Methods for diagnosis of bile acid malabsorption in clinical practice.

PubMed

Vijayvargiya, Priya; Camilleri, Michael; Shin, Andrea; Saenger, Amy

2013-10-01

Altered concentrations of bile acid (BA) in the colon can cause diarrhea or constipation. More than 25% of patients with irritable bowel syndrome with diarrhea or chronic diarrhea in Western countries have BA malabsorption (BAM). As BAM is increasingly recognized, proper diagnostic methods are needed to help direct the most effective course of treatment for the chronic bowel dysfunction. We review the methodologies, advantages, and disadvantages of tools that directly measure BAM: the (14)C-glycocholate breath and stool test, the (75)selenium homotaurocholic acid test (SeHCAT), and measurements of 7 α-hydroxy-4-cholesten-3-one (C4) and fecal BAs. The (14)C-glycocholate test is laborious and no longer widely used. The (75)SeHCAT has been validated but is not available in the United States. Measurement of serum C4 is a simple and accurate method that can be used for most patients but requires further clinical validation. Assays to quantify fecal BA (total and individual levels) are technically cumbersome and not widely available. Regrettably, none of these tests are routinely available in the United States; assessment of the therapeutic effects of a BA binder is used as a surrogate for diagnosis of BAM. Recent data indicate the advantages to studying fecal excretion of individual BAs and their role in BAM; these could support the use of the fecal BA assay, compared with other tests. Measurement of fecal BA levels could become a routine addition to the measurement of fecal fat in patients with unexplained diarrhea. Availability ultimately determines whether the C4, SeHCAT, or fecal BA test is used; more widespread availability of such tests would enhance clinical management of these patients. Copyright © 2013 AGA Institute. Published by Elsevier Inc. All rights reserved.

Biocarriers Improve Bioaugmentation Efficiency of a Rapid Sand Filter for the Treatment of 2,6-Dichlorobenzamide-Contaminated Drinking Water.

PubMed

Horemans, Benjamin; Raes, Bart; Vandermaesen, Johanna; Simanjuntak, Yanti; Brocatus, Hannelore; T'Syen, Jeroen; Degryse, Julie; Boonen, Jos; Wittebol, Janneke; Lapanje, Ales; Sørensen, Sebastian R; Springael, Dirk

2017-02-07

Aminobacter sp. MSH1 immobilized in an alginate matrix in porous stones was tested in a pilot system as an alternative inoculation strategy to the use of free suspended cells for biological removal of micropollutant concentrations of 2,6-dichlorobenzamide (BAM) in drinking water treatment plants (DWTPs). BAM removal rates and MSH1 cell numbers were recorded during operation and assessed with specific BAM degradation rates obtained in lab conditions using either freshly grown cells or starved cells to explain reactor performance. Both reactors inoculated with either suspended or immobilized cells showed immediate BAM removal under the threshold of 0.1 μg/L, but the duration of sufficient BAM removal was 2-fold (44 days) longer for immobilized cells. The longer sufficient BAM removal in case of immobilized cells compared to suspended cells was mainly explained by a lower initial loss of MSH1 cells at operational start due to volume replacement and shear. Overall loss of activity in the reactors though was due to starvation, and final removal rates did not differ between reactors inoculated with immobilized and suspended cells. Management of assimilable organic carbon, in addition to cell immobilization, appears crucial for guaranteeing long-term BAM degradation activity of MSH1 in DWTP units.

Vestibular function assessment using the NIH Toolbox

PubMed Central

Schubert, Michael C.; Whitney, Susan L.; Roberts, Dale; Redfern, Mark S.; Musolino, Mark C.; Roche, Jennica L.; Steed, Daniel P.; Corbin, Bree; Lin, Chia-Cheng; Marchetti, Greg F.; Beaumont, Jennifer; Carey, John P.; Shepard, Neil P.; Jacobson, Gary P.; Wrisley, Diane M.; Hoffman, Howard J.; Furman, Gabriel; Slotkin, Jerry

2013-01-01

Objective: Development of an easy to administer, low-cost test of vestibular function. Methods: Members of the NIH Toolbox Sensory Domain Vestibular, Vision, and Motor subdomain teams collaborated to identify 2 tests: 1) Dynamic Visual Acuity (DVA), and 2) the Balance Accelerometry Measure (BAM). Extensive work was completed to identify and develop appropriate software and hardware. More than 300 subjects between the ages of 3 and 85 years, with and without vestibular dysfunction, were recruited and tested. Currently accepted gold standard measures of static visual acuity, vestibular function, dynamic visual acuity, and balance were performed to determine validity. Repeat testing was performed to examine reliability. Results: The DVA and BAM tests are affordable and appropriate for use for individuals 3 through 85 years of age. The DVA had fair to good reliability (0.41–0.94) and sensitivity and specificity (50%–73%), depending on age and optotype chosen. The BAM test was moderately correlated with center of pressure (r = 0.42–0.48) and dynamic posturography (r = −0.48), depending on age and test condition. Both tests differentiated those with and without vestibular impairment and the young from the old. Each test was reliable. Conclusion: The newly created DVA test provides a valid measure of visual acuity with the head still and moving quickly. The novel BAM is a valid measure of balance. Both tests are sensitive to age-related changes and are able to screen for impairment of the vestibular system. PMID:23479540

In vivo roles of BamA, BamB and BamD in the biogenesis of BamA, a core protein of the β-barrel assembly machine of Escherichia coli.

PubMed

Misra, Rajeev; Stikeleather, Ryan; Gabriele, Rebecca

2015-03-13

Assembly of the β-barrel outer membrane proteins (OMPs) is an essential cellular process in Gram-negative bacteria and in the mitochondria and chloroplasts of eukaryotes--two organelles of bacterial origin. Central to this process is the conserved β-barrel OMP that belongs to the Omp85 superfamily. In Escherichia coli, BamA is the core β-barrel OMP and, together with four outer membrane lipoproteins, BamBCDE, constitutes the β-barrel assembly machine (BAM). In this paper, we investigated the roles of BamD, an essential lipoprotein, and BamB in BamA biogenesis. Depletion of BamD caused impairment in BamA biogenesis and cessation of cell growth. These defects of BamD depletion were partly reversed by single-amino-acid substitutions mapping within the β-barrel domain of BamA. However, in the absence of BamB, the positive effects of the β-barrel substitutions on BamA biogenesis under BamD depletion conditions were nullified. By employing a BamA protein bearing one such substitution, F474L, it was demonstrated that the mutant BamA protein could not only assemble without BamD but also facilitate the assembly of wild-type BamA expressed in trans. Based on these data, we propose a model in which the Bam lipoproteins, which are localized to the outer membrane by the BAM-independent Lol pathway, aid in the creation of new BAM complexes by serving as outer membrane receptors and folding factors for nascent BamA molecules. The newly assembled BAM holocomplex then catalyzes the assembly of substrate OMPs and BamA. These in vivo findings are corroborated by recently published in vitro data. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Essential β-Barrel Assembly Machinery Complex Components BamD and BamA Are Required for Autotransporter Biogenesis▿

PubMed Central

Rossiter, Amanda E.; Leyton, Denisse L.; Tveen-Jensen, Karina; Browning, Douglas F.; Sevastsyanovich, Yanina; Knowles, Timothy J.; Nichols, Katie B.; Cunningham, Adam F.; Overduin, Michael; Schembri, Mark A.; Henderson, Ian R.

2011-01-01

Autotransporter biogenesis is dependent upon BamA, a central component of the β-barrel assembly machinery (BAM) complex. In this report, we detail the role of the other BAM components (BamB-E). We identify the importance of BamD in autotransporter biogenesis and show that BamB, BamC, and BamE are not required. PMID:21665980

USDA FSIS, FDA BAM, and ISO culture methods BD BBL CHROMagar O157 media.

PubMed

Ritter, Vicki; Kircher, Susan; Dick, Nancy

2009-01-01

BBL CHROMagar O157 media (CO) was evaluated for detection of Escherichia coli O157:H7 in raw ground beef and unpasteurized apple cider. The recovery of E. coli O157:H7 on CO was compared to the U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM), U.S. Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS), and International Organization for Standardization (ISO) reference-plated media using the recommended enrichment broths. Of the 180 food samples tested, 45 were tested using BAM, 45 using the USDA method, and 90 using the ISO method. CO produced comparable results with the reference methods on all matrixes with a sensitivity of 100% and a specificity of 100%. No false negatives were found in testing the food matrixes. There was no statistical difference in recovery based on Chi-square analysis. Method agreement for raw ground beef was 85% for the USDAFSIS method and 95% for the ISO method. Method agreement for unpasteurized apple cider was 100% for the ISO and FDA BAM methods. In all cases where method agreement was <100%, CO detected more positives than the reference method media. Evaluation of known isolates on CO in inclusivity and exclusivity testing had a sensitivity and specificity of 100%. The results of this study demonstrate that CO is an effective medium for the recovery and detection of E. coli O157:H7 in raw ground beef and unpasteurized apple cider using FDA BAM, USDA FSIS, and ISO methods.

A Multicenter Prospective Study to Investigate the Diagnostic Accuracy of the SeHCAT Test in Measuring Bile Acid Malabsorption: Research Protocol

PubMed Central

Peacock, Janet; Coker, Bola; McMillan, Viktoria; Lewis, Cornelius; Keevil, Stephen; Sherwood, Roy; Vivian, Gill; Logan, Robert; Summers, Jennifer

2016-01-01

Background Bile acid malabsorption (BAM) is one possible explanation for chronic diarrhea. BAM may be idiopathic, or result from ileal resection or inflammation including Crohn’s disease, or may be secondary to other conditions, including cholecystectomy, peptic ulcer surgery, and chronic pancreatitis. No “gold standard” exists for clinical diagnosis of BAM, but response to treatment with a bile acid sequestrant (BAS) is often accepted as confirmation. The SeHCAT (tauroselcholic [selenium-75] acid) test uses a radiolabeled synthetic bile acid and provides a diagnostic test for BAM, but its performance against “trial of treatment” is unknown. Fibroblast growth factor 19 (FGF-19) and 7-alpha-hydroxy-4-cholesten-3-one (C4) also offer potential new biomarkers of BAM. Objective This protocol describes a multicenter prospective study to evaluate the diagnostic accuracy of SeHCAT and 2 biomarkers in predicting BAM as assessed by trial of treatment. Methods Participating gastroenterology centers should have a minimum workload of 30 SeHCAT patients per annum. Patients should not be pregnant, on medication that could confound follow-up, or have any severe comorbidity. All eligible patients attending a gastrointestinal appointment will be invited to participate. On attending the SeHCAT test, blood and fecal samples will be collected for analysis of FGF-19 by enzyme-linked immunosorbent assay and for C4 and fractionated bile acids by liquid chromatography–mass spectrometry. A capsule containing radiolabeled SeHCAT will be administered orally and a scan performed to measure SeHCAT activity. Patients will return on day 7 to undergo a second scan to measure percentage SeHCAT retention. The test result will be concealed from clinicians and patients. BAS will be dispensed to all patients, with a follow-up gastroenterologist appointment at 2 weeks for clinical assessment of treatment response and adherence. Patients responding positively will continue treatment for a further 2 weeks and all patients will have a final follow-up at 8 weeks. The diagnostic accuracy of the SeHCAT test and biomarkers will be analyzed at different thresholds using sensitivity, specificity, positive and negative predictive value, likelihood ratios, and area under the curve in a sample of 600 patients. Multivariable logistic regression models will be used to assess the association between presence of BAM and continuous SeHCAT retention levels after adjustment for confounders. Results Funding is being sought to conduct this research. Conclusions The SeHCAT test for diagnosis of BAM has been in common use in the United Kingdom for more than 30 years and an evidence-based assessment of its accuracy is overdue. The proposed study has some challenges. Some forms of BAS treatment are unpleasant due to the texture and taste of the resin powder, which may negatively affect recruitment and treatment adherence. Trial of treatment is not as “golden” a standard as would be ideal, and itself warrants further study. PMID:26832436

A Multicenter Prospective Study to Investigate the Diagnostic Accuracy of the SeHCAT Test in Measuring Bile Acid Malabsorption: Research Protocol.

PubMed

Reid, Fiona; Peacock, Janet; Coker, Bola; McMillan, Viktoria; Lewis, Cornelius; Keevil, Stephen; Sherwood, Roy; Vivian, Gill; Logan, Robert; Summers, Jennifer

2016-02-01

Bile acid malabsorption (BAM) is one possible explanation for chronic diarrhea. BAM may be idiopathic, or result from ileal resection or inflammation including Crohn's disease, or may be secondary to other conditions, including cholecystectomy, peptic ulcer surgery, and chronic pancreatitis. No "gold standard" exists for clinical diagnosis of BAM, but response to treatment with a bile acid sequestrant (BAS) is often accepted as confirmation. The SeHCAT (tauroselcholic [selenium-75] acid) test uses a radiolabeled synthetic bile acid and provides a diagnostic test for BAM, but its performance against "trial of treatment" is unknown. Fibroblast growth factor 19 (FGF-19) and 7-alpha-hydroxy-4-cholesten-3-one (C4) also offer potential new biomarkers of BAM. This protocol describes a multicenter prospective study to evaluate the diagnostic accuracy of SeHCAT and 2 biomarkers in predicting BAM as assessed by trial of treatment. Participating gastroenterology centers should have a minimum workload of 30 SeHCAT patients per annum. Patients should not be pregnant, on medication that could confound follow-up, or have any severe comorbidity. All eligible patients attending a gastrointestinal appointment will be invited to participate. On attending the SeHCAT test, blood and fecal samples will be collected for analysis of FGF-19 by enzyme-linked immunosorbent assay and for C4 and fractionated bile acids by liquid chromatography-mass spectrometry. A capsule containing radiolabeled SeHCAT will be administered orally and a scan performed to measure SeHCAT activity. Patients will return on day 7 to undergo a second scan to measure percentage SeHCAT retention. The test result will be concealed from clinicians and patients. BAS will be dispensed to all patients, with a follow-up gastroenterologist appointment at 2 weeks for clinical assessment of treatment response and adherence. Patients responding positively will continue treatment for a further 2 weeks and all patients will have a final follow-up at 8 weeks. The diagnostic accuracy of the SeHCAT test and biomarkers will be analyzed at different thresholds using sensitivity, specificity, positive and negative predictive value, likelihood ratios, and area under the curve in a sample of 600 patients. Multivariable logistic regression models will be used to assess the association between presence of BAM and continuous SeHCAT retention levels after adjustment for confounders. Funding is being sought to conduct this research. The SeHCAT test for diagnosis of BAM has been in common use in the United Kingdom for more than 30 years and an evidence-based assessment of its accuracy is overdue. The proposed study has some challenges. Some forms of BAS treatment are unpleasant due to the texture and taste of the resin powder, which may negatively affect recruitment and treatment adherence. Trial of treatment is not as "golden" a standard as would be ideal, and itself warrants further study.

β-Amylase1 and β-Amylase3 Are Plastidic Starch Hydrolases in Arabidopsis That Seem to Be Adapted for Different Thermal, pH, and Stress Conditions1[W][OPEN

PubMed Central

Monroe, Jonathan D.; Storm, Amanda R.; Badley, Elizabeth M.; Lehman, Michael D.; Platt, Samantha M.; Saunders, Lauren K.; Schmitz, Jonathan M.; Torres, Catherine E.

2014-01-01

Starch degradation in chloroplasts requires β-amylase (BAM) activity, which is encoded by a multigene family. Of nine Arabidopsis (Arabidopsis thaliana) BAM genes, six encode plastidic enzymes, but only four of these are catalytically active. In vegetative plants, BAM1 acts during the day in guard cells, whereas BAM3 is the dominant activity in mesophyll cells at night. Plastidic BAMs have been difficult to assay in leaf extracts, in part because of a cytosolic activity encoded by BAM5. We generated a series of double mutants lacking BAM5 and each of the active plastidic enzymes (BAM1, BAM2, BAM3, and BAM6) and found that most of the plastidic activity in 5-week-old plants was encoded by BAM1 and BAM3. Both of these activities were relatively constant during the day and the night. Analysis of leaf extracts from double mutants and purified BAM1 and BAM3 proteins revealed that these proteins have distinct properties. Using soluble starch as the substrate, BAM1 and BAM3 had optimum activity at pH 6.0 to 6.5, but at high pH, BAM1 was more active than BAM3, consistent with its known daytime role in the guard cell stroma. The optimum temperature for BAM1, which is transcriptionally induced by heat stress, was about 10°C higher than that of BAM3, which is transcriptionally induced by cold stress. The amino acid composition of BAM1 and BAM3 orthologs reflected differences that are consistent with known adaptations of proteins from heat- and cold-adapted organisms, suggesting that these day- and night-active enzymes have undergone thermal adaptation. PMID:25293962

Colonoscopy and SeHCAT for investigation of chronic diarrhea.

PubMed

Müller, Marcella; Willén, Roger; Stotzer, Per-Ove

2004-01-01

Chronic diarrhea is a common problem. Colonoscopy is the investigation of choice for diagnosis. Even a macroscopically normal mucosa on endoscopy can have abnormalities such as microscopic colitis and bile acid malabsorption (BAM). The aim of this study was to establish the value of colonoscopy with biopsies in patients with chronic diarrhea and to evaluate the additive value of a SeHCAT test for diagnosing BAM in these patients. All patients who underwent a colonoscopy between November 1999 and December 2000 were included. Patient files, colonoscopy and pathology reports and SeHCAT test results were reviewed. 205 patients were included. The most common diagnoses were diarrhea-predominant IBS (n = 76) and IBD (n = 38). 158 patients had non-bloody diarrhea, 113 (72%) of them had a macroscopically normal appearing mucosa. In 40 (35%) of these patients, a histological diagnosis could be made and microscopic colitis was the most common diagnosis (n = 27). SeHCAT test was performed in 36 patients and 15 (42%) of them had BAM. In the 47 patients with bloody diarrhea, IBD was the main diagnosis (n = 23). Colonoscopy with biopsies must be performed when investigating chronic diarrhea and BAM should be excluded.

Fixed-time stabilization of impulsive Cohen-Grossberg BAM neural networks.

PubMed

Li, Hongfei; Li, Chuandong; Huang, Tingwen; Zhang, Wanli

2018-02-01

This article is concerned with the fixed-time stabilization for impulsive Cohen-Grossberg BAM neural networks via two different controllers. By using a novel constructive approach based on some comparison techniques for differential inequalities, an improvement theorem of fixed-time stability for impulsive dynamical systems is established. In addition, based on the fixed-time stability theorem of impulsive dynamical systems, two different control protocols are designed to ensure the fixed-time stabilization of impulsive Cohen-Grossberg BAM neural networks, which include and extend the earlier works. Finally, two simulations examples are provided to illustrate the validity of the proposed theoretical results. Copyright © 2017 Elsevier Ltd. All rights reserved.

Surface Colonization and Activity of the 2,6-Dichlorobenzamide (BAM) Degrading Aminobacter sp. Strain MSH1 at Macro- and Micropollutant BAM Concentrations.

PubMed

Sekhar, Aswini; Horemans, Benjamin; Aamand, Jens; Sørensen, Sebastian R; Vanhaecke, Lynn; Bussche, Julie Vanden; Hofkens, Johan; Springael, Dirk

2016-09-20

Aminobacter sp. MSH1 uses the groundwater micropollutant 2,6-dichlorobenzamide (BAM) as a C and N source and is a potential catalyst for biotreatment of BAM-contaminated groundwater in filtration units of drinking water treatment plants (DWTPs). The oligotrophic environment of DWTPs including trace pollutant concentrations, and the high flow rates impose challenges for micropollutant biodegradation in DWTPs. To understand how trace BAM concentrations affect MSH1 surface colonization and BAM degrading activity, MSH1 was cultivated in flow channels fed continuously with BAM macro- and microconcentrations in a N- and C-limiting medium. At all BAM concentrations, MSH1 colonized the flow channel. BAM degradation efficiencies were concentration-dependent, ranging between 70 and 95%. Similarly, BAM concentration affected surface colonization, but at 100 μg/L BAM and lower, colonization was similar to that in systems without BAM, suggesting that assimilable organic carbon and nitrogen other than those supplied by BAM sustained colonization at BAM microconcentrations. Comparison of specific BAM degradation rates in flow channels and in cultures of suspended freshly grown cells indicated that starvation conditions in flow channels receiving BAM microconcentrations resulted into MSH1 biomasses with 10-100-times reduced BAM degrading activity and provided a kinetic model for predicting BAM degradation under continuous C and N starvation.

The Enzyme-Like Domain of Arabidopsis Nuclear β-Amylases Is Critical for DNA Sequence Recognition and Transcriptional Activation.

PubMed

Soyk, Sebastian; Simková, Klára; Zürcher, Evelyne; Luginbühl, Leonie; Brand, Luise H; Vaughan, Cara K; Wanke, Dierk; Zeeman, Samuel C

2014-04-01

Plant BZR1-BAM transcription factors contain a β-amylase (BAM)-like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be noncatalytic, but they determine the function of the two Arabidopsis thaliana BZR1-BAM isoforms (BAM7 and BAM8) during transcriptional initiation. Removal or swapping of the BAM domains demonstrates that the BAM7 BAM domain restricts DNA binding and transcriptional activation, while the BAM8 BAM domain allows both activities. Furthermore, we demonstrate that BAM7 and BAM8 interact on the protein level and cooperate during transcriptional regulation. Site-directed mutagenesis of residues in the BAM domain of BAM8 shows that its function as a transcriptional activator is independent of catalysis but requires an intact substrate binding site, suggesting it may bind a ligand. Microarray experiments with plants overexpressing truncated versions lacking the BAM domain indicate that the pseudo-enzymatic domain increases selectivity for the preferred cis-regulatory element BBRE (BZR1-BAM Responsive Element). Side specificity toward the G-box may allow crosstalk to other signaling networks. This work highlights the importance of the enzyme-derived domain of BZR1-BAMs, supporting their potential role as metabolic sensors. © 2014 American Society of Plant Biologists. All rights reserved.

ABL and BAM Friction Analysis Comparison

DOE PAGES

Warner, Kirstin F.; Sandstrom, Mary M.; Brown, Geoffrey W.; ...

2014-12-29

Here, the Integrated Data Collection Analysis (IDCA) program has conducted a proficiency study for Small-Scale Safety and Thermal (SSST) testing of homemade explosives (HMEs). Described here is a comparison of the Alleghany Ballistic Laboratory (ABL) friction data and Bundesanstalt fur Materialforschung und -prufung (BAM) friction data for 19 HEM and military standard explosives.

Amylases StAmy23, StBAM1 and StBAM9 regulate cold-induced sweetening of potato tubers in distinct ways

PubMed Central

Hou, Juan; Zhang, Huiling; Liu, Jun; Reid, Stephen; Liu, Tengfei; Xu, Shijing; Tian, Zhendong; Sonnewald, Uwe

2017-01-01

Abstract Cold-induced sweetening (CIS) in potato is detrimental to the quality of processed products. Conversion of starch to reducing sugars (RS) by amylases is considered one of the main pathways in CIS but is not well studied. The amylase genes StAmy23, StBAM1, and StBAM9 were studied for their functions in potato CIS. StAmy23 is localized in the cytoplasm, whereas StBAM1 and StBAM9 are targeted to the plastid stroma and starch granules, respectively. Genetic transformation of these amylases in potatoes by RNA interference showed that β-amylase activity could be decreased in cold-stored tubers by silencing of StBAM1 and collective silencing of StBAM1 and StBAM9. However, StBAM9 silencing did not decrease β-amylase activity. Silencing StBAM1 and StBAM9 caused starch accumulation and lower RS, which was more evident in simultaneously silenced lines, suggesting functional redundancy. Soluble starch content increased in RNAi-StBAM1 lines but decreased in RNAi-StBAM9 lines, suggesting that StBAM1 may regulate CIS by hydrolysing soluble starch and StBAM9 by directly acting on starch granules. Moreover, StBAM9 interacted with StBAM1 on the starch granules. StAmy23 silencing resulted in higher phytoglycogen and lower RS accumulation in cold-stored tubers, implying that StAmy23 regulates CIS by degrading cytosolic phytoglycogen. Our findings suggest that StAmy23, StBAM1, and StBAM9 function in potato CIS with varying levels of impact. PMID:28369567

Augmenting β-augmentation: structural basis of how BamB binds BamA and may support folding of outer membrane proteins.

PubMed

Heuck, Alexander; Schleiffer, Alexander; Clausen, Tim

2011-03-11

β-Barrel proteins are frequently found in the outer membrane of mitochondria, chloroplasts and Gram-negative bacteria. In Escherichia coli, these proteins are inserted in the outer membrane by the Bam (β-barrel assembly machinery) complex, a multiprotein machinery formed by the β-barrel protein BamA and the four peripheral membrane proteins BamB, BamC, BamD and BamE. The periplasmic part of BamA binds prefolded β-barrel proteins by a β-augmentation mechanism, thereby stabilizing the precursors prior to their membrane insertion. However, the role of the associated proteins within the Bam complex remains unknown. Here, we describe the crystal structure of BamB, a nonessential component of the Bam complex. The structure shows a typical eight-bladed β-propeller fold. Two sequence stretches of BamB were previously identified to be important for interaction with BamA. In our structure, both motifs are located in close proximity to each other and contribute to a conserved region forming a narrow groove on the top of the propeller. Moreover, crystal contacts reveal two interaction modes of how BamB might bind unfolded β-barrel proteins. In the crystal lattice, BamB binds to exposed β-strands by β-augmentation, whereas peptide stretches rich in aromatic residues can be accommodated in hydrophobic pockets located at the bottom of the propeller. Thus, BamB could simultaneously bind to BamA and prefolded β-barrel proteins, thereby enhancing the folding and membrane insertion capability of the Bam complex. Copyright © 2011 Elsevier Ltd. All rights reserved.

The Structure of a BamA-BamD Fusion Illuminates the Architecture of the β-Barrel Assembly Machine Core.

PubMed

Bergal, Hans Thor; Hopkins, Alex Hunt; Metzner, Sandra Ines; Sousa, Marcelo Carlos

2016-02-02

The β-barrel assembly machine (BAM) mediates folding and insertion of integral β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. Of the five BAM subunits, only BamA and BamD are essential for cell viability. Here we present the crystal structure of a fusion between BamA POTRA4-5 and BamD from Rhodothermus marinus. The POTRA5 domain binds BamD between its tetratricopeptide repeats 3 and 4. The interface structural elements are conserved in the Escherichia coli proteins, which allowed structure validation by mutagenesis and disulfide crosslinking in E. coli. Furthermore, the interface is consistent with previously reported mutations that impair BamA-BamD binding. The structure serves as a linchpin to generate a BAM model where POTRA domains and BamD form an elongated periplasmic ring adjacent to the membrane with a central cavity approximately 30 × 60 Å wide. We propose that nascent OMPs bind this periplasmic ring prior to insertion and folding by BAM. Copyright © 2016 Elsevier Ltd. All rights reserved.

Systematic review with meta-analysis: the prevalence of bile acid malabsorption in the irritable bowel syndrome with diarrhoea.

PubMed

Slattery, S A; Niaz, O; Aziz, Q; Ford, A C; Farmer, A D

2015-07-01

Irritable bowel syndrome is a widespread disorder with a marked socioeconomic burden. Previous studies support the proposal that a subset of patients with features compatible with diarrhoea-predominant IBS (IBS-D) have bile acid malabsorption (BAM). To perform a systematic review and meta-analysis to assess the prevalence of BAM in patients meeting the accepted criteria for IBS-D. MEDLINE and EMBASE were searched up to March 2015. Studies recruiting adults with IBS-D, defined by the Manning, Kruis, Rome I, II or III criteria and which used 23-seleno-25-homotaurocholic acid (SeHCAT) testing for the assessment of BAM were included. BAM was defined as 7 day SeHCAT retention of <10%. We calculated the rate of BAM and 95% confidence intervals (CI) using a random effects model. The methodological quality of included studies was evaluated using the Quality Assessment for Diagnostic Accuracy Studies (QUADAS-2). The search strategy identified six relevant studies comprising 908 individuals. The rate of BAM ranged from 16.9% to 35.3%. The pooled rate was 28.1% (95% CI: 22.6-34%). There was significant heterogeneity in effect sizes (Q-test χ(2)  = 17.9, P < 0.004; I(2)  = 72.1%). The type of diagnostic criteria used or study country did not significantly modify the effect. These data provide evidence that in excess of one quarter of patients meeting accepted criteria for IBS-D have bile acid malabsorption. This distinction has implications for the interpretation of previous studies, as well as contemporaneous clinical practice and future guideline development. © 2015 John Wiley & Sons Ltd.

β-Amylase–Like Proteins Function as Transcription Factors in Arabidopsis, Controlling Shoot Growth and Development[C][W][OA

PubMed Central

Reinhold, Heike; Soyk, Sebastian; Šimková, Klára; Hostettler, Carmen; Marafino, John; Mainiero, Samantha; Vaughan, Cara K.; Monroe, Jonathan D.; Zeeman, Samuel C.

2011-01-01

Plants contain β-amylase–like proteins (BAMs; enzymes usually associated with starch breakdown) present in the nucleus rather than targeted to the chloroplast. They possess BRASSINAZOLE RESISTANT1 (BZR1)-type DNA binding domains—also found in transcription factors mediating brassinosteroid (BR) responses. The two Arabidopsis thaliana BZR1-BAM proteins (BAM7 and BAM8) bind a cis-regulatory element that both contains a G box and resembles a BR-responsive element. In protoplast transactivation assays, these BZR1-BAMs activate gene expression. Structural modeling suggests that the BAM domain’s glucan binding cleft is intact, but the recombinant proteins are at least 1000 times less active than chloroplastic β-amylases. Deregulation of BZR1-BAMs (the bam7bam8 double mutant and BAM8-overexpressing plants) causes altered leaf growth and development. Of the genes upregulated in plants overexpressing BAM8 and downregulated in bam7bam8 plants, many carry the cis-regulatory element in their promoters. Many genes that respond to BRs are inversely regulated by BZR1-BAMs. We propose a role for BZR1-BAMs in controlling plant growth and development through crosstalk with BR signaling. Furthermore, we speculate that BZR1-BAMs may transmit metabolic signals by binding a ligand in their BAM domain, although diurnal changes in the concentration of maltose, a candidate ligand produced by chloroplastic β-amylases, do not influence their transcription factor function. PMID:21487098

β-amylase-like proteins function as transcription factors in Arabidopsis, controlling shoot growth and development.

PubMed

Reinhold, Heike; Soyk, Sebastian; Simková, Klára; Hostettler, Carmen; Marafino, John; Mainiero, Samantha; Vaughan, Cara K; Monroe, Jonathan D; Zeeman, Samuel C

2011-04-01

Plants contain β-amylase-like proteins (BAMs; enzymes usually associated with starch breakdown) present in the nucleus rather than targeted to the chloroplast. They possess BRASSINAZOLE RESISTANT1 (BZR1)-type DNA binding domains--also found in transcription factors mediating brassinosteroid (BR) responses. The two Arabidopsis thaliana BZR1-BAM proteins (BAM7 and BAM8) bind a cis-regulatory element that both contains a G box and resembles a BR-responsive element. In protoplast transactivation assays, these BZR1-BAMs activate gene expression. Structural modeling suggests that the BAM domain's glucan binding cleft is intact, but the recombinant proteins are at least 1000 times less active than chloroplastic β-amylases. Deregulation of BZR1-BAMs (the bam7bam8 double mutant and BAM8-overexpressing plants) causes altered leaf growth and development. Of the genes upregulated in plants overexpressing BAM8 and downregulated in bam7bam8 plants, many carry the cis-regulatory element in their promoters. Many genes that respond to BRs are inversely regulated by BZR1-BAMs. We propose a role for BZR1-BAMs in controlling plant growth and development through crosstalk with BR signaling. Furthermore, we speculate that BZR1-BAMs may transmit metabolic signals by binding a ligand in their BAM domain, although diurnal changes in the concentration of maltose, a candidate ligand produced by chloroplastic β-amylases, do not influence their transcription factor function.

The gene encoding the catalytically inactive beta-amylase BAM4 involved in starch breakdown in Arabidopsis leaves is expressed preferentially in vascular tissues in source and sink organs.

PubMed

Francisco, Perigio; Li, Jing; Smith, Steven M

2010-07-15

Genetic studies in Arabidopsis thaliana have shown that two members of the beta-amylase (BAM) family BAM3 and BAM4 are required for leaf starch breakdown at night. Both are plastid proteins and while BAM3 encodes an active BAM, BAM4 is not an active alpha-1,4-glucan hydrolase. To gain further insight into the possible function of BAM4 we constructed reporter genes using promoters for both BAM3 and BAM4 genes, driving beta-glucuronidase (GUS) and luciferase (LUC) expression in transgenic Arabidopsis plants. Both promoters directed expression in vascular tissue throughout the plant including cotyledons, leaves, petioles, stems, petals, siliques and roots. Tissue sections showed expression to be focused in phloem cells in stem and petiole. The BAM3 promoter was also expressed strongly throughout the photosynthetic tissues of leaves, sepals and siliques, whereas the BAM4 promoter was not. Conversely, the BAM4 promoter was active in root tip but the BAM3 promoter was not. To confirm these expression patterns and to compare with expression of other starch genes we carried-out RT-PCR analysis on RNA from vascular (replum) and non-vascular (valve) tissues of siliques. This confirmed that BAM4 expression together with RAM1 (BAM5) and GWD2 genes is stronger in the replum than the valve, whereas BAM3 is strong in both tissues. These results show that even though BAM3 and BAM4 genes apparently interact genetically in leaf starch metabolism, BAM4 is preferentially expressed in non-photosynthetic vascular tissue, so revealing a potentially greater level of complexity in the control of starch breakdown than had previously been recognised. Copyright (c) 2010 Elsevier GmbH. All rights reserved.

Robust stability of interval bidirectional associative memory neural network with time delays.

PubMed

Liao, Xiaofeng; Wong, Kwok-wo

2004-04-01

In this paper, the conventional bidirectional associative memory (BAM) neural network with signal transmission delay is intervalized in order to study the bounded effect of deviations in network parameters and external perturbations. The resultant model is referred to as a novel interval dynamic BAM (IDBAM) model. By combining a number of different Lyapunov functionals with the Razumikhin technique, some sufficient conditions for the existence of unique equilibrium and robust stability are derived. These results are fairly general and can be verified easily. To go further, we extend our investigation to the time-varying delay case. Some robust stability criteria for BAM with perturbations of time-varying delays are derived. Besides, our approach for the analysis allows us to consider several different types of activation functions, including piecewise linear sigmoids with bounded activations as well as the usual C1-smooth sigmoids. We believe that the results obtained have leading significance in the design and application of BAM neural networks.

Bioaugmentation potential of free and formulated 2,6-dichlorobenzamide (BAM) degrading Aminobacter sp. MSH1 in soil, sand and water.

PubMed

Schultz-Jensen, Nadja; Aamand, Jens; Sørensen, Sebastian R

2016-12-01

Pesticides are used extensively worldwide, which has led to the unwanted contamination of soil and water resources. Former use of the herbicide 2,6-dichlorobenzonitrile (dichlobenil) has caused pollution of ground and surface water resources by the stable degradation product 2,6-dichlorobenzamide (BAM) in several parts of Europe, which has resulted in the costly closure of several drinking water wells. One strategy for preventing this in future is bioaugmentation using bacterial degraders. BAM-degrading Aminobacter sp. MSH1 was therefore formulated into dried beads and tests undertaken to establish their potential for use in the remediation of polluted soil, sand and water. The formulation procedure included freeze drying, combined with trehalose addition for cell wall protection, thus ensuring a high amount of viable cells following prolonged storage at room temperature. The beads were round-shaped pellets with a diameter of about 1.25 mm, a dry matter content of approximately 95 % and an average viable cell content of 4.4 × 10(9) cells/g bead. Formulated MSH1 cells led to a similar, and frequently even faster, BAM mineralisation (20-65 % (14)CO2 produced from (14)C-labelled BAM) in batch tests conducted with sand, water and different soil moisture contents compared to adding free cells. Furthermore, the beads were easy to handle and had a shelf life of several months.

Comparing rapid methods for detecting Listeria in seafood and environmental samples using the most probably number (MPN) technique.

PubMed

Cruz, Cristina D; Win, Jessicah K; Chantarachoti, Jiraporn; Mutukumira, Anthony N; Fletcher, Graham C

2012-02-15

The standard Bacteriological Analytical Manual (BAM) protocol for detecting Listeria in food and on environmental surfaces takes about 96 h. Some studies indicate that rapid methods, which produce results within 48 h, may be as sensitive and accurate as the culture protocol. As they only give presence/absence results, it can be difficult to compare the accuracy of results generated. We used the Most Probable Number (MPN) technique to evaluate the performance and detection limits of six rapid kits for detecting Listeria in seafood and on an environmental surface compared with the standard protocol. Three seafood products and an environmental surface were inoculated with similar known cell concentrations of Listeria and analyzed according to the manufacturers' instructions. The MPN was estimated using the MPN-BAM spreadsheet. For the seafood products no differences were observed among the rapid kits and efficiency was similar to the BAM method. On the environmental surface the BAM protocol had a higher recovery rate (sensitivity) than any of the rapid kits tested. Clearview™, Reveal®, TECRA® and VIDAS® LDUO detected the cells but only at high concentrations (>10(2) CFU/10 cm(2)). Two kits (VIP™ and Petrifilm™) failed to detect 10(4) CFU/10 cm(2). The MPN method was a useful tool for comparing the results generated by these presence/absence test kits. There remains a need to develop a rapid and sensitive method for detecting Listeria in environmental samples that performs as well as the BAM protocol, since none of the rapid tests used in this study achieved a satisfactory result. Copyright © 2011 Elsevier B.V. All rights reserved.

Recent advances in the understanding of bile acid malabsorption.

PubMed

Pattni, Sanjeev; Walters, Julian R F

2009-01-01

Bile acid malabsorption (BAM) is a syndrome of chronic watery diarrhoea with excess faecal bile acids. Disruption of the enterohepatic circulation of bile acids following surgical resection is a common cause of BAM. The condition is easily diagnosed by the selenium homocholic acid taurine (SeHCAT) test and responds to bile acid sequestrants. Idiopathic BAM (IBAM, primary bile acid diarrhoea) is the condition where no definitive cause for low SeHCAT retention can be identified. Review of PubMed and major journals. Evidence is accumulating that BAM is more prevalent than first thought. Management of chronic diarrhoea involves excluding secondary causes. Treatment of the condition is with bile acid binders. SeHCAT testing is not widely performed, limiting awareness of how common this condition can be. The underlying mechanism for IBAM has been unclear. Increasing awareness of the condition is important. Alternative mechanisms of IBAM have been suggested which involve an increased bile acid pool size and reduced negative feedback regulation of bile acid synthesis by FGF19. New sequestrants are available. Further research into the precise mechanism of IBAM is needed. Improvements in the recognition of the condition and optimization of treatment are required.

The WD40 Protein BamB Mediates Coupling of BAM Complexes into Assembly Precincts in the Bacterial Outer Membrane.

PubMed

Gunasinghe, Sachith D; Shiota, Takuya; Stubenrauch, Christopher J; Schulze, Keith E; Webb, Chaille T; Fulcher, Alex J; Dunstan, Rhys A; Hay, Iain D; Naderer, Thomas; Whelan, Donna R; Bell, Toby D M; Elgass, Kirstin D; Strugnell, Richard A; Lithgow, Trevor

2018-05-29

The β-barrel assembly machinery (BAM) complex is essential for localization of surface proteins on bacterial cells, but the mechanism by which it functions is unclear. We developed a direct stochastic optical reconstruction microscopy (dSTORM) methodology to view the BAM complex in situ. Single-cell analysis showed that discrete membrane precincts housing several BAM complexes are distributed across the E. coli surface, with a nearest neighbor distance of ∼200 nm. The auxiliary lipoprotein subunit BamB was crucial for this spatial distribution, and in situ crosslinking shows that BamB makes intimate contacts with BamA and BamB in neighboring BAM complexes within the precinct. The BAM complex precincts swell when outer membrane protein synthesis is maximal, visual proof that the precincts are active in protein assembly. This nanoscale interrogation of the BAM complex in situ suggests a model whereby bacterial outer membranes contain highly organized assembly precincts to drive integral protein assembly. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Bile acid malabsorption: an under-investigated differential diagnosis in patients presenting with diarrhea predominant irritable bowel syndrome type symptoms.

PubMed

Kurien, Matthew; Evans, Kate E; Leeds, John S; Hopper, Andy D; Harris, Andrew; Sanders, David S

2011-07-01

Bile acid malabsorption (BAM) has been reported as a possible cause of diarrhea predominant irritable bowel syndrome (D-IBS) type symptoms. We aimed to determine how commonly patients with D-IBS type symptoms had a diagnosis of BAM as demonstrated by a positive SeHCAT (75 Selenium-homocholic acid taurine) test (retention <10% at seven days). A retrospective analysis was undertaken of patient's records for all patients who underwent a SeHCAT test between 2001 and 2009 in a tertiary hospital (Group A). Concurrently, a cohort of patients with Rome II D-IBS type symptoms was examined to determine the potential utility of SeHCAT test (Group B). In Group A 39.2% (n = 107/273) of patients had a positive SeHCAT result. The median time from first hospital visit to SeHCAT result was 30 weeks. Predictive factors for BAM: terminal ileal Crohn's disease (p < 0.01), terminal ileal resection (p < 0.01), and previous cholecystectomy (p < 0.01). 33.6% of patients who had a positive SeHCAT also had Rome II D-IBS. In Group B the D-IBS control cohort only 1.9% of patients had undergone a SeHCAT scan (p < 0.001 compared to Group A). BAM is common and should be considered earlier when investigating unselected patients with D-IBS type symptoms.

A new mechanism for bile acid diarrhea: defective feedback inhibition of bile acid biosynthesis.

PubMed

Walters, Julian R F; Tasleem, Ali M; Omer, Omer S; Brydon, W Gordon; Dew, Tracy; le Roux, Carel W

2009-11-01

Primary (idiopathic) bile acid malabsorption (BAM) is a common, yet underrecognized, chronic diarrheal syndrome. Diagnosis is difficult without selenium homocholic acid taurine (SeHCAT) testing. The diarrhea results from excess colonic bile acids, but the pathogenesis is unclear. Fibroblast growth factor 19 (FGF19), produced in the ileum in response to bile acid absorption, regulates hepatic bile acid synthesis. We proposed that FGF19 is involved in bile acid diarrhea and measured its levels in patients with BAM. Blood was collected from fasting patients with chronic diarrhea; BAM was diagnosed by SeHCAT. Serum FGF19 was measured by enzyme-linked immunosorbent assay. Serum 7alpha-hydroxy-4-cholesten-3-one (C4) was determined using high-performance liquid chromatography, to quantify bile acid synthesis. Data were compared between patients and subjects without diarrhea (controls). Samples were taken repeatedly after meals from several subjects. The median C4 level was significantly higher in patients with primary BAM than in controls (51 vs 18 ng/mL; P < .0001). The median FGF19 level was significantly lower in patients with BAM (120 vs 231 pg/mL; P < .0005). There was a significant inverse relationship between FGF19 and C4 levels (P < .0004). Low levels of FGF19 were also found in patients with postcholecystectomy and secondary bile acid diarrhea. Abnormal patterns of FGF19 levels were observed throughout the day in some patients with primary BAM. Patients with BAM have reduced serum FGF19 which may be useful in diagnosis. We propose a mechanism whereby impaired FGF19 feedback inhibition causes excessive bile acid synthesis that exceeds the normal capacity for ileal reabsorption, producing bile acid diarrhea.

Measuring Recovery in Elite Rugby Players: The Brief Assessment of Mood, Endocrine Changes, and Power.

PubMed

Shearer, David A; Kilduff, Liam P; Finn, Charlotte; Jones, Rhys M; Bracken, Richard M; Mellalieu, Stephen D; Owen, Nic; Crewther, Blair T; Cook, Christian J

2015-01-01

There is demand in applied sport settings to measure recovery briefly and accurately. Research indicates mood disturbance as the strongest psychological predictor of mental and physical recovery. The Brief Assessment of Mood (BAM) is a shortened version of the Profile of Mood States that can be completed in less than 30 s. The purpose of this study was to examine the BAM as a quick measure of mood in relation to recovery status in elite rugby players alongside established physiological markers of recovery. Using elite rugby union players (N = 12), this study examined the utility of BAM as an indicator of mental and physical recovery in elite athletes by exploring pattern change in mood disturbance, energy index, power output, cortisol, and testosterone 36 hr before and 12 hr, 36 hr, and 60 hr after a competitive rugby match. Repeated-measures multivariate analysis of variance indicated significant changes in all variables across the 4 time points (p < .05, η(2) range = .20-.48), concurrent with previous study findings. Although visual inspection of the graphs indicated that the pattern of change for mood disturbance and energy index mapped changes in all physiological variables, only a low correlation was observed for power output (r = - .34). Although BAM scores changed significantly over time in accordance with the hypotheses, further testing is required to confirm the utility of the BAM as a measure of recovery. The results indicate that the BAM could be used as 1 indicator of recovery status alongside other measures.

Comparison of the Reveal 20-hour method and the BAM culture method for the detection of Escherichia coli O157:H7 in selected foods and environmental swabs: collaborative study.

PubMed

Bird, C B; Hoerner, R J; Restaino, L

2001-01-01

Four different food types along with environmental swabs were analyzed by the Reveal for E. coli O157:H7 test (Reveal) and the Bacteriological Analytical Manual (BAM) culture method for the presence of Escherichia coli O157:H7. Twenty-seven laboratories representing academia and private industry in the United States and Canada participated. Sample types were inoculated with E. coli O157:H7 at 2 different levels. Of the 1,095 samples and controls analyzed and confirmed, 459 were positive and 557 were negative by both methods. No statistical differences (p <0.05) were observed between the Reveal and BAM methods.

BamA β16C strand and periplasmic turns are critical for outer membrane protein insertion and assembly.

PubMed

Gu, Yinghong; Zeng, Yi; Wang, Zhongshan; Dong, Changjiang

2017-11-21

Outer membrane (OM) β-barrel proteins play important roles in importing nutrients, exporting wastes and conducting signals in Gram-negative bacteria, mitochondria and chloroplasts. The outer membrane proteins (OMPs) are inserted and assembled into the OM by OMP85 family proteins. In Escherichia coli , the β-barrel assembly machinery (BAM) contains four lipoproteins such as BamB, BamC, BamD and BamE, and one OMP BamA, forming a 'top hat'-like structure. Structural and functional studies of the E. coli BAM machinery have revealed that the rotation of periplasmic ring may trigger the barrel β1C-β6C scissor-like movement that promote the unfolded OMP insertion without using ATP. Here, we report the BamA C-terminal barrel structure of Salmonella enterica Typhimurium str. LT2 and functional assays, which reveal that the BamA's C-terminal residue Trp, the β16C strand of the barrel and the periplasmic turns are critical for the functionality of BamA. These findings indicate that the unique β16C strand and the periplasmic turns of BamA are important for the outer membrane insertion and assembly. The periplasmic turns might mediate the rotation of the periplasmic ring to the scissor-like movement of BamA β1C-β6C, triggering the OMP insertion. These results are important for understanding the OMP insertion in Gram-negative bacteria, as well as in mitochondria and chloroplasts. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Periodic bidirectional associative memory neural networks with distributed delays

NASA Astrophysics Data System (ADS)

Chen, Anping; Huang, Lihong; Liu, Zhigang; Cao, Jinde

2006-05-01

Some sufficient conditions are obtained for the existence and global exponential stability of a periodic solution to the general bidirectional associative memory (BAM) neural networks with distributed delays by using the continuation theorem of Mawhin's coincidence degree theory and the Lyapunov functional method and the Young's inequality technique. These results are helpful for designing a globally exponentially stable and periodic oscillatory BAM neural network, and the conditions can be easily verified and be applied in practice. An example is also given to illustrate our results.

Puzzling with online games (BAM-COG): reliability, validity, and feasibility of an online self-monitor for cognitive performance in aging adults.

PubMed

Aalbers, Teun; Baars, Maria A E; Olde Rikkert, Marcel G M; Kessels, Roy P C

2013-12-03

Online interventions are aiming increasingly at cognitive outcome measures but so far no easy and fast self-monitors for cognition have been validated or proven reliable and feasible. This study examines a new instrument called the Brain Aging Monitor-Cognitive Assessment Battery (BAM-COG) for its alternate forms reliability, face and content validity, and convergent and divergent validity. Also, reference values are provided. The BAM-COG consists of four easily accessible, short, yet challenging puzzle games that have been developed to measure working memory ("Conveyer Belt"), visuospatial short-term memory ("Sunshine"), episodic recognition memory ("Viewpoint"), and planning ("Papyrinth"). A total of 641 participants were recruited for this study. Of these, 397 adults, 40 years and older (mean 54.9, SD 9.6), were eligible for analysis. Study participants played all games three times with 14 days in between sets. Face and content validity were based on expert opinion. Alternate forms reliability (AFR) was measured by comparing scores on different versions of the BAM-COG and expressed with an intraclass correlation (ICC: two-way mixed; consistency at 95%). Convergent validity (CV) was provided by comparing BAM-COG scores to gold-standard paper-and-pencil and computer-assisted cognitive assessment. Divergent validity (DV) was measured by comparing BAM-COG scores to the National Adult Reading Test IQ (NART-IQ) estimate. Both CV and DV are expressed as Spearman rho correlation coefficients. Three out of four games showed adequate results on AFR, CV, and DV measures. The games Conveyer Belt, Sunshine, and Papyrinth have AFR ICCs of .420, .426, and .645 respectively. Also, these games had good to very good CV correlations: rho=.577 (P=.001), rho=.669 (P<.001), and rho=.400 (P=.04), respectively. Last, as expected, DV correlations were low: rho=-.029 (P=.44), rho=-.029 (P=.45), and rho=-.134 (P=.28) respectively. The game Viewpoint provided less desirable results with an AFR ICC of .167, CV rho=.202 (P=.15), and DV rho=-.162 (P=.21). This study provides evidence for the use of the BAM-COG test battery as a feasible, reliable, and valid tool to monitor cognitive performance in healthy adults in an online setting. Three out of four games have good psychometric characteristics to measure working memory, visuospatial short-term memory, and planning capacity.

pth moment exponential stability of stochastic memristor-based bidirectional associative memory (BAM) neural networks with time delays.

PubMed

Wang, Fen; Chen, Yuanlong; Liu, Meichun

2018-02-01

Stochastic memristor-based bidirectional associative memory (BAM) neural networks with time delays play an increasingly important role in the design and implementation of neural network systems. Under the framework of Filippov solutions, the issues of the pth moment exponential stability of stochastic memristor-based BAM neural networks are investigated. By using the stochastic stability theory, Itô's differential formula and Young inequality, the criteria are derived. Meanwhile, with Lyapunov approach and Cauchy-Schwarz inequality, we derive some sufficient conditions for the mean square exponential stability of the above systems. The obtained results improve and extend previous works on memristor-based or usual neural networks dynamical systems. Four numerical examples are provided to illustrate the effectiveness of the proposed results. Copyright © 2017 Elsevier Ltd. All rights reserved.

BamA POTRA Domain Interacts with a Native Lipid Membrane Surface.

PubMed

Fleming, Patrick J; Patel, Dhilon S; Wu, Emilia L; Qi, Yifei; Yeom, Min Sun; Sousa, Marcelo Carlos; Fleming, Karen G; Im, Wonpil

2016-06-21

The outer membrane of Gram-negative bacteria is an asymmetric membrane with lipopolysaccharides on the external leaflet and phospholipids on the periplasmic leaflet. This outer membrane contains mainly β-barrel transmembrane proteins and lipidated periplasmic proteins (lipoproteins). The multisubunit protein β-barrel assembly machine (BAM) catalyzes the insertion and folding of the β-barrel proteins into this membrane. In Escherichia coli, the BAM complex consists of five subunits, a core transmembrane β-barrel with a long periplasmic domain (BamA) and four lipoproteins (BamB/C/D/E). The BamA periplasmic domain is composed of five globular subdomains in tandem called POTRA motifs that are key to BAM complex formation and interaction with the substrate β-barrel proteins. The BAM complex is believed to undergo conformational cycling while facilitating insertion of client proteins into the outer membrane. Reports describing variable conformations and dynamics of the periplasmic POTRA domain have been published. Therefore, elucidation of the conformational dynamics of the POTRA domain in full-length BamA is important to understand the function of this molecular complex. Using molecular dynamics simulations, we present evidence that the conformational flexibility of the POTRA domain is modulated by binding to the periplasmic surface of a native lipid membrane. Furthermore, membrane binding of the POTRA domain is compatible with both BamB and BamD binding, suggesting that conformational selection of different POTRA domain conformations may be involved in the mechanism of BAM-facilitated insertion of outer membrane β-barrel proteins. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules.

PubMed

Wala, Jeremiah; Zhang, Cheng-Zhong; Meyerson, Matthew; Beroukhim, Rameen

2016-07-01

We developed VariantBam, a C ++ read filtering and profiling tool for use with BAM, CRAM and SAM sequencing files. VariantBam provides a flexible framework for extracting sequencing reads or read-pairs that satisfy combinations of rules, defined by any number of genomic intervals or variant sites. We have implemented filters based on alignment data, sequence motifs, regional coverage and base quality. For example, VariantBam achieved a median size reduction ratio of 3.1:1 when applied to 10 lung cancer whole genome BAMs by removing large tags and selecting for only high-quality variant-supporting reads and reads matching a large dictionary of sequence motifs. Thus VariantBam enables efficient storage of sequencing data while preserving the most relevant information for downstream analysis. VariantBam and full documentation are available at github.com/jwalabroad/VariantBam rameen@broadinstitute.org 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.

LLNL Small-Scale Friction sensitivity (BAM) Test

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simpson, L.R.; Foltz, M.F.

1996-06-01

Small-scale safety testing of explosives, propellants and other energetic materials, is done to determine their sensitivity to various stimuli including friction, static spark, and impact. Testing is done to discover potential handling problems for either newly synthesized materials of unknown behavior, or materials that have been stored for long periods of time. This report describes the existing {open_quotes}BAM{close_quotes} Small-Scale Friction Test, and the methods used to determine the friction sensitivity pertinent to handling energetic materials. The accumulated data for the materials tested is not listed here - that information is in a database. Included is, however, a short list ofmore » (1) materials that had an unusual response, and (2), a few {open_quotes}standard{close_quotes} materials representing the range of typical responses usually seen.« less

Nitrobenzoxadiazole-Appended Cell Membrane Modifiers for Efficient Optoporation with Noncoherent Light.

PubMed

Otake, Saya; Okuro, Kou; Bochicchio, Davide; Pavan, Giovanni M; Aida, Takuzo

2018-05-24

FL NBD-BAM PEG2k , bearing a nitrobenzoxadiazole (NBD) unit and an oleyl terminus conjugated via a poly(ethylene glycol) (PEG) spacer ( M n = 2,000), was designed to fluorescently label cell membranes by docking its hydrophobic oleyl terminus. During laser scanning microscopy in a minimal essential medium (MEM), human hepatocellular carcinoma Hep3B cells labeled with FL NBD-BAM PEG2k appeared to undergo optoporation at their plasma membrane. We confirmed this unprecedented possibility by a series of cellular uptake experiments using negatively charged and therefore membrane-impermeable quantum dots (QDs; D h = 4.7 nm). Detailed studies indicated that the photoexcited NBD unit can generate singlet oxygen ( 1 O 2 ), which oxidizes the constituent phospholipids to transiently deteriorate the cell membrane. Reference membrane modifiers FL NBD-Oleyl and FL NBD-BAM PEG8k having shorter or longer hydrophilic spacers between the NBD and oleyl units showed a little or substantially no optoporation. For understanding these results, one must consider the following contradictory factors: (1) The photosensitized 1 O 2 generation efficiently occurs only when the NBD unit is in aqueous media, and (2) the lifetime of 1 O 2 in aqueous media is very short (3.0-3.5 μs). As supported experimentally and computationally, the hydrophilic spacer length of FL NBD-BAM PEG2k is optimal for compromising these factors. Further to note, the optoporation using FL NBD-BAM PEG2k is not accompanied by cytotoxicity.

Deterministic transfection drives efficient nonviral reprogramming and uncovers reprogramming barriers.

PubMed

Gallego-Perez, Daniel; Otero, Jose J; Czeisler, Catherine; Ma, Junyu; Ortiz, Cristina; Gygli, Patrick; Catacutan, Fay Patsy; Gokozan, Hamza Numan; Cowgill, Aaron; Sherwood, Thomas; Ghatak, Subhadip; Malkoc, Veysi; Zhao, Xi; Liao, Wei-Ching; Gnyawali, Surya; Wang, Xinmei; Adler, Andrew F; Leong, Kam; Wulff, Brian; Wilgus, Traci A; Askwith, Candice; Khanna, Savita; Rink, Cameron; Sen, Chandan K; Lee, L James

2016-02-01

Safety concerns and/or the stochastic nature of current transduction approaches have hampered nuclear reprogramming's clinical translation. We report a novel non-viral nanotechnology-based platform permitting deterministic large-scale transfection with single-cell resolution. The superior capabilities of our technology are demonstrated by modification of the well-established direct neuronal reprogramming paradigm using overexpression of the transcription factors Brn2, Ascl1, and Myt1l (BAM). Reprogramming efficiencies were comparable to viral methodologies (up to ~9-12%) without the constraints of capsid size and with the ability to control plasmid dosage, in addition to showing superior performance relative to existing non-viral methods. Furthermore, increased neuronal complexity could be tailored by varying BAM ratio and by including additional proneural genes to the BAM cocktail. Furthermore, high-throughput NEP allowed easy interrogation of the reprogramming process. We discovered that BAM-mediated reprogramming is regulated by AsclI dosage, the S-phase cyclin CCNA2, and that some induced neurons passed through a nestin-positive cell stage. In the field of regenerative medicine, the ability to direct cell fate by nuclear reprogramming is an important facet in terms of clinical application. In this article, the authors described their novel technique of cell reprogramming through overexpression of the transcription factors Brn2, Ascl1, and Myt1l (BAM) by in situ electroporation through nanochannels. This new technique could provide a platform for further future designs. Copyright © 2016 Elsevier Inc. All rights reserved.

Backscatter Mossbauer Spectrometer (BaMS) for extraterrestrial applications

NASA Technical Reports Server (NTRS)

Agresti, D. G.; Shelfer, T. D.; Pimperl, M. M.; Wills, E. L.; Shen, M. H.; Morris, R. V.

1993-01-01

Mossbauer spectroscopy is a nuclear gamma resonance technique particularly well suited to the study of materials that contain iron (Fe-57). It can provide information on the oxidation state of iron as well as the type and proportion of iron-containing mineral species in a sample of interest. Iron Mossbauer spectroscopy (FeMS) has been applied to samples believed to have come from Mars (SNC meteorites) and has been helpful in refining the choice among putative Martian surface materials by suggesting a likely nanophase component of the Martian regolity. FeMS spectrum of a Martial analogue material (Hawaiian palagonite) is shown; it is dominated by ferric-bearing phases and shows evidence of a nanophase component. FeMS has also been applied to lunar materials. It can be used to measure the maturity of lunar surface material and has been proposed as a prospector for lunar ilmenite, an oxygen resource mineral. Several years ago we suggested a backscatter Mossbauer spectrometer (BaMS) for a Mars rover mission. Backscatter design was selected as most appropriate for in-situ application because no sample preparation is required. Since that time, we have continued to develop the BaMS instrument in anticipation that it would eventually find a home on a NASA planetary mission. Gooding proposed BaMS as a geochemistry instrument on MESUR. More recently, an LPI workshop has recommended that BaMS be included in a three-instrument payload on the next (1996?) lunar lander.

Systematic review: the management of chronic diarrhoea due to bile acid malabsorption.

PubMed

Wilcox, C; Turner, J; Green, J

2014-05-01

Bile acid malabsorption (BAM) is a common, yet under-recognised, cause of chronic diarrhoea, with limited guidance available on the appropriate management of patients with BAM. To summarise the evidence supporting different treatments available for patients with bile acid malabsorption, noting their impact on clinical outcomes, tolerability and associated side effects. A literature search was conducted through PubMed, the Cochrane Database of Systematic Reviews and Scopus. Relevant articles studied patients who had been diagnosed with BAM and were clinically assessed before and after therapy. A total of 30 relevant publications (1241 adult patients) were identified, which investigated the clinical response to drugs, including colestyramine, colestipol, colesevelam, aluminium hydroxide and obeticholic acid. The most commonly used diagnostic test of bile acid malabsorption was the SeHCAT test (24 studies). Colestyramine treatment was by far the most studied of these agents, and was successful in 70% of 801 patients (range: 63-100%). Colestyramine and colestipol are generally effective treatments of gastrointestinal symptoms from BAM, but may be poorly tolerated and reduce the bioavailability of co-administered agents. Alternative therapies (including colesevelam and aluminium hydroxide) as well as dietary intervention may also have a role, and the promising results of the first proof-of-concept study of obeticholic acid suggest that its novel approach may have an exciting future in the treatment of this condition. Future trials should employ accurate diagnostic testing and be conducted over longer periods so that the long-term benefits and tolerability of these different approaches can be evaluated. © 2014 John Wiley & Sons Ltd.

Hadoop-BAM: directly manipulating next generation sequencing data in the cloud

PubMed Central

Niemenmaa, Matti; Kallio, Aleksi; Schumacher, André; Klemelä, Petri; Korpelainen, Eija; Heljanko, Keijo

2012-01-01

Summary: Hadoop-BAM is a novel library for the scalable manipulation of aligned next-generation sequencing data in the Hadoop distributed computing framework. It acts as an integration layer between analysis applications and BAM files that are processed using Hadoop. Hadoop-BAM solves the issues related to BAM data access by presenting a convenient API for implementing map and reduce functions that can directly operate on BAM records. It builds on top of the Picard SAM JDK, so tools that rely on the Picard API are expected to be easily convertible to support large-scale distributed processing. In this article we demonstrate the use of Hadoop-BAM by building a coverage summarizing tool for the Chipster genome browser. Our results show that Hadoop offers good scalability, and one should avoid moving data in and out of Hadoop between analysis steps. Availability: Available under the open-source MIT license at http://sourceforge.net/projects/hadoop-bam/ Contact: matti.niemenmaa@aalto.fi Supplementary information: Supplementary material is available at Bioinformatics online. PMID:22302568

Genetic (In)stability of 2,6-Dichlorobenzamide Catabolism in Aminobacter sp. Strain MSH1 Biofilms under Carbon Starvation Conditions

PubMed Central

Raes, Bart; Brocatus, Hannelore; T'Syen, Jeroen; Rombouts, Caroline; Vanhaecke, Lynn; Hofkens, Johan; Springael, Dirk

2017-01-01

ABSTRACT Aminobacter sp. strain MSH1 grows on and mineralizes the groundwater micropollutant 2,6-dichlorobenzamide (BAM) and is of interest for BAM removal in drinking water treatment plants (DWTPs). The BAM-catabolic genes in MSH1 are located on plasmid pBAM1, carrying bbdA, which encodes the conversion of BAM to 2,6-dichlorobenzoic acid (2,6-DCBA) (BbdA+ phenotype), and plasmid pBAM2, carrying gene clusters encoding the conversion of 2,6-DCBA to tricarboxylic acid (TCA) cycle intermediates (Dcba+ phenotype). There are indications that MSH1 easily loses its BAM-catabolic phenotype. We obtained evidence that MSH1 rapidly develops a population that lacks the ability to mineralize BAM when grown on nonselective (R2B medium) and semiselective (R2B medium with BAM) media. Lack of mineralization was explained by loss of the Dcba+ phenotype and corresponding genes. The ecological significance of this instability for the use of MSH1 for BAM removal in the oligotrophic environment of DWTPs was explored in lab and pilot systems. A higher incidence of BbdA+ Dcba− MSH1 cells was also observed when MSH1 was grown as a biofilm in flow chambers under C and N starvation conditions due to growth on nonselective residual assimilable organic carbon. Similar observations were made in experiments with a pilot sand filter reactor bioaugmented with MSH1. BAM conversion to 2,6-DCBA was not affected by loss of the DCBA-catabolic genes. Our results show that MSH1 is prone to BAM-catabolic instability under the conditions occurring in a DWTP. While conversion of BAM to 2,6-DCBA remains unaffected, BAM mineralization activity is at risk, and monitoring of metabolites is warranted. IMPORTANCE Bioaugmentation of dedicated biofiltration units with bacterial strains that grow on and mineralize micropollutants was suggested as an alternative for treating micropollutant-contaminated water in drinking water treatment plants (DWTPs). Organic-pollutant-catabolic genes in bacteria are often easily lost, especially under nonselective conditions, which affects the bioaugmentation success. In this study, we provide evidence that Aminobacter sp. strain MSH1, which uses the common groundwater micropollutant 2,6-dichlorobenzamide (BAM) as a C source, shows a high frequency of loss of its BAM-mineralizing phenotype due to the loss of genes that convert 2,6-DCBA to Krebs cycle intermediates when nonselective conditions occur. Moreover, we show that catabolic-gene loss also occurs in the oligotrophic environment of DWTPs, where growth of MSH1 depends mainly on the high fluxes of low concentrations of assimilable organic carbon, and hence show the ecological relevance of catabolic instability for using strain MSH1 for BAM removal in DWTPs. PMID:28363960

Hadoop-BAM: directly manipulating next generation sequencing data in the cloud.

PubMed

Niemenmaa, Matti; Kallio, Aleksi; Schumacher, André; Klemelä, Petri; Korpelainen, Eija; Heljanko, Keijo

2012-03-15

Hadoop-BAM is a novel library for the scalable manipulation of aligned next-generation sequencing data in the Hadoop distributed computing framework. It acts as an integration layer between analysis applications and BAM files that are processed using Hadoop. Hadoop-BAM solves the issues related to BAM data access by presenting a convenient API for implementing map and reduce functions that can directly operate on BAM records. It builds on top of the Picard SAM JDK, so tools that rely on the Picard API are expected to be easily convertible to support large-scale distributed processing. In this article we demonstrate the use of Hadoop-BAM by building a coverage summarizing tool for the Chipster genome browser. Our results show that Hadoop offers good scalability, and one should avoid moving data in and out of Hadoop between analysis steps.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bidlack, J.M.; Frey, D.K.; Seyed-Mozaffari, A.

The binding properties of 14{beta}-(bromoacetamido)morphine (BAM) and the ability of BAM to irreversibly inhibit opioid binding to rat brain membranes were examined to characterize the affinity and selectivity of BAM as an irreversible affinity ligand for opioid receptors. BAM had the same receptor selectivity as morphine, with a 3-5-fold decrease in affinity for the different types of opioid receptors. When brain membranes were incubated with BAM, followed by extensive washing, opioid binding was restored to control levels. However, when membranes were incubated with dithiothreitol (DTT), followed by BAM, and subsequently washed, 90% of the 0.25 nM ({sup 3}H)(D-Ala{sup 2},(Me)Phe{sup 4},Gly(ol){supmore » 5})enkephalin (DAGO) binding was irreversibly inhibited as a result of the specific alkylation of a sulfhydryl group at the {mu} binding site. This inhibition was dependent on the concentrations of both DTT and BAM. The {mu} receptor specificity of BAM alkylation was demonstrated by the ability of BAM alkylated membranes to still bind the {delta}-selective peptide ({sup 3}H)(D-penicillamine{sup 2},D-penicillamine{sup 5})enkephalin (DPDPE) and (-)-({sup 3}H)bremazocine in the presence of {mu} and {delta} blockers, selective for {kappa} binding sites. Morphine and naloxone partially protected the binding site from alkylation with BAM, while ligands that did not bind to the {mu}s site did not afford protection. These studies have demonstrated that when a disulfide bond at or near {mu} opioid binding sites was reduced, BAM could then alkylate this site, resulting in the specific irreversible labeling of {mu} opioid receptors.« less

The caBIG® Life Science Business Architecture Model.

PubMed

Boyd, Lauren Becnel; Hunicke-Smith, Scott P; Stafford, Grace A; Freund, Elaine T; Ehlman, Michele; Chandran, Uma; Dennis, Robert; Fernandez, Anna T; Goldstein, Stephen; Steffen, David; Tycko, Benjamin; Klemm, Juli D

2011-05-15

Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG®) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research. LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model's current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases. The LS BAM is freely available as UML, PDF and HTML (https://wiki.nci.nih.gov/x/OFNyAQ).

Puzzling With Online Games (BAM-COG): Reliability, Validity, and Feasibility of an Online Self-Monitor for Cognitive Performance in Aging Adults

PubMed Central

Baars, Maria A E; Olde Rikkert, Marcel G M; Kessels, Roy P C

2013-01-01

Background Online interventions are aiming increasingly at cognitive outcome measures but so far no easy and fast self-monitors for cognition have been validated or proven reliable and feasible. Objective This study examines a new instrument called the Brain Aging Monitor–Cognitive Assessment Battery (BAM-COG) for its alternate forms reliability, face and content validity, and convergent and divergent validity. Also, reference values are provided. Methods The BAM-COG consists of four easily accessible, short, yet challenging puzzle games that have been developed to measure working memory (“Conveyer Belt”), visuospatial short-term memory (“Sunshine”), episodic recognition memory (“Viewpoint”), and planning (“Papyrinth”). A total of 641 participants were recruited for this study. Of these, 397 adults, 40 years and older (mean 54.9, SD 9.6), were eligible for analysis. Study participants played all games three times with 14 days in between sets. Face and content validity were based on expert opinion. Alternate forms reliability (AFR) was measured by comparing scores on different versions of the BAM-COG and expressed with an intraclass correlation (ICC: two-way mixed; consistency at 95%). Convergent validity (CV) was provided by comparing BAM-COG scores to gold-standard paper-and-pencil and computer-assisted cognitive assessment. Divergent validity (DV) was measured by comparing BAM-COG scores to the National Adult Reading Test IQ (NART-IQ) estimate. Both CV and DV are expressed as Spearman rho correlation coefficients. Results Three out of four games showed adequate results on AFR, CV, and DV measures. The games Conveyer Belt, Sunshine, and Papyrinth have AFR ICCs of .420, .426, and .645 respectively. Also, these games had good to very good CV correlations: rho=.577 (P=.001), rho=.669 (P<.001), and rho=.400 (P=.04), respectively. Last, as expected, DV correlations were low: rho=−.029 (P=.44), rho=−.029 (P=.45), and rho=−.134 (P=.28) respectively. The game Viewpoint provided less desirable results with an AFR ICC of .167, CV rho=.202 (P=.15), and DV rho=−.162 (P=.21). Conclusions This study provides evidence for the use of the BAM-COG test battery as a feasible, reliable, and valid tool to monitor cognitive performance in healthy adults in an online setting. Three out of four games have good psychometric characteristics to measure working memory, visuospatial short-term memory, and planning capacity. PMID:24300212

C and N isotope fractionation during biodegradation of the pesticide metabolite 2,6-dichlorobenzamide (BAM): potential for environmental assessments.

PubMed

Reinnicke, Sandra; Simonsen, Allan; Sørensen, Sebastian R; Aamand, Jens; Elsner, Martin

2012-02-07

2,6-Dichlorobenzamide (BAM) is a metabolite of the herbicide 2,6-dichlorobenzonitrile (dichlobenil), and a prominent groundwater contaminant. Observable compound-specific isotope fractionation during BAM formation-through transformation of dichlobenil by Rhodococcus erythropolis DSM 9685-was small. In contrast, isotope fractionation during BAM degradation-with Aminobacter sp. MSH1 and ASI1, the only known bacterial strains capable of mineralizing BAM-was large, with pronounced carbon (ε(C) = -7.5‰ to -7.8‰) and nitrogen (ε(N) = -10.7‰ to -13.5‰) isotopic enrichment factors. BAM isotope values in natural samples are therefore expected to be dominated by the effects of its degradation rather than formation. Dual isotope slopes Δ (=Δδ(15)N/Δδ(13)C ≈ ε(N)/ε(C)) showed only small differences for MSH1 (1.75 ± 0.03) and ASI1 (1.45 ± 0.03) suggesting similar transformation mechanisms of BAM hydrolysis. Observations are in agreement with either a tetrahedral intermediate promoted by OH(-) or H(3)O(+) catalysis, or a concerted reaction mechanism. Therefore, owing to consistent carbon isotopic fractionation, isotope shifts of BAM can be linked to BAM biodegradation, and may even be used to quantify degradation of this persistent metabolite. In contrast, nitrogen isotope values may be rather indicative of different sources. Our results delineate a new approach to assessing the fate of BAM in the environment.

Recombinant proteins secreted from tissue-engineered bioartificial muscle improve cardiac dysfunction and suppress cardiomyocyte apoptosis in rats with heart failure.

PubMed

Rong, Shu-Ling; Wang, Yong-Jin; Wang, Xiao-Lin; Lu, Yong-Xin; Wu, Yin; Liu, Qi-Yun; Mi, Shao-Hua; Xu, Yu-Lan

2010-12-01

Tissue-engineered bioartificial muscle-based gene therapy represents a promising approach for the treatment of heart diseases. Experimental and clinical studies suggest that systemic administration of insulin-like growth factor-1 (IGF-1) protein or overexpression of IGF-1 in the heart exerts a favorable effect on cardiovascular function. This study aimed to investigate a chronic stage after myocardial infarction (MI) and the potential therapeutic effects of delivering a human IGF-1 gene by tissue-engineered bioartificial muscles (BAMs) following coronary artery ligation in Sprague-Dawley rats. Ligation of the left coronary artery or sham operation was performed. Primary skeletal myoblasts were retrovirally transduced to synthesize and secrete recombinant human insulin-like growth factor-1 (rhIGF-1), and green fluorescent protein (GFP), and tissue-engineered into implantable BAMs. The rats that underwent ligation were randomly assigned to 2 groups: MI-IGF group (n = 6) and MI-GFP group (n = 6). The MI-IGF group received rhIGF-secreting BAM (IGF-BAMs) transplantation, and the MI-GFP group received GFP-secreting BAM (GFP-BAMs) transplantation. Another group of rats served as the sham operation group, which was also randomly assigned to 2 subgroups: S-IGF group (n = 6) and S-GFP group (n = 6). The S-IGF group underwent IGF-1-BAM transplantation, and S-GFP group underwent GFP-BAM transplantation. IGF-1-BAMs and GFP-BAMs were implanted subcutaneously into syngeneic rats after two weeks of operation was performed. Four weeks after the treatment, hemodynamics was performed. IGF-1 was measured by radioimmunoassay, and then the rats were sacrificed and ventricular samples were subjected to immunohistochemistry. Reverse transcriptase-polymerase chain reaction (RT-PCR) was used to examine the mRNA expression of bax and Bcl-2. TNF-α and caspase 3 expression in myocardium was examined by Western blotting. Primary rat myoblasts were retrovirally transduced to secrete rhIGF-1 and tissue-engineered into implantable BAMs containing parallel arrays of postmitotic myofibers. In vitro, they secreted consistent levels of hIGF (0.4 - 1.2 µg×BAM(-1)×d(-1)). When implanted into syngeneic rat, IGF-BAMs secreted and delivered rhIGF. Four weeks after therapy, the hemodynamics was improved significantly in MI rats treated with IGF-BAMs compared with those treated with GFP-BAMs. The levels of serum IGF-1 were increased significantly in both MI and sham rats treated with IGF-BAM. The mRNA expression of bax was lower and Bcl-2 expression was higher in MI-IGF group than MI-GFP group (P < 0.05). Western blotting assay showed TNF-α and caspase 3 expression was lower in MI-IGF group than MI-GFP group after therapy. rhIGF-1 significantly improves left ventricular function and suppresses cardiomyocyte apoptosis in rats with chronic heart failure. Genetically modified tissue-engineered BAMs provide a method delivering recombinant protein for the treatment of heart failure.

Extent and Durability of Contamination of Groundwater and Water Works With The Pesticide Metabolite Bam (2,6 -dichlorbenzamide) Evaluated For Representative Aquifers In Denmark

NASA Astrophysics Data System (ADS)

Jørgensen, Peter R.; Clausen, Liselotte; Larsen, Flemming

The pesticide metabolite BAM (2,6-dichlorbenzamide) is the most frequently found pesticide contaminant in Danish groundwater. In 1999 BAM was found in 26% of Danish water supply wells and the drinking water standard (0.1 µg/L) was exceeded in 11% of the wells. BAM is a metabolite from the active ingredient dichlobenil (DCB), which was used for non-agricultural total weed protection during 1966 ­ 1997. By using the numerical codes FRAC3Dvs and MODFLOW/MT3D it is the aim of the study to evaluate the extent and durability of the BAM pollution in Danish groundwater and to recommend planning strategies to avoid or minimize BAM in future water supply. The modeling was based on the total amount sold of the DCB (29.000 ton/year) combined with data for sorption and degradation of the DCB and BAM measured from comprehensive laboratory experiments with soil material representing root zone and main aquifer soil types in Denmark. As a main result the laboratory experiments revealed that BAM was only very slowly degraded in the root zone, while no degradation was observed in the sub-soil environments. Combining these model in-put data with representative data for the main aquifer types and overriding fractured clay aquitards, the modeling indicates that more than 99% of infiltrated dichlobenile has been transformed to its metabolite BAM (approximately 500 tons in total), and that currently (year 2001) approximately 100% of this compound appears widely in the groundwater and/or in the above aquitards. The modeling shows that the BAM pollution will appear in the groundwater with a high frequency in extensive parts of Denmark during the following 20 years to more than 100 years. The highest current BAM concentrations, but however also the shortest durability of the BAM pollution, will occur in contaminated aquifers, which are not covered with clay layers. Short durability in such areas is furthermore dependent on the lack of further up-stream BAM sources. The modeling moreover indicates that aquifers will be less vulnerable in contaminated areas with high run-of in the surface layers and small groundwater recharge. In contrast to the current vulnerability of the free water table aquifers, BAM contamination underneath thick clay layers (30 m or more) will not break through to the aquifers before year 2050 to 2070. However, hereafter the BAM concentration will increase until approximately year 2150. Hence, the modeling indicates that water extraction may proceed without influence of the BAM pollution from aquifers underneath thick clay aquitards until the middle or late end of the current century, and hereafter, may be moved to areas with no clay layers above aquifers, since such aquifers will have no measurable concentrations of BAM after approximately year 2050. The modeling moreover show that the extent and future evolution of the BAM pollution is a strong function of local geological and hydrological conditions, which indicates a promising potential for minimizing problems for the water supply through planning and management. The project was funded by the Danish Environmental Protection Agency and the EU-project "PEGASE".

The caBIG® Life Science Business Architecture Model

PubMed Central

Boyd, Lauren Becnel; Hunicke-Smith, Scott P.; Stafford, Grace A.; Freund, Elaine T.; Ehlman, Michele; Chandran, Uma; Dennis, Robert; Fernandez, Anna T.; Goldstein, Stephen; Steffen, David; Tycko, Benjamin; Klemm, Juli D.

2011-01-01

Motivation: Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG®) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research. Results: LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model's current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases. Availability and Implementation: The LS BAM is freely available as UML, PDF and HTML (https://wiki.nci.nih.gov/x/OFNyAQ). Contact: lbboyd@bcm.edu; laurenbboyd@gmail.com Supplementary information: Supplementary data) are avaliable at Bioinformatics online. PMID:21450709

BamTools: a C++ API and toolkit for analyzing and managing BAM files.

PubMed

Barnett, Derek W; Garrison, Erik K; Quinlan, Aaron R; Strömberg, Michael P; Marth, Gabor T

2011-06-15

Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit. BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools.

Ames Lab 101: BAM (Boron-Aluminum-Magnesium)

ScienceCinema

Cook, Bruce

2017-12-13

Materials scientist, Bruce Cook, discusses the super hard, low friction, and lubricious alloy know as BAM (Boron-Aluminum-Magnesium). BAM was discovered by Bruce Cook and his team at the Ames Laboratory.

BamTools: a C++ API and toolkit for analyzing and managing BAM files

PubMed Central

Barnett, Derek W.; Garrison, Erik K.; Quinlan, Aaron R.; Strömberg, Michael P.; Marth, Gabor T.

2011-01-01

Motivation: Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. Results: We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit. Availability: BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools. Contact: barnetde@bc.edu PMID:21493652

The structure of the β-barrel assembly machinery complex

DOE PAGES

Bakelar, Jeremy; Buchanan, Susan K.; Noinaj, Nicholas

2016-01-08

β-Barrel outer membrane proteins (OMPs) are found in the outer membranes of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. A 200-kilodalton five-component complex called the β-barrel assembly machinery (BAM) complex has been implicated in the biogenesis of OMPs. In this paper, we report the structure of the BAM complex from Escherichia coli, revealing that binding of BamCDE modulates the conformation of BamA, the central component, which may serve to regulate the BAM complex. The periplasmic domain of BamA was in a closed state that prevents access to the barrel lumen, which indicates substrate OMPs may notmore » be threaded through the barrel during biogenesis. Finally and further, conformational shifts in the barrel domain lead to opening of the exit pore and rearrangement at the lateral gate.« less

The structure of the β-barrel assembly machinery complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bakelar, Jeremy; Buchanan, Susan K.; Noinaj, Nicholas

β-Barrel outer membrane proteins (OMPs) are found in the outer membranes of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. A 200-kilodalton five-component complex called the β-barrel assembly machinery (BAM) complex has been implicated in the biogenesis of OMPs. In this paper, we report the structure of the BAM complex from Escherichia coli, revealing that binding of BamCDE modulates the conformation of BamA, the central component, which may serve to regulate the BAM complex. The periplasmic domain of BamA was in a closed state that prevents access to the barrel lumen, which indicates substrate OMPs may notmore » be threaded through the barrel during biogenesis. Finally and further, conformational shifts in the barrel domain lead to opening of the exit pore and rearrangement at the lateral gate.« less

Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools

PubMed Central

Cheng, Yinhe; Tzeng, Tzy-Hwa Kathy

2016-01-01

This paper introduces a high-throughput software tool framework called sam2bam that enables users to significantly speed up pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156–186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize multiple processors, available memory, high-bandwidth storage, and hardware compression accelerators, if available. The sam2bam provides file format conversion between well-known genome file formats, from SAM to BAM, as a basic feature. Additional features such as analyzing, filtering, and converting input data are provided by using plug-in tools, e.g., duplicate marking, which can be attached to sam2bam at runtime. We demonstrated that sam2bam could significantly reduce the runtime of next generation sequencing (NGS) data pre-processing from about two hours to about one minute for a whole-exome data set on a 16-core single-node system using up to 130 GB of memory. The sam2bam could reduce the runtime of NGS data pre-processing from about 20 hours to about nine minutes for a whole-genome sequencing data set on the same system using up to 711 GB of memory. PMID:27861637

Induced formation and maturation of acetylcholine receptor clusters in a defined 3D bio-artificial muscle.

PubMed

Wang, Lin; Shansky, Janet; Vandenburgh, Herman

2013-12-01

Dysfunction of the neuromuscular junction is involved in a wide range of muscular diseases. The development of neuromuscular junction through which skeletal muscle is innervated requires the functional modulation of acetylcholine receptor (AchR) clustering on myofibers. However, studies on AchR clustering in vitro are mostly done on monolayer muscle cell culture, which lacks a three-dimensional (3D) structure, a prominent limitation of the two-dimensional (2D) system. To enable a better understanding on the structure-function correlation underlying skeletal muscle innervation, a muscle system with a well-defined geometry mimicking the in vivo muscular setting is needed. Here, we report a 3D bio-artificial muscle (BAM) bioengineered from green fluorescent protein-transduced C3H murine myoblasts as a novel in vitro tissue-based model for muscle innervation studies. Our cell biological and molecular analysis showed that this BAM is structurally similar to in vivo muscle tissue and can reach the perinatal differentiation stage, higher than does 2D culture. Effective clustering and morphological maturation of AchRs on BAMs induced by agrin and laminin indicate the functional activity and plasticity of this BAM system toward innervation. Taken together, our results show that the BAM provides a favorable 3D environment that at least partially recapitulates real physiological skeletal muscle with regard to innervation. With a convenience of fabrication and manipulation, this 3D in vitro system offers a novel model for studying mechanisms underlying skeletal muscle innervation and testing therapeutic strategies for relevant nervous and muscular diseases.

Refolding, crystallization and preliminary X-ray crystallographic studies of the β-barrel domain of BamA, a membrane protein essential for outer membrane protein biogenesis.

PubMed

Ni, Dongchun; Yang, Kun; Huang, Yihua

2014-03-01

In Gram-negative bacteria, the assembly of outer membrane proteins (OMPs) requires a five-protein β-barrel assembly machinery (BAM) complex, of which BamA is an essential and evolutionarily conserved integral outer membrane protein. Here, the refolding, crystallization and preliminary X-ray crystallographic characterization of the β-barrel domain of BamA from Escherichia coli (EcBamA) are reported. Native and selenomethionine-substituted EcBamA proteins were crystallized at 16°C and X-ray diffraction data were collected to 2.6 and 3.7 Å resolution, respectively. The native crystals belonged to space group P21212, with unit-cell parameters a = 118.492, b = 159.883, c = 56.000 Å and two molecules in one asymmetric unit; selenomethionine-substituted protein crystals belonged to space group P4322, with unit-cell parameters a = b = 163.162, c = 46.388 Å and one molecule in one asymmetric unit. Initial phases for EcBamA β-barrel domain were obtained from a SeMet SAD data set. These preliminary X-ray crystallographic studies paved the way for further structural determination of the β-barrel domain of EcBamA.

Formative evaluation on cultural tailoring breathing awareness meditation smartphone apps to reduce stress and blood pressure

PubMed Central

Adams, Zachary W.; Nemeth, Lynne; Brunner-Jackson, Brenda; Mueller, Martina; Anderson, Ashley; Patel, Sachin; Sox, Luke; Treiber, Frank A.

2017-01-01

Background Chronic stress is an independent risk factor for essential hypertension (EH), cardiovascular disease (CVD), and is sometimes confronted by mal-adaptive coping behaviors (e.g., stress eating, excessive alcohol consumption, etc.). Pre-essential hypertension (preEH) is the leading predictor of future EH status. Breathing awareness meditation (BAM) can result in clinically beneficial blood pressure (BP) reductions, though face-to-face sessions presents barriers to reach those in need. The purpose of this study was to identify if a culturally tailored approach is needed in the design and preferences between groups of preEH African American and White adults toward using a smartphone BAM app, the Tension Tamer (TT) app. Methods TT includes audio delivered BAM instructions, real-time heart rate, feedback graphs and motivational reinforcement text messaging. Questionnaires and two focus groups each of African American and White adults, [n=34, mean age =43.1 years, (SD 13.8 years), 44.1% African American] were conducted to understand stress, EH knowledge, app usage along with feedback from a hands-on demonstration of TT. Grounded theory using NVivo 10 was used to develop themes and combined with the questionnaires in the analysis. Results No racial differences were found in the analysis including app use scenarios, preferences, knowledge, technology use or the attitudes and acceptance toward mobile health (mHealth) programs. Reported stress was high for African Americans [PSS-4: mean 6.87 (SD 3.3) versus mean 4.56 (SD 2.6); P=0.03]. Four main themes were found: (I) stress was pervasive; (II) coping strategies were both positive and negative; (III) BAM training was easy to incorporated; and (IV) tracking stress responses was useful. Responses suggest that additional personalization of app interfaces may drive ownership and adherence to protocols. Measures and reports of heart rate monitoring while in session were favorably viewed with low issues with confidentiality or trust issues on collected session data. Conclusions Results suggest that a culturally tailored approach may be unnecessary in the design of BAM apps. Further investigation is warranted for other racial groups, age ranges, and disease conditions. PMID:29184896

Roche/BIOTECON Diagnostics LightCycler foodproof L. monocytogenes detection kit in combination with ShortPrep foodproof II Kit. Performance-Tested Method 070401.

PubMed

Junge, Benjamin; Berghof-Jäger, Kornelia

2006-01-01

A method was developed for the detection of L. monocytogenes in food based on real-time polymerase chain reaction (PCR). This advanced PCR method was designed to reduce the time needed to achieve results from PCR reactions and to enable the user to monitor the amplification of the PCR product simultaneously, in real-time. After DNA isolation using the Roche/BIOTECON Diagnostics ShortPrep foodproof II Kit (formerly called Listeria ShortPrep Kit) designed for the rapid preparation of L. monocytogenes DNA for direct use in PCR, the real-time detection of L. monocytogenes DNA is performed by using the Roche/BIOTECON Diagnostics LightCycler foodproof L. monocytogenes Detection Kit. This kit provides primers and hybridization probes for sequence-specific detection, convenient premixed reagents, and different controls for reliable interpretation of results. For repeatability studies, 20 different foods, covering the 15 food groups recommended from the AOAC Research Institute (AOAC RI) for L. monocytogenes detection were analyzed: raw meats, fresh produce/vegetables, processed meats, seafood, egg and egg products, dairy (cultured/noncultured), spices, dry foods, fruit/juices, uncooked pasta, nuts, confectionery, pet food, food dyes and colorings, and miscellaneous. From each food 20, samples were inoculated with a low level (1-10 colony-forming units (CFU)/25 g) and 20 samples with a high level (10-50 CFU/25 g) of L. monocytogenes. Additionally, 5 uninoculated samples were prepared from each food. The food samples were examined with the test kits and in correlation with the cultural methods according to U.S. Food and Drug Administration (FDA) Bacteriological Analytical Manual (BAM) or U.S. Department of Agriculture (USDA)/Food Safety and Inspection Service (FSIS) Microbiology Laboratory Guidebook. After 48 h of incubation, the PCR method in all cases showed equal or better results than the reference cultural FDA/BAM or USDA/FSIS methods. Fifteen out of 20 tested food types gave exactly the same amount of positive samples for both methods in both inoculation levels. For 5 out of 20 foodstuffs, the PCR method resulted in more positives than the reference method after 48 h of incubation. Following AOAC RI definition, these were false positives because they were not confirmed by the reference method (false-positive rate for low inoculated foodstuffs: 5.4%; for high inoculated foodstuffs: 7.1%). Without calculating these unconfirmed positives, the PCR method showed equal sensitivity results compared to the alternative method. With the unconfirmed PCR-positives included into the calculations, the alternative PCR method showed a higher sensitivity than the microbiological methods (low inoculation level: 100 vs 98.0%; sensitivity rate: 1; high inoculation level: 99.7 vs 97.7%; sensitivity rate, 1). All in-house and independently tested uninoculated food samples were negative for L. monocytogenes. The ruggedness testing of both ShortPrep foodproof II Kit and Roche/BIOTECON LightCycler foodproof L. monocytogenes Detection Kit showed no noteworthy influences to any variation of the parameters component concentration, apparatus comparison, tester comparison, and sample volumes. In total, 102 L. monocytogenes isolates (cultures and pure DNA) were tested and detected for the inclusivity study, including all isolates claimed by the AOAC RI. The exclusivity study included 60 non-L. monocytogenes bacteria. None of the tested isolates gave a false-positive result; specificity was 100%. Three different lots were tested in the lot-to-lot study. All 3 lots gave equal results. The stability study was subdivided into 3 parts: long-term study, stress test, and freeze-defrost test. Three lots were tested in 4 time intervals within a period of 13 months. They all gave comparable results for all test intervals. For the stress test, LightCycler L. monocytogenes detection mixes were stored at different temperatures and tested at different time points during 1 month. Stable results were produced at all storage temperatures. The freeze-defrost analysis showed no noteworthy aggravation of test results. The independent validation study examined by Campden and Chorleywood Food Research Association Group (CCFRA) demonstrated again that the LightCycler L. monocytogenes detection system shows a comparable sensitivity to reference methods. With both the LightCycler PCR and BAM methods, 19 out of 20 inoculated food samples were detected. The 24 h PCR results generated by the LightCycler system corresponded directly with the FDA/BAM culture results. However, the 48 h PCR results did not relate exactly to the FDA/BAM results, as one sample found to be positive by the 48 h PCR could not be culturally confirmed and another sample which was negative by the 48 h PCR was culturally positive.

Evaluation of the 3M™ Petrifilm™ Salmonella express system for the detection of Salmonella species in selected foods: collaborative study.

PubMed

Bird, Patrick; Flannery, Jonathan; Crowley, Erin; Agin, James; Goins, David; Jechorek, Robert

2014-01-01

The 3M™ Petriflm™ Salmonella Express (SALX) System is a simple, ready-to-use chromogenic culture medium system for the rapid qualitative detection and biochemical confirmation of Salmonella spp. in food and food process environmental samples. The 3M Petrifilm SALX System was compared using an unpaired study design in a multilaboratory collaborative study to the U.S. Department of Agriculture/Food Safety and Inspection Service (USDA/FSIS) Microbiology Laboratory Guidebook (MLG) 4.07 (2013) Isolation and Identification of Salmonella from Meat, Poultry, Pasteurized Egg and Catfish Products and Carcass and Environmental Sponges for raw ground beef and the U.S. Food and Drug Administration Bacteriological Analytical Manual (FDA/BAM) Chapter 5, Salmonella (2011) reference method for dry dog food following the current AOAC validation guidelines. For this study, a total of 17 laboratories located throughout the continental United States evaluated 1872 test portions. For the 3M Petrifilm SALX System, raw ground beef was analyzed using 25 g test portions, and dry dog food was analyzed using 375 g test portions. For the reference methods, 25 g test portions of each inatrix were analyzed. The two matrices were artificially contaminated with Salmonella at three inoculation levels: an uninoculated control level (0 CFU/test portion), a low inoculum level (0.2-2 CFU/test portion), and a high inoculum level (2-5 CFU/test portion). Each inoculation level was statistically analyzed using the probability of detection statistical model. For the raw ground beef and dry dog food test portions, no significant differences at the 95% confidence interval were observed in the number of positive samples detected by the 3M Petrifilm SALX System versus either the USDA/FSIS-MLG or FDA/BAM methods.

Anti-synchronization control of BAM memristive neural networks with multiple proportional delays and stochastic perturbations

NASA Astrophysics Data System (ADS)

Wang, Weiping; Yuan, Manman; Luo, Xiong; Liu, Linlin; Zhang, Yao

2018-01-01

Proportional delay is a class of unbounded time-varying delay. A class of bidirectional associative memory (BAM) memristive neural networks with multiple proportional delays is concerned in this paper. First, we propose the model of BAM memristive neural networks with multiple proportional delays and stochastic perturbations. Furthermore, by choosing suitable nonlinear variable transformations, the BAM memristive neural networks with multiple proportional delays can be transformed into the BAM memristive neural networks with constant delays. Based on the drive-response system concept, differential inclusions theory and Lyapunov stability theory, some anti-synchronization criteria are obtained. Finally, the effectiveness of proposed criteria are demonstrated through numerical examples.

biobambam: tools for read pair collation based algorithms on BAM files

PubMed Central

2014-01-01

Background Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs. Results In this paper we introduce biobambam, a set of tools based on the efficient collation of alignments in BAM files by read name. The employed collation algorithm avoids time and space consuming sorting of alignments by read name where this is possible without using more than a specified amount of main memory. Using this algorithm tasks like duplicate marking in BAM files and conversion of BAM files to the FastQ format can be performed very efficiently with limited resources. We also make the collation algorithm available in the form of an API for other projects. This API is part of the libmaus package. Conclusions In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities our approach can often perform an equivalent task more efficiently in terms of the required main memory and run-time. Our BAM to FastQ conversion is faster than all widely known alternatives including Picard and bamUtil. Our duplicate marking is about as fast as the closest competitor bamUtil for small data sets and faster than all known alternatives on large and complex data sets.

The Microstructure Analysis of Barium M- Hexaferrite Particles Coated by Pani Conducting Material with In Situ Polymerization Process

NASA Astrophysics Data System (ADS)

Zainuri, M.; Amalia, L.

2017-05-01

Barium M-Hexaferrite (BaM) was synthesized by coprecipitation method and doped with Zn. Polyaniline (PANI) was synthesized by chemically and doped DBSA. The composite of PANI/BaM was synthesized by in situ polymerization method. The phase identification of the sample was performed by XRD, FTIR and SEM. Based on XRD data, the phase composition of BaM and hematite are 85.52 % and 14.48%. The characteristic peaks of PANI occur at 3435, 1637, 1473, 1298, 1127, 1009, and 799 cm-1. The characteristic metal oxide stretching peaks of BaM occurs at 575 and 437 cm-1. There is no phase changing in PANI/BaM composite. Based on SEM photography, the shape of BaM is hexagonal. The particle size of BaM powder ranges from 400-700 nm. The qualitative interfacial bonding between PANI and BaM particles are conducted very well and the both materials have good wettability.

Comparison of a novel strategy for the detection and isolation of Salmonella in shell eggs with the Food and Drug Administration Bacteriological Analytical Manual method.

PubMed

Zhang, Guodong; Thau, Eve; Brown, Eric W; Hammack, Thomas S

2013-12-01

The current FDA Bacteriological Analytical Manual (BAM) method for the detection of Salmonella in eggs requires 2 wk to complete. The objective of this project was to improve the BAM method for the detection and isolation of Salmonella in whole shell eggs. A novel protocol, using 1,000 g of liquid eggs for direct preenrichment with 2 L of tryptic soy broth (TSB) followed by enrichment using Rappaport-Vassiliadis and Tetrathionate broths, was compared with the standard BAM method, which requires 96 h room temperature incubation of whole shell egg samples followed by preenrichment in TSB supplemented with FeSO4. Four Salmonella ser. Enteritidis (4 phage types) and one Salmonella ser. Heidelberg isolates were used in the study. Bulk inoculated pooled liquid eggs, weighing 52 or 56 kg (approximately 1,100 eggs) were used in each trial. Twenty 1,000-g test portions were withdrawn from the pooled eggs for both the alternative and the reference methods. Test portions were inoculated with Salmonella at 1 to 5 cfu/1,000 g eggs. Two replicates were performed for each isolate. In the 8 trials conducted with Salmonella ser. Enteritidis, the alternative method was significantly (P < 0.05) more productive than the reference method in 3 trials, and significantly (P < 0.05) less productive than the reference method in 1 trial. There were no significant (P < 0.05) differences between the 2 methods for the other 4 trials. For Salmonella ser. Heidelberg, combined data from 2 trials showed the alternative method was significantly (P < 0.05) more efficient than the BAM method. We have concluded that the alternative method, described herein, has the potential to replace the current BAM culture method for detection and isolation of Salmonella from shell eggs based on the following factors: 1) the alternative method is 4 d shorter than the reference method; 2) it uses regular TSB instead of the more complicated TSB supplemented with FeSO4; and 3) it was equivalent or superior to the reference method in 9 out of 10 trials for the detection of Salmonella in shell eggs.

DHS small-scale safety and thermal testing of improvised explosives-comparison of testing performance

NASA Astrophysics Data System (ADS)

Reynolds, J. G.; Sandstrom, M. M.; Brown, G. W.; Warner, K. F.; Phillips, J. J.; Shelley, T. J.; Reyes, J. A.; Hsu, P. C.

2014-05-01

One of the first steps in establishing safe handling procedures for explosives is small-scale safety and thermal (SSST) testing. To better understand the response of improvised materials or homemade explosives (HMEs) to SSST testing, 16 HME materials were compared to three standard military explosives in a proficiency-type round robin study among five laboratories-two DoD and three DOE-sponsored by DHS. The testing matrix has been designed to address problems encountered with improvised materials-powder mixtures, liquid suspensions, partially wetted solids, immiscible liquids, and reactive materials. More than 30 issues have been identified that indicate standard test methods may require modification when applied to HMEs to derive accurate sensitivity assessments needed for developing safe handling and storage practices. This paper presents a generalized comparison of the results among the testing participants, comparison of friction results from BAM (German Bundesanstalt für Materi-alprüfung) and ABL (Allegany Ballistics Laboratory) designed testing equipment, and an overview of the statistical results from the RDX (1,3,5-Trinitroperhydro-1,3,5-triazine) standard tested throughout the proficiency test.

Isolation of equine herpesvirus 3 (EHV-3) from equine coital exanthema of two stallions and sero-epidemiology of EHV-3 infection in Japan

PubMed Central

KIRISAWA, Rikio; TOISHI, Yuko; AKAMATSU, Ai; SOEJIMA, Kosuke; MIYASHITA, Taisuke; TSUNODA, Nobuo

2017-01-01

In the spring of 2015, two stallions reared in Farms A and B in Hokkaido in Japan showed symptoms of equine coital exanthema. Equine herpesvirus 3 (EHV-3) was isolated from penis swab samples of both stallions, and the isolates from each stallion in Farms A and B were designated as SS-1 and YS-1 strains, respectively. BamHI restriction profiles of SS-1 and Japanese reference strain Iwate-1 were indistinguishable, but the BamHI-A fragment of YS-1 was larger than those of SS-1 and Iwate-1 by 1.9 kbp because of the lack of two BamHI sites. Nucleotide sequence analyses of glycoprotein G (gG), gB, gC and VP13/14 coding regions revealed that SS-1 and YS-1 had 99.77% to 100% identities to each other. These results suggested that the origins of SS-1 and YS-1 were different. For a sero-epidemiological survey, serum neutralizing tests using SS-1 against 319 sera of horses from eight farms in Hokkaido were conducted. Six of the eight farms were EHV-3 antibody-positive, and positive rates ranged from 2.6% to 17.6%. To determine the infection time of four EHV-3 antibody-positive horses, a retrospective study was conducted. Infection time of the four horses was in the breeding season, and re-infection or reactivation of latently infected EHV-3 might have occurred in one horse. However, these four horses had never shown any clinical symptoms. The results suggested that several EHV-3 strains are distributed in Japan and that infection is maintained widely in horses without clinical symptoms. PMID:28132964

In situ hybridisation of EBV DNA-DNA hybrids using wet heat in polypropylene containers.

PubMed Central

Labrecque, L G

1992-01-01

AIMS: To explore procedures designed to optimise DNA-DNA in situ hybridisation, using cells infected with Epstein-Barr virus (EBV) and tissues and subfragments of the EBV DNA as probes. METHODS: The denaturation step occurred in a polypropylene container, using wet heat generated by a hot water container, the pressure cooker, or the microwave oven, without coverslips, reaching a temperature of 121 degrees C or more in these two last systems. Two different visualisation systems were used. RESULTS: Fixed cells and tumours harbouring a high and medium to low copy number (a few hundreds to 33 copies per cell), were clearly labelled, using a simple reiterated subfragment (BamW) of the EBV DNA, and fresh frozen cells, harbouring a very low copy number (one to two on average) labelled using BamW as well as BamH (single non-reiterated 6 kilobase subfragment). CONCLUSION: This is a valuable alternative technique for DNA-DNA ISH that can be used in fresh frozen samples as well as fixed samples. Images PMID:1336018

Discrete-time BAM neural networks with variable delays

NASA Astrophysics Data System (ADS)

Liu, Xin-Ge; Tang, Mei-Lan; Martin, Ralph; Liu, Xin-Bi

2007-07-01

This Letter deals with the global exponential stability of discrete-time bidirectional associative memory (BAM) neural networks with variable delays. Using a Lyapunov functional, and linear matrix inequality techniques (LMI), we derive a new delay-dependent exponential stability criterion for BAM neural networks with variable delays. As this criterion has no extra constraints on the variable delay functions, it can be applied to quite general BAM neural networks with a broad range of time delay functions. It is also easy to use in practice. An example is provided to illustrate the theoretical development.

A targeted boost-and-sort immunization strategy using Escherichia coli BamA identifies rare growth inhibitory antibodies.

PubMed

Vij, Rajesh; Lin, Zhonghua; Chiang, Nancy; Vernes, Jean-Michel; Storek, Kelly M; Park, Summer; Chan, Joyce; Meng, Y Gloria; Comps-Agrar, Laetitia; Luan, Peng; Lee, Sophia; Schneider, Kellen; Bevers, Jack; Zilberleyb, Inna; Tam, Christine; Koth, Christopher M; Xu, Min; Gill, Avinash; Auerbach, Marcy R; Smith, Peter A; Rutherford, Steven T; Nakamura, Gerald; Seshasayee, Dhaya; Payandeh, Jian; Koerber, James T

2018-05-08

Outer membrane proteins (OMPs) in Gram-negative bacteria are essential for a number of cellular functions including nutrient transport and drug efflux. Escherichia coli BamA is an essential component of the OMP β-barrel assembly machinery and a potential novel antibacterial target that has been proposed to undergo large (~15 Å) conformational changes. Here, we explored methods to isolate anti-BamA monoclonal antibodies (mAbs) that might alter the function of this OMP and ultimately lead to bacterial growth inhibition. We first optimized traditional immunization approaches but failed to identify mAbs that altered cell growth after screening >3000 hybridomas. We then developed a "targeted boost-and-sort" strategy that combines bacterial cell immunizations, purified BamA protein boosts, and single hybridoma cell sorting using amphipol-reconstituted BamA antigen. This unique workflow improves the discovery efficiency of FACS + mAbs by >600-fold and enabled the identification of rare anti-BamA mAbs with bacterial growth inhibitory activity in the presence of a truncated lipopolysaccharide layer. These mAbs represent novel tools for dissecting the BamA-mediated mechanism of β-barrel folding and our workflow establishes a new template for the efficient discovery of novel mAbs against other highly dynamic membrane proteins.

Bile acid malabsorption after pelvic and prostate intensity modulated radiation therapy: an uncommon but treatable condition.

PubMed

Harris, Victoria; Benton, Barbara; Sohaib, Aslam; Dearnaley, David; Andreyev, H Jervoise N

2012-12-01

Intensity modulated radiation therapy (IMRT) is a significant therapeutic advance in prostate cancer, allowing increased tumor dose delivery and increased sparing of normal tissues. IMRT planning uses strict dose constraints to nearby organs to limit toxicity. Bile acid malabsorption (BAM) is a treatable disorder of the terminal ileum (TI) that presents with symptoms similar to radiation therapy toxicity. It has not been described in patients receiving RT for prostate cancer in the contemporary era. We describe new-onset BAM in men after IMRT for prostate cancer. Diagnosis of new-onset BAM was established after typical symptoms developed, selenium-75 homocholic acid taurine (SeHCAT) scanning showed 7-day retention of <15%, and patients' symptoms unequivocally responded to a bile acid sequestrant. The TI was identified on the original radiation therapy plan, and the radiation dose delivered was calculated and compared with accepted dose-volume constraints. Five of 423 men treated in a prospective series of high-dose prostate and pelvic IMRT were identified with new onset BAM (median age, 65 years old). All reported having normal bowel habits before RT. The volume of TI ranged from 26-141 cc. The radiation dose received by the TI varied between 11.4 Gy and 62.1 Gy (uncorrected). Three of 5 patients had TI treated in excess of 45 Gy (equivalent dose calculated in 2-Gy fractions, using an α/β ratio of 3) with volumes ranging from 1.6 cc-49.0 cc. One patient had mild BAM (SeHCAT retention, 10%-15%), 2 had moderate BAM (SeHCAT retention, 5%-10%), and 2 had severe BAM (SeHCAT retention, <5%). The 3 patients whose TI received ≥45 Gy developed moderate to severe BAM, whereas those whose TI received <45 Gy had only mild to moderate BAM. Radiation delivered to the TI during IMRT may cause BAM. Identification of the TI from unenhanced RT planning computed tomography scans is difficult and may impede accurate dosimetric evaluation. Thorough toxicity assessment and close liaison between oncologist and gastroenterologist allow timely diagnosis and treatment. Copyright © 2012 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harris, Victoria; Benton, Barbara; Sohaib, Aslam

Purpose: Intensity modulated radiation therapy (IMRT) is a significant therapeutic advance in prostate cancer, allowing increased tumor dose delivery and increased sparing of normal tissues. IMRT planning uses strict dose constraints to nearby organs to limit toxicity. Bile acid malabsorption (BAM) is a treatable disorder of the terminal ileum (TI) that presents with symptoms similar to radiation therapy toxicity. It has not been described in patients receiving RT for prostate cancer in the contemporary era. We describe new-onset BAM in men after IMRT for prostate cancer. Methods and Materials: Diagnosis of new-onset BAM was established after typical symptoms developed, selenium-75more » homocholic acid taurine (SeHCAT) scanning showed 7-day retention of <15%, and patients' symptoms unequivocally responded to a bile acid sequestrant. The TI was identified on the original radiation therapy plan, and the radiation dose delivered was calculated and compared with accepted dose-volume constraints. Results: Five of 423 men treated in a prospective series of high-dose prostate and pelvic IMRT were identified with new onset BAM (median age, 65 years old). All reported having normal bowel habits before RT. The volume of TI ranged from 26-141 cc. The radiation dose received by the TI varied between 11.4 Gy and 62.1 Gy (uncorrected). Three of 5 patients had TI treated in excess of 45 Gy (equivalent dose calculated in 2-Gy fractions, using an {alpha}/{beta} ratio of 3) with volumes ranging from 1.6 cc-49.0 cc. One patient had mild BAM (SeHCAT retention, 10%-15%), 2 had moderate BAM (SeHCAT retention, 5%-10%), and 2 had severe BAM (SeHCAT retention, <5%). The 3 patients whose TI received {>=}45 Gy developed moderate to severe BAM, whereas those whose TI received <45 Gy had only mild to moderate BAM. Conclusions: Radiation delivered to the TI during IMRT may cause BAM. Identification of the TI from unenhanced RT planning computed tomography scans is difficult and may impede accurate dosimetric evaluation. Thorough toxicity assessment and close liaison between oncologist and gastroenterologist allow timely diagnosis and treatment.« less

Interaction of Elastic Waves with Corrosion Damage

DTIC Science & Technology

2010-08-01

Joachim Schneider -Gloetzl, Gloetzl GmbH, Rheinstetten, Germany Rainer Gloetzl, RG Research, Ettlingen, Germany...Katerina Krebber, Sascha Liehr, Mario Wendt, Aleksander Wosniok, BAM, Federal Institute for Materials, Research and Testing, Berlin, Germany

Design Framework Validation for a Hot Spot on Complex Aircraft Structures

DTIC Science & Technology

2010-08-01

LEONARD, S. E. OLSON AND M. P. DESIMIO Joachim Schneider -Gloetzl, Gloetzl GmbH, Rh instetten, Germany...Rainer Gloetzl, RG Research, Ettlingen, Ger any Katerina Krebber, Sascha Liehr, Mario Wendt, Aleksander Wosniok, BAM, Federal Institute for

Are bile acid malabsorption and bile acid diarrhoea important causes of loose stool complicating cancer therapy?

PubMed

Phillips, F; Muls, A C G; Lalji, A; Andreyev, H J N

2015-08-01

Gastrointestinal (GI) symptoms during and after cancer therapy can significantly affect quality of life and interfere with treatment. This study assessed whether bile acid malabsorption (BAM) or bile acid diarrhoea (BAD) are important causes of diarrhoea associated with cancer treatment. A retrospective analysis was carried out of consecutive patients assessed for BAM using ((75) Se) Selenium homocholic acid taurocholate (SeHCAT) scanning, after reporting any episodes of loose stool, attending a gastroenterology clinic in a cancer centre. Between 2009 and 2013, 506 consecutive patients (54.5% male; age range: 20-91 years), were scanned. BAM/BAD was diagnosed in 215 (42.5%). It was mild in 25.6%, moderate in 29.3% and severe in 45.1%. Pelvic chemoradiation had induced BAM in > 50% of patients. BAM was also frequent after treatment for conditions not previously associated with BAM, such as anal and colorectal cancer, and was present in > 75% of patients referred after pancreatic surgery. It was also unexpectedly frequent in patients who were treated for malignancy outside the GI tract, such as breast cancer and haematological malignancy. BAM/BAD are very common and under-appreciated causes of GI symptoms after cancer treatment. Health professionals should have a low threshold in suspecting this condition, as diagnosis and treatment can significantly improve quality of life. Colorectal Disease © 2015 The Association of Coloproctology of Great Britain and Ireland.

BAM! Physical Activity

MedlinePlus

... Vegetables Desserts Dining Decisions Mobile App – Dining Decisions Game Online Game – Dining Decisions Questions Answered Under the Microscope Xpert ... Test Your Smarts Feeling Frazzled…? Feeling Stressed Out? Game Grind Your Mind Game Kabam! Comic Creator Best ...

Effect of Novel Starter Culture on Reduction of Biogenic Amines, Quality Improvement, and Sensory Properties of Doenjang, a Traditional Korean Soybean Fermented Sauce Variety.

PubMed

Shukla, Shruti; Lee, Jong Suk; Park, Hae-Kyong; Yoo, Jung-Ah; Hong, Sung-Yong; Kim, Jong-Kyu; Kim, Myunghee

2015-08-01

To select appropriate microorganisms as starter cultures for the reliable and reproducible fermentation of soybean fermented products of Korean Doenjang, various ratios of fungi (Aspergillus oryzae J, Mucor racemosus 15, M. racemosus 42) combined with Bacillus subtilis TKSP 24 were selected as either single, double, or multiple Meju strains for commercial mass production of Doenjang, followed by analysis of sensory characteristics. In the sensory evaluation, Doenjang BAM15-1 and BAM42-1, which were fermented with multiple strains (1:1:1), showed the highest sensory scores as compared to control. Based on sensory characteristics, 6 Doenjang samples were subjected to quantitative determination of amino acids, free sugars, and organic acids (volatile and nonvolatile) contents, followed by determination of biogenic amines. Total sweet taste amino acid contents were highest in BAM15-1 and BAM42-1 samples (333.7 and 295.8 mg/100 g, respectively) and similar that of control (391.1 mg/100 g). Samples BAM15-1 and BAM42-1 showed the relatively high volatile and nonvolatile organic acid contents (154.24, 192.26, and 71.31, 82.42 mg/100 g, respectively). In addition, BAM15-1 and BAM42-1 showed negligible biogenic amine formation, ranging from 0.00 to 1.02 and 0.00 to 3.92 mg/100 g, respectively. These findings indicate that determination of food components along with sensory and quality attributes using multiple microbial Meju strains as a starter culture may provide substantial results on improved quality fermented Doenjang products. © 2015 Institute of Food Technologists®

Existence and global exponential stability of periodic solution of memristor-based BAM neural networks with time-varying delays.

PubMed

Li, Hongfei; Jiang, Haijun; Hu, Cheng

2016-03-01

In this paper, we investigate a class of memristor-based BAM neural networks with time-varying delays. Under the framework of Filippov solutions, boundedness and ultimate boundedness of solutions of memristor-based BAM neural networks are guaranteed by Chain rule and inequalities technique. Moreover, a new method involving Yoshizawa-like theorem is favorably employed to acquire the existence of periodic solution. By applying the theory of set-valued maps and functional differential inclusions, an available Lyapunov functional and some new testable algebraic criteria are derived for ensuring the uniqueness and global exponential stability of periodic solution of memristor-based BAM neural networks. The obtained results expand and complement some previous work on memristor-based BAM neural networks. Finally, a numerical example is provided to show the applicability and effectiveness of our theoretical results. Copyright © 2015 Elsevier Ltd. All rights reserved.

BAM! Guide to Getting Along

MedlinePlus

... Vegetables Desserts Dining Decisions Mobile App – Dining Decisions Game Online Game – Dining Decisions Questions Answered Under the Microscope Xpert ... Test Your Smarts Feeling Frazzled…? Feeling Stressed Out? Game Grind Your Mind Game Kabam! Comic Creator Best ...

BAM! Body and Mind

MedlinePlus

... Vegetables Desserts Dining Decisions Mobile App – Dining Decisions Game Online Game – Dining Decisions Questions Answered Under the Microscope Xpert ... Test Your Smarts Feeling Frazzled…? Feeling Stressed Out? Game Grind Your Mind Game Kabam! Comic Creator Best ...

Impact of breathing awareness meditation on ambulatory blood pressure and sodium handling in prehypertensive African American adolescents.

PubMed

Barnes, Vernon A; Pendergrast, Robert A; Harshfield, Gregory A; Treiber, Frank A

2008-01-01

This study evaluated the impact of a breathing awareness meditation (BAM) program on ambulatory blood pressure and sodium handling in African American adolescents with high-normal systolic blood pressure (SBP) levels. Following three consecutive days of SBP screenings, 66 eligible ninth graders were randomly assigned by school to either BAM (n = 20) or health education control (n = 46) groups. The BAM group engaged in 10-minute BAM sessions at school and at home each day for three months. Teachers conducted sessions at school during health classes. Before and after the intervention, overnight urine samples were collected, and ambulatory SBP, diastolic blood pressure, and heart rate were recorded periodically for 24 hours. Significant changes before and after the intervention were observed between BAM and control groups for SBP during school hours (-4.7 vs .9 mm Hg, P < .05), SBP at night (-4.8 vs -.6 mm Hg, P < .01), and heart rate during school hours (-6.7 vs -2.3 bpm, P < .02), adjusted for their respective preintervention levels. The overnight urinary sodium excretion rate decreased in the BAM group but increased in the control group (-.3 +/- 4.9 vs 1.1 +/- 4.0 mEq/hour, P < .03). These findings demonstrate the potential beneficial impact of BAM taught by school health teachers on blood pressure control in the natural environment in African American youth at risk for development of hypertension.

Regulation of Leaf Starch Degradation by Abscisic Acid Is Important for Osmotic Stress Tolerance in Plants[OPEN

PubMed Central

Thalmann, Matthias; Pazmino, Diana; Seung, David; Horrer, Daniel; Nigro, Arianna; Meier, Tiago; Zeeman, Samuel C.; Santelia, Diana

2016-01-01

Starch serves functions that range over a timescale of minutes to years, according to the cell type from which it is derived. In guard cells, starch is rapidly mobilized by the synergistic action of β-AMYLASE1 (BAM1) and α-AMYLASE3 (AMY3) to promote stomatal opening. In the leaves, starch typically accumulates gradually during the day and is degraded at night by BAM3 to support heterotrophic metabolism. During osmotic stress, starch is degraded in the light by stress-activated BAM1 to release sugar and sugar-derived osmolytes. Here, we report that AMY3 is also involved in stress-induced starch degradation. Recently isolated Arabidopsis thaliana amy3 bam1 double mutants are hypersensitive to osmotic stress, showing impaired root growth. amy3 bam1 plants close their stomata under osmotic stress at similar rates as the wild type but fail to mobilize starch in the leaves. 14C labeling showed that amy3 bam1 plants have reduced carbon export to the root, affecting osmolyte accumulation and root growth during stress. Using genetic approaches, we further demonstrate that abscisic acid controls the activity of BAM1 and AMY3 in leaves under osmotic stress through the AREB/ABF-SnRK2 kinase-signaling pathway. We propose that differential regulation and isoform subfunctionalization define starch-adaptive plasticity, ensuring an optimal carbon supply for continued growth under an ever-changing environment. PMID:27436713

Trends of Serum Electrolyte Changes in Crush syndrome patients of Bam Earthquake; a Cross sectional Study.

PubMed

Safari, Saeed; Eshaghzade, Mehdi; Najafi, Iraj; Baratloo, Alireza; Hashemi, Behrooz; Forouzanfar, Mohammad Mehdi; Rahmati, Farhad

2017-01-01

Electrolyte imbalances are very common among crushed earthquake victims but there is not enough data regarding their trend of changes. The present study was designed to evaluate the trend of changes in sodium, calcium, and phosphorus ions among crush syndrome patients. In this retrospective cross-sectional study, using the database of Bam earthquake victims, which was developed by Iranian Society of Nephrology following Bam earthquake, Iran, 2003, the 10-day trend of sodium, calcium, and phosphorus ions changes in > 15 years old crush syndrome patients was evaluated. 118 patients with the mean age of 25.6 ± 6.9 years were studied (57.3 male). On the first day of admission, 52.5% (95% CI: 42.7 - 62.3) of the patients had hyponatremia, which reached 43.9% (95% CI: 28.5 - 59.3) on day 10. 100.0% of patients were hypocalcemic on admission and serum calcium level did not change dramatically during the 10 days of hospitalization. The prevalence of hyperphosphatemia on the first day was 90.5% (95% CI: 81.5 - 99.5) and on the 10 th day of hospitalization 66.7% (95% CI: 48.5 - 84.8) of the patients were still affected. The results of the present study shows the 52.5% prevalence of hyponatremia, 100% hypocalcemia, and 90.5% hyperphosphatemia among crush syndrome patients of Bam earthquake victims on the first day of admission. Evaluation of 10-day trend shows a slow decreasing pattern of these imbalances as after 10 days, 43.9% still remain hyponatremic, 92.3% hypocalcemic, and 66.7% hypophosphatemic.

BioAerosol Mass Spectrometry: Reagentless Detection of Individual Airborne Spores and Other Bioagent Particles Based on Laser Desorption/Ionization Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steele, Paul Thomas

2004-09-01

Better devices are needed for the detection of aerosolized biological warfare agents. Advances in the ongoing development of one such device, the BioAerosol Mass Spectrometry (BAMS) system, are described here in detail. The system samples individual, micrometer-sized particles directly from the air and analyzes them in real-time without sample preparation or use of reagents. At the core of the BAMS system is a dual-polarity, single-particle mass spectrometer with a laser based desorption and ionization (DI) system. The mass spectra produced by early proof-of-concept instruments were highly variable and contained limited information to differentiate certain types of similar biological particles. Themore » investigation of this variability and subsequent changes to the DI laser system are described. The modifications have reduced the observed variability and thereby increased the usable information content in the spectra. These improvements would have little value without software to analyze and identify the mass spectra. Important improvements have been made to the algorithms that initially processed and analyzed the data. Single particles can be identified with an impressive level of accuracy, but to obtain significant reductions in the overall false alarm rate of the BAMS instrument, alarm decisions must be made dynamically on the basis of multiple analyzed particles. A statistical model has been developed to make these decisions and the resulting performance of a hypothetical BAMS system is quantitatively predicted. The predictions indicate that a BAMS system, with reasonably attainable characteristics, can operate with a very low false alarm rate (orders of magnitude lower than some currently fielded biodetectors) while still being sensitive to small concentrations of biological particles in a large range of environments. Proof-of-concept instruments, incorporating some of the modifications described here, have already performed well in independent testing.« less

Romer Labs RapidChek®Listeria monocytogenes Test System for the Detection of L. monocytogenes on Selected Foods and Environmental Surfaces.

PubMed

Juck, Gregory; Gonzalez, Verapaz; Allen, Ann-Christine Olsson; Sutzko, Meredith; Seward, Kody; Muldoon, Mark T

2018-04-27

The Romer Labs RapidChek ® Listeria monocytogenes test system (Performance Tested Method ℠ 011805) was validated against the U.S. Department of Agriculture-Food Safety and Inspection Service Microbiology Laboratory Guidebook (USDA-FSIS/MLG), U.S. Food and Drug Association Bacteriological Analytical Manual (FDA/BAM), and AOAC Official Methods of Analysis ℠ (AOAC/OMA) cultural reference methods for the detection of L. monocytogenes on selected foods including hot dogs, frozen cooked breaded chicken, frozen cooked shrimp, cured ham, and ice cream, and environmental surfaces including stainless steel and plastic in an unpaired study design. The RapidChek method uses a proprietary enrichment media system, a 44-48 h enrichment at 30 ± 1°C, and detects L. monocytogenes on an immunochromatographic lateral flow device within 10 min. Different L. monocytogenes strains were used to spike each of the matrixes. Samples were confirmed based on the reference method confirmations and an alternate confirmation method. A total of 140 low-level spiked samples were tested by the RapidChek method after enrichment for 44-48 h in parallel with the cultural reference method. There were 88 RapidChek presumptive positives. One of the presumptive positives was not confirmed culturally. Additionally, one of the culturally confirmed samples did not exhibit a presumptive positive. No difference between the alternate confirmation method and reference confirmation method was observed. The respective cultural reference methods (USDA-FSIS/MLG, FDA/BAM, and AOAC/OMA) produced a total of 63 confirmed positive results. Nonspiked samples from all foods were reported as negative for L. monocytogenes by all methods. Probability of detection analysis demonstrated no significant differences in the number of positive samples detected by the RapidChek method and the respective cultural reference method.

The Drosophila nuclear lamina protein otefin is required for germline stem cell survival.

PubMed

Barton, Lacy J; Pinto, Belinda S; Wallrath, Lori L; Geyer, Pamela K

2013-06-24

LEM domain (LEM-D) proteins are components of an extensive protein network that assembles beneath the inner nuclear envelope. Defects in LEM-D proteins cause tissue-restricted human diseases associated with altered stem cell homeostasis. Otefin (Ote) is a Drosophila LEM-D protein that is intrinsically required for female germline stem cell (GSC) maintenance. Previous studies linked Ote loss with transcriptional activation of the key differentiation gene bag-of-marbles (bam), leading to the model in which Ote tethers the bam gene to the nuclear periphery for gene silencing. Using genetic and phenotypic analyses of multiple ote(-/-) backgrounds, we obtained evidence that is inconsistent with this model. We show that bam repression is maintained in ote(-/-) GSCs and that germ cell loss persists in ote(-/-), bam(-/-) mutants, together demonstrating that GSC loss is independent of bam transcription. We show that the primary defect in ote(-/-) GSCs is a block of differentiation, which ultimately leads to germ cell death. Copyright © 2013 Elsevier Inc. All rights reserved.

The Drosophila bag of marbles Gene Interacts Genetically with Wolbachia and Shows Female-Specific Effects of Divergence

PubMed Central

Flores, Heather A.; Bubnell, Jaclyn E.; Aquadro, Charles F.; Barbash, Daniel A.

2015-01-01

Many reproductive proteins from diverse taxa evolve rapidly and adaptively. These proteins are typically involved in late stages of reproduction such as sperm development and fertilization, and are more often functional in males than females. Surprisingly, many germline stem cell (GSC) regulatory genes, which are essential for the earliest stages of reproduction, also evolve adaptively in Drosophila. One example is the bag of marbles (bam) gene, which is required for GSC differentiation and germline cyst development in females and for regulating mitotic divisions and entry to spermatocyte differentiation in males. Here we show that the extensive divergence of bam between Drosophila melanogaster and D. simulans affects bam function in females but has no apparent effect in males. We further find that infection with Wolbachia pipientis, an endosymbiotic bacterium that can affect host reproduction through various mechanisms, partially suppresses female sterility caused by bam mutations in D. melanogaster and interacts differentially with bam orthologs from D. melanogaster and D. simulans. We propose that the adaptive evolution of bam has been driven at least in part by the long-term interactions between Drosophila species and Wolbachia. More generally, we suggest that microbial infections of the germline may explain the unexpected pattern of evolution of several GSC regulatory genes. PMID:26291077

Optimal design of stormwater basins with bio-sorption activated media (BAM) in karst environments - phase I : site screening and selection.

DOT National Transportation Integrated Search

2015-12-01

Anthropogenic activities within the Silver Springs springshed over recent decades may have contributed : to elevated nutrient concentrations in stormwater runoff and groundwater, leading to the eutrophication : of Silver Springs. To remove the nutrie...

Fixed-time synchronization of memristor-based BAM neural networks with time-varying discrete delay.

PubMed

Chen, Chuan; Li, Lixiang; Peng, Haipeng; Yang, Yixian

2017-12-01

This paper is devoted to studying the fixed-time synchronization of memristor-based BAM neural networks (MBAMNNs) with discrete delay. Fixed-time synchronization means that synchronization can be achieved in a fixed time for any initial values of the considered systems. In the light of the double-layer structure of MBAMNNs, we design two similar feedback controllers. Based on Lyapunov stability theories, several criteria are established to guarantee that the drive and response MBAMNNs can realize synchronization in a fixed time. In particular, by changing the parameters of controllers, this fixed time can be adjusted to some desired value in advance, irrespective of the initial values of MBAMNNs. Numerical simulations are included to validate the derived results. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synthesis and Characterization Materials M-Barium Hexaferrite Doping Ions Co-Mn Nano Particle

NASA Astrophysics Data System (ADS)

Susilawati; Doyan, A.; Sahlam

2017-05-01

This research has been success in the synthesis of M-Barium hexaferrite (BaM) doping Co-Mn ions using coprecipitation method are expected to be applied as a base material in the coating RADAR. M-Barium hexaferrite (BaM) are BaFe12-2xCoxMnxO19 synthesized with various concentrations (x = 0.0, 0.1, 0.2, 0.3) and the calcinations temperature (T = 400°C, 600°C, 800°C). The materials characterization using a X-Ray Diffraction (XRD), Transmission Electron Microscope (TEM), Inductance Capacitance and resistance (LCR) meter, and Vibrating Sample Magnetometer (VSM) Instruments. The measurement results using XRD shows the material has a hexagonal crystalline structure. The measurement results using a TEM show a sample of nano crystal materials with grain diameters up to 40 nm and spacing of the crystal lattice. The measurement results using a LCR-meter shows the electric conductivity of 1.15 × 10-6 S/cm to BaM without doping, 3.75 × 10-6 S/cm to 0.1 doping concentration calcination temperature of 400 °C, and 1,23 × 10-5 S/cm to 0.3 doping concentration calcination temperature of 800 °C, thus including semiconductor materials. The magnetic properties of materials using a VSM test results show the value of coercivity of 0.1 T; remanence value of 0.06 emu/g; and the saturation value of 0.42 emu/g. The results above show BaM Co-Mn metal doping potential as anti-radar material.

Optical metrology for DMD™ characterization

NASA Astrophysics Data System (ADS)

Miller, Seth A.; Mezenner, Rabah; Doane, Dennis

2001-01-01

The Digital Micromirror Device™ (DMD™) developed at Texas Instruments is a spatial light modulator composed of 500,000 to 1.3 million movable micromachined aluminum mirrors. The DMD™ serves as the engine for the current generation of computer-driven slide and video projectors, and for next generation devices in digital television and movie projectors. Because of the unique architecture and applications of the device, Texas Instruments has developed a series of customized optical testers for characterizing DMD™ performance. This paper provides a general overview of the MirrorMaster, a custom optical inspection tool. Particular attention is given to Bias Adhesion Mapping (BAM) as a device performance metric. BAM is an optical test that monitors the performance of the mirrors as a function of an applied voltage. This voltage drives the mirrors to the `on' or `off' position, and as the bias is stepped down the mirrors return to their neutral orientations. Important forces involved in this process include the electrostatic field applied, the compliance of the hinge, and static friction (stiction). BAM curves can help characterize device stiction and allow us to examine the efficacy of the lubrication system over the lifetime of the device.

Multicentre prospective survey of SeHCAT provision and practice in the UK

PubMed Central

Peacock, Janet; Coker, Bolaji; McMillan, Viktoria; Ofuya, Mercy; Lewis, Cornelius; Keevil, Stephen; Logan, Robert; McLaughlin, John; Reid, Fiona

2016-01-01

Objective A clinical diagnosis of bile acid malabsorption (BAM) can be confirmed using SeHCAT (tauroselcholic (75selenium) acid), a radiolabelled synthetic bile acid. However, while BAM can be the cause of chronic diarrhoea, it is often overlooked as a potential diagnosis. Therefore, we investigated the use of SeHCAT for diagnosis of BAM in UK hospitals. Design A multicentre survey was conducted capturing centre and patient-level information detailing patient care-pathways, clinical history, SeHCAT results, treatment with bile acid sequestrants (BAS), and follow-up in clinics. Eligible data from 38 centres and 1036 patients were entered into a validated management system. Results SeHCAT protocol varied between centres, with no standardised patient positioning, and differing referral systems. Surveyed patients had a mean age of 50 years and predominantly women (65%). The mean SeHCAT retention score for all patients was 19% (95% CI 17.8% to 20.3%). However, this differed with suspected BAM type: type 1: 9% (95% CI 6.3% to 11.4%), type 2: 21% (95% CI 19.2% to 23.0%) and type 3: 22% (95% CI 19.6% to 24.2%). Centre-defined ‘abnormal’ and ‘borderline’ results represented over 50% of the survey population. BAS treatment was prescribed to only 73% of patients with abnormal results. Conclusions The study identified a lack of consistent cut-off/threshold values, with differing centre criteria for defining an ‘abnormal’ SeHCAT result. BAS prescription was not related in a simple way to the SeHCAT result, nor to the centre-defined result, highlighting a lack of clear patient care-pathways. There is a clear need for a future diagnostic accuracy study and a better understanding of optimal management pathways. PMID:27252882

Experimental and computational study of the effect of breath-actuated mechanism built in the NEXThaler® dry powder inhaler.

PubMed

Farkas, Árpád; Lewis, David; Church, Tanya; Tweedie, Alan; Mason, Francesca; Haddrell, Allen E; Reid, Jonathan P; Horváth, Alpár; Balásházy, Imre

2017-11-25

The breath-actuated mechanism (BAM) is a mechanical unit included in NEXThaler ® with the role of delaying the emission of the drug until the inhalation flow rate of the patient is sufficiently high to detach the drug particles from their carriers. The main objective of this work was to analyse the effect of the presence of BAM on the size distribution of the emitted drug and its airway deposition efficiency and distribution. Study of the hygroscopic growth of the emitted drug particles and its effect on the deposition was another goal of this study. Size distributions of Foster ® NEXThaler ® drug particles emitted by dry powder inhalers with and without BAM have been measured by a Next Generation Impactor. Three characteristic inhalation profiles of asthmatic patients (low, moderate and high flow rates) were used for both experimental and modelling purposes. Particle hygroscopic growth was determined by a new method, where experimental measurements are combined with simulations. Upper airway and lung deposition fractions were computed assuming 5s and 10s breath-hold times. By the inclusion of BAM the fine particle fraction of the steroid component increased from 24 to 30% to 47-51%, while that of bronchodilator from 25-34% to 52-55%. The predicted upper airway steroid and bronchodilator doses decreased from about 60% to 35-40% due to BAM. At the same time, predicted lung doses increased from about 20%-35% (steroid) and from 22% to 38% (bronchodilator) for the moderate flow profile and from about 25% to 40% (steroid) and from 29% to 47% (bronchodilator) for the high inhalation flow profile. Although BDP and FF upper airway doses decreased by a factor of about two when BAM was present, lung doses of both components were about the same in the BAM and no-BAM configurations at the weakest flow profile. However, lung dose increased by 2-3% even for this profile when hygroscopic growth was taken into account. In conclusion, the NEXThaler ® BAM mechanism is a unique feature enabling high emitted fine particle fraction and enhanced drug delivery to the lungs. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Pasteurella haemolytica leukotoxin and endotoxin induced cytokine gene expression in bovine alveolar macrophages requires NF-kappaB activation and calcium elevation.

PubMed

Hsuan, S L; Kannan, M S; Jeyaseelan, S; Prakash, Y S; Malazdrewich, C; Abrahamsen, M S; Sieck, G C; Maheswaran, S K

1999-05-01

In bovine alveolar macrophages (BAMs), exposure to leukotoxin (Lkt) and endotoxin (LPS) from Pasteurella haemolytica results in expression of inflammatory cytokine genes and intracellular calcium ([Ca2+]i) elevation. Leukotoxin from P. haemolytica interacts only with leukocytes and platelets from ruminant species. Upregulation of cytokine genes in different cells by LPS involves activation of the transcription factor NF-kappaB (NF-kappaB), resulting in its translocation from the cytoplasm to the nucleus. Using immunocytochemical staining and confocal imaging, we studied whether NF-kappaB activation represents a common mechanism for the expression of multiple cytokine genes in BAMs (Lkt-susceptible cells) stimulated with Lkt and LPS. Bovine pulmonary artery endothelial cells and porcine alveolar macrophages were used as nonsusceptible cells. The role of Ca2+ and tyrosine kinases in NF-kappaB activation and inflammatory cytokine gene expression was studied, since an inhibitor of tyrosine kinases attenuates LPS-induced [Ca2+]i elevation in BAMs. The results are summarized as follows: (a) Lkt induced NF-kappaB activation and [Ca2+]i elevation only in BAMs, while LPS effects were demonstrable in all cell types; (b) chelation of [Ca2+]i blocked NF-kappaB activation and IL-1beta, TNFalpha, and IL-8 mRNA expression; and (c) tyrosine kinase inhibitor herbimycin A blocked expression of all three cytokine genes in BAMs stimulated with Lkt, while only the expression of IL-1beta was blocked in BAMs stimulated with LPS. We conclude that cytokine gene expression in BAMs requires NF-kappaB activation and [Ca2+]i elevation, and Lkt effects exhibit cell type- and species specificity. Copyright 1999 Academic Press.

BAM 1 and RECEPTOR-LIKE PROTEIN KINASE 2 constitute a signaling pathway and modulate CLE peptide-triggered growth inhibition in Arabidopsis root.

PubMed

Shimizu, Noriko; Ishida, Takashi; Yamada, Masashi; Shigenobu, Shuji; Tabata, Ryo; Kinoshita, Atsuko; Yamaguchi, Katsushi; Hasebe, Mitsuyasu; Mitsumasu, Kanako; Sawa, Shinichiro

2015-12-01

Ligand receptor-based signaling is a means of cell-to-cell communication for coordinating developmental and physiological processes in multicellular organisms. In plants, cell-producing meristems utilize this signaling to regulate their activities and ensure for proper development. Shoot and root systems share common requirements for carrying out this process; however, its molecular basis is largely unclear. It has been suggested that synthetic CLV3/EMBRYO SURROUNDING REGION (CLE) peptide shrinks the root meristem through the actions of CLAVATA2 (CLV2) and the RECEPTOR-LIKE PROTEIN KINASE 2 (RPK2) pathway in Arabidopsis thaliana. Our genetic screening for mutations that resist CLE peptide signaling in roots determined that BAM1, which is a member of the leucine-rich repeat receptor-like kinase (LRR-RLK) family, is also involved in this pathway. BAM1 is preferentially expressed in the root tip, including the quiescent center and its surrounding stem cells. Our genetic analysis revealed that BAM1 functions together with RPK2. Using coimmunoprecipitation assay, we showed that BAM1 is capable of forming heteromeric complexes with RPK2. These findings suggest that the BAM1 and RPK2 receptors constitute a signaling pathway that modulates cell proliferation in the root meristem and that related molecules are employed in root and shoot meristems. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

The effect of BaM/PANI composition with epoxy paint matrix on single and double layers coating with spray coating method for radar absorbing materials applications

NASA Astrophysics Data System (ADS)

Widyastuti, Fajarin, Rindang; Pratiwi, Vania Mitha; Kholid, Rifki Rachman; Habib, Abdulloh

2018-04-01

In this study, RAM composite has been succesfully synthesized by mixing BaM as magnetic materials and PANI as conductive materials. BaM and PANI materials were prepared separately by solid state method and polymerization method, respectively. To investigated the presence of BaM phase and magnetic property of the as prepared BaM, XRD pert PAN analytical and VSM 250 Dexing Magnet were employed. Inductance Capacitance Resistance technique was carried out to measure electrical conductivity of the synthesized PANI materials. In order to further characterized the structural features of BaM and PANI, SEM-EDX FEI 850 and FTIR characterizations were conducted. RAM composite was prepared by mixing BaM and PANI powders with ultrasonic cleaner. Afterwards, VNA (Vector Network Analyzer) characterization was carried out to determine reflection loss value of RAM by applying mixed RAM composite and epoxy paint on aluminum plate using spray gun. Microscopic characterization was employed to investigated the distribution of RAM particles on the substrate. It was found that reflection loss value as low as -27.153 dB was achieved when applied 15 wt% BaM/PANi composite at 100.6 µm thickness. In addition, the absorption of electromagnetic waves value increase as the addition of RAM composite composition increases.

Optimal design of stormwater basins with bio-sorption activated media (BAM) in karst environments - phase I : site screening and selection, [summary].

DOT National Transportation Integrated Search

2015-11-01

Nutrient content is a concern in Floridas aquifers and springs sources of drinking water, : recreation, and the states natural beauty. In recent years, the nitrogen content of Floridas : aquifer springs has risen. This increase in nutrie...

Tissue Engineered Skeletal Myofibers can Directly "Sense" Gravitational Force Changes

NASA Technical Reports Server (NTRS)

Vandenburgh, Herman H.; Shansky, J.; DelTatto, M.; Lee, Peter; Meir, J.

1999-01-01

Long-term manned space flight requires a better understanding of skeletal muscle atrophy resulting from microgravity. Atrophy most likely results from changes at both the systemic level (e.g. decreased circulating growth hormone, increased circulating glucocorticoids) and locally (e.g. decreased myofiber resting tension). Differentiated skeletal myofibers in tissue culture have provided a model system over the last decade for gaining a better understanding of the interactions of exogenous growth factors, endogenous growth factors, and muscle fiber tension in regulating protein turnover rates and muscle cell growth. Tissue engineering these cells into three dimensional bioartificial muscle (BAM) constructs has allowed us to extend their use to Space flight studies for the potential future development of countermeasures. Embryonic avian muscle cells were isolated and BAMs tissue engineered as described previously. The myoblasts proliferate and fuse into aligned postmitotic myofibers after ten to fourteen days in vitro. A cylindrical muscle-like structure containing several thousand myofibers is formed which is approximately 30 mm in length, 2-3 mm in diameter, and attached at each end. For the Space Shuttle experiments, the BAMs were transferred to 55 mL bioreactor cartridges (6 BAMs/cartridge). At Kennedy Space Center, the cartridges were mounted in two Space Tissue Loss (STL) Modules (three to four cartridges per Module) and either maintained as ground controls or loaded in a Mid-Deck locker of the Space Shuttle. The BAM cartridges were continuously perfused during the experiment at 1.5 mL/ min with tissue culture medium. Eighteen BAMs were flown for nine days on Mission STS66 while eighteen BAMs served as ground controls. The complete experiment was repeated on Mission STS77 with twenty four BAMs in each group. BAMs could be maintained in a healthy state for at least 30 days in the perfusion bioreactor cartridges. The BAM muscle fibers directly detected both the loss of gravity and the reloading effects of 1 x g. While total cellular metabolism and total protein degradation rates were not altered during 9 to 10 days in Space, protein synthesis rates were significantly reduced and resulted in significant myofiber atrophy compared to ground controls. One g reloading of the flight muscle cells post-flight significantly increased protein synthesis rates and the synthesis rates of myosin heavy chain, fibronectin, and collagen. Tissue cultured muscle cells can directly "sense" changes in gravity and provide a valid model to begin the study of countermeasures. Based on our ground based experiments, and the experiments of others, growth hormone and/or insulin-like growth factors are attractive protein therapeutics which may assisting attenuating skeletal muscle wasting in space. Our laboratory is developing a new cell-based delivery system for this and other potential therapeutic factors for attenuating muscle and bone wasting.

Global exponential stability of BAM neural networks with time-varying delays: The discrete-time case

NASA Astrophysics Data System (ADS)

Raja, R.; Marshal Anthoni, S.

2011-02-01

This paper deals with the problem of stability analysis for a class of discrete-time bidirectional associative memory (BAM) neural networks with time-varying delays. By employing the Lyapunov functional and linear matrix inequality (LMI) approach, a new sufficient conditions is proposed for the global exponential stability of discrete-time BAM neural networks. The proposed LMI based results can be easily checked by LMI control toolbox. Moreover, an example is also provided to demonstrate the effectiveness of the proposed method.

Anti-scratch AlMgB14 Gorilla® Glass coating

NASA Astrophysics Data System (ADS)

Putrolaynen, V. V.; Grishin, A. M.; Rigoev, I. V.

2017-10-01

Hard aluminum-magnesium boride (BAM) films were fabricated onto Corning® Gorilla® Glass by radio-frequency magnetron sputtering of a single stoichiometric AlMgB14 target. BAM films exhibit a Vickers hardness from 10 to 30 GPa and a Young's modulus from 80 to 160 GPa depending on applied loading forces. Deposited hard coating increases the critical load at which glass substrate cracks. The adhesion energy of BAM films on Gorilla® Glass is 6.4 J/m2.

75SeHCAT scan in bile acid malabsorption in chronic diarrhoea.

PubMed

Mena Bares, L M; Carmona Asenjo, E; García Sánchez, M V; Moreno Ortega, E; Maza Muret, F R; Guiote Moreno, M V; Santos Bueno, A M; Iglesias Flores, E; Benítez Cantero, J M; Vallejo Casas, J A

Chronic diarrhoea is a common entity in daily clinical practice and it leads to a loss in these patients quality of life. It may be the main symptom of multiple ethiologies including bile acid malabsorption (BAM) which has a comparable prevalence to celiac disease. The BAM results from imbalances in the homeostasis of bile acids in the enterohepatic circulation. It can be a consequence of ileal disease or ileal dysfunction (BAM type i), it can be considered idiopathic or primary (BAM type ii) or associated with other gastrointestinal entities (BAM type iii). Among the different diagnostic methods available, 75 SeHCAT study is the primary current method due to its sensitivity, specificity, safety and low cost. The main disadvantage is that it's not available in all countries, so other diagnostic methods have appeared, such as serum measurement of FGF19 and C4, however they are significantly more complex and costly. The first-line treatment of bile acid diarrhoea is bile acid sequestrant, such as cholestyramine, which can be difficult to administer due to its poor tolerability and gastrointestinal side effects. These are less prominent with newer agents such as colesevelam. In summary, the BAM is a common entity underdiagnosed and undertreated, so it is essential to establish a diagnosis algorithm of chronic diarrhoea in which the 75 SeHCAT study would be first or second line in the differential diagnosis of these patients. Copyright © 2016 Elsevier España, S.L.U. y SEMNIM. All rights reserved.

Challenging current views on bile acid diarrhoea and malabsorption.

PubMed

Kurien, Matthew; Thurgar, Elizabeth; Davies, Ashley; Akehurst, Ron; Andreyev, Jervoise

2018-04-01

In 2012, the National Institute for Health and Care Excellence (NICE) assessed guidance (DG7) on the use of tauroselcholic ( 75 selenium) acid (also known as SeHCAT) for the investigation of diarrhoea due to bile acid malabsorption (BAM) in patients with IBS-D and in patients with Crohn's disease who have not had an ileal resection. NICE concluded that tauroselcholic ( 75 selenium) acid was recommended for use in research only. NICE will be reviewing the decision to update the guidance for tauroselcholic ( 75 selenium) acid, for these populations, in March 2017. Our aim is to summarise advances in BAM, also known as bile acid diarrhoea (BAD), and encourage clinicians to re-evaluate their understanding of this disorder. We review the prevalence, diagnosis and treatment of BAD/BAM. We describe the new evidence available since the original NICE review in 2012, and discuss the economic issues associated with failure to diagnose or to treat BAD/BAM accurately. There is new and compelling evidence available since DG7, which shows that tauroselcholic ( 75 selenium) acid scanning is a powerful tool in the diagnosis of BAD/BAM. We summarise published prevalence data (approximately 1% prevalence in the UK, as suggested by clinical practice diagnosis rates), and highlight that the true prevalence of BAD/BAM could be far greater than this. We present evidence that challenges current opinion about this disorder, and we commend both clinicians and health technology assessment (HTA) agencies for being open to arguments and new evidence in any future HTAs.

Epitaxially grown BaM hexaferrite films having uniaxial axis in the film plane for self-biased devices

PubMed Central

Zhang, Xiaozhi; Meng, Siqin; Song, Dongsheng; Zhang, Yao; Yue, Zhenxing; Harris, Vincent G.

2017-01-01

Barium hexaferrite (BaM) films with in-plane c-axis orientation are promising and technically important materials for self-biased magnetic microwave devices. In this work, highly oriented BaM films with different thickness and an in-plane easy axis (c-axis) of magnetization were grown on a-plane single-crystal sapphire substrates by direct current magnetron sputtering. A procedure involving seed layers, layer-by-layer annealing was adopted to reduce the substrate-induced strains and allow for the growth of thick (~3.44 μm) films. The epitaxial growth of the BaM film on sapphire was revealed by high-resolution transmission electron microscopy with dislocations being observed at the film-substrate interface. The orientation was also verified by X-ray diffraction and more notably, polarized Raman scattering. The magnetic properties and ferromagnetic resonant frequencies were experimentally characterized by a vibrating sample magnetometry and a frequency-swept ferromagnetic resonant flip-chip technique, respectively. The micron-thick BaM films exhibited a large remanence ratio of 0.92 along in-plane easy axis and a small one of 0.09 for the in-plane hard axis loop measurement. The FMR frequency was 50.3 GHz at zero field and reached 57.9 GHz under a magnetic field of 3 kOe, indicating that the epitaxial BaM films with strong self-biased behaviors have good electromagnetic properties in millimeter-wave range. PMID:28276492

Distribution of Anaerobic Hydrocarbon-Degrading Bacteria in Soils from King George Island, Maritime Antarctica.

PubMed

Sampaio, Dayanna Souza; Almeida, Juliana Rodrigues Barboza; de Jesus, Hugo E; Rosado, Alexandre S; Seldin, Lucy; Jurelevicius, Diogo

2017-11-01

Anaerobic diesel fuel Arctic (DFA) degradation has already been demonstrated in Antarctic soils. However, studies comparing the distribution of anaerobic bacterial groups and of anaerobic hydrocarbon-degrading bacteria in Antarctic soils containing different concentrations of DFA are scarce. In this study, functional genes were used to study the diversity and distribution of anaerobic hydrocarbon-degrading bacteria (bamA, assA, and bssA) and of sulfate-reducing bacteria (SRB-apsR) in highly, intermediate, and non-DFA-contaminated soils collected during the summers of 2009, 2010, and 2011 from King George Island, Antarctica. Signatures of bamA genes were detected in all soils analyzed, whereas bssA and assA were found in only 4 of 10 soils. The concentration of DFA was the main factor influencing the distribution of bamA-containing bacteria and of SRB in the analyzed soils, as shown by PCR-DGGE results. bamA sequences related to genes previously described in Desulfuromonas, Lautropia, Magnetospirillum, Sulfuritalea, Rhodovolum, Rhodomicrobium, Azoarcus, Geobacter, Ramlibacter, and Gemmatimonas genera were dominant in King George Island soils. Although DFA modulated the distribution of bamA-hosting bacteria, DFA concentration was not related to bamA abundance in the soils studied here. This result suggests that King George Island soils show functional redundancy for aromatic hydrocarbon degradation. The results obtained in this study support the hypothesis that specialized anaerobic hydrocarbon-degrading bacteria have been selected by hydrocarbon concentrations present in King George Island soils.

Epitaxially grown BaM hexaferrite films having uniaxial axis in the film plane for self-biased devices.

PubMed

Zhang, Xiaozhi; Meng, Siqin; Song, Dongsheng; Zhang, Yao; Yue, Zhenxing; Harris, Vincent G

2017-03-09

Barium hexaferrite (BaM) films with in-plane c-axis orientation are promising and technically important materials for self-biased magnetic microwave devices. In this work, highly oriented BaM films with different thickness and an in-plane easy axis (c-axis) of magnetization were grown on a-plane single-crystal sapphire substrates by direct current magnetron sputtering. A procedure involving seed layers, layer-by-layer annealing was adopted to reduce the substrate-induced strains and allow for the growth of thick (~3.44 μm) films. The epitaxial growth of the BaM film on sapphire was revealed by high-resolution transmission electron microscopy with dislocations being observed at the film-substrate interface. The orientation was also verified by X-ray diffraction and more notably, polarized Raman scattering. The magnetic properties and ferromagnetic resonant frequencies were experimentally characterized by a vibrating sample magnetometry and a frequency-swept ferromagnetic resonant flip-chip technique, respectively. The micron-thick BaM films exhibited a large remanence ratio of 0.92 along in-plane easy axis and a small one of 0.09 for the in-plane hard axis loop measurement. The FMR frequency was 50.3 GHz at zero field and reached 57.9 GHz under a magnetic field of 3 kOe, indicating that the epitaxial BaM films with strong self-biased behaviors have good electromagnetic properties in millimeter-wave range.

SeHCAT [tauroselcholic (selenium-75) acid] for the investigation of bile acid malabsorption and measurement of bile acid pool loss: a systematic review and cost-effectiveness analysis.

PubMed

Riemsma, R; Al, M; Corro Ramos, I; Deshpande, S N; Armstrong, N; Lee, Y-C; Ryder, S; Noake, C; Krol, M; Oppe, M; Kleijnen, J; Severens, H

2013-12-01

The principal diagnosis/indication for this assessment is chronic diarrhoea due to bile acid malabsorption (BAM). Diarrhoea can be defined as the abnormal passage of loose or liquid stools more than three times daily and/or a daily stool weight > 200 g per day and is considered to be chronic if it persists for more than 4 weeks. The cause of chronic diarrhoea in adults is often difficult to ascertain and patients may undergo several investigations without a definitive cause being identified. BAM is one of several causes of chronic diarrhoea and results from failure to absorb bile acids (which are required for the absorption of dietary fats and sterols in the intestine) in the distal ileum. For people with chronic diarrhoea with unknown cause and in people with Crohn's disease and chronic diarrhoea with unknown cause (i.e. before resection): (1) What are the effects of selenium-75-homocholic acid taurine (SeHCAT) compared with no SeHCAT in terms of chronic diarrhoea, other health outcomes and costs? (2) What are the effects of bile acid sequestrants (BASs) compared with no BASs in people with a positive or negative SeHCAT test? (3) Does a positive or negative SeHCAT test predict improvement in terms of chronic diarrhoea, other health outcomes and costs? A systematic review was conducted to summarise the evidence on the clinical effectiveness of SeHCAT for the assessment of BAM and the measurement of bile acid pool loss. Search strategies were based on target condition and intervention, as recommended in the Centre for Reviews and Dissemination (CRD) guidance for undertaking reviews in health care and the Cochrane Handbook for Diagnostic Test Accuracy Reviews. The following databases were searched up to April 2012: MEDLINE; MEDLINE In-Process & Other Non-Indexed Citations; EMBASE; the Cochrane Databases; Database of Abstracts of Reviews of Effects; Health Technology Assessment (HTA) Database; and Science Citation Index. Research registers and conference proceedings were also searched. Systematic review methods followed the principles outlined in the CRD guidance for undertaking reviews in health care and the National Institute for Health and Care Excellence (NICE) Diagnostic Assessment Programme interim methods statement. In the health economic analysis, the cost-effectiveness of SeHCAT for the assessment of BAM, in patients with chronic diarrhoea, was estimated in two different populations. The first is the population of patients with chronic diarrhoea with unknown cause and symptoms suggestive of diarrhoea-predominant irritable bowel syndrome (IBS-D) and the second population concerns patients with Crohn's disease without ileal resection with chronic diarrhoea. For each population, three models were combined: (1) a short-term decision tree that models the diagnostic pathway and initial response to treatment (first 6 months); (2) a long-term Markov model that estimates the lifetime costs and effects for patients initially receiving BAS; and (3) a long-term Markov model that estimates the lifetime costs and effects for patients initially receiving regular treatment (IBS-D treatment in the first population and Crohn's treatment in the second population). Incremental cost-effectiveness ratios were estimated as additional cost per additional responder in the short term (first 6 months) and per additional quality-adjusted life-year (QALY) in the long term (lifetime). We found three studies assessing the relationship between the SeHCAT test and response to treatment with cholestyramine. However, the studies had small numbers of patients with unknown cause chronic diarrhoea, and they used different cut-offs to define BAM. For the short term (first 6 months), when trial of treatment is not considered as a comparator, the optimal choice depends on the willingness to pay for an additional responder. For lower values (between £1500 and £4600) the choice will be no SeHCAT in all scenarios; for higher values either SeHCAT 10% or SeHCAT 15% becomes cost-effective. For the lifetime perspective, the various scenarios showed widely differing results: in the threshold range of £20,000-30,000 per QALY gained we found as optimal choice either no SeHCAT, SeHCAT 5% (only IBS-D) or SeHCAT 15%. When trial of treatment is considered a comparator, the analysis showed that for the short term, trial of treatment is the optimal choice across a range of scenarios. For the lifetime perspective with trial of treatment, again the various scenarios show widely differing results. Depending on the scenario, in the threshold range of £20,000-30,000 per QALY gained, we found as optimal choice either trial of treatment, no SeHCAT or SeHCAT 15%. In conclusion, the various analyses show that for both populations considerable decision uncertainty exists and that no firm conclusions can be formulated about which strategy is optimal. Standardisation of the definition of a positive SeHCAT test should be the first step in assessing the usefulness of this test. As there is no reference standard for the diagnosis of BAM and SeHCAT testing provides a continuous measure of metabolic function, diagnostic test accuracy (DTA) studies are not the most appropriate study design. However, in studies where all patients are tested with SeHCAT and all patients are treated with BASs, response to treatment can provide a surrogate reference standard; further DTA studies of this type may provide information on the ability of SeHCAT to predict response to BASs. A potentially more informative option would be multivariate regression modelling of treatment response (dependent variable), with SeHCAT result and other candidate clinical predictors as covariates. Such a study design could also inform the definition of a positive SeHCAT result. The study is registered as PROSPERO CRD42012001911. The National Institute for Health Research Health Technology Assessment programme.

Crisis management aspects of bam catastrophic earthquake: review article.

PubMed

Sadeghi-Bazargani, Homayoun; Azami-Aghdash, Saber; Kazemi, Abdolhassan; Ziapour, Behrad

2015-01-01

Bam earthquake was the most catastrophic natural disasters in recent years. The aim of this study was to review different aspects of crisis management during and after the catastrophic earthquake in Bam City, Iran. Data needed for this systematic review were collected through searching PubMed, EMBASE and SID databases, for the period from 2003 to 2011. Keywords included earthquake, Iran and Bam earthquake. The data were summarized and were analyzed using Content Analysis. Out of 422 articles, 25 articles were included in the study. Crisis Management aspects and existing pitfalls were classified into seven categories including planning and organization, human resource management, management of logistics, international humanitarian aids, field performance of the military and security forces, health and medical service provision, and information management. Positive aspects and major pitfalls of crisis management have been introduced in all the mentioned categories. The available evidence indicated poor crisis management during Bam earthquake that resulted in aggravating the losses as well as diminishing the effect of interventions. Thus, concerning the importance of different aspects of the crisis management and the high prevalence of disasters in Iran, the observed vulnerability in disaster management process should be addressed.

CIDR

Science.gov Websites

Sequencing Information Investigators have a wealth of study design options available to them using next (whole exome and custom only). SNVs and indels called and annotated Data quality evaluated using a robust contamination is estimated using VerifyBamID. The QC report is used in-house to monitor QC metrics real-time and

Targeting human Mas-related G protein-coupled receptor X1 to inhibit persistent pain

PubMed Central

Li, Zhe; Tseng, Pang-Yen; Tiwari, Vinod; Xu, Qian; He, Shao-Qiu; Wang, Yan; Zheng, Qin; Han, Liang; Wu, Zhiping; Blobaum, Anna L.; Cui, Yiyuan; Tiwari, Vineeta; Sun, Shuohao; Cheng, Yingying; Huang-Lionnet, Julie H. Y.; Geng, Yixun; Xiao, Bo; Peng, Junmin; Hopkins, Corey; Raja, Srinivasa N.; Guan, Yun; Dong, Xinzhong

2017-01-01

Human Mas-related G protein-coupled receptor X1 (MRGPRX1) is a promising target for pain inhibition, mainly because of its restricted expression in nociceptors within the peripheral nervous system. However, constrained by species differences across Mrgprs, drug candidates that activate MRGPRX1 do not activate rodent receptors, leaving no responsive animal model to test the effect on pain in vivo. Here, we generated a transgenic mouse line in which we replaced mouse Mrgprs with human MrgprX1. This humanized mouse allowed us to characterize an agonist [bovine adrenal medulla 8–22 (BAM8–22)] and a positive allosteric modulator (PAM), ML382, of MRGPRX1. Cellular studies suggested that ML382 enhances the ability of BAM8–22 to inhibit high-voltage-activated Ca2+ channels and attenuate spinal nociceptive transmission. Importantly, both BAM8–22 and ML382 effectively attenuated evoked, persistent, and spontaneous pain without causing obvious side effects. Notably, ML382 by itself attenuated both evoked pain hypersensitivity and spontaneous pain in MrgprX1 mice after nerve injury without acquiring coadministration of an exogenous agonist. Our findings suggest that humanized MrgprX1 mice provide a promising preclinical model and that activating MRGPRX1 is an effective way to treat persistent pain. PMID:28223516

New Passivity Criteria for Fuzzy Bam Neural Networks with Markovian Jumping Parameters and Time-Varying Delays

NASA Astrophysics Data System (ADS)

Vadivel, P.; Sakthivel, R.; Mathiyalagan, K.; Thangaraj, P.

2013-02-01

This paper addresses the problem of passivity analysis issue for a class of fuzzy bidirectional associative memory (BAM) neural networks with Markovian jumping parameters and time varying delays. A set of sufficient conditions for the passiveness of the considered fuzzy BAM neural network model is derived in terms of linear matrix inequalities by using the delay fractioning technique together with the Lyapunov function approach. In addition, the uncertainties are inevitable in neural networks because of the existence of modeling errors and external disturbance. Further, this result is extended to study the robust passivity criteria for uncertain fuzzy BAM neural networks with time varying delays and uncertainties. These criteria are expressed in the form of linear matrix inequalities (LMIs), which can be efficiently solved via standard numerical software. Two numerical examples are provided to demonstrate the effectiveness of the obtained results.

Quenching and annealing in the minority game

NASA Astrophysics Data System (ADS)

Burgos, E.; Ceva, Horacio; Perazzo, R. P. J.

2001-05-01

We study the bar attendance model (BAM) and a generalized version of the minority game (MG) in which a number of agents self organize to match an attendance that is fixed externally as a control parameter. We compare the probabilistic dynamics used in the MG with one that we introduce for the BAM that makes better use of the same available information. The relaxation dynamics of the MG leads the system to long lived, metastable (quenched) configurations in which adaptive evolution stops in spite of being far from equilibrium. On the contrary, the BAM relaxation dynamics avoids the MG glassy state, leading to an equilibrium configuration. Finally, we introduce in the MG model the concept of annealing by defining a new procedure with which one can gradually overcome the metastable MG states, bringing the system to an equilibrium that coincides with the one obtained with the BAM.

Investigating the Magneto Electric Coupling of [90 wt%Na0.5Bi0.5TiO3 (NBT)-10 wt% BaFe12O19 (BaM)] novel multiferroiccomposite system by increasing of BaM grain size

NASA Astrophysics Data System (ADS)

Pattanayak, Ranjit; Raut, Subhajit; Kuila, Sourav; Chandrasekhar, Mallam; Panigrahi, Simanchala

2017-02-01

Polycrystalline three novel [90 wt%Na0.5Bi0.5TiO3 (NBT)-10 wt% BaFe12O19 (BaM)] magnetoelctricmultiferroic composite systems were fabricated by considering the variation (increasing) of BaM grain size. The desired formation of composites was confirmed by X-ray diffraction study. The FESEM and SEM study were verified the variation of grain size and 0-3 type connectivity of composite systems. To predict the room temperature multiferroicbehaviour of theses composite systems we were taken PE and MH loop. For investigating the extrinsic and intrinsic magnetoelctric effect magneto impedance spectroscopy was considered for theses composite systems. The variation of intrinsic magnetoelctric coupling was predicted by proposing a simple mechanical model.

A simple process to obtain anisotropic self-biased magnets constituted of stacked barium ferrite single domain particles

NASA Astrophysics Data System (ADS)

Mattei, Jean-Luc; Le, Cong Nha; Chevalier, Alexis; Maalouf, Azar; Noutehou, Nathan; Queffelec, Patrick; Laur, Vincent

2018-04-01

An efficient and inexpensive process is presented that produces highly oriented bulk compacts made of BaM particles. Barium hexaferrite particles (BaM, nominal composition BaFe11O19) were prepared by a chemical coprecipitation method, using different rates and types of precipitating agents (NaOH and Na2CO3). It was demonstrated that when a large excess of Na2CO3 is used, a noteworthy packing of hexagonal BaM platelets is obtained, after mechanical compaction and firing at moderate temperature (1140 °C), without including any more steps than those required for a conventional sintering process. The hysteresis loop displays a very competitive squareness of 0.88 (normalized remanent magnetization) and a coercivity of 215 kA/m, which make this BaM bulk ferrite suitable for self-biased applications.

Spectroscopic study and enhanced thermostability of combustion-derived BaMgAl10O17:Eu2+ blue phosphors for solid-state lighting

NASA Astrophysics Data System (ADS)

Pradal, Nathalie; Potdevin, Audrey; Chadeyron, Geneviève; Bonville, Pierre; Caillier, Bruno; Mahiou, Rachid

2017-02-01

Blue-emitting BaMgAl10O17:Eu2+ (BAM:Eu), suitable for applications in a next generation of Hg-free lamps based on UV LEDs, was prepared by a microwave induced solution combustion synthesis, using urea as combustion fuel and nitrates as oxidizers. Purity control of the as-synthesized blue phosphor was undertaken by a washing step followed by a reduction one. Structural and morphological properties of the outcoming phosphors have been considered. Synthesis process allows producing a well-crystallized and nanostructured BAM phase within only few minutes. The influence of reduction treatment on the relative amounts of Eu2+/Eu3+ in our samples has been investigated through an original study by magnetization and Mössbauer spectroscopy. Furthermore, a complete optical study has been carried out and allowed us to determine the europium localization in the three possible sites in BAM matrix. The percentage of Eu2+ increased twofold after the reduction treatment, entailing an increase in the luminescence efficiency upon UV excitation. Finally, temperature-dependent luminescence of combustion-derived powders has been studied till 170 °C and compared to that of commercial BAM:Eu. MISCS-derived phosphors present a higher thermal stability than commercial one: whereas the emission efficiency of this last was reduced by 64%, the one of combustion-derived BAM:Eu experienced an only 12% decline. Furthermore, while commercial BAM suffered from a severe blue-shift with increasing temperature, our phosphors keep its color quality with a good stability of the photometric parameters.

Breathing awareness meditation and LifeSkills Training programs influence upon ambulatory blood pressure and sodium excretion among African American adolescents.

PubMed

Gregoski, Mathew J; Barnes, Vernon A; Tingen, Martha S; Harshfield, Gregory A; Treiber, Frank A

2011-01-01

To evaluate the effect of breathing awareness meditation (BAM), Botvin LifeSkills Training (LST), and health education control (HEC) on ambulatory blood pressure and sodium excretion in African American adolescents. Following 3 consecutive days of systolic blood pressure (SBP) screenings, 166 eligible participants (i.e., SBP >50th-95th percentile) were randomized by school to either BAM (n = 53), LST (n = 69), or HEC (n = 44). In-school intervention sessions were administered for 3 months by health education teachers. Before and after the intervention, overnight urine samples and 24-hour ambulatory SBP, diastolic blood pressure, and heart rate were obtained. Significant group differences were found for changes in overnight SBP and SBP, diastolic blood pressure, and heart rate over the 24-hour period and during school hours. The BAM treatment exhibited the greatest overall decreases on these measures (Bonferroni adjusted, ps < .05). For example, for school-time SBP, BAM showed a change of -3.7 mmHg compared with no change for LST and a change of -.1 mmHg for HEC. There was a nonsignificant trend for overnight urinary sodium excretion (p = .07), with the BAM group displaying a reduction of -.92 ± 1.1 mEq/hr compared with increases of .89 ± 1.2 mEq/hr for LST and .58 ± .9 mEq/hr for HEC group. BAM appears to improve hemodynamic function and may affect sodium handling among African American adolescents who are at increased risk for development of cardiovascular disease. Published by Elsevier Inc.

Evaluation of Modification of the 3M™ Molecular Detection Assay (MDA) Salmonella Method (2013.09) for the Detection of Salmonella in Selected Foods: Collaborative Study.

PubMed

Bird, Patrick; Fisher, Kiel; Boyle, Megan; Huffman, Travis; Benzinger, M Joseph; Bedinghaus, Paige; Flannery, Jonathon; Crowley, Erin; Agin, James; Goins, David; Benesh, DeAnn; David, John

2014-01-01

The 3M(™) Molecular Detection Assay (MDA) Salmonella utilizes isothermal amplification of nucleic acid sequences with high specificity, efficiency, rapidity and bioluminescence to detect amplification of Salmonella spp. in food, food-related, and environmental samples after enrichment. A method modification and matrix extension study of the previously approved AOAC Official Method(SM) 2013.09 was conducted, and approval of the modification was received on March 20, 2014. Using an unpaired study design in a multilaboratory collaborative study, the 3M MDA Salmonella method was compared to the U.S. Department of Agriculture/Food Safety and Inspection Service (USDA/FSIS) Microbiology Laboratory Guidebook (MLG) 4.05 (2011), Isolation and Identification of Salmonella from Meat, Poultry, Pasteurized Egg, and Catfish Products for raw ground beef and the U.S. Food and Drug Administration (FDA)/Bacteriological Analytical Manual (BAM) Chapter 5, Salmonella reference method for wet dog food following the current AOAC guidelines. A total of 20 laboratories participated. For the 3M MDA Salmonella method, raw ground beef was analyzed using 25 g test portions, and wet dog food was analyzed using 375 g test portions. For the reference methods, 25 g test portions of each matrix were analyzed. Each matrix was artificially contaminated with Salmonella at three inoculation levels: an uninoculated control level (0 CFU/test portion), a low inoculum level (0.2-2 CFU/test portion), and a high inoculum level (2-5 CFU/test portion). In this study, 1512 unpaired replicate samples were analyzed. Statistical analysis was conducted according to the probability of detection (POD). For the low-level raw ground beef test portions, the following dLPOD (difference between the LPODs of the reference and candidate method) values with 95% confidence intervals were obtained: -0.01 (-0.14, +0.12). For the low-level wet dog food test portions, the following dLPOD with 95% confidence intervals were obtained: -0.04 (-0.16, +0.09). No significant differences were observed in the number of positive samples detected by the 3M MDA Salmonella method versus either the USDA/FSIS-MLG or FDA/BAM methods.

Evaluation of 3M molecular detection assay (MDA) Salmonella for the detection of Salmonella in selected foods: collaborative study.

PubMed

Bird, Patrick; Fisher, Kiel; Boyle, Megan; Huffman, Travis; Benzinger, M Joseph; Bedinghaus, Paige; Flannery, Jonathan; Crowley, Erin; Agin, James; Goins, David; Benesh, DeAnn; David, John

2013-01-01

The 3M Molecular Detection Assay (MDA) Salmonella is used with the 3M Molecular Detection System for the detection of Salmonella spp. in food, food-related, and environmental samples after enrichment. The assay utilizes loop-mediated isothermal amplification to rapidly amplify Salmonella target DNA with high specificity and sensitivity, combined with bioluminescence to detect the amplification. The 3M MDA Salmonella method was compared using an unpaired study design in a multilaboratory collaborative study to the U.S. Department of Agriculture/Food Safety and Inspection Service-Microbiology Laboratory Guidebook (USDA/FSIS-MLG 4.05), Isolation and Identification of Salmonella from Meat, Poultry, Pasteurized Egg and Catfish Products for raw ground beef and the U.S. Food and Drug Administration/Bacteriological Analytical Manual (FDA/BAM) Chapter 5 Salmonella reference method for wet dog food following the current AOAC guidelines. A total of 20 laboratories participated. For the 3M MDA Salmonella method, raw ground beef was analyzed using 25 g test portions, and wet dog food was analyzed using 375 g test portions. For the reference methods, 25 g test portions of each matrix were analyzed. Each matrix was artificially contaminated with Salmonella at three inoculation levels: an uninoculated control level (0 CFU/test portion), a low inoculum level (0.2-2 CFU/test portion), and a high inoculum level (2-5 CFU/test portion). In this study, 1512 unpaired replicate samples were analyzed. Statistical analysis was conducted according to the probability of detection (POD). For the low-level raw ground beef test portions, the following dLPOD (difference between the POD of the reference and candidate method) values with 95% confidence intervals were obtained: -0.01 (-0.14, +0.12). For the low-level wet dog food test portions, the following dLPOD with 95% confidence intervals were obtained: -0.04 (-0.16, +0.09). No significant differences were observed in the number of positive samples detected by the 3M MDA Salmonella method versus either the USDA/FSIS-MLG or FDA/BAM methods.

Nutrient removal using biosorption activated media: preliminary biogeochemical assessment of an innovative stormwater infiltration basin

USGS Publications Warehouse

O'Reilly, Andrew M.; Wanielista, Martin P.; Chang, Ni-Bin; Xuan, Zhemin; Harris, Willie G.

2012-01-01

Soil beneath a stormwater infiltration basin receiving runoff from a 22.7 ha predominantly residential watershed in central Florida, USA, was amended using biosorption activated media (BAM) to study the effectiveness of this technology in reducing inputs of nitrogen and phosphorus to groundwater. The functionalized soil amendment BAM consists of a 1.0:1.9:4.1 mixture (by volume) of tire crumb (to increase sorption capacity), silt and clay (to increase soil moisture retention), and sand (to promote sufficient infiltration), which was applied to develop a prototype stormwater infiltration basin utilizing nutrient reduction and flood control sub-basins. Comparison of nitrate/chloride (NO3-/Cl-) ratios for the shallow groundwater indicate that prior to using BAM, NO3- concentrations were substantially influenced by nitrification or variations in NO3- input. In contrast, for the prototype basin utilizing BAM, NO3-/Cl- ratios indicate minor nitrification and NO3- losses with the exception of one summer sample that indicated a 45% loss. Biogeochemical indicators (denitrifier activity derived from real-time polymerase chain reaction and variations in major ions, nutrients, dissolved and soil gases, and stable isotopes) suggest NO3- losses are primarily attributable to denitrification, whereas dissimilatory nitrate reduction to ammonium is a minor process. Denitrification was likely occurring intermittently in anoxic microsites in the unsaturated zone, which was enhanced by increased soil moisture within the BAM layer and resultant reductions in surface/subsurface oxygen exchange that produced conditions conducive to increased denitrifier activity. Concentrations of total dissolved phosphorus and orthophosphate (PO43-) were reduced by more than 70% in unsaturated zone soil water, with the largest decreases in the BAM layer where sorption was the most likely mechanism for removal. Post-BAM PO43-/Cl- ratios for shallow groundwater indicate predominantly minor increases and decreases in PO43- with the exception of one summer sample that indicated a 50% loss. Differences in nutrient variations between the unsaturated zone and shallow groundwater may be the result of the intensity and duration of nutrient removal processes and mixing ratios with water that had not undergone significant chemical changes. Observed nitrogen and phosphorus losses demonstrate the potential, as well as future research needs to improve performance, of the prototype stormwater infiltration basin using BAM for providing passive, economical, stormwater nutrient-treatment technology to support green infrastructure.

Bam, Iran, Radar Interferometry -- Earthquake

NASA Image and Video Library

2004-06-25

A magnitude 6.5 earthquake devastated the small city of Bam in southeast Iran on December 26, 2003. The two images from ESA Envisat show similar measures of the radar interferometric correlation in grayscale on the left and in false colors on the right.

Multistability in bidirectional associative memory neural networks

NASA Astrophysics Data System (ADS)

Huang, Gan; Cao, Jinde

2008-04-01

In this Letter, the multistability issue is studied for Bidirectional Associative Memory (BAM) neural networks. Based on the existence and stability analysis of the neural networks with or without delay, it is found that the 2 n-dimensional networks can have 3 equilibria and 2 equilibria of them are locally exponentially stable, where each layer of the BAM network has n neurons. Furthermore, the results has been extended to (n+m)-dimensional BAM neural networks, where there are n and m neurons on the two layers respectively. Finally, two numerical examples are presented to illustrate the validity of our results.

The 2003 Bam (Iran) earthquake: Rupture of a blind strike-slip fault

NASA Technical Reports Server (NTRS)

Talebian, M.; Fielding, E. J.; Funning, G. J.; Ghorashi, M.; Jackson, J.; Nazari, H.; Parsons, B.; Priestley, K.; Rosen, P. A.; Walker, R.;

Thin films sputtered from Ba{sub 2}NdFeNb{sub 4}O{sub 15} multiferroic targets on BaFe{sub 12}O{sub 19} coated substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bodeux, Romain; Univ. Bordeaux, ICMCB, UPR 9048, F-33600 Pessac; Michau, Dominique, E-mail: dominique.michau@icmcb.cnrs.fr

2016-09-15

Highlights: • Synthesis of Ba{sub 2}NdFeNb{sub 4}O{sub 15}/BaFe{sub 12}O{sub 19} (BaM) heterostructures by RF magnetron sputtering. • Growth of TTB layer were retained regardless of the underlayer (Pt bottom electrode or BaM). • Dielectric and magnetic properties were obtained from the Pt/TTB/BaM/Pt stacks. - Abstract: Ba{sub 2}NdFeNb{sub 4}O{sub 15} tetragonal tungsten bronze (TTB)/BaFe{sub 12}O{sub 19} (BaM) hexaferrite bilayers have been grown by RF magnetron sputtering on Pt/TiO{sub 2}/SiO{sub 2}/Si (PtS) substrates. The BaM layer is textured along (0 0 1) while the TTB layer is multioriented regardless of the PtS or BaM/PtS substrate. Dielectric properties of TTB films are similarmore » to those of bulk, i.e., ε ∼ 150 and a magnetic hysteresis loop is obtained from TTB/BaM bilayers, thanks to the BaM component. This demonstrates the possibility of transferring to 2 dimensional structures the composite multiferroic system TTB/BaM previously identified in 3 dimensional bulk ceramics.« less

Magnetic properties of in-plane oriented barium hexaferrite thin films prepared by direct current magnetron sputtering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xiaozhi; Yue, Zhenxing, E-mail: yuezhx@mail.tsinghua.edu.cn; Meng, Siqin

2014-12-28

In-plane c-axis oriented Ba-hexaferrite (BaM) thin films were prepared on a-plane (112{sup ¯}0) sapphire (Al{sub 2}O{sub 3}) substrates by DC magnetron sputtering followed by ex-situ annealing. The DC magnetron sputtering was demonstrated to have obvious advantages over the traditionally used RF magnetron sputtering in sputtering rate and operation simplicity. The sputtering power had a remarkable influence on the Ba/Fe ratio, the hematite secondary phase, and the grain morphology of the as-prepared BaM films. Under 80 W of sputtering power, in-plane c-axis highly oriented BaM films were obtained. These films had strong magnetic anisotropy with high hysteresis loop squareness (M{sub r}/M{sub s}more » of 0.96) along the in-plane easy axis and low M{sub r}/M{sub s} of 0.03 along the in-plane hard axis. X-ray diffraction patterns and pole figures revealed that the oriented BaM films grew via an epitaxy-like growth process with the crystallographic relationship BaM (101{sup ¯}0)//α-Fe{sub 2}O{sub 3}(112{sup ¯}0)//Al{sub 2}O{sub 3}(112{sup ¯}0)« less

Evolution of the Translocation and Assembly Module (TAM)

PubMed Central

Heinz, Eva; Selkrig, Joel; Belousoff, Matthew J.; Lithgow, Trevor

2015-01-01

Bacterial outer membrane proteins require the beta-barrel assembly machinery (BAM) for their correct folding and function. The central component of this machinery is BamA, an Omp85 protein that is essential and found in all Gram-negative bacteria. An additional feature of the BAM is the translocation and assembly module (TAM), comprised TamA (an Omp85 family protein) and TamB. We report that TamA and a closely related protein TamL are confined almost exclusively to Proteobacteria and Bacteroidetes/Chlorobi respectively, whereas TamB is widely distributed across the majority of Gram-negative bacterial lineages. A comprehensive phylogenetic and secondary structure analysis of the TamB protein family revealed that TamB was present very early in the evolution of bacteria. Several sequence characteristics were discovered to define the TamB protein family: A signal-anchor linkage to the inner membrane, beta-helical structure, conserved domain architecture and a C-terminal region that mimics outer membrane protein beta-strands. Taken together, the structural and phylogenetic analyses suggest that the TAM likely evolved from an original combination of BamA and TamB, with a later gene duplication event of BamA, giving rise to an additional Omp85 sequence that evolved to be TamA in Proteobacteria and TamL in Bacteroidetes/Chlorobi. PMID:25994932

Fungal hyphae stimulate bacterial degradation of 2,6-dichlorobenzamide (BAM).

PubMed

Knudsen, Berith Elkær; Ellegaard-Jensen, Lea; Albers, Christian Nyrop; Rosendahl, Søren; Aamand, Jens

2013-10-01

Introduction of specific degrading microorganisms into polluted soil or aquifers is a promising remediation technology provided that the organisms survive and spread in the environment. We suggest that consortia, rather than single strains, may be better suited to overcome these challenges. Here we introduced a fungal-bacterial consortium consisting of Mortierella sp. LEJ702 and the 2,6-dichlorobenzamide (BAM)-degrading Aminobacter sp. MSH1 into small sand columns. A more rapid mineralisation of BAM was obtained by the consortium compared to MSH1 alone especially at lower moisture contents. Results from quantitative real-time polymerase chain reaction (qPCR) demonstrated better spreading of Aminobacter when Mortierella was present suggesting that fungal hyphae may stimulate bacterial dispersal. Extraction and analysis of BAM indicated that translocation of the compound was also affected by the fungal hyphae in the sand. This suggests that fungal-bacterial consortia are promising for successful bioremediation of pesticide contamination. Copyright © 2013 Elsevier Ltd. All rights reserved.

Using the Mixed Rasch Model to analyze data from the beliefs and attitudes about memory survey.

PubMed

Smith, Everett V; Ying, Yuping; Brown, Scott W

2012-01-01

In this study, we used the Mixed Rasch Model (MRM) to analyze data from the Beliefs and Attitudes About Memory Survey (BAMS; Brown, Garry, Silver, and Loftus, 1997). We used the original 5-point BAMS data to investigate the functioning of the "Neutral" category via threshold analysis under a 2-class MRM solution. The "Neutral" category was identified as not eliciting the model expected responses and observations in the "Neutral" category were subsequently treated as missing data. For the BAMS data without the "Neutral" category, exploratory MRM analyses specifying up to 5 latent classes were conducted to evaluate data-model fit using the consistent Akaike information criterion (CAIC). For each of three BAMS subscales, a two latent class solution was identified as fitting the mixed Rasch rating scale model the best. Results regarding threshold analysis, person parameters, and item fit based on the final models are presented and discussed as well as the implications of this study.

Three-dimensional deformation caused by the Bam, Iran, earthquake and the origin of shallow slip deficit.

PubMed

Fialko, Yuri; Sandwell, David; Simons, Mark; Rosen, Paul

2005-05-19

Our understanding of the earthquake process requires detailed insights into how the tectonic stresses are accumulated and released on seismogenic faults. We derive the full vector displacement field due to the Bam, Iran, earthquake of moment magnitude 6.5 using radar data from the Envisat satellite of the European Space Agency. Analysis of surface deformation indicates that most of the seismic moment release along the 20-km-long strike-slip rupture occurred at a shallow depth of 4-5 km, yet the rupture did not break the surface. The Bam event may therefore represent an end-member case of the 'shallow slip deficit' model, which postulates that coseismic slip in the uppermost crust is systematically less than that at seismogenic depths (4-10 km). The InSAR-derived surface displacement data from the Bam and other large shallow earthquakes suggest that the uppermost section of the seismogenic crust around young and developing faults may undergo a distributed failure in the interseismic period, thereby accumulating little elastic strain.

Evaluation and single-laboratory verification of a proposed modification to the U.S. Food and Drug Administration method for detection and identification of Campylobacter jejuni or Campylobacter coli from raw silo milk.

PubMed

Gharst, Greg; Bark, Don H; Newkirk, Robert; Guillen, Lacey; Wang, Qian; Abeyta, Carlos

2013-01-01

The current U.S. Food and Drug Administration (FDA) methodology for detection of Campylobacter, a leading source for foodborne illness, is outdated. The purpose of this study, therefore, was to improve and update the cultural and identification methods found in the FDA/Bacteriological Analytical Manual (BAM). Raw silo milk samples containing typical and atypical strains of Campylobacter jejuni and Campylobacter coli at different levels (5 CFU/25 g, 50 CFU/25 g, and 125 CFU/25 g) were analyzed. Valid results were obtained from 240 test portions. Six inoculated (at the levels described above) and two uninoculated samples were sent to a participating laboratory to mimic a "real-world" scenario. These combined data indicated that the use of sheep blood in combination with enrichment is not necessary. R & F Campylobacter jejuni/Campylobacter coli Chromogenic Plating Medium is significantly (P < 0.05) more sensitive for detection of C. jejuni or C. coli at low inoculation levels than the modified Cefoperazone Charcoal Deoxycholate Agar used in the BAM. The quantitative PCR method described demonstrated rapid confirmation and identification of C. jejuni or C. coli. It reduced the time to isolate C. jejuni or C. coli, and increased the sensitivity compared to the current BAM protocol.

BAM: Bayesian AMHG-Manning Inference of Discharge Using Remotely Sensed Stream Width, Slope, and Height

NASA Astrophysics Data System (ADS)

Hagemann, M. W.; Gleason, C. J.; Durand, M. T.

2017-11-01

The forthcoming Surface Water and Ocean Topography (SWOT) NASA satellite mission will measure water surface width, height, and slope of major rivers worldwide. The resulting data could provide an unprecedented account of river discharge at continental scales, but reliable methods need to be identified prior to launch. Here we present a novel algorithm for discharge estimation from only remotely sensed stream width, slope, and height at multiple locations along a mass-conserved river segment. The algorithm, termed the Bayesian AMHG-Manning (BAM) algorithm, implements a Bayesian formulation of streamflow uncertainty using a combination of Manning's equation and at-many-stations hydraulic geometry (AMHG). Bayesian methods provide a statistically defensible approach to generating discharge estimates in a physically underconstrained system but rely on prior distributions that quantify the a priori uncertainty of unknown quantities including discharge and hydraulic equation parameters. These were obtained from literature-reported values and from a USGS data set of acoustic Doppler current profiler (ADCP) measurements at USGS stream gauges. A data set of simulated widths, slopes, and heights from 19 rivers was used to evaluate the algorithms using a set of performance metrics. Results across the 19 rivers indicate an improvement in performance of BAM over previously tested methods and highlight a path forward in solving discharge estimation using solely satellite remote sensing.

A comparison of the BAX system method to the U.S. Food and Drug Administration's Bacteriological Analytical Manual and International Organization for Standardization reference methods for the detection of Salmonella in a variety of soy ingredients.

PubMed

Belete, Tamrat; Crowley, Erin; Bird, Patrick; Gensic, Joseph; Wallace, F Morgan

2014-10-01

The performances of two DuPont BAX System PCR assays for detecting Salmonella on a variety of low-moisture soy ingredients were evaluated against the U. S. Food and Drug Administration's Bacteriological Analytical Manual (FDA BAM) method or the International Organization for Standardization (ISO) 6579 reference method. These evaluations were conducted as a single laboratory validation at an ISO 17025 accredited third-party laboratory. Validations were conducted on five soy ingredients: isolated soy protein (ISP), soy fiber, fluid soy lecithin, deoiled soy lecithin, and soy nuggets, using a paired-study design. The ISP was analyzed as both 25- and 375-g composite test portions, whereas all other sample matrices were analyzed as 375-g composite test portions. To evaluate 25-g test portions of ISP, the test material was inoculated using Salmonella enterica subsp. enterica serovar Mbandaka (Q Laboratories isolate 11031.1). Salmonella enterica subsp. enterica serovar Tennessee (Q Laboratories isolate 11031.3) was used for all other trials. For each trial of the method comparison, 25 samples were analyzed for each matrix: 5 uninoculated controls and 20 samples inoculated at low levels (0.2 to 2 CFU per test portion) that were targeted to achieve fractionally positive results (25 to 75%). Using McNemar's chi-square analysis, no significant difference at P ≥ 0.05 (χ(2) ≤ 3.84) was observed between the number of positives obtained by the BAX System and the reference methods for all five test matrices evaluated. These studies indicate that the BAX System PCR assays, in combination with the single buffered peptone water primary enrichment and subsequent brain heart infusion regrowth step, demonstrate equivalent sensitivity and robustness compared with the FDA BAM and ISO reference methods for both 25- and 375-g composite samples. Moreover, there was no observed reduction of sensitivity in the larger 375-g composite samples for all five matrices.

76 FR 22045 - Fluopicolide; Pesticide Tolerances

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-20

... increased quantitative susceptibility of rat or rabbit fetuses to in utero or postnatal exposure to... is identified as docket ID number EPA-HQ-OPP-2006-0481. A quantitative reassessment of the BAM risk... fluopicolide and separately, its metabolite, BAM in food as follows: i. Acute exposure. Quantitative acute...

Nutrient removal using biosorption activated media: preliminary biogeochemical assessment of an innovative stormwater infiltration basin.

PubMed

O'Reilly, Andrew M; Wanielista, Martin P; Chang, Ni-Bin; Xuan, Zhemin; Harris, Willie G

2012-08-15

Soil beneath a stormwater infiltration basin receiving runoff from a 23 ha predominantly residential watershed in north-central Florida, USA, was amended using biosorption activated media (BAM) to study the effectiveness of this technology in reducing inputs of nitrogen and phosphorus to groundwater. The functionalized soil amendment BAM consists of a 1.0:1.9:4.1 mixture (by volume) of tire crumb (to increase sorption capacity), silt and clay (to increase soil moisture retention), and sand (to promote sufficient infiltration), which was applied to develop an innovative stormwater infiltration basin utilizing nutrient reduction and flood control sub-basins. Comparison of nitrate/chloride (NO(3)(-)/Cl(-)) ratios for the shallow groundwater indicates that prior to using BAM, NO(3)(-) concentrations were substantially influenced by nitrification or variations in NO(3)(-) input. In contrast, for the new basin utilizing BAM, NO(3)(-)/Cl(-) ratios indicate minor nitrification and NO(3)(-) losses with the exception of one summer sample that indicated a 45% loss. Biogeochemical indicators (denitrifier activity derived from real-time polymerase chain reaction and variations in major ions, nutrients, dissolved and soil gases, and stable isotopes) suggest that NO(3)(-) losses are primarily attributable to denitrification, whereas dissimilatory nitrate reduction to ammonium is a minor process. Denitrification was likely occurring intermittently in anoxic microsites in the unsaturated zone, which was enhanced by the increased soil moisture within the BAM layer and resultant reductions in surface/subsurface oxygen exchange that produced conditions conducive to increased denitrifier activity. Concentrations of total dissolved phosphorus and orthophosphate (PO(4)(3-)) were reduced by more than 70% in unsaturated zone soil water, with the largest decreases in the BAM layer where sorption was the most likely mechanism for removal. Post-BAM PO(4)(3-)/Cl(-) ratios for shallow groundwater indicate predominantly minor increases and decreases in PO(4)(3-) with the exception of one summer sample that indicated a 50% loss. Differences in nutrient variations between the unsaturated zone and shallow groundwater may be the result of the intensity and duration of nutrient removal processes and mixing ratios with water that had undergone little biogeochemical transformation. Observed nitrogen and phosphorus losses demonstrate the potential, as well as the future research needs to improve performance, of the innovative stormwater infiltration basin using BAM for providing passive, economical, stormwater nutrient-treatment technology to support green infrastructure. Copyright © 2012 Elsevier B.V. All rights reserved.

Oligoclonal T cell receptor gene rearrangements in blood lymphocytes of patients with acute Epstein-Barr virus-induced infectious mononucleosis.

PubMed Central

Strickler, J G; Movahed, L A; Gajl-Peczalska, K J; Horwitz, C A; Brunning, R D; Weiss, L M

1990-01-01

Gene rearrangement studies were performed on blood lymphocytes from eight patients with acute Epstein-Barr virus-induced infectious mononucleosis. The diagnosis in each case was based on characteristic clinical, hematologic, and serologic findings. The blood lymphocytes in each patient consisted predominantly of CD8+ T cells. EBV DNA was detected in seven patients by Southern blot analysis (EBV Bam HI W probe, Bam HI). A germline configuration was found for the immunoglobulin heavy and light chain genes (JH probe, Bam HI and Eco RI; C kappa probe, Bam HI; and C lambda probe, Eco RI). T cell receptor gene rearrangements were detected with J gamma and J beta 1 + 2 probes. Using a J gamma probe with two different restriction enzymes (Bgl II and Eco RI), the blood from each patient showed several bands corresponding to the polyclonal pattern previously described in the blood of normal individuals. Using J beta 1 + 2 probes with two different restriction enzymes (Bgl II and Bam HI), each case showed from 3 to about 12 extragermline bands of varying intensity and in different locations from case to case. In addition, each case showed relative deletion of the J beta 1 germline band. This oligoclonal pattern of T cell receptor gene rearrangements has not been previously reported in benign or malignant T cell populations. Images PMID:2170451

SeHCAT [tauroselcholic (selenium-75) acid] for the investigation of bile acid malabsorption and measurement of bile acid pool loss: a systematic review and cost-effectiveness analysis.

PubMed Central

Riemsma, R; Al, M; Corro Ramos, I; Deshpande, S N; Armstrong, N; Lee, Y-C; Ryder, S; Noake, C; Krol, M; Oppe, M; Kleijnen, J; Severens, H

2013-01-01

BACKGROUND The principal diagnosis/indication for this assessment is chronic diarrhoea due to bile acid malabsorption (BAM). Diarrhoea can be defined as the abnormal passage of loose or liquid stools more than three times daily and/or a daily stool weight > 200 g per day and is considered to be chronic if it persists for more than 4 weeks. The cause of chronic diarrhoea in adults is often difficult to ascertain and patients may undergo several investigations without a definitive cause being identified. BAM is one of several causes of chronic diarrhoea and results from failure to absorb bile acids (which are required for the absorption of dietary fats and sterols in the intestine) in the distal ileum. OBJECTIVE For people with chronic diarrhoea with unknown cause and in people with Crohn's disease and chronic diarrhoea with unknown cause (i.e. before resection): (1) What are the effects of selenium-75-homocholic acid taurine (SeHCAT) compared with no SeHCAT in terms of chronic diarrhoea, other health outcomes and costs? (2) What are the effects of bile acid sequestrants (BASs) compared with no BASs in people with a positive or negative SeHCAT test? (3) Does a positive or negative SeHCAT test predict improvement in terms of chronic diarrhoea, other health outcomes and costs? DATA SOURCES A systematic review was conducted to summarise the evidence on the clinical effectiveness of SeHCAT for the assessment of BAM and the measurement of bile acid pool loss. Search strategies were based on target condition and intervention, as recommended in the Centre for Reviews and Dissemination (CRD) guidance for undertaking reviews in health care and the Cochrane Handbook for Diagnostic Test Accuracy Reviews. The following databases were searched up to April 2012: MEDLINE; MEDLINE In-Process & Other Non-Indexed Citations; EMBASE; the Cochrane Databases; Database of Abstracts of Reviews of Effects; Health Technology Assessment (HTA) Database; and Science Citation Index. Research registers and conference proceedings were also searched. REVIEW METHODS Systematic review methods followed the principles outlined in the CRD guidance for undertaking reviews in health care and the National Institute for Health and Care Excellence (NICE) Diagnostic Assessment Programme interim methods statement. In the health economic analysis, the cost-effectiveness of SeHCAT for the assessment of BAM, in patients with chronic diarrhoea, was estimated in two different populations. The first is the population of patients with chronic diarrhoea with unknown cause and symptoms suggestive of diarrhoea-predominant irritable bowel syndrome (IBS-D) and the second population concerns patients with Crohn's disease without ileal resection with chronic diarrhoea. For each population, three models were combined: (1) a short-term decision tree that models the diagnostic pathway and initial response to treatment (first 6 months); (2) a long-term Markov model that estimates the lifetime costs and effects for patients initially receiving BAS; and (3) a long-term Markov model that estimates the lifetime costs and effects for patients initially receiving regular treatment (IBS-D treatment in the first population and Crohn's treatment in the second population). Incremental cost-effectiveness ratios were estimated as additional cost per additional responder in the short term (first 6 months) and per additional quality-adjusted life-year (QALY) in the long term (lifetime). RESULTS We found three studies assessing the relationship between the SeHCAT test and response to treatment with cholestyramine. However, the studies had small numbers of patients with unknown cause chronic diarrhoea, and they used different cut-offs to define BAM. For the short term (first 6 months), when trial of treatment is not considered as a comparator, the optimal choice depends on the willingness to pay for an additional responder. For lower values (between £1500 and £4600) the choice will be no SeHCAT in all scenarios; for higher values either SeHCAT 10% or SeHCAT 15% becomes cost-effective. For the lifetime perspective, the various scenarios showed widely differing results: in the threshold range of £20,000-30,000 per QALY gained we found as optimal choice either no SeHCAT, SeHCAT 5% (only IBS-D) or SeHCAT 15%. When trial of treatment is considered a comparator, the analysis showed that for the short term, trial of treatment is the optimal choice across a range of scenarios. For the lifetime perspective with trial of treatment, again the various scenarios show widely differing results. Depending on the scenario, in the threshold range of £20,000-30,000 per QALY gained, we found as optimal choice either trial of treatment, no SeHCAT or SeHCAT 15%. CONCLUSIONS In conclusion, the various analyses show that for both populations considerable decision uncertainty exists and that no firm conclusions can be formulated about which strategy is optimal. Standardisation of the definition of a positive SeHCAT test should be the first step in assessing the usefulness of this test. As there is no reference standard for the diagnosis of BAM and SeHCAT testing provides a continuous measure of metabolic function, diagnostic test accuracy (DTA) studies are not the most appropriate study design. However, in studies where all patients are tested with SeHCAT and all patients are treated with BASs, response to treatment can provide a surrogate reference standard; further DTA studies of this type may provide information on the ability of SeHCAT to predict response to BASs. A potentially more informative option would be multivariate regression modelling of treatment response (dependent variable), with SeHCAT result and other candidate clinical predictors as covariates. Such a study design could also inform the definition of a positive SeHCAT result. STUDY REGISTRATION The study is registered as PROSPERO CRD42012001911. FUNDING The National Institute for Health Research Health Technology Assessment programme. PMID:24351663

Robust stability for uncertain stochastic fuzzy BAM neural networks with time-varying delays

NASA Astrophysics Data System (ADS)

Syed Ali, M.; Balasubramaniam, P.

2008-07-01

In this Letter, by utilizing the Lyapunov functional and combining with the linear matrix inequality (LMI) approach, we analyze the global asymptotic stability of uncertain stochastic fuzzy Bidirectional Associative Memory (BAM) neural networks with time-varying delays which are represented by the Takagi-Sugeno (TS) fuzzy models. A new class of uncertain stochastic fuzzy BAM neural networks with time varying delays has been studied and sufficient conditions have been derived to obtain conservative result in stochastic settings. The developed results are more general than those reported in the earlier literatures. In addition, the numerical examples are provided to illustrate the applicability of the result using LMI toolbox in MATLAB.

Growth and high rate reactive ion etching of epitaxially grown barium hexaferrite films on single crystal silicon carbide substrates

NASA Astrophysics Data System (ADS)

Chen, Zhaohui

Ferrites are an invaluable group of insulating magnetic materials used for high frequency microwave applications in such passive electronic devices as isolators, phase shifters, and circulators. Because of their high permeability, non-reciprocal electromagnetic properties, and low eddy current losses, there are no other materials that serve such a broad range of applications. Until recently, they have been widely employed in bulk form, with little success in thin film-based applications in commercial or military microwave technologies. In today's technology, emerging electronic systems, such as high frequency, high power wireless and satellite communications (GPS, Bluetooth, WLAN, commercial radar, etc) thin film materials are in high demand. It is widely recognized that as high frequency devices shift to microwave frequencies the integration of passive devices with semiconductor electronics holds significant advantages in the realization of miniaturization, broader bandwidths, higher performance, speed, power and lower production costs. Thus, the primary objective of this thesis is to explore the integration of ferrite films with wide band gap semiconductor substrates for the realization of monolithic integrated circuits (MICs). This thesis focuses on two key steps for the integration of barium hexaferrite (Ba M-type or BaM) devices on semiconductor substrates. First, the development of high crystal quality ferrite film growth via pulsed laser deposition on wide band gap silicon carbide semiconductor substrates, and second, the effective patterning of BaM films using dry etching techniques. To address part one, BaM films were deposited on 6H silicon carbide (0001) substrates by Pulsed Laser Deposition. X-ray diffraction showed strong crystallographic alignment while pole figures exhibited reflections consistent with epitaxial growth. After optimized annealing, BaM films have a perpendicular magnetic anisotropy field of 16,900 Oe, magnetization (4piMs) of 4.4 kG, and ferromagnetic resonance peak-to-peak derivative linewidth at 53 GHz of 96 Oe. This combination of properties qualifies these films for microwave device applications. This marks the first growth of a microwave ferrite on SiC substrates and offers a new approach in the design and development of mu-wave and mm-wave monolithic integrated circuits. In part two, high-rate reactive ion etching using CHF3/SF6 gas mixtures was successfully demonstrated on BaM films, resulting in high aspect profile features of less than 50 nm in lateral dimension. These demonstrations enable the future integration of ferrites into MIC devices and technologies.

Robust state estimation for uncertain fuzzy bidirectional associative memory networks with time-varying delays

NASA Astrophysics Data System (ADS)

Vadivel, P.; Sakthivel, R.; Mathiyalagan, K.; Arunkumar, A.

2013-09-01

This paper addresses the issue of robust state estimation for a class of fuzzy bidirectional associative memory (BAM) neural networks with time-varying delays and parameter uncertainties. By constructing the Lyapunov-Krasovskii functional, which contains the triple-integral term and using the free-weighting matrix technique, a set of sufficient conditions are derived in terms of linear matrix inequalities (LMIs) to estimate the neuron states through available output measurements such that the dynamics of the estimation error system is robustly asymptotically stable. In particular, we consider a generalized activation function in which the traditional assumptions on the boundedness, monotony and differentiability of the activation functions are removed. More precisely, the design of the state estimator for such BAM neural networks can be obtained by solving some LMIs, which are dependent on the size of the time derivative of the time-varying delays. Finally, a numerical example with simulation result is given to illustrate the obtained theoretical results.

Optimization of rotational speed for growing BaFe12O19 thin films using spin coating

NASA Astrophysics Data System (ADS)

Budiawanti, S.; Soegijono, B.; Mudzakir, I.; Suharno, Fadillah, L.

2017-07-01

Barium ferrite (BaFe12O19, BaM) thin films were fabricated by the spin coating of precursors obtained by using a sol-gel method. The effects of the rotational speed on the spin-coating process for growing a BaM thin film were investigated in this study. Coated films were heat-deposited at different rotational speeds ranging from 2000 to 4000 rpm, while the number of layers was set to nine. Further, the effect of the number of layers on the growth of BaM thin films was discussed. For this purpose, we take the layers number 1 to 12 and take the constant rotational speed of 3000 rpm. All the film were characterized using X-Ray diffraction, Scanning Electron microscope, and Energy-dispersive X-Ray spectroscopy and Vibrating Sample Magnetometer. It was found that by increasing the rotational speed the amount of material deposited on the Si substrate decreased. The measured grain size of the BaM thin film was nearly similar for three three different rotational speeds. However, the grain size was found to increase the number of layers.

THE USE OF KETAMINE-XYLAZINE OR BUTORPHANOL-AZAPERONE-MEDETOMIDINE TO IMMOBILIZE AMERICAN BLACK BEARS ( URSUS AMERICANUS).

PubMed

Williamson, Ryan H; Muller, Lisa L; Blair, Coy

2018-04-04

  Wildlife anesthetic protocols must offer rapid inductions and recoveries, be physiologically safe, and be minimally regulated. With this in mind, we evaluated differences in induction and recovery times and physiological parameters in 33 American black bears ( Ursus americanus) anesthetized with ketamine-xylazine (KX) or immobilized with a commercial drug combination of butorphanol, azaperone, and medetomidine (BAM). Dose was based on mass estimated from field observations. Bears were housed at Appalachian Bear Rescue, Townsend, Tennessee, US, or free-ranging within the Great Smoky Mountains National Park (Tennessee and North Carolina, US) and chemically immobilized for management purposes. From 11 April to 29 June 2016, we immobilized bears with injection via pole syringe or disposable dart projected from an air-powered dart rifle. Once immobilized, we measured each bear's temperature, respiration (breaths/min), heart rate (beats/min), hemoglobin oxygen saturation (via pulse oximetry), arterial blood gases, and mass (kg). We found no differences in the induction parameters, partial pressures of CO 2 , and rectal temperatures. The BAM-treated bears had lower heart and respiratory rates that led to lower hemoglobin oxygen saturation levels (from blood gas analysis, SaO 2 ). The SaO 2 after treatment with BAM (91.1±0.8%) was lower than with KX (93.4±0.9%). After handling, we reversed KX-treated bears with a x̄=0.2±0.02 mg/kg yohimbine and BAM-treated bears with x̄=1.5±0.1 mg/kg atipamezole and 0.8±0.1 mg/kg naltrexone. We found no differences in the recovery times to increased respiration and to the bear assuming a head-up position. The BAM-treated bears stood and recovered quicker than did KX-treated animals. Based on our observations, BAM appears to offer safe, predictable immobilizations with fewer drawbacks and faster recovery times than KX-treated bears.

Evaluation of Apoptosis and Autophagy Inducing Potential of Berberis aristata, Azadirachta indica, and Their Synergistic Combinations in Parental and Resistant Human Osteosarcoma Cells

PubMed Central

Sengupta, Pracheta; Raman, Sukanya; Chowdhury, Rajdeep; Lohitesh, K.; Saini, Heena; Mukherjee, Sudeshna; Paul, Atish

2017-01-01

Cancer is a multifactorial disease and hence can be effectively overcome by a multi-constituently therapeutic strategy. Medicinal plant extracts represent a perfect example of such stratagem. However, minimal studies have been done till date that portray the effect of extraction techniques on the phyto-constituent profile of plant extracts and its impact on anticancer activity. In the present study, we have evaluated the anticancer potential of methanolic extracts of Berberis aristata root and Azadirachta indica seeds prepared by various extraction techniques in human osteosarcoma (HOS) cells. Soxhlation extract of B. aristata (BAM-SX) and sonication extract of A. indica (AIM-SO) were most effective in inducing apoptosis in parental drug sensitive, as well as resistant cell type developed by repeated drug exposure. Generation of reactive oxygen species and cell cycle arrest preceded caspase-mediated apoptosis in HOS cells. Interestingly, inhibition of autophagy enhanced cell death suggesting the cytoprotective role of autophagy. Combination studies of different methanolic extracts of BAM and AIM were performed, among which, the combination of BAM-SO and AIM-SO (BAAISO) was found to show synergism (IC50 10.27 µg/ml) followed by combination of BAM-MC and AIM-MC (BAAIMC) with respect to other combinations in the ratio of 1:1. BAAISO also showed synergism when it was added to cisplatin-resistant HOS cells (HCR). Chromatographic profiling of BAM-SX and AIM-SO by high performance thin layer chromatography resulted in identification of berberine (Rf 0.55), palmitine (Rf 0.50) in BAM-SX and azadirachtin A (Rf 0.36), azadirachtin B (Rf 0.56), nimbin (Rf 0.80), and nimbolide (Rf 0.43) in AIM-SO. The cytotoxic sensitivity obtained can be attributed to the above compounds. Our results highlight the importance of extraction technique and subsequent mechanism of action of multi-constituential B. aristata and A. indica against both sensitive and drug refractory HOS cells. PMID:29312880

Evaluation of Apoptosis and Autophagy Inducing Potential of Berberis aristata, Azadirachta indica, and Their Synergistic Combinations in Parental and Resistant Human Osteosarcoma Cells.

PubMed

Sengupta, Pracheta; Raman, Sukanya; Chowdhury, Rajdeep; Lohitesh, K; Saini, Heena; Mukherjee, Sudeshna; Paul, Atish

2017-01-01

Cancer is a multifactorial disease and hence can be effectively overcome by a multi-constituently therapeutic strategy. Medicinal plant extracts represent a perfect example of such stratagem. However, minimal studies have been done till date that portray the effect of extraction techniques on the phyto-constituent profile of plant extracts and its impact on anticancer activity. In the present study, we have evaluated the anticancer potential of methanolic extracts of Berberis aristata root and Azadirachta indica seeds prepared by various extraction techniques in human osteosarcoma (HOS) cells. Soxhlation extract of B. aristata (BAM-SX) and sonication extract of A. indica (AIM-SO) were most effective in inducing apoptosis in parental drug sensitive, as well as resistant cell type developed by repeated drug exposure. Generation of reactive oxygen species and cell cycle arrest preceded caspase-mediated apoptosis in HOS cells. Interestingly, inhibition of autophagy enhanced cell death suggesting the cytoprotective role of autophagy. Combination studies of different methanolic extracts of BAM and AIM were performed, among which, the combination of BAM-SO and AIM-SO (BAAISO) was found to show synergism (IC 50 10.27 µg/ml) followed by combination of BAM-MC and AIM-MC (BAAIMC) with respect to other combinations in the ratio of 1:1. BAAISO also showed synergism when it was added to cisplatin-resistant HOS cells (HCR). Chromatographic profiling of BAM-SX and AIM-SO by high performance thin layer chromatography resulted in identification of berberine (R f 0.55), palmitine (R f 0.50) in BAM-SX and azadirachtin A (R f 0.36), azadirachtin B (R f 0.56), nimbin (R f 0.80), and nimbolide (R f 0.43) in AIM-SO. The cytotoxic sensitivity obtained can be attributed to the above compounds. Our results highlight the importance of extraction technique and subsequent mechanism of action of multi-constituential B. aristata and A. indica against both sensitive and drug refractory HOS cells.

Prevalence of mip virulence gene and PCR-base sequence typing of Legionella pneumophila from cooling water systems of two cities in Iran.

PubMed

Ahmadrajabi, Roya; Shakibaie, Mohammad Reza; Iranmanesh, Zahra; Mollaei, Hamid Reza; Sobhanipoor, Mohammad Hossein

2016-07-03

Legionella pneumophila is the primary respiratory pathogen and mostly transmitted to human through water cooling systems and cause mild to severe pneumonia with high mortality rate especially in elderly both in hospitals and community. However, current Legionella risk assessments may be compromised by uncertainties in Legionella detection methods. Here, we investigated the presence of L. pneumophila mip gene in water samples collected from different hospitals cooling towers, nursing homes and building/hotels water coolants from two geographical locations of Iran (Kerman and Bam cities) during summer season of 2015 by both nested and real-time PCR methods. Analysis of the 128 water samples for presence of the mip gene by nested-PCR revealed, 18 (23%) positive cases in Kerman and 7(14%) in Bam. However, when samples were tested by real-time PCR, we identified 4 more new cases of L. pneumophila in the hospitals as well as nursing homes water systems that were missed by nested-PCR. The highest rate of contamination was detected in water obtained from hospitals cooling towers in both the cities (p≤0.05). Dendrogram analysis and clonal relationship by PCR-base sequence typing (SBT) of the L. pneumophila genomic DNAs in Kerman water samples showed close clonal similarities among the isolates, in contrast, isolates identified from Bam city demonstrated two fingerprint patterns. The clones from hospital water samples were more related to the L. pneumophila serogroup- 1.

Prevalence of mip virulence gene and PCR-base sequence typing of Legionella pneumophila from cooling water systems of two cities in Iran

PubMed Central

Ahmadrajabi, Roya; Shakibaie, Mohammad Reza; Iranmanesh, Zahra; Mollaei, Hamid Reza; Sobhanipoor, Mohammad Hossein

2016-01-01

ABSTRACT Legionella pneumophila is the primary respiratory pathogen and mostly transmitted to human through water cooling systems and cause mild to severe pneumonia with high mortality rate especially in elderly both in hospitals and community. However, current Legionella risk assessments may be compromised by uncertainties in Legionella detection methods. Here, we investigated the presence of L. pneumophila mip gene in water samples collected from different hospitals cooling towers, nursing homes and building/hotels water coolants from two geographical locations of Iran (Kerman and Bam cities) during summer season of 2015 by both nested and real-time PCR methods. Analysis of the 128 water samples for presence of the mip gene by nested-PCR revealed, 18 (23%) positive cases in Kerman and 7(14%) in Bam. However, when samples were tested by real-time PCR, we identified 4 more new cases of L. pneumophila in the hospitals as well as nursing homes water systems that were missed by nested-PCR. The highest rate of contamination was detected in water obtained from hospitals cooling towers in both the cities (p≤0.05). Dendrogram analysis and clonal relationship by PCR-base sequence typing (SBT) of the L. pneumophila genomic DNAs in Kerman water samples showed close clonal similarities among the isolates, in contrast, isolates identified from Bam city demonstrated two fingerprint patterns. The clones from hospital water samples were more related to the L. pneumophila serogroup- 1. PMID:27028760

Global exponential stability of BAM neural networks with time-varying delays and diffusion terms

NASA Astrophysics Data System (ADS)

Wan, Li; Zhou, Qinghua

2007-11-01

The stability property of bidirectional associate memory (BAM) neural networks with time-varying delays and diffusion terms are considered. By using the method of variation parameter and inequality technique, the delay-independent sufficient conditions to guarantee the uniqueness and global exponential stability of the equilibrium solution of such networks are established.

Learning Systematically from Experience through a Research-to-Practice Pipeline in Chicago

ERIC Educational Resources Information Center

Fine, Wendy; Lansing, Jiffy; Bacon, Marshaun

2018-01-01

The Becoming A Man (BAM) program is a school-based group counseling and mentoring program run by Youth Guidance (YG), a community organization that serves children in Chicago schools who are at risk. BAM guides young men to learn, internalize, and practice social cognitive skills, make responsible decisions for their future, and become positive…

Mei-P26 Cooperates with Bam, Bgcn and Sxl to Promote Early Germline Development in the Drosophila Ovary

PubMed Central

Li, Yun; Zhang, Qiao; Carreira-Rosario, Arnaldo; Maines, Jean Z.; McKearin, Dennis M.; Buszczak, Michael

2013-01-01

In the Drosophila female germline, spatially and temporally specific translation of mRNAs governs both stem cell maintenance and the differentiation of their progeny. However, the mechanisms that control and coordinate different modes of translational repression within this lineage remain incompletely understood. Here we present data showing that Mei-P26 associates with Bam, Bgcn and Sxl and nanos mRNA during early cyst development, suggesting that this protein helps to repress the translation of nanos mRNA. Together with recently published studies, these data suggest that Mei-P26 mediates both GSC self-renewal and germline differentiation through distinct modes of translational repression depending on the presence of Bam. PMID:23526974

Surface Ruptures and Building Damage of the 2003 Bam, Iran, Earthquake Mapped by Satellite Synthetic Aperture Radar Interferometric Correlation

NASA Technical Reports Server (NTRS)

Fielding, Eric J.; Talebian, M.; Rosen, P. A.; Nazari, H.; Jackson, J. A.; Ghorashi, M.; Walker, R.

2005-01-01

We use the interferometric correlation from Envisat synthetic aperture radar (SAR) images to map the details of the surface ruptures related to the 26 December 2003 earthquake that devastated Bam, Iran. The main strike-slip fault rupture south of the city of Bam has a series of four segments with left steps shown by a narrow line of low correlation in the coseismic interferogram. This also has a clear expression in the field because of the net extension across the fault. Just south of the city limits, the surface strain becomes distributed over a width of about 500 m, probably because of a thicker layer of soft sedimentary material.

Rv1458c: a new diagnostic marker for identification of Mycobacterium tuberculosis complex in a novel duplex PCR assay.

PubMed

Shrivastava, Kamal; Garima, Kushal; Narang, Anshika; Bhattacharyya, Kausik; Vishnoi, Ekta; Singh, Roshan Kumar; Chaudhry, Anil; Prasad, Rajendra; Bose, Mridula; Varma-Basil, Mandira

2017-03-01

We explored the efficiency of Rv1458c, the gene encoding a putative ABC drug transporter specific for the Mycobacterium tuberculosis complex (MTBC), as a diagnostic marker. A 190 bp region of Rv1458c and a 300 bp region of hsp65 were targeted in a novel duplex PCR assay and the results were compared with those for PCR restriction analysis(PRA) using the restriction enzymes NruI and BamHI. Species identification of a subset of the isolates (n=50) was confirmed by sequencing. Clinical isolates of M. tuberculosis (n=426) obtained from clinically suspected patients of pulmonary tuberculosis and mycobacterial (n=13) and non-mycobacterial (n=8) reference strains were included in the study. The duplex PCR assay correctly identified 320/426 isolates as MTBC and 106/426 isolates as non-tuberculous mycobacteria(NTM). The test was 100 % specific and sensitive when compared with NruI/BamHI PCR restriction analysis and highlighted the use of Rv1458c as a diagnostic marker for MTBC. The duplex PCR assay could be developed for use as a screening test to identify MTBC in clinical specimens in peripheral laboratories with limited resources.

Synthesis and Characterization of BaFe12O19/Poly(aniline, pyrrole, ethylene terephthalate) Composites Coatings as Radar Absorbing Material (RAM)

NASA Astrophysics Data System (ADS)

Sasria, Nia; Ardhyananta, H.; Fajarin, R.; Widyastuti

2017-07-01

This research shows the processing and design of radar absorbing material (RAM) based on barium hexaferrite (BaM) and poly(aniline, pyrrole, ethylene terephthalate) (PAni,PPy,PET). BaM was prepared by sol gel method with Ni-Zn doping at mole fraction of 0. 4 to obtain soft magnetic material. BaM/(PAni,PPy) composites were synthesized by in-situ polymerization method at ˜0 °C. (BaM/PET) composite was prepared by melt compounding at 220°C. The composites were coated on A-grade AH36 steel using Dallenbach Layer, Salisbury Screen and Jaumann Layer methods with thickness of 2, 4, and 6 mm. The composites were evaluated using XRD, SEM, FTIR, VSM, LCM-meter and VNA. Results showed that doped BaM showed BaNixZnxFe12-2xO19 structure. BaM/(PAni,PPy,PET) composites possessed globular morphology with M-O and C-H bonds. BaNixZnxFe12-2xO19 exhibited the value of Ms and Hc, 56.6 emu/g and 60 Oe respectively. High electrical conductivity of 1.77744 × 10-5 S/cm was achieved of BaM/PAni composite. The maximum reflection loss (RL) was reached at - 48.720 dB and 8.1 GHz for BaM/PAni composite coating with 6 mm thickness at Jaumann Layer. These results indicated that BaM/PAni composite was a soft magnetic material with a high RL value that is suitable for RAM, which used in stealth technology on naval vessels.

RGB-Switchable Porous Electrospun Nanofiber Chemoprobe-Filter Prepared from Multifunctional Copolymers for Versatile Sensing of pH and Heavy Metals.

PubMed

Liang, Fang-Cheng; Kuo, Chi-Ching; Chen, Bo-Yu; Cho, Chia-Jung; Hung, Chih-Chien; Chen, Wen-Chang; Borsali, Redouane

2017-05-17

Novel red-green-blue (RGB) switchable probes based on fluorescent porous electrospun (ES) nanofibers exhibiting high sensitivity to pH and mercury ions (Hg 2+ ) were prepared with one type of copolymer (poly(methyl methacrylatete-co-1,8-naphthalimide derivatives-co-rhodamine derivative); poly(MMA-co-BNPTU-co-RhBAM)) by using a single-capillary spinneret. The MMA, BNPTU, and RhBAM moieties were designed to (i) permit formation of porous fibers, (ii) fluoresce for Hg 2+ detection, and (iii) fluoresce for pH, respectively. The fluorescence emission of BNPTU (fluorescence resonance energy transfer (FRET) donor) changed from green to blue as it detected Hg 2+ . The fluorescence emission of RhBAM (FRET acceptor) was highly selective for pH, changing from nonfluorescent (pH 7) to exhibiting strong red fluorescence (pH 2). The full-color emission of the ES nanofibers included green, red, blue, purple, and white depending on the particular pH and Hg 2+ -concentration combination of the solution. The porous ES nanofibers with 30 nm pores were fabricated using hydrophobic MMA, low-boiling-point solvent, and at a high relative humidity (80%). These porous ES nanofibers had a higher surface-to-volume ratio than did the corresponding thin films, which enhanced their performance. The present study demonstrated that the FRET-based full-color-fluorescence porous nanofibrous membranes, which exhibit on-off switching and can be used as naked eye probes, have potential for application in water purification sensing filters.

Bile acid malabsorption in persistent diarrhoea.

PubMed

Smith, M J; Cherian, P; Raju, G S; Dawson, B F; Mahon, S; Bardhan, K D

2000-01-01

We have investigated bile acid malabsorption (BAM), and its response to treatment, in patients seen in this district general hospital with chronic continuous or recurrent diarrhoea. Seven-day retention of 75-SeHCAT was measured (normal: > 10%). Patients were initially given conventional therapy (prednisolone +/- ASA drugs in Crohn's disease, and antidiarrhoeals in the others). If this therapy failed, bile acid sequestrants (BAS) were prescribed. The definition of successful response was based on the patient's perception of sustained improvement. The 304 patients were categorised as follows: Group 1: Crohn's disease patients with ileal resection, in clinical remission (n = 37). Group 2: Crohn's disease, unoperated and in clinical remission (n = 44). Group 3: vagotomy and pyloroplasty, with/without cholecystectomy (n = 26). Group 4: diarrhoea predominant 'irritable bowel syndrome' (IBS) (n = 197). BAM was found in 97% (36/37), 54% (24/44) and 58% (15/26) of patients in groups 1, 2 and 3 respectively. One third (65/197) of patients with IBS had BAM. The outcome of treatment was available in 96 patients with BAM: of the patients with ileal resection 32% responded to antidiarrhoeals, 60% to BAS. Of the unoperated Crohn's patients 55% responded to disease-specific therapy, 40% to BAS. Of the gastric surgery patients 18% responded to conventional treatment, 64% to BAS. Of the IBS patients 15% of responded to conventional therapy, 70% to BAS. This observational study indicates that BAM is common in patients with chronic diarrhoea, and is frequently found in IBS. The results of open treatment suggest that, where antidiarrhoeal drugs fail in such patients, BAS are often effective.

Perpendicularly oriented barium ferrite thin films with low microwave loss, prepared by pulsed laser deposition

NASA Astrophysics Data System (ADS)

Da-Ming, Chen; Yuan-Xun, Li; Li-Kun, Han; Chao, Long; Huai-Wu, Zhang

2016-06-01

Barium ferrite (BaM) thin films are deposited on platinum coated silicon wafers by pulsed laser deposition (PLD). The effects of deposition substrate temperature on the microstructure, magnetic and microwave properties of BaM thin films are investigated in detail. It is found that microstructure, magnetic and microwave properties of BaM thin film are very sensitive to deposition substrate temperature, and excellent BaM thin film is obtained when deposition temperature is 910 °C and oxygen pressure is 300 mTorr (1 Torr = 1.3332 × 102 Pa). X-ray diffraction patterns and atomic force microscopy images show that the best thin film has perpendicular orientation and hexagonal morphology, and the crystallographic alignment degree can be calculated to be 0.94. Hysteresis loops reveal that the squareness ratio (M r/M s) is as high as 0.93, the saturated magnetization is 4004 Gs (1 Gs = 104 T), and the anisotropy field is 16.5 kOe (1 Oe = 79.5775 A·m-1). Ferromagnetic resonance measurements reveal that the gyromagnetic ratio is 2.8 GHz/kOe, and the ferromagnetic resonance linewith is 108 Oe at 50 GHz, which means that this thin film has low microwave loss. These properties make the BaM thin films have potential applications in microwave devices. Project supported by the Open Foundation of State Key Laboratory of Electronic Thin Films and Integrated Devices (Grant No. KFJJ201506), the Scientific Research Starting Foundation of Hainan University (Grant No. kyqd1539), and the Natural Science Foundation of Hainan Province (Grant No. 20165187).

Assessment of butorphanol-azaperone-medetomidine combination as anesthesia for semen collection and evaluation of semen quality in white-tailed deer (Odocoileus virginianus).

PubMed

Kirschner, S M; Rodenkirch, R

2017-09-01

The aim of this current study was to evaluate the level of anesthesia produced by a combination of butorphanol-azaperone-medetomidine (BAM) for semen collection by electroejaculation on captive white-tailed bucks (Odocoileus virginianus). Ten male white-tailed deer, weighing 68.2-115.9kg, ranging in age from one to four years were randomly selected from housing pens and anesthetized with the BAM drug combination at a dose volume of 2.0mL each. Semen was collected from each animal using a standard cervid electroejaculation protocol while under BAM anesthesia. Physiological data was recorded following induction of anesthesia and during semen collection. Collected ejaculates were prepared for analysis using a standard extender protocol for cryopreservation. Eleven sperm viability parameters were quantified for each sample using a Computerized Assisted Sperm Analysis system, including total seminal volume; sperm concentration and total sperm number. kinematic parameters of motile spermatozoa were also assessed. Results demonstrated that BAM provided an effective plane of anesthesia for successful collection of viable sperm. Measured physiological variables of heart rate, respiration and body temperature all remained within safe, normal limits. Data recorded on semen characteristics from all collected ejaculates correlated well with key traits determined to be important for successful fertilization through measurement of total semen volume; sperm concentration; total sperm number; and kinematic parameters of motile spermatozoa. There were no serious adverse events. This field study indicates that BAM anesthesia is suitable for semen collection in white-tailed deer. Copyright © 2017 Elsevier B.V. All rights reserved.

Fault Mechanics and Post-seismic Deformation at Bam, SE Iran

NASA Astrophysics Data System (ADS)

Wimpenny, S. E.; Copley, A.

2017-12-01

The extent to which aseismic deformation relaxes co-seismic stress changes on a fault zone is fundamental to assessing the future seismic hazard following any earthquake, and in understanding the mechanical behaviour of faults. We used models of stress-driven afterslip and visco-elastic relaxation, in conjunction with a dense time series of post-seismic InSAR measurements, to show that there has been minimal release of co-seismic stress changes through post-seismic deformation following the 2003 Mw 6.6 Bam earthquake. Our modelling indicates that the faults at Bam may remain predominantly locked, and that the co- plus inter-seismically accumulated elastic strain stored down-dip of the 2003 rupture patch may be released in a future Mw 6 earthquake. Modelling also suggests parts of the fault that experienced post-seismic creep between 2003-2009 overlapped with areas that also slipped co-seismically. Our observations and models also provide an opportunity to probe how aseismic fault slip leads to the growth of topography at Bam. We find that, for our modelled afterslip distribution to be consistent with forming the sharp step in the local topography at Bam over repeated earthquake cycles, and also to be consistent with the geodetic observations, requires either (1) far-field tectonic loading equivalent to a 2-10 MPa deviatoric stress acting across the fault system, which suggests it supports stresses 60-100 times less than classical views of static fault strength, or (2) that the fault surface has some form of mechanical anisotropy, potentially related to corrugations on the fault plane, that controls the sense of slip.

The Small Breathing Amplitude at the Upper Lobes Favors the Attraction of Polymorphonuclear Neutrophils to Mycobacterium tuberculosis Lesions and Helps to Understand the Evolution toward Active Disease in An Individual-Based Model

PubMed Central

Cardona, Pere-Joan; Prats, Clara

2016-01-01

Infection with Mycobacterium tuberculosis (Mtb) can induce two kinds of lesions, namely proliferative and exudative. The former are based on the presence of macrophages with controlled induction of intragranulomatous necrosis, and are even able to stop its physical progression, thus avoiding the induction of active tuberculosis (TB). In contrast, the most significant characteristic of exudative lesions is their massive infiltration with polymorphonuclear neutrophils (PMNs), which favor enlargement of the lesions and extracellular growth of the bacilli. We have built an individual-based model (IBM) (known as “TBPATCH”) using the NetLogo interface to better understand the progression from Mtb infection to TB. We have tested four main factors previously identified as being able to favor the infiltration of Mtb-infected lesions with PMNs, namely the tolerability of infected macrophages to the bacillary load; the capacity to modulate the Th17 response; the breathing amplitude (BAM) (large or small in the lower and upper lobes respectively), which influences bacillary drainage at the alveoli; and the encapsulation of Mtb-infected lesions by the interlobular septae that structure the pulmonary parenchyma into secondary lobes. Overall, although all the factors analyzed play some role, the small BAM is the major factor determining whether Mtb-infected lesions become exudative, and thus induce TB, thereby helping to understand why this usually takes place in the upper lobes. This information will be very useful for the design of future prophylactic and therapeutic approaches against TB. PMID:27065951

The Small Breathing Amplitude at the Upper Lobes Favors the Attraction of Polymorphonuclear Neutrophils to Mycobacterium tuberculosis Lesions and Helps to Understand the Evolution toward Active Disease in An Individual-Based Model.

PubMed

Cardona, Pere-Joan; Prats, Clara

2016-01-01

Infection with Mycobacterium tuberculosis (Mtb) can induce two kinds of lesions, namely proliferative and exudative. The former are based on the presence of macrophages with controlled induction of intragranulomatous necrosis, and are even able to stop its physical progression, thus avoiding the induction of active tuberculosis (TB). In contrast, the most significant characteristic of exudative lesions is their massive infiltration with polymorphonuclear neutrophils (PMNs), which favor enlargement of the lesions and extracellular growth of the bacilli. We have built an individual-based model (IBM) (known as "TBPATCH") using the NetLogo interface to better understand the progression from Mtb infection to TB. We have tested four main factors previously identified as being able to favor the infiltration of Mtb-infected lesions with PMNs, namely the tolerability of infected macrophages to the bacillary load; the capacity to modulate the Th17 response; the breathing amplitude (BAM) (large or small in the lower and upper lobes respectively), which influences bacillary drainage at the alveoli; and the encapsulation of Mtb-infected lesions by the interlobular septae that structure the pulmonary parenchyma into secondary lobes. Overall, although all the factors analyzed play some role, the small BAM is the major factor determining whether Mtb-infected lesions become exudative, and thus induce TB, thereby helping to understand why this usually takes place in the upper lobes. This information will be very useful for the design of future prophylactic and therapeutic approaches against TB.

Indexation Rules for Metallurgy in PASCAL. Original Title: Regles d'Indexation de la Metallurgie'--Technical Note Issued by Informascience--January 1980. Translated by Marie Wallin.

ERIC Educational Resources Information Center

Royal Inst. of Tech., Stockholm (Sweden). Library.

The indexing rules presented are designed for use with a new French-German database on metallurgy being developed under an agreement by CNRS (Centre National de la Recherche Scientifique, Paris) and BAM (Bundesanstalt fur Materialprufung, Berlin). The new database, which will feature multilingual titles and index terms (French-German-English-) and…

A promising lightweight multicomponent microwave absorber based on doped barium hexaferrite/calcium titanate/multiwalled carbon nanotubes

NASA Astrophysics Data System (ADS)

Afghahi, Seyyed Salman Seyyed; Jafarian, Mojtaba; Atassi, Yomen

2016-07-01

We present the design of a microwave absorber in the X band based on ternary nanocomposite of doped barium hexaferrite (Ba-M)/calcium titanate (CTO)/multiwall carbon nanotubes (MWCNTs) in epoxy matrix. The hydrothermal method has been used to synthesize Ba-M and CTO nanopowder. The phase identification has been investigated using XRD patterns. Scanning electron microscope, transmission electron microscope, vibrating sample magnetometer, and vector network analyzer are used to analyze the morphology of the different components and the magnetic, electromagnetic, and microwave absorption properties of the final composite absorbers, respectively. As far as we know, the design of this type of multicomponent microwave absorber has not been investigated before. The results reveal that the combination of these three components with their different loss mechanisms has a synergistic effect that enhances the attenuation properties of the final composite. The absorber of only 2.5-mm thickness and 35 wt% of loading ratio exhibits a minimum reflection loss of -43 dB at 10.2 GHz with a bandwidth of 3.6 GHz, while the corresponding absorber based on pure (Ba-M) shows a minimum reflection loss of -34 dB at 9.8 GHz with a bandwidth of 0.256 GHz and a thickness of 4 mm.

Global Hopf bifurcation analysis on a BAM neural network with delays

NASA Astrophysics Data System (ADS)

Sun, Chengjun; Han, Maoan; Pang, Xiaoming

2007-01-01

A delayed differential equation that models a bidirectional associative memory (BAM) neural network with four neurons is considered. By using a global Hopf bifurcation theorem for FDE and a Bendixon's criterion for high-dimensional ODE, a group of sufficient conditions for the system to have multiple periodic solutions are obtained when the sum of delays is sufficiently large.

Impact of Stress Reduction Interventions on Hostility and Ambulatory Systolic Blood Pressure in African American Adolescents

ERIC Educational Resources Information Center

Wright, Lynda Brown; Gregoski, Mathew J.; Tingen, Martha S.; Barnes, Vernon A.; Treiber, Frank A.

2011-01-01

This study examined the impact of breathing awareness meditation (BAM), life skills (LS) training, and health education (HE) interventions on self-reported hostility and 24-hour ambulatory blood pressure (ABP) in 121 African American (AA) ninth graders at increased risk for development of essential hypertension. They were randomly assigned to BAM,…

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.

PubMed

Takeuchi, Toshiki; Yamada, Atsuo; Aoki, Takashi; Nishimura, Kunihiro

2016-01-01

Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast. However, SAMtools requires an additional implementation to be used in parallel with, for example, OpenMP (Open Multi-Processing) libraries. For the accumulation of next-generation sequencing data, a simple parallelization program, which can support cloud and PC cluster environments, is required. We have developed cljam using the Clojure programming language, which simplifies parallel programming, to handle SAM/BAM data. Cljam can run in a Java runtime environment (e.g., Windows, Linux, Mac OS X) with Clojure. Cljam can process and analyze SAM/BAM files in parallel and at high speed. The execution time with cljam is almost the same as with SAMtools. The cljam code is written in Clojure and has fewer lines than other similar tools.

Dimension dependence of clustering dynamics in models of ballistic aggregation and freely cooling granular gas

NASA Astrophysics Data System (ADS)

Paul, Subhajit; Das, Subir K.

2018-03-01

Via event-driven molecular dynamics simulations we study kinetics of clustering in assemblies of inelastic particles in various space dimensions. We consider two models, viz., the ballistic aggregation model (BAM) and the freely cooling granular gas model (GGM), for each of which we quantify the time dependence of kinetic energy and average mass of clusters (that form due to inelastic collisions). These quantities, for both the models, exhibit power-law behavior, at least in the long time limit. For the BAM, corresponding exponents exhibit strong dimension dependence and follow a hyperscaling relation. In addition, in the high packing fraction limit the behavior of these quantities become consistent with a scaling theory that predicts an inverse relation between energy and mass. On the other hand, in the case of the GGM we do not find any evidence for such a picture. In this case, even though the energy decay, irrespective of packing fraction, matches quantitatively with that for the high packing fraction picture of the BAM, it is inversely proportional to the growth of mass only in one dimension, and the growth appears to be rather insensitive to the choice of the dimension, unlike the BAM.

Modification of the BAX System PCR assay for detecting Salmonella in beef, produce, and soy protein isolate. Performance Tested Method 100201.

PubMed

Peng, Linda X; Wallace, Morgan; Andaloro, Bridget; Fallon, Dawn; Fleck, Lois; Delduco, Dan; Tice, George

2011-01-01

The BAX System PCR assay for Salmonella detection in foods was previously validated as AOAC Research Institute (RI) Performance Tested Method (PTM) 100201. New studies were conducted on beef and produce using the same media and protocol currently approved for the BAX System PCR assay for E. coli O157:H7 multiplex (MP). Additionally, soy protein isolate was tested for matrix extension using the U.S. Food and Drug Administration-Bacteriological Analytical Manual (FDA-BAM) enrichment protocols. The studies compared the BAX System method to the U.S. Department of Agriculture culture method for detecting Salmonella in beef and the FDA-BAM culture method for detecting Salmonella in produce and soy protein isolate. Method comparison studies on low-level inoculates showed that the BAX System assay for Salmonella performed as well as or better than the reference method for detecting Salmonella in beef and produce in 8-24 h enrichment when the BAX System E. coli O157:H7 MP media was used, and soy protein isolate in 20 h enrichment with lactose broth followed by 3 h regrowth in brain heart infusion broth. An inclusivity panel of 104 Salmonella strains with diverse serotypes was tested by the BAX System using the proprietary BAX System media and returned all positive results. Ruggedness factors involved in the enrichment phase were also evaluated by testing outside the specified parameters, and none of the factors examined affected the performance of the assay.

Concussion Assessment With Smartglasses: Validation Study of Balance Measurement Toward a Lightweight, Multimodal, Field-Ready Platform

PubMed Central

Salisbury, Joseph P; Keshav, Neha U; Sossong, Anthony D

2018-01-01

Background Lightweight and portable devices that objectively measure concussion-related impairments could improve injury detection and critical decision-making in contact sports and the military, where brain injuries commonly occur but remain underreported. Current standard assessments often rely heavily on subjective methods such as symptom self-reporting. Head-mounted wearables, such as smartglasses, provide an emerging platform for consideration that could deliver the range of assessments necessary to develop a rapid and objective screen for brain injury. Standing balance assessment, one parameter that may inform a concussion diagnosis, could theoretically be performed quantitatively using current off-the-shelf smartglasses with an internal accelerometer. However, the validity of balance measurement using smartglasses has not been investigated. Objective This study aimed to perform preliminary validation of a smartglasses-based balance accelerometer measure (BAM) compared with the well-described and characterized waist-based BAM. Methods Forty-two healthy individuals (26 male, 16 female; mean age 23.8 [SD 5.2] years) participated in the study. Following the BAM protocol, each subject performed 2 trials of 6 balance stances while accelerometer and gyroscope data were recorded from smartglasses (Glass Explorer Edition). Test-retest reliability and correlation were determined relative to waist-based BAM as used in the National Institutes of Health’s Standing Balance Toolbox. Results Balance measurements obtained using a head-mounted wearable were highly correlated with those obtained through a waist-mounted accelerometer (Spearman rho, ρ=.85). Test-retest reliability was high (intraclass correlation coefficient, ICC2,1=0.85, 95% CI 0.81-0.88) and in good agreement with waist balance measurements (ICC2,1=0.84, 95% CI 0.80-0.88). Considering the normalized path length magnitude across all 3 axes improved interdevice correlation (ρ=.90) while maintaining test-retest reliability (ICC2,1=0.87, 95% CI 0.83-0.90). All subjects successfully completed the study, demonstrating the feasibility of using a head-mounted wearable to assess balance in a healthy population. Conclusions Balance measurements derived from the smartglasses-based accelerometer were consistent with those obtained using a waist-mounted accelerometer. Additional research is necessary to determine to what extent smartglasses-based accelerometry measures can detect balance dysfunction associated with concussion. However, given the potential for smartglasses to perform additional concussion-related assessments in an integrated, wearable platform, continued development and validation of a smartglasses-based balance assessment is warranted. This approach could lead to a wearable platform for real-time assessment of concussion-related impairments that could be further augmented with telemedicine capabilities to integrate professional clinical guidance. Smartglasses may be superior to fully immersive virtual reality headsets for this application, given their lighter weight and reduced likelihood of potential safety concerns. PMID:29362210

proBAMconvert: A Conversion Tool for proBAM/proBed.

PubMed

Olexiouk, Volodimir; Menschaert, Gerben

2017-07-07

The introduction of new standard formats, proBAM and proBed, improves the integration of genomics and proteomics information, thus aiding proteogenomics applications. These novel formats enable peptide spectrum matches (PSM) to be stored, inspected, and analyzed within the context of the genome. However, an easy-to-use and transparent tool to convert mass spectrometry identification files to these new formats is indispensable. proBAMconvert enables the conversion of common identification file formats (mzIdentML, mzTab, and pepXML) to proBAM/proBed using an intuitive interface. Furthermore, ProBAMconvert enables information to be output both at the PSM and peptide levels and has a command line interface next to the graphical user interface. Detailed documentation and a completely worked-out tutorial is available at http://probam.biobix.be .

Global asymptotic stability to a generalized Cohen-Grossberg BAM neural networks of neutral type delays.

PubMed

Zhang, Zhengqiu; Liu, Wenbin; Zhou, Dongming

2012-01-01

In this paper, we first discuss the existence of a unique equilibrium point of a generalized Cohen-Grossberg BAM neural networks of neutral type delays by means of the Homeomorphism theory and inequality technique. Then, by applying the existence result of an equilibrium point and constructing a Lyapunov functional, we study the global asymptotic stability of the equilibrium solution to the above Cohen-Grossberg BAM neural networks of neutral type. In our results, the hypothesis for boundedness in the existing paper, which discussed Cohen-Grossberg neural networks of neutral type on the activation functions, are removed. Finally, we give an example to demonstrate the validity of our global asymptotic stability result for the above neural networks. Copyright © 2011 Elsevier Ltd. All rights reserved.

Growing barium hexaferrite (BaFe{sub 12}O{sub 19}) thin films using chemical solution deposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Budiawanti, Sri, E-mail: awanty77@yahoo.com; Faculty of Teacher Training and Education, Sebelas Maret University; Soegijono, Bambang

Barium hexaferrite (BaFe{sub 12}O{sub 19}, or simply known as BaM) thin films has been recognized as a potential candidate for microwave-based devices, magnetic recording media and data storage. To grow BaM thin films, chemical solution deposition is conducted using the aqueous solution of metal nitrates, which involves spin coatings on Si substrates. Furthermore, Thermal Gravimeter Analysis (TGA), X-Ray Diffractometer (XRD), Scanning Electron Microscopy (SEM) and Vibrating Sample Magnetometer (VSM) are applied to evaluate the decomposition behavior, structure, morphology, and magnetic properties of BaM thin films. Additionally, the effects of number of layers variation are also investigated. Finally, magnetic properties analysismore » indicates the isotropic nature of the films.« less

Bam35 tectivirus intraviral interaction map unveils new function and localization of phage ORFan proteins.

PubMed

Berjón-Otero, Mónica; Lechuga, Ana; Mehla, Jitender; Uetz, Peter; Salas, Margarita; Redrejo-Rodríguez, Modesto

2017-07-26

Tectiviridae comprises a group of tail-less, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria.In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology. With the aim of increasing the knowledge of the viral proteome, we carried out a comprehensive yeast two-hybrid analysis among all the putative proteins encoded by the Bam35 genome. The resulting protein interactome comprises 76 unique interactions among 24 proteins, of which 12 have an unknown function. These results suggested that the P17 protein is the minor capsid protein of Bam35 and P24 is the penton protein, being the latter also supported by iterative threading protein modeling. Moreover, the inner membrane transglycosylase protein P26 could have an additional structural role. We also detected interactions involving non-structural proteins, such as the DNA binding protein P1 and the genome terminal protein (P4), which was confirmed by co-immunoprecipitation of recombinant proteins. Altogether, our results provide a functional view of the Bam35 viral proteome, with a focus on the composition and organization of the viral particle. IMPORTANCE Tail-less viruses of the family Tectiviridae can infect commensal and pathogenic Gram-positive and Gram-negative bacteria. Moreover, they have been proposed to be at the evolutionary origin of several groups of large eukaryotic DNA viruses and self-replicating plasmids. However, due to their ancient origin and complex diversity, many tectiviral proteins are ORFans of unknown function.Comprehensive protein-protein interaction (PPI) analysis among viral proteins can eventually disclose biological mechanisms and thus provide new insights into protein function unattainable by studying proteins one by one. Here we comprehensively describe intraviral PPIs among tectivirus Bam35 proteins using multi-vector yeast two-hybrid screening that was further supported by co-immunoprecipitation assays and protein structural models. This approach allowed us to propose new functions for known proteins and hypothesize on the biological role localization within the viral particle of some viral ORFan proteins that will be helpful for understanding the biology of Gram-positive tectivirus. Copyright © 2017 American Society for Microbiology.

Bam35 Tectivirus Intraviral Interaction Map Unveils New Function and Localization of Phage ORFan Proteins

PubMed Central

Berjón-Otero, Mónica; Lechuga, Ana; Mehla, Jitender; Uetz, Peter

2017-01-01

ABSTRACT The family Tectiviridae comprises a group of tailless, icosahedral, membrane-containing bacteriophages that can be divided into two groups by their hosts, either Gram-negative or Gram-positive bacteria. While the first group is composed of PRD1 and nearly identical well-characterized lytic viruses, the second one includes more variable temperate phages, like GIL16 or Bam35, whose hosts are Bacillus cereus and related Gram-positive bacteria. In the genome of Bam35, nearly half of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being putative proteins of unknown function, which hinders the understanding of their biology. With the aim of increasing knowledge about the viral proteome, we carried out a comprehensive yeast two-hybrid analysis of all the putative proteins encoded by the Bam35 genome. The resulting protein interactome comprised 76 unique interactions among 24 proteins, of which 12 have an unknown function. These results suggest that the P17 protein is the minor capsid protein of Bam35 and P24 is the penton protein, with the latter finding also being supported by iterative threading protein modeling. Moreover, the inner membrane transglycosylase protein P26 could have an additional structural role. We also detected interactions involving nonstructural proteins, such as the DNA-binding protein P1 and the genome terminal protein (P4), which was confirmed by coimmunoprecipitation of recombinant proteins. Altogether, our results provide a functional view of the Bam35 viral proteome, with a focus on the composition and organization of the viral particle. IMPORTANCE Tailless viruses of the family Tectiviridae can infect commensal and pathogenic Gram-positive and Gram-negative bacteria. Moreover, they have been proposed to be at the evolutionary origin of several groups of large eukaryotic DNA viruses and self-replicating plasmids. However, due to their ancient origin and complex diversity, many tectiviral proteins are ORFans of unknown function. Comprehensive protein-protein interaction (PPI) analysis of viral proteins can eventually disclose biological mechanisms and thus provide new insights into protein function unattainable by studying proteins one by one. Here we comprehensively describe intraviral PPIs among tectivirus Bam35 proteins determined using multivector yeast two-hybrid screening, and these PPIs were further supported by the results of coimmunoprecipitation assays and protein structural models. This approach allowed us to propose new functions for known proteins and hypothesize about the biological role of the localization of some viral ORFan proteins within the viral particle that will be helpful for understanding the biology of tectiviruses infecting Gram-positive bacteria. PMID:28747494

An ABC of Drumming: Children's Narratives about Beat, Rhythm and Groove in a Primary Classroom

ERIC Educational Resources Information Center

Mackinlay, Elizabeth

2014-01-01

In this paper, I use a bricolage of arts-based research and writing practices to explore narratives by Grade 4 children about their experiences in a drumming circle called "Bam Bam" as represented in a text they created with me called An ABC of drumming. The term "narrative" is used here in a contemporary sense to…

Transcriptional activity across the Epstein-Barr virus genome in Raji cells during latency and after induction of an abortive lytic cycle.

PubMed

Kirchner, E A; Bornkamm, G W; Polack, A

1991-10-01

We have studied the relative rate of transcription across the Epstein-Barr virus genome in the Burkitt's lymphoma cell line Raji by nuclear run-on analysis during latency and after induction of an abortive lytic cycle with 12-0-tetradecanoylphorbol 13-acetate (TPA) and 5-iodo-2'-deoxyuridine (IUdR). During latency the entire, or almost the entire, viral genome was found to be transcriptionally active to a low or intermediate extent, with some variation in activity along the genome. The fragment with the highest transcriptional activity was EcoRI J, which contains the genes encoding the small nuclear RNAs EBER1 and -2, transcribed predominantly by RNA polymerase III. An intermediate level of transcription was observed between positions 10 and 138 (kb), with areas of slightly higher activity on the large internal repeats and the left duplicated region (DL). The remaining part of the viral genome, between position 138 and the termini, and the termini and position 10 (kb) (with the exception of the EcoRI J fragment), showed very little transcriptional activity, except for the intermediately active regions carrying the righthand oriLyt (DR) and the terminal repeats. Upon induction of the viral genome with TPA and IUdR, the viral genome was transcriptionally active at a rate at least tenfold that seen during latency. Polymerases were not equally distributed along the genome after induction; the highest density was found in regions 48 to 58 kb, 82 to 84 kb, 102 to 104 kb, 118 to 122 kb and 142 to 145 kb of the viral genome. High transcriptional activity correlated with distinct transcription units in some cases, i.e. BamHI H1LF1 (DL), BamHI MLF1, BamHI ZLF1/BamHI RLF1 and BamHI X (thymidine kinase), but not in others (BamHI H2). Besides initiation of transcription, other regulatory processes such as stabilization and processing of primary transcripts may also contribute to regulation of virus gene expression. Addition of cycloheximide completely abolished the transcriptional activation of the genome mediated by TPA and IUdR.

Validation of a Salmonella loop-mediated isothermal amplification assay in animal food.

PubMed

Domesle, Kelly J; Yang, Qianru; Hammack, Thomas S; Ge, Beilei

2018-01-02

Loop-mediated isothermal amplification (LAMP) has emerged as a promising alternative to PCR for pathogen detection in food testing and clinical diagnostics. This study aimed to validate a Salmonella LAMP method run on both turbidimetry (LAMP I) and fluorescence (LAMP II) platforms in representative animal food commodities. The U.S. Food and Drug Administration (FDA)'s culture-based Bacteriological Analytical Manual (BAM) method was used as the reference method and a real-time quantitative PCR (qPCR) assay was also performed. The method comparison study followed the FDA's microbiological methods validation guidelines, which align well with those from the AOAC International and ISO. Both LAMP assays were 100% specific among 300 strains (247 Salmonella of 185 serovars and 53 non-Salmonella) tested. The detection limits ranged from 1.3 to 28 cells for six Salmonella strains of various serovars. Six commodities consisting of four animal feed items (cattle feed, chicken feed, horse feed, and swine feed) and two pet food items (dry cat food and dry dog food) all yielded satisfactory results. Compared to the BAM method, the relative levels of detection (RLODs) for LAMP I ranged from 0.317 to 1 with a combined value of 0.610, while those for LAMP II ranged from 0.394 to 1.152 with a combined value of 0.783, which all fell within the acceptability limit (2.5) for an unpaired study. This also suggests that LAMP was more sensitive than the BAM method at detecting low-level Salmonella contamination in animal food and results were available 3days sooner. The performance of LAMP on both platforms was comparable to that of qPCR but notably faster, particularly LAMP II. Given the importance of Salmonella in animal food safety, the LAMP assays validated in this study holds great promise as a rapid, reliable, and robust method for routine screening of Salmonella in these commodities. Published by Elsevier B.V.

Thinking, Fast and Slow? Some Field Experiments to Reduce Crime and Dropout in Chicago. NBER Working Paper 21178

ERIC Educational Resources Information Center

Heller, Sara B.; Shah, Anuj K.; Guryan, Jonathan; Ludwig, Jens; Mullainathan, Sendhil; Pollack, Harold A.

2015-01-01

We present the results of three large-scale randomized controlled trials (RCTs) carried out in Chicago, testing interventions to reduce crime and dropout by changing the decision-making of economically disadvantaged youth. We study a program called Becoming a Man (BAM), developed by the non-profit Youth Guidance, in two RCTs implemented in 2009-10…

Digital optical correlator x-ray telescope alignment monitoring system

NASA Astrophysics Data System (ADS)

Lis, Tomasz; Gaskin, Jessica; Jasper, John; Gregory, Don A.

2018-01-01

The High-Energy Replicated Optics to Explore the Sun (HEROES) program is a balloon-borne x-ray telescope mission to observe hard x-rays (˜20 to 70 keV) from the sun and multiple astrophysical targets. The payload consists of eight mirror modules with a total of 114 optics that are mounted on a 6-m-long optical bench. Each mirror module is complemented by a high-pressure xenon gas scintillation proportional counter. Attached to the payload is a camera that acquires star fields and then matches the acquired field to star maps to determine the pointing of the optical bench. Slight misalignments between the star camera, the optical bench, and the telescope elements attached to the optical bench may occur during flight due to mechanical shifts, thermal gradients, and gravitational effects. These misalignments can result in diminished imaging and reduced photon collection efficiency. To monitor these misalignments during flight, a supplementary Bench Alignment Monitoring System (BAMS) was added to the payload. BAMS hardware comprises two cameras mounted directly to the optical bench and rings of light-emitting diodes (LEDs) mounted onto the telescope components. The LEDs in these rings are mounted in a predefined, asymmetric pattern, and their positions are tracked using an optical/digital correlator. The BAMS analysis software is a digital adaption of an optical joint transform correlator. The aim is to enhance the observational proficiency of HEROES while providing insight into the magnitude of mechanically and thermally induced misalignments during flight. Results from a preflight test of the system are reported.

CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.

PubMed

Li, Pei; Ji, Guoli; Dong, Min; Schmidt, Emily; Lenox, Douglas; Chen, Liangliang; Liu, Qi; Liu, Lin; Zhang, Jie; Liang, Chun

2012-09-15

To address the impending need for exploring rapidly increased transcriptomics data generated for non-model organisms, we developed CBrowse, an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs. Designed in a standard three-tier architecture with a data pre-processing pipeline, CBrowse is essentially a Rich Internet Application that offers many seamlessly integrated web interfaces and allows users to navigate, sort, filter, search and visualize data smoothly. The pre-processing pipeline takes the contig sequence file in FASTA format and its relevant SAM/BAM file as the input; detects putative polymorphisms, simple sequence repeats and sequencing errors in contigs and generates image, JSON and database-compatible CSV text files that are directly utilized by different web interfaces. CBowse is a generic visualization and analysis tool that facilitates close examination of assembly quality, genetic polymorphisms, sequence repeats and/or sequencing errors in transcriptome sequencing projects. CBrowse is distributed under the GNU General Public License, available at http://bioinfolab.muohio.edu/CBrowse/ liangc@muohio.edu or liangc.mu@gmail.com; glji@xmu.edu.cn Supplementary data are available at Bioinformatics online.

Thermal treatment of the minority game

NASA Astrophysics Data System (ADS)

Burgos, E.; Ceva, Horacio; Perazzo, R. P.

2002-03-01

We study a cost function for the aggregate behavior of all the agents involved in the minority game (MG) or the bar attendance model (BAM). The cost function allows us to define a deterministic, synchronous dynamic that yields results that have the main relevant features than those of the probabilistic, sequential dynamics used for the MG or the BAM. We define a temperature through a Langevin approach in terms of the fluctuations of the average attendance. We prove that the cost function is an extensive quantity that can play the role of an internal energy of the many-agent system while the temperature so defined is an intensive parameter. We compare the results of the thermal perturbation to the deterministic dynamics and prove that they agree with those obtained with the MG or BAM in the limit of very low temperature.

Thermal treatment of the minority game.

PubMed

Burgos, E; Ceva, Horacio; Perazzo, R P J

2002-03-01

We study a cost function for the aggregate behavior of all the agents involved in the minority game (MG) or the bar attendance model (BAM). The cost function allows us to define a deterministic, synchronous dynamic that yields results that have the main relevant features than those of the probabilistic, sequential dynamics used for the MG or the BAM. We define a temperature through a Langevin approach in terms of the fluctuations of the average attendance. We prove that the cost function is an extensive quantity that can play the role of an internal energy of the many-agent system while the temperature so defined is an intensive parameter. We compare the results of the thermal perturbation to the deterministic dynamics and prove that they agree with those obtained with the MG or BAM in the limit of very low temperature.

A Decadal Regional and Global Trend Analysis of the Aerosol Optical Depth using a Data-Assimilation Grade Over-Water MODIS and Level 2 MISR Aerosol Products

DTIC Science & Technology

2010-01-01

and seasonal sensitivities to clear sky fraction and emissions (e.g., see annual state of the climate summaries in the BAMS, http://www.ncdc.noaa...gov/bams- state - of - the - climate /). Long term changes are as- sumed to be attributable to more background changes of en- ergy use and economic development

The EP-3E vs. the BAMS UAS: An Operating and Support Cost Comparison

DTIC Science & Technology

2012-09-01

Accountability Office HALE High Altitude Long Endurance ISR Intelligence, Surveillance and Reconnaissance JCC Joint Architecture...others are very complex high altitude long endurance (HALE) aircraft. However, most share the common need for satellite bandwidth. The DoD plan is...collection sites, and risks as they apply to the BAMS UAS. These factors were not adequately considered in the original O&S analysis . Once the analysis

Removal and retention of phosphorus by periphyton from wastewater with high organic load.

PubMed

Cao, Jinxiang; Hong, Xiaoxing; Pei, Guofeng

2014-01-01

The total phosphorus (TP) removal efficiency from organic wastewater (pig farm and distillery wastewater) were estimated by using filamentous green algae (FGA) and benthic algal mats (BAM) treatment systems under laboratory conditions, and the contents of periphyton phosphorus fractions were determined by using a sequential extraction. The removal rates of TP reached 59-78% within the first 8 days of all treatment systems and could achieve average 80% during 30 day period, and the phosphorus removal rates by using BAM was higher than that of FGA. The ability of retention TP of periphyton enhanced gradually, the BAM TP contents were higher than that of FGA, the highest TP concentrations of BAM and FGA were 26.24 and 10.52 mg P g(-1)·dry weight. Inorganic phosphorus (IP) always exceeded 67.5% of TP, but the organic phosphorus fraction only made up less than 20% of TP. The calcium-binding phosphorus (Ca-P) was the dominant fraction and its relative contribution to TP was more than 40%. The TP was also strongly and positively correlated with the IP and Ca-P (p < 0.01) in periphyton. It showed that the periphyton had a potential ability of rapid phosphorus removing and remarkable retention from wastewater with high load phosphorus.

Identification of a conjunctivitis-associated gene locus from the virulence plasmid of Yersinia enterocolitica.

PubMed

Miliotis, M D; Morris, J G; Cianciosi, S; Wright, A C; Wood, P K; Robins-Browne, R M

1990-08-01

The virulence plasmid (pYV) of Yersinia enterocolitica is necessary for production of conjunctivitis in guinea pigs and for mouse lethality. To identify the genes responsible for production of conjunctivitis in guinea pigs, we subcloned the BamHI and SalI restriction fragments of the virulence plasmid of Y. enterocolitica A2635 (serotype O:8) into derivatives of the broad-host-range plasmid pRK290 and introduced the constructions into plasmid-negative Y. enterocolitica strains. A mild, transient conjunctivitis was evident 24 h after inoculation with strains containing a 2.8-kilobase (kb) BamHI fragment of pYV. These strains were cytotoxic to HEp-2 cells but did not cause death in iron-loaded adult mice. When the 2.8- and adjacent 0.5-kb BamHI fragments were deleted from the virulence plasmid of a fully virulent Y. enterocolitica isolate, the resultant strain did not cause conjunctivitis in guinea pigs and was not cytotoxic to HEp-2 cells. However, the strain with the deletion appeared to be more virulent for mice, with more rapid dissemination after orogastric inoculation, compared with that of the parent strain. When the deletion was complemented by introduction of a plasmid containing the 2.8-kb BamHI fragment, the strain again caused conjunctivitis but had decreased virulence for mice.

Fabrication and characterization of magnetically tunable metal-semiconductor schottky diode using barium hexaferrite thin film on gold

NASA Astrophysics Data System (ADS)

Kaur, Jotinder; Sharma, Vinay; Sharma, Vipul; Veerakumar, V.; Kuanr, Bijoy K.

2016-05-01

Barium Hexaferrite (BaM) is an extensively studied magnetic material due to its potential device application. In this paper, we study Schottky junction diodes fabricated using gold and BaM and demonstrate the function of a spintronic device. Gold (50 nm)/silicon substrate was used to grow the BaM thin films (100-150 nm) using pulsed laser deposition. I-V characteristics were measured on the Au/BaM structure sweeping the voltage from ±5 volts. The forward and reverse bias current-voltage curves show diode like rectifying characteristics. The threshold voltage decreases while the output current increases with increase in the applied external magnetic field showing that the I-V characteristics of the BaM based Schottky junction diodes can be tuned by external magnetic field. It is also demonstrated that, the fabricated Schottky diode can be used as a half-wave rectifier, which could operate at high frequencies in the range of 1 MHz compared to the regular p-n junction diodes, which rectify below 10 kHz. In addition, it is found that above 1 MHz, Au/BaM diode can work as a rectifier as well as a capacitor filter, making the average (dc) voltage much larger.

Profile-Based LC-MS Data Alignment—A Bayesian Approach

PubMed Central

Tsai, Tsung-Heng; Tadesse, Mahlet G.; Wang, Yue; Ressom, Habtom W.

2014-01-01

A Bayesian alignment model (BAM) is proposed for alignment of liquid chromatography-mass spectrometry (LC-MS) data. BAM belongs to the category of profile-based approaches, which are composed of two major components: a prototype function and a set of mapping functions. Appropriate estimation of these functions is crucial for good alignment results. BAM uses Markov chain Monte Carlo (MCMC) methods to draw inference on the model parameters and improves on existing MCMC-based alignment methods through 1) the implementation of an efficient MCMC sampler and 2) an adaptive selection of knots. A block Metropolis-Hastings algorithm that mitigates the problem of the MCMC sampler getting stuck at local modes of the posterior distribution is used for the update of the mapping function coefficients. In addition, a stochastic search variable selection (SSVS) methodology is used to determine the number and positions of knots. We applied BAM to a simulated data set, an LC-MS proteomic data set, and two LC-MS metabolomic data sets, and compared its performance with the Bayesian hierarchical curve registration (BHCR) model, the dynamic time-warping (DTW) model, and the continuous profile model (CPM). The advantage of applying appropriate profile-based retention time correction prior to performing a feature-based approach is also demonstrated through the metabolomic data sets. PMID:23929872

Skeletal muscle atrophy in bioengineered skeletal muscle: a new model system.

PubMed

Lee, Peter H U; Vandenburgh, Herman H

2013-10-01

Skeletal muscle atrophy has been well characterized in various animal models, and while certain pathways that lead to disuse atrophy and its associated functional deficits have been well studied, available drugs to counteract these deficiencies are limited. An ex vivo tissue-engineered skeletal muscle offers a unique opportunity to study skeletal muscle physiology in a controlled in vitro setting. Primary mouse myoblasts isolated from adult muscle were tissue engineered into bioartificial muscles (BAMs) containing hundreds of aligned postmitotic muscle fibers expressing sarcomeric proteins. When electrically stimulated, BAMs generated measureable active forces within 2-3 days of formation. The maximum isometric tetanic force (Po) increased for ∼3 weeks to 2587±502 μN/BAM and was maintained at this level for greater than 80 days. When BAMs were reduced in length by 25% to 50%, muscle atrophy occurred in as little as 6 days. Length reduction resulted in significant decreases in Po (50.4%), mean myofiber cross-sectional area (21.7%), total protein synthesis rate (22.0%), and noncollagenous protein content (6.9%). No significant changes occurred in either the total metabolic activity or protein degradation rates. This study is the first in vitro demonstration that length reduction alone can induce skeletal muscle atrophy, and establishes a novel in vitro model for the study of skeletal muscle atrophy.

Results from a round robin test for the ecotoxicological evaluation of construction products using two leaching tests and an aquatic test battery.

PubMed

Gartiser, Stefan; Heisterkamp, Ines; Schoknecht, Ute; Burkhardt, Michael; Ratte, Monika; Ilvonen, Outi; Brauer, Frank; Brückmann, Jan; Dabrunz, André; Egeler, Philipp; Eisl, Andrea-Maria; Feiler, Ute; Fritz, Ines; König, Sabina; Lebertz, Herbert; Pandard, Pascal; Pötschke, Gabriele; Scheerbaum, Dirk; Schreiber, Frank; Soldán, Přemysl; Weiß, Roland; Weltens, Reinhilde

2017-05-01

A European round robin test according to ISO 5725-2 was conceptually prepared, realised, and evaluated. The aim was to determine the inter-laboratory variability of the overall process for the ecotoxicological characterization of construction products in eluates and bioassays. To this end, two construction products BAM-G1 (granulate) and HSR-2 (roof sealing sheet), both made of EPDM polymers (rubber), were selected. The granular construction product was eluted in a one stage batch test, the planar product in the Dynamic Surface Leaching test (DSLT). A total of 17 laboratories from 5 countries participated in the round robin test: Germany (12), Austria (2), Belgium (1), Czech Republic (1) and France (1). A test battery of four standardised ecotoxicity tests with algae, daphnia, luminescent bacteria and zebrafish eggs was used. As toxicity measures, EC50 and LID values were calculated. All tests, except the fish egg test, were basically able to demonstrate toxic effects and the level of toxicity. The reproducibility of test results depended on the test specimens and the test organisms. Generally, the variability of the EC50 or LID values increased with the overall level of toxicity. For the very toxic BAM-G1 eluate a relative high variability of CV = 73%-110% was observed for EC50 in all biotests, while for the less toxic HSR-2 eluate the reproducibility of EC50 varied with sensitivity: it was very good (CV = 9.3%) for the daphnia test with the lowest sensitivity, followed by the algae test (CV = 36.4%). The luminescent bacteria test, being the most sensitive bioassay for HSR-2 Eluate, showed the highest variability (CV = 74.8%). When considering the complex overall process the reproducibility of bioassays with eluates from construction products was acceptable. Copyright © 2017. Published by Elsevier Ltd.

Seroprevalence of canine visceral leishmaniasis in southeast of Iran.

PubMed

Mahshid, Mostafavi; Baharak, Akhtardanesh; Iraj, Sharifi; Sina, Kakooei; Javad, Khedri; Mehdi, Bamorovat

2014-06-01

Visceral leishmaniasis is an endemic disease in many parts of Iran and infected dogs constitute the main domestic reservoirs that play a key role in transmission to humans. The objective of this study was to assess the seroprevalence of canine visceral leishmaniasis (CVL) by enzyme linked immunosorbent assay (ELISA) in southeast of Iran. This survey was carried out from 2009 to 2011 in Kerman, Bam and Baft districts in Kerman province and Zabol in Sistan-Baluchestan province. Blood samples were taken from 201 dogs after complete clinical examination. Following hematological evaluation; collected sera were tested by indirect ELISA method for the presence of anti Leishmania infantum antibodies. Overall seroprevalence was 15.4 %, including 6.4, 3.5, 3 and 2.4 % in Bam, Zabol, Baft and Kerman, respectively. However, seroprevalence of disease was not significantly related to age, gender, presence of clinical signs and hematological disorders. Based to the results of the present study, CVL is endemic in southeastern Iran. Delayed diagnosis and euthanasia of potentially infectious animals may occur with an increased transmission risk to sand flies and subsequently to humans. Implementation of potent screening tests with high validity is essential for rapid detection and successful dog elimination programs in endemic parts of Iran.

Integrated Data Collection and Analysis Project: Friction Correlation Study

DTIC Science & Technology

2015-08-01

methods authorized in AOP-7 include Pendulum Friction, Rotary Friction, Sliding Friction (ABL), BAM Friction and Steel/Fiber Shoe Methods. The...sensitivity can be obtained by Pendulum Friction, Rotary Friction, Sliding Friction (such as the ABL), BAM Friction and Steel/Fiber Shoe Methods.3, 4 Within...Figure 4.16 A variable compressive force is applied downward through the wheel hydraulically (50-1995 psi). The 5 kg pendulum impacts (8 ft/sec is the

Exponential stability preservation in semi-discretisations of BAM networks with nonlinear impulses

NASA Astrophysics Data System (ADS)

Mohamad, Sannay; Gopalsamy, K.

2009-01-01

This paper demonstrates the reliability of a discrete-time analogue in preserving the exponential convergence of a bidirectional associative memory (BAM) network that is subject to nonlinear impulses. The analogue derived from a semi-discretisation technique with the value of the time-step fixed is treated as a discrete-time dynamical system while its exponential convergence towards an equilibrium state is studied. Thereby, a family of sufficiency conditions governing the network parameters and the impulse magnitude and frequency is obtained for the convergence. As special cases, one can obtain from our results, those corresponding to the non-impulsive discrete-time BAM networks and also those corresponding to continuous-time (impulsive and non-impulsive) systems. A relation between the Lyapunov exponent of the non-impulsive system and that of the impulsive system involving the size of the impulses and the inter-impulse intervals is obtained.

Dynamical quenching and annealing in self-organization multiagent models.

PubMed

Burgos, E; Ceva, H; Perazzo, R P

2001-07-01

We study the dynamics of a generalized minority game (GMG) and of the bar attendance model (BAM) in which a number of agents self-organize to match an attendance that is fixed externally as a control parameter. We compare the usual dynamics used for the minority game with one for the BAM that makes a better use of the available information. We study the asymptotic states reached in both frameworks. We show that states that can be assimilated to either thermodynamic equilibrium or quenched configurations can appear in both models, but with different settings. We discuss the relevance of the parameter G that measures the value of the prize for winning in units of the fine for losing. We also provide an annealing protocol by which the quenched configurations of the GMG can progressively be modified to reach an asymptotic equilibrium state that coincides with the one obtained with the BAM.

Dynamical quenching and annealing in self-organization multiagent models

NASA Astrophysics Data System (ADS)

Burgos, E.; Ceva, Horacio; Perazzo, R. P.

2001-07-01

We study the dynamics of a generalized minority game (GMG) and of the bar attendance model (BAM) in which a number of agents self-organize to match an attendance that is fixed externally as a control parameter. We compare the usual dynamics used for the minority game with one for the BAM that makes a better use of the available information. We study the asymptotic states reached in both frameworks. We show that states that can be assimilated to either thermodynamic equilibrium or quenched configurations can appear in both models, but with different settings. We discuss the relevance of the parameter G that measures the value of the prize for winning in units of the fine for losing. We also provide an annealing protocol by which the quenched configurations of the GMG can progressively be modified to reach an asymptotic equilibrium state that coincides with the one obtained with the BAM.

Investigations on antibody binding to a micro-cantilever coated with a BAM pesticide residue.

PubMed

Bache, Michael; Taboryski, Rafael; Schmid, Silvan; Aamand, Jens; Jakobsen, Mogens Havsteen

2011-05-16

The attachment of an antibody to an antigen-coated cantilever has been investigated by repeated experiments, using a cantilever-based detection system by Cantion A/S. The stress induced by the binding of a pesticide residue BAM (2,6 dichlorobenzamide) immobilized on a cantilever surface to anti-BAM antibody is measured using the CantiLab4© system from Cantion A/S with four gold-coated cantilevers and piezo resistive readout. The detection mechanism is in principle label-free, but fluorescent-marked antibodies have been used to subsequently verify the binding on the cantilever surface. The bending and increase in mass of each cantilever has also been investigated using a light interferometer and a Doppler Vibrometer. The system has been analyzed during repeated measurements to investigate whether the CantiLab4© system is a suited platform for a pesticide assay system.

Enhanced robust finite-time passivity for Markovian jumping discrete-time BAM neural networks with leakage delay.

PubMed

Sowmiya, C; Raja, R; Cao, Jinde; Rajchakit, G; Alsaedi, Ahmed

2017-01-01

This paper is concerned with the problem of enhanced results on robust finite-time passivity for uncertain discrete-time Markovian jumping BAM delayed neural networks with leakage delay. By implementing a proper Lyapunov-Krasovskii functional candidate, the reciprocally convex combination method together with linear matrix inequality technique, several sufficient conditions are derived for varying the passivity of discrete-time BAM neural networks. An important feature presented in our paper is that we utilize the reciprocally convex combination lemma in the main section and the relevance of that lemma arises from the derivation of stability by using Jensen's inequality. Further, the zero inequalities help to propose the sufficient conditions for finite-time boundedness and passivity for uncertainties. Finally, the enhancement of the feasible region of the proposed criteria is shown via numerical examples with simulation to illustrate the applicability and usefulness of the proposed method.

A Homology Model Reveals Novel Structural Features and an Immunodominant Surface Loop/Opsonic Target in the Treponema pallidum BamA Ortholog TP_0326

PubMed Central

Luthra, Amit; Anand, Arvind; Hawley, Kelly L.; LeDoyt, Morgan; La Vake, Carson J.; Caimano, Melissa J.; Cruz, Adriana R.; Salazar, Juan C.

2015-01-01

ABSTRACT We recently demonstrated that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses characteristic BamA bipartite topology. Herein, we used immunofluorescence analysis (IFA) to show that only the β-barrel domain of TP_0326 contains surface-exposed epitopes in intact T. pallidum. Using the solved structure of Neisseria gonorrhoeae BamA, we generated a homology model of full-length TP_0326. Although the model predicts a typical BamA fold, the β-barrel harbors features not described in other BamAs. Structural modeling predicted that a dome comprised of three large extracellular loops, loop 4 (L4), L6, and L7, covers the barrel's extracellular opening. L4, the dome's major surface-accessible loop, contains mainly charged residues, while L7 is largely neutral and contains a polyserine tract in a two-tiered conformation. L6 projects into the β-barrel but lacks the VRGF/Y motif that anchors L6 within other BamAs. IFA and opsonophagocytosis assay revealed that L4 is surface exposed and an opsonic target. Consistent with B cell epitope predictions, immunoblotting and enzyme-linked immunosorbent assay (ELISA) confirmed that L4 is an immunodominant loop in T. pallidum-infected rabbits and humans with secondary syphilis. Antibody capture experiments using Escherichia coli expressing OM-localized TP_0326 as a T. pallidum surrogate further established the surface accessibility of L4. Lastly, we found that a naturally occurring substitution (Leu593 → Gln593) in the L4 sequences of T. pallidum strains affects antibody binding in sera from syphilitic patients. Ours is the first study to employ a “structure-to-pathogenesis” approach to map the surface topology of a T. pallidum OMP within the context of syphilitic infection. IMPORTANCE Previously, we reported that TP_0326 is a bona fide rare outer membrane protein (OMP) in Treponema pallidum and that it possesses the bipartite topology characteristic of a BamA ortholog. Using a homology model as a guide, we found that TP_0326 displays unique features which presumably relate to its function(s) in the biogenesis of T. pallidum's unorthodox OM. The model also enabled us to identify an immunodominant epitope in a large extracellular loop that is both an opsonic target and subject to immune pressure in a human population. Ours is the first study to follow a structure-to-pathogenesis approach to map the surface topology of a T. pallidum rare OMP within the context of syphilitic infection. PMID:25825429

MoS2-Filled PEEK Composite as a Self-Lubricating Material for Aerospace Applications

NASA Technical Reports Server (NTRS)

Theiler, Geraldine; Gradt, Thomas

2010-01-01

At BAM, several projects were conducted in the past years dealing with the tribological properties of friction couples at cryogenic temperature and in vacuum environment. Promising candidates for vacuum application are MoS2-filled PEEK/PTFE composites, which showed a friction coefficient as low as 0.03 in high vacuum. To complete the tribological profile of these composites, further tests were performed in ultra-high vacuum (UHV) at room temperature. In this paper, friction and stick slip behavior, as well as outgassing characteristics during the test are presented.

Concussion Assessment With Smartglasses: Validation Study of Balance Measurement Toward a Lightweight, Multimodal, Field-Ready Platform.

PubMed

Salisbury, Joseph P; Keshav, Neha U; Sossong, Anthony D; Sahin, Ned T

2018-01-23

Lightweight and portable devices that objectively measure concussion-related impairments could improve injury detection and critical decision-making in contact sports and the military, where brain injuries commonly occur but remain underreported. Current standard assessments often rely heavily on subjective methods such as symptom self-reporting. Head-mounted wearables, such as smartglasses, provide an emerging platform for consideration that could deliver the range of assessments necessary to develop a rapid and objective screen for brain injury. Standing balance assessment, one parameter that may inform a concussion diagnosis, could theoretically be performed quantitatively using current off-the-shelf smartglasses with an internal accelerometer. However, the validity of balance measurement using smartglasses has not been investigated. This study aimed to perform preliminary validation of a smartglasses-based balance accelerometer measure (BAM) compared with the well-described and characterized waist-based BAM. Forty-two healthy individuals (26 male, 16 female; mean age 23.8 [SD 5.2] years) participated in the study. Following the BAM protocol, each subject performed 2 trials of 6 balance stances while accelerometer and gyroscope data were recorded from smartglasses (Glass Explorer Edition). Test-retest reliability and correlation were determined relative to waist-based BAM as used in the National Institutes of Health's Standing Balance Toolbox. Balance measurements obtained using a head-mounted wearable were highly correlated with those obtained through a waist-mounted accelerometer (Spearman rho, ρ=.85). Test-retest reliability was high (intraclass correlation coefficient, ICC 2,1 =0.85, 95% CI 0.81-0.88) and in good agreement with waist balance measurements (ICC 2,1 =0.84, 95% CI 0.80-0.88). Considering the normalized path length magnitude across all 3 axes improved interdevice correlation (ρ=.90) while maintaining test-retest reliability (ICC 2,1 =0.87, 95% CI 0.83-0.90). All subjects successfully completed the study, demonstrating the feasibility of using a head-mounted wearable to assess balance in a healthy population. Balance measurements derived from the smartglasses-based accelerometer were consistent with those obtained using a waist-mounted accelerometer. Additional research is necessary to determine to what extent smartglasses-based accelerometry measures can detect balance dysfunction associated with concussion. However, given the potential for smartglasses to perform additional concussion-related assessments in an integrated, wearable platform, continued development and validation of a smartglasses-based balance assessment is warranted. This approach could lead to a wearable platform for real-time assessment of concussion-related impairments that could be further augmented with telemedicine capabilities to integrate professional clinical guidance. Smartglasses may be superior to fully immersive virtual reality headsets for this application, given their lighter weight and reduced likelihood of potential safety concerns. ©Joseph P Salisbury, Neha U Keshav, Anthony D Sossong, Ned T Sahin. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 23.01.2018.

NAMRU-3 Reprint Accession List 1982. Number 12.

DTIC Science & Technology

1983-01-01

1316 * VETERINARY MEDICINE Canine parvovirus infection 1288 Congenital osteopetrosis in o/op mouse 1317 History of rabies vaccination 1278 Liver biopsy...Entomol., 19(2):209- 210, 1982. _ 1288 8UCCIO T.J., BOTROS, B.A.-M. and EL tiOLLA, M.: Canine Parvovirus Infe~tion: A Brief Review and Report of First...1278 BOTROS, B.A.M.: History of Rabies Vaccination . Review and Comments. J. Egypt. Public Health Assoc., 55(566):309-318, 1980. 1279 KLOOS, H

Modeling East Asian Dust and Its Radiative Feedbacks in CAM4-BAM

NASA Astrophysics Data System (ADS)

Xie, Xiaoning; Liu, Xiaodong; Che, Huizheng; Xie, Xiaoxun; Wang, Hongli; Li, Jiandong; Shi, Zhengguo; Liu, Yangang

2018-01-01

East Asian dust and its radiative feedbacks are analyzed by the use of the fourth version of the Community Atmosphere Model (CAM4) with a bulk aerosol model parameterization (BAM) for the dust size distribution (CAM4-BAM). Two numerical experiments are conducted and intercompared: one with (Active) and one without (Passive) the radiative effects of dust aerosols. This CAM4-BAM captures the main spatial distribution of the dust aerosol optical depth (AOD) and the dust surface concentrations over East Asia, with positive correlations with the local observational data on annual and seasonal means. A comparative analysis of the Active and Passive experiments reveals that consideration of the dust-radiation interaction can significantly reduce dust emissions, loading, transport, and dry and wet depositions over East Asia, which is opposite to the enhanced dust cycle over North Africa. Further analysis of the contrasting dust-radiation feedbacks between North Africa and East Asia shows that over North Africa, the dust radiative forcing significantly increases the surface temperature and 10 m wind speed, whereas it decreases the surface temperature and the surface wind speeds over East Asia. These contrasting radiative effects, in turn, result in distinct dust cycle changes over these two regions. Mechanistic analysis reveals that the radiative contrasts between East Asia and North Africa are mainly due to the differences in their regional surface albedo, dust vertical distribution, and size distribution.

A Supercomplex Spanning the Inner and Outer Membranes Mediates the Biogenesis of β-Barrel Outer Membrane Proteins in Bacteria.

PubMed

Wang, Yan; Wang, Rui; Jin, Feng; Liu, Yang; Yu, Jiayu; Fu, Xinmiao; Chang, Zengyi

2016-08-05

β-barrel outer membrane proteins (OMPs) are ubiquitously present in Gram-negative bacteria, mitochondria and chloroplasts, and function in a variety of biological processes. The mechanism by which the hydrophobic nascent β-barrel OMPs are transported through the hydrophilic periplasmic space in bacterial cells remains elusive. Here, mainly via unnatural amino acid-mediated in vivo photo-crosslinking studies, we revealed that the primary periplasmic chaperone SurA interacts with nascent β-barrel OMPs largely via its N-domain but with β-barrel assembly machine protein BamA mainly via its satellite P2 domain, and that the nascent β-barrel OMPs interact with SurA via their N- and C-terminal regions. Additionally, via dual in vivo photo-crosslinking, we demonstrated the formation of a ternary complex involving β-barrel OMP, SurA, and BamA in cells. More importantly, we found that a supercomplex spanning the inner and outer membranes and involving the BamA, BamB, SurA, PpiD, SecY, SecE, and SecA proteins appears to exist in living cells, as revealed by a combined analyses of sucrose-gradient ultra-centrifugation, Blue native PAGE and mass spectrometry. We propose that this supercomplex integrates the translocation, transportation, and membrane insertion events for β-barrel OMP biogenesis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

A Supercomplex Spanning the Inner and Outer Membranes Mediates the Biogenesis of β-Barrel Outer Membrane Proteins in Bacteria*

PubMed Central

Wang, Yan; Wang, Rui; Jin, Feng; Liu, Yang; Yu, Jiayu; Fu, Xinmiao; Chang, Zengyi

2016-01-01

β-barrel outer membrane proteins (OMPs) are ubiquitously present in Gram-negative bacteria, mitochondria and chloroplasts, and function in a variety of biological processes. The mechanism by which the hydrophobic nascent β-barrel OMPs are transported through the hydrophilic periplasmic space in bacterial cells remains elusive. Here, mainly via unnatural amino acid-mediated in vivo photo-crosslinking studies, we revealed that the primary periplasmic chaperone SurA interacts with nascent β-barrel OMPs largely via its N-domain but with β-barrel assembly machine protein BamA mainly via its satellite P2 domain, and that the nascent β-barrel OMPs interact with SurA via their N- and C-terminal regions. Additionally, via dual in vivo photo-crosslinking, we demonstrated the formation of a ternary complex involving β-barrel OMP, SurA, and BamA in cells. More importantly, we found that a supercomplex spanning the inner and outer membranes and involving the BamA, BamB, SurA, PpiD, SecY, SecE, and SecA proteins appears to exist in living cells, as revealed by a combined analyses of sucrose-gradient ultra-centrifugation, Blue native PAGE and mass spectrometry. We propose that this supercomplex integrates the translocation, transportation, and membrane insertion events for β-barrel OMP biogenesis. PMID:27298319

Toward a Better Nutritional Aiding in Disasters: Relying on Lessons Learned during the Bam Earthquake.

PubMed

Nekouie Moghadam, Mahmoud; Amiresmaieli, Mohammadreza; Hassibi, Mohammad; Doostan, Farideh; Khosravi, Sajad

2017-08-01

Introduction Examining various problems in the aftermath of disasters is very important to the disaster victims. Managing and coordinating food supply and its distribution among the victims is one of the most important problems after an earthquake. Therefore, the purpose of this study was to recognize problems and experiences in the field of nutritional aiding during an earthquake. This qualitative study was of phenomenological type. Using the purposive sampling method, 10 people who had experienced nutritional aiding during the Bam Earthquake (Iran; 2003) were interviewed. Colaizzi's method of analysis was used to analyze interview data. The findings of this study identified four main categories and 19 sub-categories concerning challenges in the nutritional aiding during the Bam Earthquake. The main topics included managerial, aiding, infrastructural, and administrative problems. The major problems in nutritional aiding include lack of prediction and development of a specific program of suitable nutritional pattern and nutritional assessment of the victims in critical conditions. Forming specialized teams, educating team members about nutrition, and making use of experts' knowledge are the most important steps to resolve these problems in the critical conditions; these measures are the duties of the relevant authorities. Nekouie Moghadam M , Amiresmaieli M , Hassibi M , Doostan F , Khosravi S . Toward a better nutritional aiding in disasters: relying on lessons learned during the Bam Earthquake. Prehosp Disaster Med. 2017;32(4):382-386.

Parental cigarette smoking, transforming growth factor-alpha gene variant and the risk of orofacial cleft in Iranian infants

PubMed Central

Ebadifar, Asghar; Hamedi, Roya; KhorramKhorshid, Hamid Reza; Kamali, Koorosh; Moghadam, Fatemeh Aghakhani

2016-01-01

Objective(s): We investigated the influence of genetic variation of the transforming growth-factor alpha (TGFA) locus on the relationship between smoking and oral clefts. Materials and Methods: In this study 105 Iranian infants with non-syndromic cleft lip/palate and 218 controls with non-cleft birth defects were examined to test for associations among maternal exposures, genetic markers, and oral clefts. Maternal and parental smoking histories during pregnancy were obtained through questionnaire. DNA was extracted from newborn screening blood samples, and genotyping of the BamHI polymorphism in the TGFA gene was performed by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) methods. A number of factors including gender of the newborns, type of oral cleft, consanguinity of the parents, as well as the mother’s age and education were evaluated as potential confounders and effect modifiers. Results: Maternal smoking, in the absence of paternal smoking, was associated with an increased risk for CL/P (OR = 19.2, 95% CI = [(6.2-59.5)]) and cleft palate only (OR =48.7, 95% CI = [(8-29.3)]). If both parents smoked, risks were generally greater (OR = 55.6, 95% CI = [12-20.25]). Analyses for the risk of clefting from maternal smoking, stratified by the presence or absence of the TGFA/BamH1variant, revealed that the risk of clefting among the infants with the TGFA/BamH1 variant when their mothers smoked cigarettes was much greater than the infants who had non-smoker mothers (P=0.001, OR=10.4,95% CI=[3.2,33.6]). Conclusion: The results of this study indicate that first-trimester maternal smoking and infant TGFA locus mutations are both associated with nonsyndromic cleft lip and/or palate (CL/P). PMID:27279979

Psychological distress among Bam earthquake survivors in Iran: a population-based study.

PubMed

Montazeri, Ali; Baradaran, Hamid; Omidvari, Sepideh; Azin, Seyed Ali; Ebadi, Mehdi; Garmaroudi, Gholamreza; Harirchi, Amir Mahmood; Shariati, Mohammad

2005-01-11

An earthquake measuring 6.3 on the Richter scale struck the city of Bam in Iran on the 26th of December 2003 at 5.26 A.M. It was devastating, and left over 40,000 dead and around 30,000 injured. The profound tragedy of thousands killed has caused emotional and psychological trauma for tens of thousands of people who have survived. A study was carried out to assess psychological distress among Bam earthquake survivors and factors associated with severe mental health in those who survived the tragedy. This was a population-based study measuring psychological distress among the survivors of Bam earthquake in Iran. Using a multi-stage stratified sampling method a random sample of individuals aged 15 years and over living in Bam were interviewed. Psychological distress was measured using the 12-item General Health Questionnaire (GHQ-12). In all 916 survivors were interviewed. The mean age of the respondents was 32.9 years (SD = 12.4), mostly were males (53%), married (66%) and had secondary school education (50%). Forty-one percent reported they lost 3 to 5 members of their family in the earthquake. In addition the findings showed that 58% of the respondents suffered from severe mental health as measured by the GHQ-12 and this was three times higher than reported psychological distress among the general population. There were significant differences between sub-groups of the study sample with regard to their psychological distress. The results of the logistic regression analysis also indicated that female gender; lower education, unemployment, and loss of family members were associated with severe psychological distress among earthquake victims. The study findings indicated that the amount of psychological distress among earthquake survivors was high and there is an urgent need to deliver mental health care to disaster victims in local medical settings and to reduce negative health impacts of the earthquake adequate psychological counseling is needed for those who survived the tragedy.

Psychological distress among Bam earthquake survivors in Iran: a population-based study

PubMed Central

Montazeri, Ali; Baradaran, Hamid; Omidvari, Sepideh; Azin, Seyed Ali; Ebadi, Mehdi; Garmaroudi, Gholamreza; Harirchi, Amir Mahmood; Shariati, Mohammad

2005-01-01

Background An earthquake measuring 6.3 on the Richter scale struck the city of Bam in Iran on the 26th of December 2003 at 5.26 A.M. It was devastating, and left over 40,000 dead and around 30,000 injured. The profound tragedy of thousands killed has caused emotional and psychological trauma for tens of thousands of people who have survived. A study was carried out to assess psychological distress among Bam earthquake survivors and factors associated with severe mental health in those who survived the tragedy. Methods This was a population-based study measuring psychological distress among the survivors of Bam earthquake in Iran. Using a multi-stage stratified sampling method a random sample of individuals aged 15 years and over living in Bam were interviewed. Psychological distress was measured using the 12-item General Health Questionnaire (GHQ-12). Results In all 916 survivors were interviewed. The mean age of the respondents was 32.9 years (SD = 12.4), mostly were males (53%), married (66%) and had secondary school education (50%). Forty-one percent reported they lost 3 to 5 members of their family in the earthquake. In addition the findings showed that 58% of the respondents suffered from severe mental health as measured by the GHQ-12 and this was three times higher than reported psychological distress among the general population. There were significant differences between sub-groups of the study sample with regard to their psychological distress. The results of the logistic regression analysis also indicated that female gender; lower education, unemployment, and loss of family members were associated with severe psychological distress among earthquake victims. Conclusion The study findings indicated that the amount of psychological distress among earthquake survivors was high and there is an urgent need to deliver mental health care to disaster victims in local medical settings and to reduce negative health impacts of the earthquake adequate psychological counseling is needed for those who survived the tragedy. PMID:15644145

Distinctive Roles for Periplasmic Proteases in the Maintenance of Essential Outer Membrane Protein Assembly.

PubMed

Soltes, Garner R; Martin, Nicholas R; Park, Eunhae; Sutterlin, Holly A; Silhavy, Thomas J

2017-10-15

Outer membrane protein (OMP) biogenesis in Escherichia coli is a robust process essential to the life of the organism. It is catalyzed by the β-barrel assembly machine (Bam) complex, and a number of quality control factors, including periplasmic chaperones and proteases, maintain the integrity of this trafficking pathway. Little is known, however, about how periplasmic proteases recognize and degrade OMP substrates when assembly is compromised or whether different proteases recognize the same substrate at distinct points in the assembly pathway. In this work, we use well-defined assembly-defective mutants of LptD, the essential lipopolysaccharide assembly translocon, to show that the periplasmic protease DegP degrades substrates with assembly defects that prevent or impair initial contact with Bam, causing the mutant protein to accumulate in the periplasm. In contrast, another periplasmic protease, BepA, degrades a LptD mutant substrate that has engaged the Bam complex and formed a nearly complete barrel. Furthermore, we describe the role of the outer membrane lipoprotein YcaL, a protease of heretofore unknown function, in the degradation of a LptD substrate that has engaged the Bam complex but is stalled at an earlier step in the assembly process that is not accessible to BepA. Our results demonstrate that multiple periplasmic proteases monitor OMPs at distinct points in the assembly process. IMPORTANCE OMP assembly is catalyzed by the essential Bam complex and occurs in a cellular environment devoid of energy sources. Assembly intermediates that misfold can compromise this essential molecular machine. Here we demonstrate distinctive roles for three different periplasmic proteases that can clear OMP substrates with folding defects that compromise assembly at three different stages. These quality control factors help ensure the integrity of the permeability barrier that contributes to the intrinsic resistance of Gram-negative organisms to many antibiotics. Copyright © 2017 American Society for Microbiology.

Reveal Listeria 2.0 test for detection of Listeria spp. in foods and environmental samples.

PubMed

Alles, Susan; Curry, Stephanie; Almy, David; Jagadeesan, Balamurugan; Rice, Jennifer; Mozola, Mark

2012-01-01

A Performance Tested Method validation study was conducted for a new lateral flow immunoassay (Reveal Listeria 2.0) for detection of Listeria spp. in foods and environmental samples. Results of inclusivity testing showed that the test detects all species of Listeria, with the exception of L. grayi. In exclusivity testing conducted under nonselective growth conditions, all non-listeriae tested produced negative Reveal assay results, except for three strains of Lactobacillus spp. However, these lactobacilli are inhibited by the selective Listeria Enrichment Single Step broth enrichment medium used with the Reveal method. Six foods were tested in parallel by the Reveal method and the U.S. Food and Drug Administration/Bacteriological Analytical Manual (FDA/BAM) reference culture procedure. Considering data from both internal and independent laboratory trials, overall sensitivity of the Reveal method relative to that of the FDA/BAM procedure was 101%. Four foods were tested in parallel by the Reveal method and the U.S. Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS) reference culture procedure. Overall sensitivity of the Reveal method relative to that of the USDA-FSIS procedure was 98.2%. There were no statistically significant differences in the number of positives obtained by the Reveal and reference culture procedures in any food trials. In testing of swab or sponge samples from four types of environmental surfaces, sensitivity of Reveal relative to that of the USDA-FSIS reference culture procedure was 127%. For two surface types, differences in the number of positives obtained by the Reveal and reference methods were statistically significant, with more positives by the Reveal method in both cases. Specificity of the Reveal assay was 100%, as there were no unconfirmed positive results obtained in any phase of the testing. Results of ruggedness experiments showed that the Reveal assay is tolerant of modest deviations in test sample volume and device incubation time.

Passivity analysis for uncertain BAM neural networks with time delays and reaction-diffusions

NASA Astrophysics Data System (ADS)

Zhou, Jianping; Xu, Shengyuan; Shen, Hao; Zhang, Baoyong

2013-08-01

This article deals with the problem of passivity analysis for delayed reaction-diffusion bidirectional associative memory (BAM) neural networks with weight uncertainties. By using a new integral inequality, we first present a passivity condition for the nominal networks, and then extend the result to the case with linear fractional weight uncertainties. The proposed conditions are expressed in terms of linear matrix inequalities, and thus can be checked easily. Examples are provided to demonstrate the effectiveness of the proposed results.

Samsung Salmonella Detection Kit. AOAC Performance Tested Method(SM) 021203.

PubMed

Li, Jun; Cheung, Win Den; Opdyke, Jason; Harvey, John; Chong, Songchun; Moon, Cheol Gon

2012-01-01

Salmonella, one of the most common causes of foodborne illness, is a significant public health concern worldwide. There is a need in the food industry for methods that are simple, rapid, and sensitive for the detection of foodborne pathogens. In this study, the Samsung Salmonella Detection Kit, a real-time PCR assay for the detection of Salmonella, was evaluated according to the current AOAC guidelines. The validation consisted of lot-to-lot consistency, stability, robustness, and inclusivity/exclusivity studies, as well as a method comparison of 10 different food matrixes. In the validation, the Samsung Salmonella Detection Kit was used in conjunction with the Applied Biosystems StepOnePlus PCR system and the Samsung Food Testing Software for the detection of Salmonella species. The performance of the assays was compared to the U.S. Department of Agriculture/Food Safety and Inspection Service-Microbiology Laboratory Guidebook (USDA/FSIS-MLG) 4.05: Isolation and Identification of Salmonella from Meat, Poultry, Pasteurized Egg, and Catfish and the and U.S. Food and Drug Administration/Bacteriological Analytical Manual (FDA/BAM) Chapter 5 Salmonella reference methods. The validation was conducted using an unpaired study design for detection of Salmonella spp. in raw ground beef, raw pork, raw ground pork, raw chicken wings, raw salmon, alfalfa sprouts, pasteurized orange juice, peanut butter, pasteurized whole milk, and shell eggs. The Samsung Salmonella Detection Kit demonstrated lot-to-lot consistency among three independent lots as well as ruggedness with minor modifications to changes in enrichment incubation time, enrichment incubation temperature, and DNA sample volume for PCR reaction. Stability was observed for 13 months at -20 degrees C and 3 months at 5 degrees C. For the inclusivity/exclusivity study, the Samsung Salmonella Detection Kit correctly identified 147 Salmonella species isolates out of 147 isolates tested from each of three different enrichment broths (a total of 441 isolates detected), and correctly excluded all 31 nontarget strains analyzed. For the method comparison, statistical analysis was conducted according to the Mantel-Haenszel Chi-square formula for unpaired test portions, and there was no significant difference in the number of positive samples detected between the Samsung Salmonella Detection Kit and the USDA/FSIS-MLG and FDA/BAM reference methods for all 10 food matrixes.

An investigation of cell growth and detachment from thermoresponsive physically crosslinked networks.

PubMed

Healy, Deirdre; Nash, Maria; Gorleov, Alexander; Thompson, Kerry; Dockery, Peter; Rochev, Yury

2017-11-01

The primary aim of this investigation was to determine the biocompatibility and cell culture potential of a newly designed class of thermoresponsive polymers. The attractiveness of these polymers lies in the fact that they swell rather than dissolve when the temperature is reduced below their respective lower critical solution temperature, due to the incorporation of octadecyl methacrylate (ODMA). The ODMA monomer acts as a physical crosslinker, preventing polymer dissolution upon temperature reduction. Two polymers were studied in this investigation poly(N isorpoylacrylamide (NIPAm)(99.25%)-co-ODMA(0.75%)) and poly(NIPAm(65%)-co-N-tert-butylacrylamide (NtBAm)(34.25%)-co-ODMA(0.75%)). Thin thermoresponsive films of the polymers were prepared via spin coating. 3T3 cells were then seeded on the prepared films and cell viability was assessed quantitatively through cell viability and activity assays and qualitatively by light microscopy. Cells were successfully seeded and grown on the poly(NIPAm-co-ODMA) and poly(NIPAm-co-NtBAm-co-ODMA) copolymer films after film modification with cell adhesion promoters (CAPs). Cell sheets successfully detached from the CAP coated poly(NIPAm-co-ODMA) platforms upon temperature reduction. Copyright © 2017 Elsevier B.V. All rights reserved.

Strain monitoring of a newly developed precast concrete track for high speed railway traffic using embedded fiber optic sensors

NASA Astrophysics Data System (ADS)

Crail, Stephanie; Reichel, D.; Schreiner, U.; Lindner, E.; Habel, Wolfgang R.; Hofmann, Detlef; Basedau, Frank; Brandes, K.; Barner, A.; Ecke, Wolfgang; Schroeder, Kerstin

2002-07-01

In a German slab track system (Feste Fahrbahn FF, system Boegl) for speeds up to 300 km/h and more different fiber optic sensors have been embedded in several levels and locations of the track system. The track system consists of prestressed precast panels of steel fiber concrete which are supported by a cat-in-situ concrete or asphalt base course. The sensors are to measure the bond behavior or the stress transfer in the track system. For that, tiny fiber-optic sensors - fiber Fabry-Perot and Bragg grating sensors - have been embedded very near to the interface of the layers. Measurements were taken on a full scale test sample (slab track panel of 6.45 m length) as well as on a real high speed track. The paper describes the measurement task and discusses aspects with regard to sensor design and prefabrication of the sensor frames as well as the embedding procedure into the concrete track. Results from static and dynamic full scale tests carried out in the testing laboratory of BAM and from measurements on a track are given.

High dispersibility and enhanced luminescence properties of BaMgAl10O17:Eu2+ phosphors derived from molten salt synthesis

NASA Astrophysics Data System (ADS)

Wang, Xiang; Li, Jin-hong; Shi, Ping-lu; Guan, Wei-min; Zhang, Hong-yao

2015-08-01

BaMgAl10O17:Eu2+ (BAM) phosphors were prepared via the molten salt synthesis (MSS) method. The NaCl-KCl eutectic mixture and LiF were used as the molten salt and flux, respectively. X-ray powder diffraction (XRD) patterns indicate that the BAM phase is formed above 1200 °C and that the addition of LiF leads to an obvious improvement in crystallinity. The emission intensity of the BAM phosphor with 10 wt% LiF is about 85% higher than that of the phosphor without LiF and about 200% higher than that of the phosphor without molten salt and LiF. Scanning electron microscopy (SEM) reveal that the as-prepared phosphors have good crystallinity and regular morphology, and most importantly, they are not aggregated. Li+ doping is benefit for the thermal stability and results in a slightly longer decay times of 1.17 μs.

Bio-Aerosol Detection Using Mass Spectrometry: Public Health Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ludvigson, Laura D.

2004-01-01

I recently spent a summer as an intern at the Lawrence Livermore National Laboratory. I worked on a project involving the real-time, reagentless, single cell detection of aerosolized pathogens using a novel mass spectrometry approach called Bio-Aerosol Mass Spectrometry (BAMS). Based upon preliminary results showing the differentiation capabilities of BAMS, I would like to explore the development and use of this novel detection system in the context of both environmental and clinical sample pathogen detection. I would also like to explore the broader public health applications that a system such as BAMS might have in terms of infectious disease preventionmore » and control. In order to appreciate the potential of this instrument, I will demonstrate the need for better pathogen detection methods, and outline the instrumentation, data analysis and preliminary results that lead me toward a desire to explore this technology further. I will also discuss potential experiments for the future along with possible problems that may be encountered along the way.« less

Modeling East Asian Dust and Its Radiative Feedbacks in CAM4-BAM

DOE PAGES

Xie, Xiaoning; Liu, Xiaodong; Che, Huizheng; ...

2018-01-18

East Asian dust and its radiative feedbacks are analyzed by the use of the fourth version of the Community Atmosphere Model (CAM4) with a bulk aerosol model parameterization (BAM) for the dust size distribution (CAM4-BAM). Two numerical experiments are conducted and intercompared: one with (Active) and one without (Passive) the radiative effects of dust aerosols. This CAM4-BAM captures the main spatial distribution of the dust aerosol optical depth (AOD) and the dust surface concentrations over East Asia, with positive correlations with the local observational data on annual and seasonal means. A comparative analysis of the Active and Passive experiments revealsmore » that consideration of the dust-radiation interaction can significantly reduce dust emissions, loading, transport, and dry and wet depositions over East Asia, which is opposite to the enhanced dust cycle over North Africa. Further analysis of the contrasting dust-radiation feedbacks between North Africa and East Asia shows that over North Africa, the dust radiative forcing significantly increases the surface temperature and 10-m wind speed, whereas it decreases the surface temperature and the surface wind speeds over East Asia. These contrasting radiative effects, in turn, result in distinct dust cycle changes over these two regions. Thus, mechanistic analysis reveals that the radiative contrasts between East Asia and North Africa are mainly due to the differences in their regional surface albedo, dust vertical distribution and size distribution.« less

Anti-tumor immunity of BAM-SiPc-mediated vascular photodynamic therapy in a BALB/c mouse model.

PubMed

Yeung, Hing-Yuen; Lo, Pui-Chi; Ng, Dennis K P; Fong, Wing-Ping

2017-02-01

In recent decades, accumulating evidence from both animal and clinical studies has suggested that a sufficiently activated immune system may strongly augment various types of cancer treatment, including photodynamic therapy (PDT). Through the generation of reactive oxygen species, PDT eradicates tumors by triggering localized tumor damage and inducing anti-tumor immunity. As the major component of anti-tumor immunity, the involvement of a cell-mediated immune response in PDT has been well investigated in the past decade, whereas the role of humoral immunity has remained relatively unexplored. In the present investigation, using the photosensitizer BAM-SiPc and the CT26 tumor-bearing BALB/c mouse model, it was demonstrated that both cell-mediated and humoral adaptive immune components could be involved in PDT. With a vascular PDT (VPDT) regimen, BAM-SiPc could eradicate the tumors of ∼70% of tumor-bearing mice and trigger an anti-tumor immune response that could last for more than 1 year. An elevation of Th2 cytokines was detected ex vivo after VPDT, indicating the potential involvement of a humoral response. An analysis of serum from the VPDT-cured mice also revealed elevated levels of tumor-specific antibodies. Moreover, this serum could effectively hinder tumor growth and protect the mice against further re-challenge in a T-cell-dependent manner. Taken together, these results show that the humoral components induced after BAM-SiPc-VPDT could assist the development of anti-tumor immunity.

Modeling East Asian Dust and Its Radiative Feedbacks in CAM4-BAM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Xiaoning; Liu, Xiaodong; Che, Huizheng

East Asian dust and its radiative feedbacks are analyzed by the use of the fourth version of the Community Atmosphere Model (CAM4) with a bulk aerosol model parameterization (BAM) for the dust size distribution (CAM4-BAM). Two numerical experiments are conducted and intercompared: one with (Active) and one without (Passive) the radiative effects of dust aerosols. This CAM4-BAM captures the main spatial distribution of the dust aerosol optical depth (AOD) and the dust surface concentrations over East Asia, with positive correlations with the local observational data on annual and seasonal means. A comparative analysis of the Active and Passive experiments revealsmore » that consideration of the dust-radiation interaction can significantly reduce dust emissions, loading, transport, and dry and wet depositions over East Asia, which is opposite to the enhanced dust cycle over North Africa. Further analysis of the contrasting dust-radiation feedbacks between North Africa and East Asia shows that over North Africa, the dust radiative forcing significantly increases the surface temperature and 10-m wind speed, whereas it decreases the surface temperature and the surface wind speeds over East Asia. These contrasting radiative effects, in turn, result in distinct dust cycle changes over these two regions. Thus, mechanistic analysis reveals that the radiative contrasts between East Asia and North Africa are mainly due to the differences in their regional surface albedo, dust vertical distribution and size distribution.« less

Discrete-time bidirectional associative memory neural networks with variable delays

NASA Astrophysics Data System (ADS)

Liang, variable delays [rapid communication] J.; Cao, J.; Ho, D. W. C.

2005-02-01

Based on the linear matrix inequality (LMI), some sufficient conditions are presented in this Letter for the existence, uniqueness and global exponential stability of the equilibrium point of discrete-time bidirectional associative memory (BAM) neural networks with variable delays. Some of the stability criteria obtained in this Letter are delay-dependent, and some of them are delay-independent, they are less conservative than the ones reported so far in the literature. Furthermore, the results provide one more set of easily verified criteria for determining the exponential stability of discrete-time BAM neural networks.

Characterization of a Laser-Generated Perturbation in High-Speed Flow for Receptivity Studies

DTIC Science & Technology

2014-01-01

to trip the boundary layer. Figure 1. Schematic of the Boeing/AFOSR Mach-6 Quiet Tunnel (BAM6QT) The BAM6QT is a Ludwieg tube with a double- burst ...reduced to a 4-mm beam diameter by an aperture. Although the PIV-400 is a double- pulse laser, only the first pulse is used to generate perturbations in the...also both seeded, and pulse at 10 Hz, with a pulse width of about 7 ns. 2. Forming Optics The laser-generated perturbation is created by focusing a

Unique variations of Epstein-Barr virus-encoded BARF1 gene in nasopharyngeal carcinoma biopsies.

PubMed

Wang, Yun; Wang, Xiao-Feng; Sun, Zhi-Fu; Luo, Bing

2012-06-01

The Epstein-Barr virus (EBV) BamHI-A rightward frame 1 (BARF1) gene is frequently expressed in EBV-associated epithelial malignancies and involves in oncogenicity and immunomodulation. To characterize the variations of BARF1 gene in different populations, the sequences of BARF1 gene in Northern Chinese nasopharyngeal carcinoma (NPC), EBV-associated gastric carcinoma (EBVaGC) and healthy donors were analyzed. The correlation of BARF1 variation with polymorphisms of BamHI F fragment (type F and f variants) and EBV-coded viral interleukin-10 (vIL-10) gene (B95-8 and SPM patterns) was also explored. Two major subtypes of BARF1 gene, designated as B95-8 and V29A, were identified. B95-8 subtype had identical amino acid sequence to B95-8 and was the dominant subtype among the EBV isolates from Northern China. V29A subtype, with one consistent amino acid change at residue 29 (V→A) and several nucleotide changes, showed higher frequency in NPC cases (25.3%, 20/79) than in EBVaGC cases (0/45) or healthy donors (4.3%, 2/46) (NPC vs. EBVaGC: P=0.0001; NPC vs. healthy donor: P=0.004). A preferential linkage between BamHI F and BARF1/vIL-10 polymorphisms was found. Type f isolates was specially correlated with the V29A/SPM genotype in NPC isolates and type f/V29A/SPM was preferentially found in NPC. BARF1/c-fms homology domain, transforming domain and cytotoxic T lymphocyte (CTL) epitopes of BARF1 were highly conserved in most isolates, suggesting the important role of BARF1 in virus infection and the potential usefulness in EBV-targeting immunotherapy of EBV-associated tumors. The relatively higher prevalence of type f/V29A/SPM strains in NPC may also suggest the association between these variations in multiple viral genes and NPC. Copyright © 2012 Elsevier B.V. All rights reserved.

DuPont Qualicon BAX System polymerase chain reaction assay. Performance Tested Method 100201.

PubMed

Tice, George; Andaloro, Bridget; Fallon, Dawn; Wallace, F Morgan

2009-01-01

A recent outbreak of Salmonella in peanut butter has highlighted the need for validation of rapid detection methods. A multilaboratory study for detecting Salmonella in peanut butter was conducted as part of the AOAC Research Institute Emergency Response Validation program for methods that detect outbreak threats to food safety. Three sites tested spiked samples from the same master mix according to the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA-BAM) method and the BAX System method. Salmonella Typhimurium (ATCC 14028) was grown in brain heart infusion for 24 h at 37 degrees C, then diluted to appropriate levels for sample inoculation. Master samples of peanut butter were spiked at high and low target levels, mixed, and allowed to equilibrate at room temperature for 2 weeks. Spike levels were low [1.08 most probable number (MPN)/25 g]; high (11.5 MPN/25 g) and unspiked to serve as negative controls. Each master sample was divided into 25 g portions and coded to blind the samples. Twenty portions of each spiked master sample and five portions of the unspiked sample were tested at each site. At each testing site, samples were blended in 25 g portions with 225 mL prewarmed lactose broth until thoroughly homogenized, then allowed to remain at room temperature for 55-65 min. Samples were adjusted to a pH of 6.8 +/- 0.2, if necessary, and incubated for 22-26 h at 35 degrees C. Across the three reporting laboratories, the BAX System detected Salmonella in 10/60 low-spike samples and 58/60 high-spike samples. The reference FDA-BAM method yielded positive results for 11/60 low-spike and 58/60 high-spike samples. Neither method demonstrated positive results for any of the 15 unspiked samples.

Implantation of In Vitro Tissue Engineered Muscle Repair Constructs and Bladder Acellular Matrices Partially Restore In Vivo Skeletal Muscle Function in a Rat Model of Volumetric Muscle Loss Injury

PubMed Central

Corona, Benjamin T.; Ward, Catherine L.; Baker, Hannah B.; Walters, Thomas J.

2014-01-01

The frank loss of a large volume of skeletal muscle (i.e., volumetric muscle loss [VML]) can lead to functional debilitation and presents a significant problem to civilian and military medicine. Current clinical treatment for VML involves the use of free muscle flaps and physical rehabilitation; however, neither are effective in promoting regeneration of skeletal muscle to replace the tissue that was lost. Toward this end, skeletal muscle tissue engineering therapies have recently shown great promise in offering an unprecedented treatment option for VML. In the current study, we further extend our recent progress (Machingal et al., 2011, Tissue Eng; Corona et al., 2012, Tissue Eng) in the development of tissue engineered muscle repair (TEMR) constructs (i.e., muscle-derived cells [MDCs] seeded on a bladder acellular matrix (BAM) preconditioned with uniaxial mechanical strain) for the treatment of VML. TEMR constructs were implanted into a VML defect in a tibialis anterior (TA) muscle of Lewis rats and observed up to 12 weeks postinjury. The salient findings of the study were (1) TEMR constructs exhibited a highly variable capacity to restore in vivo function of injured TA muscles, wherein TEMR-positive responders (n=6) promoted an ≈61% improvement, but negative responders (n=7) resulted in no improvement compared to nonrepaired controls, (2) TEMR-positive and -negative responders exhibited differential immune responses that may underlie these variant responses, (3) BAM scaffolds (n=7) without cells promoted an ≈26% functional improvement compared to uninjured muscles, (4) TEMR-positive responders promoted muscle fiber regeneration within the initial defect area, while BAM scaffolds did so only sparingly. These findings indicate that TEMR constructs can improve the in vivo functional capacity of the injured musculature at least, in part, by promoting generation of functional skeletal muscle fibers. In short, the degree of functional recovery observed following TEMR implantation (BAM+MDCs) was 2.3×-fold greater than that observed following implantation of BAM alone. As such, this finding further underscores the potential benefits of including a cellular component in the tissue engineering strategy for VML injury. PMID:24066899

Attenuation of skeletal muscle wasting with recombinant human growth hormone secreted from a tissue-engineered bioartificial muscle

NASA Technical Reports Server (NTRS)

Vandenburgh, H.; Del Tatto, M.; Shansky, J.; Goldstein, L.; Russell, K.; Genes, N.; Chromiak, J.; Yamada, S.

1998-01-01

Skeletal muscle wasting is a significant problem in elderly and debilitated patients. Growth hormone (GH) is an anabolic growth factor for skeletal muscle but is difficult to deliver in a therapeutic manner by injection owing to its in vivo instability. A novel method is presented for the sustained secretion of recombinant human GH (rhGH) from genetically modified skeletal muscle implants, which reduces host muscle wasting. Proliferating murine C2C12 skeletal myoblasts stably transduced with the rhGH gene were tissue engineered in vitro into bioartificial muscles (C2-BAMs) containing organized postmitotic myofibers secreting 3-5 microg of rhGH/day in vitro. When implanted subcutaneously into syngeneic mice, C2-BAMs delivered a sustained physiologic dose of 2.5 to 11.3 ng of rhGH per milliliter of serum. rhGH synthesized and secreted by the myofibers was in the 22-kDa monomeric form and was biologically active, based on downregulation of a GH-sensitive protein synthesized in the liver. Skeletal muscle disuse atrophy was induced in mice by hindlimb unloading, causing the fast plantaris and slow soleus muscles to atrophy by 21 to 35% ( < 0.02). This atrophy was significantly attenuated 41 to 55% (p < 0.02) in animals that received C2-BAM implants, but not in animals receiving daily injections of purified rhGH (1 mg/kg/day). These data support the concept that delivery of rhGH from BAMs may be efficacious in treating muscle-wasting disorders.

Molecularly imprinted phloroglucinol-formaldehyde-melamine resin prepared in a deep eutectic solvent for selective recognition of clorprenaline and bambuterol in urine.

PubMed

Liang, Shiru; Yan, Hongyuan; Cao, Jiankun; Han, Yehong; Shen, Shigang; Bai, Ligai

2017-01-25

A new molecularly imprinted phloroglucinol-formaldehyde-melamine resin (MIPFMR) was synthesized in a deep eutectic solvent (DES) using phenylephrine as a dummy template. The MIPFMR was used as a solid phase extraction (SPE) sorbent for the selective isolation and recognition of clorprenaline (CLP) and bambuterol (BAM) in urine. Phloroglucinol and melamine were used as double functional monomers that introduced abundant hydrophilic groups (such as hydroxyl groups, imino groups, and ether linkages) into the MIPFMR, making it compatible with aqueous solvents. In addition, the formation of DES by combining the quaternary ammonium salt of choline chloride with ethylene glycol as a hydrogen bond donor was an environmentally safe alternative to toxic organic solvents such as chloroform and dimethylsulfoxide that are typically used in the preparation of most molecularly imprinted polymers (MIPs). Moreover, MIPFMR-based SPE of CLP and BAM in urine resulted in higher recoveries and purer extracts than those obtained by using other SPE materials (e.g., SCX, C 18 , HLB, and non-imprinted phloroglucinol-formaldehyde-melamine resin (NIPFMR)). The optimized MIPFMR-SPE-HPLC-UV method had good linearity (r 2  ≥ 0.9996) ranging from 15.0 to 3000.0 ng mL -1 for CLP and BAM, and the recoveries at three spiked levels ranged from 91.7% to 100.1% with RSDs ≤7.6%. The novel MIPFMR-SPE-HPLC-UV method is simple, selective, and accurate, and can be used for the determination of CLP and BAM in urine samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Lineage-Specific Evolutionary Histories and Regulation of Major Starch Metabolism Genes during Banana Ripening

PubMed Central

Jourda, Cyril; Cardi, Céline; Gibert, Olivier; Giraldo Toro, Andrès; Ricci, Julien; Mbéguié-A-Mbéguié, Didier; Yahiaoui, Nabila

2016-01-01

Starch is the most widespread and abundant storage carbohydrate in plants. It is also a major feature of cultivated bananas as it accumulates to large amounts during banana fruit development before almost complete conversion to soluble sugars during ripening. Little is known about the structure of major gene families involved in banana starch metabolism and their evolution compared to other species. To identify genes involved in banana starch metabolism and investigate their evolutionary history, we analyzed six gene families playing a crucial role in plant starch biosynthesis and degradation: the ADP-glucose pyrophosphorylases (AGPases), starch synthases (SS), starch branching enzymes (SBE), debranching enzymes (DBE), α-amylases (AMY) and β-amylases (BAM). Using comparative genomics and phylogenetic approaches, these genes were classified into families and sub-families and orthology relationships with functional genes in Eudicots and in grasses were identified. In addition to known ancestral duplications shaping starch metabolism gene families, independent evolution in banana and grasses also occurred through lineage-specific whole genome duplications for specific sub-families of AGPase, SS, SBE, and BAM genes; and through gene-scale duplications for AMY genes. In particular, banana lineage duplications yielded a set of AGPase, SBE and BAM genes that were highly or specifically expressed in banana fruits. Gene expression analysis highlighted a complex transcriptional reprogramming of starch metabolism genes during ripening of banana fruits. A differential regulation of expression between banana gene duplicates was identified for SBE and BAM genes, suggesting that part of starch metabolism regulation in the fruit evolved in the banana lineage. PMID:27994606

Impact of leakage delay on bifurcation in high-order fractional BAM neural networks.

PubMed

Huang, Chengdai; Cao, Jinde

2018-02-01

The effects of leakage delay on the dynamics of neural networks with integer-order have lately been received considerable attention. It has been confirmed that fractional neural networks more appropriately uncover the dynamical properties of neural networks, but the results of fractional neural networks with leakage delay are relatively few. This paper primarily concentrates on the issue of bifurcation for high-order fractional bidirectional associative memory(BAM) neural networks involving leakage delay. The first attempt is made to tackle the stability and bifurcation of high-order fractional BAM neural networks with time delay in leakage terms in this paper. The conditions for the appearance of bifurcation for the proposed systems with leakage delay are firstly established by adopting time delay as a bifurcation parameter. Then, the bifurcation criteria of such system without leakage delay are successfully acquired. Comparative analysis wondrously detects that the stability performance of the proposed high-order fractional neural networks is critically weakened by leakage delay, they cannot be overlooked. Numerical examples are ultimately exhibited to attest the efficiency of the theoretical results. Copyright © 2017 Elsevier Ltd. All rights reserved.

On-sky verification of the 6-h periodic basic angle variations of the Gaia satellite

NASA Astrophysics Data System (ADS)

Liao, Shilong; Lattanzi, Mario G.; Vecchiato, Alberto; Qi, Zhaoxiang; Crosta, Mariateresa; Tang, Zhenghong

2018-04-01

A Basic Angle (BA) of 106.5° separates the view directions of Gaia's two fields of view (FoV). A precise determination of the BA variations (BAV) is essential to guarantee a correct reconstruction of the global astrometric sphere, as residual systematic errors would result in, e.g., a bias in the parallaxes of the final Gaia catalog. The Basic Angle Monitoring (BAM) device, which provides a reliable and accurate estimation of BAV, shows that there exists a ~1 mas amplitude, 6-h period BA oscillation. It's essential to verify to what extent this signal is caused by real BAV, or is at least in part an effect of the BAM device itself. Here, we propose an astrometric on-sky approach to re-determine the 6-h periodic BAV. The results of this experiment, which treated a full day (17 Oct 2016) of Gaia astrometric data, recover a value for the 6-h oscillation of 1.856+/-0.857 mas. This is consistent, within the errors, with the BAM finding for that day.

Compositions and methods for detecting gene rearrangements and translocations

DOEpatents

Rowley, Janet D.; Diaz, Manuel O.

2000-01-01

Disclosed is a series of nucleic acid probes for use in diagnosing and monitoring certain types of leukemia using, e.g., Southern and Northern blot analyses and fluorescence in situ hybridization (FISH). These probes detect rearrangements, such as translocations involving chromosome band 11q23 with other chromosomes bands, including 4q21, 6q27, 9p22, 19p13.3, in both dividing leukemic cells and interphase nuclei. The breakpoints in all such translocations are clustered within an 8.3 kb BamHI genomic region of the MLL gene. A novel 0.7 kb BamH1 cDNA fragment derived from this gene detects rearrangements on Southern blot analysis with a single BamHI restriction digest in all patients with the common 11q23 translocations and in patients with other 11q23 anomalies. Northern blot analyses are presented demonstrating that the MLL gene has multiple transcripts and that transcript size differentiates leukemic cells from normal cells. Also disclosed are MLL fusion proteins, MLL protein domains and anti-MLL antibodies.

A bat algorithm with mutation for UCAV path planning.

PubMed

Wang, Gaige; Guo, Lihong; Duan, Hong; Liu, Luo; Wang, Heqi

2012-01-01

Path planning for uninhabited combat air vehicle (UCAV) is a complicated high dimension optimization problem, which mainly centralizes on optimizing the flight route considering the different kinds of constrains under complicated battle field environments. Original bat algorithm (BA) is used to solve the UCAV path planning problem. Furthermore, a new bat algorithm with mutation (BAM) is proposed to solve the UCAV path planning problem, and a modification is applied to mutate between bats during the process of the new solutions updating. Then, the UCAV can find the safe path by connecting the chosen nodes of the coordinates while avoiding the threat areas and costing minimum fuel. This new approach can accelerate the global convergence speed while preserving the strong robustness of the basic BA. The realization procedure for original BA and this improved metaheuristic approach BAM is also presented. To prove the performance of this proposed metaheuristic method, BAM is compared with BA and other population-based optimization methods, such as ACO, BBO, DE, ES, GA, PBIL, PSO, and SGA. The experiment shows that the proposed approach is more effective and feasible in UCAV path planning than the other models.

Molecular cloning and physical mapping of the genome of fish lymphocystis disease virus.

PubMed

Darai, G; Delius, H; Clarke, J; Apfel, H; Schnitzler, P; Flügel, R M

1985-10-30

A defined and complete gene library of the fish lymphocystis disease virus (FLDV) genome was established. FLDV DNA was cleaved with EcoRI, BamHI, EcoRI/BamHI and EcoRI/HindIII and the resulting fragments were inserted into the corresponding sites of the pACYC184 or pAT153 plasmid vectors using T4 DNA ligase. Since FLDV DNA is highly methylated at CpG sequences (Darai et al., 1983; Wagner et al., 1985), an Escherichia coli GC-3 strain was required to amplify the recombinant plasmids harboring the FLDV DNA fragments. Bacterial colonies harboring recombinant plasmids were selected. All cloned fragments were individually identified by digestion of the recombinant plasmid DNA with different restriction enzymes and screened by hybridization of recombinant plasmid DNA to viral DNA. This analysis revealed that sequences representing 100% of the viral genome were cloned. Using these recombinant plasmids, the physical maps of the genome were constructed for BamHI, EcoRI, BestEII, and PstI restriction endonucleases. Although the FLDV genome is linear, due to circular permutation the restriction maps are circular.

Magnetic bead/capture DNA/glucose-loaded nanoliposomes for amplifying the glucometer signal in the rapid screening of hepatitis C virus RNA.

PubMed

Tu, Haijian; Lin, Kun; Lun, Yongzhi; Yu, Liuming

2018-06-01

A digital detection strategy based on a portable personal glucometer (PGM) was developed for the simple, rapid, and sensitive detection of hepatitis C virus (HCV) RNA, involving the release of glucose-loaded nanoliposomes due to coupling-site-specific cleavage by the endonuclease BamHI. The glucose-loaded nanoliposomes were synthesized using a reversed-phase evaporation method and provided an amplified signal at the PGM in the presence of HCV RNA. Initially, a 21-mer oligonucleotide complementary to HCV RNA was covalently conjugated to a magnetic bead through the amino group at the 5' end of the oligonucleotide, and then bound to a glucose-loaded liposome by typical carbodiimide coupling at its 3' end. In the presence of the target HCV RNA, the target hybridized with the oligonucleotide to form double-stranded DNA. The symmetrical duplex sequence 5'-GGATCC-3' between guanines was then catalytically cleaved by BamHI, which detached the glucose-loaded liposome from the magnetic bead. Following magnetic separation of the bead, the detached glucose-loaded liposome was lysed using Triton X-100 to release the glucose molecules within it, which were then detected as an amplified signal at the digital PGM. Under optimal conditions, the PGM signal increased with increasing HCV RNA, and displayed a strongly linear dependence on the level of HCV RNA for concentrations ranging from 10 pM to 1.0 μM. The detection limit (LOD) of the system was 1.9 pM. Good reproducibility and favorable specificity were achieved in the analysis of the target HCV RNA. Human serum samples containing HCV RNA were analyzed using this strategy, and the developed sensing platform was observed to yield satisfactory results based on a comparison with the corresponding results from a Cobas ® Amplicor HCV Test Analyzer. Graphical abstract A digital detection strategy utilizing a personal glucometer was developed for the detection of hepatitis C virus RNA. The strategy involved the use of the endonuclease BamHI along with a 21-mer oligonucleotide conjugated to both a magnetic bead and a glucose-loaded nanoliposome. Hybridization of the nucleotide with the target RNA triggered the coupling-site-specific cleavage of the duplex by BamHI, leading to the release of the glucose-loaded nanoliposome. Following separation of the magnetic bead, the free nanoliposome was dissolved, liberating the glucose molecules within it, which in turn were detected as an amplified signal by the glucometer.

Global exponential stability analysis on impulsive BAM neural networks with distributed delays

NASA Astrophysics Data System (ADS)

Li, Yao-Tang; Yang, Chang-Bo

2006-12-01

Using M-matrix and topological degree tool, sufficient conditions are obtained for the existence, uniqueness and global exponential stability of the equilibrium point of bidirectional associative memory (BAM) neural networks with distributed delays and subjected to impulsive state displacements at fixed instants of time by constructing a suitable Lyapunov functional. The results remove the usual assumptions that the boundedness, monotonicity, and differentiability of the activation functions. It is shown that in some cases, the stability criteria can be easily checked. Finally, an illustrative example is given to show the effectiveness of the presented criteria.

Existence and global exponential stability of periodic solution to BAM neural networks with periodic coefficients and continuously distributed delays

NASA Astrophysics Data System (ADS)

Zhou, distributed delays [rapid communication] T.; Chen, A.; Zhou, Y.

2005-08-01

By using the continuation theorem of coincidence degree theory and Liapunov function, we obtain some sufficient criteria to ensure the existence and global exponential stability of periodic solution to the bidirectional associative memory (BAM) neural networks with periodic coefficients and continuously distributed delays. These results improve and generalize the works of papers [J. Cao, L. Wang, Phys. Rev. E 61 (2000) 1825] and [Z. Liu, A. Chen, J. Cao, L. Huang, IEEE Trans. Circuits Systems I 50 (2003) 1162]. An example is given to illustrate that the criteria are feasible.

Fundamental study of phosphor separation by controlling magnetic force

NASA Astrophysics Data System (ADS)

Wada, Kohei; Mishima, Fumihito; Akiyama, Yoko; Nishijima, Shigehiro

2013-11-01

The phosphor wastes consist of phosphors with different emission colors, green (LAP), red (YOX), blue (BAM) and white (HP). It is required to recover and reuse the rare earth phosphors with high market value. In this study, we tried to separate the phosphor using the magnetic separation by HTS bulk magnet utilizing the differences of magnetic susceptibility by the type of phosphors. We succeeded in the successive separation of HP with low market value from YOX and BAM including the rare earth using the magnetic Archimedes method. In this method, vertical and radial components of the magnetic force were used.

Structure and Dynamics of Interfaces: Drops and Films

NASA Technical Reports Server (NTRS)

Mann, J. Adin, Jr.; Mann, Elizabeth K.; Meyer, William V.; Neumann, A. Wilhelm; Tavana, Hossein

2015-01-01

We aim to acquire measurements of the structure and dynamics of certain liquid-fluid interfaces using an ensemble of techniques in collaboration: (1) Total internal reflection (TIR) Surface light scattering spectroscopy (SLSS), (2) Brewster angle microscopy (BAM), and (3) Drop-shape analysis. SLSS and BAM can be done on a shared interfacial footprint. Results using a 50-50 mixture of pentane-isohexane, which extends the range of NASA's Confined Vapor Bubble (CVB) experiment, yield surface tension results that differ from the expected Langmuir Fit. These results were confirmed using both the SLSS and drop-shape analysis approaches.

Climate Change Accuracy: Requirements and Economic Value

NASA Astrophysics Data System (ADS)

Wielicki, B. A.; Cooke, R.; Mlynczak, M. G.; Lukashin, C.; Thome, K. J.; Baize, R. R.

2014-12-01

Higher than normal accuracy is required to rigorously observe decadal climate change. But what level is needed? How can this be quantified? This presentation will summarize a new more rigorous and quantitative approach to determining the required accuracy for climate change observations (Wielicki et al., 2013, BAMS). Most current global satellite observations cannot meet this accuracy level. A proposed new satellite mission to resolve this challenge is CLARREO (Climate Absolute Radiance and Refractivity Observatory). CLARREO is designed to achieve advances of a factor of 10 for reflected solar spectra and a factor of 3 to 5 for thermal infrared spectra (Wielicki et al., Oct. 2013 BAMS). The CLARREO spectrometers are designed to serve as SI traceable benchmarks for the Global Satellite Intercalibration System (GSICS) and to greatly improve the utility of a wide range of LEO and GEO infrared and reflected solar passive satellite sensors for climate change observations (e.g. CERES, MODIS, VIIIRS, CrIS, IASI, Landsat, SPOT, etc). Providing more accurate decadal change trends can in turn lead to more rapid narrowing of key climate science uncertainties such as cloud feedback and climate sensitivity. A study has been carried out to quantify the economic benefits of such an advance as part of a rigorous and complete climate observing system. The study concludes that the economic value is $12 Trillion U.S. dollars in Net Present Value for a nominal discount rate of 3% (Cooke et al. 2013, J. Env. Sys. Dec.). A brief summary of these two studies and their implications for the future of climate science will be presented.

Cloning, Expression, and Purification of Histidine-Tagged Escherichia coli Dihydrodipicolinate Reductase.

PubMed

Trigoso, Yvonne D; Evans, Russell C; Karsten, William E; Chooback, Lilian

2016-01-01

The enzyme dihydrodipicolinate reductase (DHDPR) is a component of the lysine biosynthetic pathway in bacteria and higher plants. DHDPR catalyzes the NAD(P)H dependent reduction of 2,3-dihydrodipicolinate to the cyclic imine L-2,3,4,5,-tetrahydropicolinic acid. The dapB gene that encodes dihydrodipicolinate reductase has previously been cloned, but the expression of the enzyme is low and the purification is time consuming. Therefore the E. coli dapB gene was cloned into the pET16b vector to improve the protein expression and simplify the purification. The dapB gene sequence was utilized to design forward and reverse oligonucleotide primers that were used to PCR the gene from Escherichia coli genomic DNA. The primers were designed with NdeI or BamHI restriction sites on the 5'and 3' terminus respectively. The PCR product was sequenced to confirm the identity of dapB. The gene was cloned into the expression vector pET16b through NdeI and BamHI restriction endonuclease sites. The resulting plasmid containing dapB was transformed into the bacterial strain BL21 (DE3). The transformed cells were utilized to grow and express the histidine-tagged reductase and the protein was purified using Ni-NTA affinity chromatography. SDS/PAGE gel analysis has shown that the protein was 95% pure and has approximate subunit molecular weight of 28 kDa. The protein purification is completed in one day and 3 liters of culture produced approximately 40-50 mgs of protein, an improvement on the previous protein expression and multistep purification.

Cloning, Expression, and Purification of Histidine-Tagged Escherichia coli Dihydrodipicolinate Reductase

PubMed Central

Trigoso, Yvonne D.; Evans, Russell C.; Karsten, William E.; Chooback, Lilian

2016-01-01

The enzyme dihydrodipicolinate reductase (DHDPR) is a component of the lysine biosynthetic pathway in bacteria and higher plants. DHDPR catalyzes the NAD(P)H dependent reduction of 2,3-dihydrodipicolinate to the cyclic imine L-2,3,4,5,-tetrahydropicolinic acid. The dapB gene that encodes dihydrodipicolinate reductase has previously been cloned, but the expression of the enzyme is low and the purification is time consuming. Therefore the E. coli dapB gene was cloned into the pET16b vector to improve the protein expression and simplify the purification. The dapB gene sequence was utilized to design forward and reverse oligonucleotide primers that were used to PCR the gene from Escherichia coli genomic DNA. The primers were designed with NdeI or BamHI restriction sites on the 5’and 3’ terminus respectively. The PCR product was sequenced to confirm the identity of dapB. The gene was cloned into the expression vector pET16b through NdeI and BamHI restriction endonuclease sites. The resulting plasmid containing dapB was transformed into the bacterial strain BL21 (DE3). The transformed cells were utilized to grow and express the histidine-tagged reductase and the protein was purified using Ni-NTA affinity chromatography. SDS/PAGE gel analysis has shown that the protein was 95% pure and has approximate subunit molecular weight of 28 kDa. The protein purification is completed in one day and 3 liters of culture produced approximately 40–50 mgs of protein, an improvement on the previous protein expression and multistep purification. PMID:26815040

Multicentre prospective survey of SeHCAT provision and practice in the UK.

PubMed

Summers, Jennifer A; Peacock, Janet; Coker, Bolaji; McMillan, Viktoria; Ofuya, Mercy; Lewis, Cornelius; Keevil, Stephen; Logan, Robert; McLaughlin, John; Reid, Fiona

2016-01-01

A clinical diagnosis of bile acid malabsorption (BAM) can be confirmed using SeHCAT (tauroselcholic ((75)selenium) acid), a radiolabelled synthetic bile acid. However, while BAM can be the cause of chronic diarrhoea, it is often overlooked as a potential diagnosis. Therefore, we investigated the use of SeHCAT for diagnosis of BAM in UK hospitals. A multicentre survey was conducted capturing centre and patient-level information detailing patient care-pathways, clinical history, SeHCAT results, treatment with bile acid sequestrants (BAS), and follow-up in clinics. Eligible data from 38 centres and 1036 patients were entered into a validated management system. SeHCAT protocol varied between centres, with no standardised patient positioning, and differing referral systems. Surveyed patients had a mean age of 50 years and predominantly women (65%). The mean SeHCAT retention score for all patients was 19% (95% CI 17.8% to 20.3%). However, this differed with suspected BAM type: type 1: 9% (95% CI 6.3% to 11.4%), type 2: 21% (95% CI 19.2% to 23.0%) and type 3: 22% (95% CI 19.6% to 24.2%). Centre-defined 'abnormal' and 'borderline' results represented over 50% of the survey population. BAS treatment was prescribed to only 73% of patients with abnormal results. The study identified a lack of consistent cut-off/threshold values, with differing centre criteria for defining an 'abnormal' SeHCAT result. BAS prescription was not related in a simple way to the SeHCAT result, nor to the centre-defined result, highlighting a lack of clear patient care-pathways. There is a clear need for a future diagnostic accuracy study and a better understanding of optimal management pathways.

20-Day Trend of Serum Potassium Changes in Bam Earthquake Victims with Crush Syndrome; a Cross-sectional Study.

PubMed

Safari, Saeed; Najafi, Iraj; Hosseini, Mostafa; Baratloo, Alireza; Yousefifard, Mahmoud; Mohammadi, Hamidreza

2017-01-01

Many of those who survive following an earthquake die in the next phase due to preventable and treatable medical conditions such as hyperkalemia. The present study aimed to evaluate the trend of potassium changes in crush syndrome patients of Bam earthquake. In this retrospective cross-sectional study, using the database of Bam earthquake victims, which were developed by Iranian Society of Nephrology following Bam earthquake, Iran, 2003, the 20-day trend of potassium changes in > 15 years old crush syndrome patients was evaluated. 135 crush syndrome patients with the mean age of 29.9 ± 9.91 years were evaluated (56.3% male). Mean potassium concentration during the first 3 days of admission was 5.6 ± 1.3 mEq/L. On the day of admission, 43.1% (95% CI: 34.0 - 52.2) had normal potassium concentration, 3.4% (95% CI: 0.1 - 6.8) had hypokalemia, and 53.4% (44.3 - 62.6) had hyperkalemia. During 20-day follow-up, 62.3% (95% CI: 66.7-71.9) of the patients had normal potassium. While, 11.5% (95% CI: 9.7-13.3) had hypokalemia and 19.2% (95% CI: 17.0-21.5) had hyperkalemia. As the days of hospitalization increased, prevalence of hyperkalemia decreased while hypokalemia increased. On the 17 th day 21.2% (95% CI: 2.2-39.9) had hypokalemia and 10.5% (95% CI: 0.1 - 24.7) had hyperkalemia. Findings of the present study showed that following urine alkalinization and fluid resuscitation, the prevalence of hyperkalemia reduced, but hypokalemia developed. It seems that the correction of serum potassium level should be accompanied by precise monitoring of intake and output of the patient and prescription of reasonable amount of intravenous fluid.

Motivating Latino caregivers of children with asthma to quit smoking: a randomized trial.

PubMed

Borrelli, Belinda; McQuaid, Elizabeth L; Novak, Scott P; Hammond, S Katharine; Becker, Bruce

2010-02-01

Secondhand smoke exposure is associated with asthma onset and exacerbation. Latino children have higher rates of asthma morbidity than other groups. The current study compared the effectiveness of a newly developed smoking cessation treatment with existing clinical guidelines for smoking cessation. Latino caregivers who smoked (N = 133; 72.9% female; mean age = 36.8 years) and had a child with asthma were randomly assigned to receive 1 of 2 smoking cessation counseling interventions during a home-based asthma program: (a) behavioral action model (BAM; modeled on clinical guidelines for smoking cessation) or (b) precaution adoption model (PAM; feedback on the caregiver's carbon monoxide level and child's secondhand smoke exposure using Motivational Interviewing). Counseling was delivered by a bilingual Latina health educator, and the content was tailored to Latino values and culture. It was not necessary for smokers to want to quit smoking to participate. Smoking cessation was biochemically verified and secondhand smoke exposure was objectively measured through passive nicotine monitors. Intent-to-treat analyses showed that 20.5% of participants in the PAM condition and 9.1% of those in the BAM condition were continuously abstinent at 2 months posttreatment (OR = 2.54; 95% CI = 0.91-7.10), whereas 19.1% of participants in the PAM condition and 12.3% of those in BAM condition were continuously abstinent at 3 months posttreatment (OR = 1.68; 95% CI = 0.64-4.37). Secondhand smoke exposure decreased only in the BAM condition (p < .001), an effect due to less smoking around the child among nonquitters in this condition. Asthma morbidity showed significant decreases in the posttreatment period for the PAM group only (p < .001). Results provide support for targeting specific populations with theory-based interventions.

Réalisation de couches minces magnétiques d'hexaferrite de baryum en vue de concevoir un isolateur coplanaire passif

NASA Astrophysics Data System (ADS)

Capraro, S.; Nader, C.; Chatelon, J. P.; Le Berre, M.; Rouiller, T.; Bayard, B.; Joisten, H.; Barbier, D.; Rousseau, J. J.

2005-05-01

Le développement des dispositifs intégrés employant un ferrite est un objectif majeur pour des applications électroniques dans la gamme hyperfréquence (circulateurs et isolateurs). Les ferrites hexagonaux, tel que l'hexaferrite de baryum (BaFe{12}O{19} ou BaM), présentent un grand intérêt pour de tels dispositifs en raison de leurs grandes résistivités et de leurs perméabilités élevées aux hautes fréquences. Dans cette étude, les couches minces de BaM, sont déposées et optimisées par pulvérisation cathodique RF sur des substrats d'alumine et de silicium. Après dépôt, les films sont amorphes et un recuit thermique à 800° C est nécessaire pour que les couches de BaM cristallisent et présentent des propriétés magnétiques. Les propriétés magnétiques des couches minces de BaM ont été déterminées par VSM, et on constate que le champ coercitif et l'aimantation à saturation atteignent respectivement 330 kA/m et 500 mT. Des isolateurs sont réalisés par dépôt d'une couche conductrice d'or en utilisant la technique du lift-off qui permet la mise en place du ruban signal ainsi que des plans de masse. Les premiers résultats de mesure en transmission ont montré un effet non réciproque qui atteint 8 dB/cm à 50 GHz.

Effect of Mas-related gene (Mrg) receptors on hyperalgesia in rats with CFA-induced inflammation via direct and indirect mechanisms.

PubMed

Jiang, Jianping; Wang, Dongmei; Zhou, Xiaolong; Huo, Yuping; Chen, Tingjun; Hu, Fenjuan; Quirion, Rémi; Hong, Yanguo

2013-11-01

Mas oncogene-related gene (Mrg) receptors are exclusively distributed in small-sized neurons in trigeminal and dorsal root ganglia (DRG). We investigated the effects of MrgC receptor activation on inflammatory hyperalgesia and its mechanisms. A selective MrgC receptor agonist, bovine adrenal medulla peptide 8-22 (BAM8-22) or melanocyte-stimulating hormone (MSH) or the μ-opioid receptor (MOR) antagonist CTAP was administered intrathecally (i.t.) in rats injected with complete Freund's adjuvant (CFA) in one hindpaw. Thermal and mechanical nociceptive responses were assessed. Neurochemicals were measured by immunocytochemistry, Western blot, ELISA and RT-PCR. CFA injection increased mRNA for MrgC receptors in lumbar DRG. BAM8-22 or MSH, given i.t., generated instant short and delayed long-lasting attenuations of CFA-induced thermal hyperalgesia, but not mechanical allodynia. These effects were associated with decreased up-regulation of neuronal NOS (nNOS), CGRP and c-Fos expression in the spinal dorsal horn and/or DRG. However, i.t. administration of CTAP blocked the induction by BAM8-22 of delayed anti-hyperalgesia and inhibition of nNOS and CGRP expression in DRG. BAM8-22 also increased mRNA for MORs and pro-opiomelanocortin, along with β-endorphin content in the lumbar spinal cord and/or DRG. MrgC receptors and nNOS were co-localized in DRG neurons. Activation of MrgC receptors suppressed up-regulation of pronociceptive mediators and consequently inhibited inflammatory pain, because of the activation of up-regulated MrgC receptors and subsequent endogenous activity at MORs. The uniquely distributed MrgC receptors could be a novel target for relieving inflammatory pain. © 2013 The British Pharmacological Society.

Evaluation of PCR detection of Salmonella in alfalfa sprouts and spent irrigation water collected during sprouting of naturally contaminated seed.

PubMed

Maks, Nicole; Fu, Tong-Jen

2013-02-01

This study evaluated the efficacy of a PCR-based system (DuPont Qualicon BAX) for detection of Salmonella in sprouts and spent irrigation water collected during sprouting of seeds naturally contaminated with Salmonella. Alfalfa seeds were grown in Mason jars at 20 and 30°C for 3 days. Levels of Salmonella present in the water and sprouts were determined by most-probable-number (MPN) analysis. Background microflora levels were also determined. Samples of spent irrigation water and sprouts were enriched overnight individually in tetrathionate broth and in buffered peptone water with novobiocin at 42°C and then run in the BAX system. Samples were also enriched according to the U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA BAM) method for Salmonella as a comparison. Salmonella levels were lower at 20°C compared with 30°C for some trials, and background microflora levels ranged from 10(7) to 10(8) CFU/g or ml at 20°C and 10(8) to 10(9) CFU/g or ml at 30°C. In trials with a Salmonella level >1.1 MPN/g or ml, both the BAX and FDA BAM methods were able to detect Salmonella in all samples. In trials with lower levels (0.21 MPN/g or ml or lower) of Salmonella, BAX was able to detect more positive samples than FDA BAM. For one trial with <0.003 MPN/g or ml of Salmonella, the presence of the pathogen was not indicated by either the BAX or the FDA BAM method. The results suggest that PCR detected low levels of Salmonella in sprouts or spent irrigation water collected from sprouting of naturally contaminated seeds.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giri, R. P., E-mail: rajendra.giri@saha.ac.in; Mukhopadhyay, M. K.

The spontaneous surface aggregation of diblock copolymer, containing polystyrene-polydimethylsiloxane or PS-PDMS, have been studied at air-water interface using Brewster’s angle microscopy (BAM) and grazing incidence small angle x-ray scattering (GISAXS) technique. Pronounced differences in the molecular weight and solvent dependence of the size of aggregation on the water surface are observed. Structural characterization is done using atomic force microscopy (AFM) for a monolayer transferred to Si substrate. It shows that, individual polymer chains coalesce to form some disc like micelle aggregation on the Si surface which is also evident from the BAM image of the water floated monolayer. GISAXS studymore » is also corroborating the same result.« less

Using GBrowse 2.0 to visualize and share next-generation sequence data

PubMed Central

2013-01-01

GBrowse is a mature web-based genome browser that is suitable for deployment on both public and private web sites. It supports most of genome browser features, including qualitative and quantitative (wiggle) tracks, track uploading, track sharing, interactive track configuration, semantic zooming and limited smooth track panning. As of version 2.0, GBrowse supports next-generation sequencing (NGS) data by providing for the direct display of SAM and BAM sequence alignment files. SAM/BAM tracks provide semantic zooming and support both local and remote data sources. This article provides step-by-step instructions for configuring GBrowse to display NGS data. PMID:23376193

SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly

PubMed Central

Wala, Jeremiah; Beroukhim, Rameen

2017-01-01

Abstract We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. Availability and Implementation: SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. Contact: jwala@broadinstitue.org; rameen@broadinstitute.org PMID:28011768

A Bat Algorithm with Mutation for UCAV Path Planning

PubMed Central

Wang, Gaige; Guo, Lihong; Duan, Hong; Liu, Luo; Wang, Heqi

2012-01-01

Path planning for uninhabited combat air vehicle (UCAV) is a complicated high dimension optimization problem, which mainly centralizes on optimizing the flight route considering the different kinds of constrains under complicated battle field environments. Original bat algorithm (BA) is used to solve the UCAV path planning problem. Furthermore, a new bat algorithm with mutation (BAM) is proposed to solve the UCAV path planning problem, and a modification is applied to mutate between bats during the process of the new solutions updating. Then, the UCAV can find the safe path by connecting the chosen nodes of the coordinates while avoiding the threat areas and costing minimum fuel. This new approach can accelerate the global convergence speed while preserving the strong robustness of the basic BA. The realization procedure for original BA and this improved metaheuristic approach BAM is also presented. To prove the performance of this proposed metaheuristic method, BAM is compared with BA and other population-based optimization methods, such as ACO, BBO, DE, ES, GA, PBIL, PSO, and SGA. The experiment shows that the proposed approach is more effective and feasible in UCAV path planning than the other models. PMID:23365518

Structural and magnetic properties of Ni-Zn doped BaM nanocomposite via citrate precursor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rana, Kush; Thakur, Preeti; Thakur, Atul, E-mail: atulphysics@gmail.com

2016-05-23

Ni-Zn substituted M-type barium ferrite nanocomposite has been prepared via citrate precursor method. Nanocomposite having composition BaNi{sub 0.5}Zn{sub 0.5}Fe{sub 11}O{sub 19} was sintered at 900°C for 3hrs and characterized by using different characterization techniques. X-ray diffraction (XRD) confirmed the formation of double phase with most prominent peak at (114). Average crystallite size for pure BaM and BNZFO were found to be 36 nm & 45 nm. Field emission scanning electron microscopy (FESEM) confirmed the formation of hexagonal platelets with a layered structure. Magnetic properties of these samples were investigated by using vibrating sample magnetometer (VSM). Magnetic parameters like saturation magnetization (M{sub s}),more » coericivity (H{sub c}) and squareness ratio (SQR) of nanocomposite were found to be 60 emu/g, 3663 Oe and 0.6163 respectively. These values were noticed to be higher as compared to pure BaM. Enhanced magnetic properties of nanocomposite were strongly dependent on exchange coupling. Therefore these properties make this nanocomposite a suitable candidate for magnetic recording and high frequency applications.« less

SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.

PubMed

Wala, Jeremiah; Beroukhim, Rameen

2017-03-01

We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. jwala@broadinstitue.org ; rameen@broadinstitute.org. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Preparation of Scandium-Doped, Textured, M-Type Barium Ferrite via a Wet Magnetizing Orientation Process

NASA Astrophysics Data System (ADS)

Wang, Yu; Liu, Yingli; Zhang, Huaiwu; Li, Jie; Gao, Liwen; Chen, Daming; Chen, Yong

2018-02-01

In this paper, a wet magnetizing orientation process was applied to synthesize c-axis-textured, M-type barium ferrite (BaFe12O19 or BaM), which is widely used to produce hard magnetic materials. To modify the magnetic properties of the BaM ferrite and make it suitable for certain operating frequencies, Sc3+ was substituted into Fe3+ sites of the BaM crystal structure. A BaSc x Fe12- x O19 ferrite with a typical relative density of ˜ 75% was successfully obtained. We used x-ray diffraction, scanning electronic microscopy, and a vibrating sample magnetometer to obtain phase information, detail of the microstructure, and magnetic properties of the BaSc x Fe12- x O19, respectively. The composition BaSc x Fe12- x O19 ( x = 0.1) featured a superior squareness ratio of ˜ 67% and a saturation magnetization ( M S) of ˜ 5300 Gauss in magnetic hysteresis loop measurements. These features match well with requirements for self-biased passive devices. Moreover, the site preference of Sc3+ in the hexagonal crystal structure was investigated.

Monohalogenated acetamide-induced cellular stress and genotoxicity are related to electrophilic softness and thiol/thiolate reactivity.

PubMed

Pals, Justin A; Wagner, Elizabeth D; Plewa, Michael J; Xia, Menghang; Attene-Ramos, Matias S

2017-08-01

Haloacetamides (HAMs) are cytotoxic, genotoxic, and mutagenic byproducts of drinking water disinfection. They are soft electrophilic compounds that form covalent bonds with the free thiol/thiolate in cysteine residues through an S N 2 reaction mechanism. Toxicity of the monohalogenated HAMs (iodoacetamide, IAM; bromoacetamide, BAM; or chloroacetamide, CAM) varied depending on the halogen substituent. The aim of this research was to investigate how the halogen atom affects the reactivity and toxicological properties of HAMs, measured as induction of oxidative/electrophilic stress response and genotoxicity. Additionally, we wanted to determine how well in silico estimates of electrophilic softness matched thiol/thiolate reactivity and in vitro toxicological endpoints. Each of the HAMs significantly induced nuclear Rad51 accumulation and ARE signaling activity compared to a negative control. The rank order of effect was IAM>BAM>CAM for Rad51, and BAM≈IAM>CAM for ARE. In general, electrophilic softness and in chemico thiol/thiolate reactivity provided a qualitative indicator of toxicity, as the softer electrophiles IAM and BAM were more thiol/thiolate reactive and were more toxic than CAM. Copyright © 2017. Published by Elsevier B.V.

Setting Foundations for Developing Disaster Response Metrics.

PubMed

Abir, Mahshid; Bell, Sue Anne; Puppala, Neha; Awad, Osama; Moore, Melinda

2017-08-01

There are few reported efforts to define universal disaster response performance measures. Careful examination of responses to past disasters can inform the development of such measures. As a first step toward this goal, we conducted a literature review to identify key factors in responses to 3 recent events with significant loss of human life and economic impact: the 2003 Bam, Iran, earthquake; the 2004 Indian Ocean tsunami; and the 2010 Haiti earthquake. Using the PubMed (National Library of Medicine, Bethesda, MD) database, we identified 710 articles and retained 124 after applying inclusion and exclusion criteria. Seventy-two articles pertained to the Haiti earthquake, 38 to the Indian Ocean tsunami, and 14 to the Bam earthquake. On the basis of this review, we developed an organizational framework for disaster response performance measurement with 5 key disaster response categories: (1) personnel, (2) supplies and equipment, (3) transportation, (4) timeliness and efficiency, and (5) interagency cooperation. Under each of these, and again informed by the literature, we identified subcategories and specific items that could be developed into standardized performance measures. The validity and comprehensiveness of these measures can be tested by applying them to other recent and future disaster responses, after which standardized performance measures can be developed through a consensus process. (Disaster Med Public Health Preparedness. 2017;11:505-509).

Integrated Data Collection Analysis (IDCA) Program - NaClO 3/Icing Sugar

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sandstrom, Mary M.; Brown, Geoffrey W.; Preston, Daniel N.

The Integrated Data Collection Analysis (IDCA) program is conducting a proficiency study for Small- Scale Safety and Thermal (SSST) testing of homemade explosives (HMEs). Described here are the results for impact, friction, electrostatic discharge, and differential scanning calorimetry analysis of a mixture of NaClO 3 and icing sugar—NaClO 3/icing sugar mixture. The mixture was found to: be more sensitive than RDX but less sensitive than PETN in impact testing (180-grit sandpaper); be more sensitive than RDX and about the same sensitivity as PETN in BAM fiction testing; be less sensitive than RDX and PETN except for one participant found themore » mixture more sensitive than PETN in ABL ESD testing; and to have one to three exothermic features with the lowest temperature event occurring at ~ 160°C always observed in thermal testing. Variations in testing parameters also affected the sensitivity.« less

Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case.

PubMed

Russ, Thomas A; Ramakrishnan, Cartic; Hovy, Eduard H; Bota, Mihail; Burns, Gully A P C

2011-08-22

We address the goal of curating observations from published experiments in a generalizable form; reasoning over these observations to generate interpretations and then querying this interpreted knowledge to supply the supporting evidence. We present web-application software as part of the 'BioScholar' project (R01-GM083871) that fully instantiates this process for a well-defined domain: using tract-tracing experiments to study the neural connectivity of the rat brain. The main contribution of this work is to provide the first instantiation of a knowledge representation for experimental observations called 'Knowledge Engineering from Experimental Design' (KEfED) based on experimental variables and their interdependencies. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a 'neural connection matrix' interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. BioScholar is built in Flex 3.5. It uses Persevere (a noSQL database) as a flexible data store and PowerLoom® (a mature First Order Logic reasoning system) to execute queries using spatial reasoning over the BAMS neuroanatomical ontology. We first introduce the KEfED approach as a general approach and describe its possible role as a way of introducing structured reasoning into models of argumentation within new models of scientific publication. We then describe the design and implementation of our example application: the BioScholar software. This is presented as a possible biocuration interface and supplementary reasoning toolkit for a larger, more specialized bioinformatics system: the Brain Architecture Management System (BAMS).

Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case

PubMed Central

2011-01-01

Background We address the goal of curating observations from published experiments in a generalizable form; reasoning over these observations to generate interpretations and then querying this interpreted knowledge to supply the supporting evidence. We present web-application software as part of the 'BioScholar' project (R01-GM083871) that fully instantiates this process for a well-defined domain: using tract-tracing experiments to study the neural connectivity of the rat brain. Results The main contribution of this work is to provide the first instantiation of a knowledge representation for experimental observations called 'Knowledge Engineering from Experimental Design' (KEfED) based on experimental variables and their interdependencies. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a 'neural connection matrix' interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. BioScholar is built in Flex 3.5. It uses Persevere (a noSQL database) as a flexible data store and PowerLoom® (a mature First Order Logic reasoning system) to execute queries using spatial reasoning over the BAMS neuroanatomical ontology. Conclusions We first introduce the KEfED approach as a general approach and describe its possible role as a way of introducing structured reasoning into models of argumentation within new models of scientific publication. We then describe the design and implementation of our example application: the BioScholar software. This is presented as a possible biocuration interface and supplementary reasoning toolkit for a larger, more specialized bioinformatics system: the Brain Architecture Management System (BAMS). PMID:21859449

Paraconsistent Annotated Logic in Viability Analysis: an Approach to Product Launching

NASA Astrophysics Data System (ADS)

Romeu de Carvalho, Fábio; Brunstein, Israel; Abe, Jair Minoro

2004-08-01

In this paper we present an application of the Para-analyzer, a logical analyzer based on the Paraconsistent Annotated Logic Pτ, introduced by Da Silva Filho and Abe in the decision-making systems. An example is analyzed in detail showing how uncertainty, inconsistency and paracompleteness can be elegantly handled with this logical system. As application for the Para-analyzer in decision-making, we developed the BAM — Baricenter Analysis Method. In order to make the presentation easier, we present the BAM applied in the viability analysis of product launching. Some of the techniques of Paraconsistent Annotated Logic have been applied in Artificial Intelligence, Robotics, Information Technolgy (Computer Sciences), etc..

Indexcov: fast coverage quality control for whole-genome sequencing.

PubMed

Pedersen, Brent S; Collins, Ryan L; Talkowski, Michael E; Quinlan, Aaron R

2017-11-01

The BAM and CRAM formats provide a supplementary linear index that facilitates rapid access to sequence alignments in arbitrary genomic regions. Comparing consecutive entries in a BAM or CRAM index allows one to infer the number of alignment records per genomic region for use as an effective proxy of sequence depth in each genomic region. Based on these properties, we have developed indexcov, an efficient estimator of whole-genome sequencing coverage to rapidly identify samples with aberrant coverage profiles, reveal large-scale chromosomal anomalies, recognize potential batch effects, and infer the sex of a sample. Indexcov is available at https://github.com/brentp/goleft under the MIT license. © The Authors 2017. Published by Oxford University Press.

DuPont qualicon BAX system real-time PCR assay for Escherichia coli O157:H7.

PubMed

Burns, Frank; Fleck, Lois; Andaloro, Bridget; Davis, Eugene; Rohrbeck, Jeff; Tice, George; Wallace, Morgan

2011-01-01

Evaluations were conducted to test the performance of the BAX System Real-Time PCR assay, which was certified as Performance Tested Method 031002 for screening E. coli O157:H7 in ground beef, beef trim, spinach, and lettuce. Method comparison studies performed on samples with low-level inoculates showed that the BAX System demonstrates a sensitivity equivalent or superior to the FDA-BAM and the USDA-FSIS culture methods, but with a significantly shorter time to result. Tests to evaluate inclusivity and exclusivity returned no false-negative and no false-positive results on a diverse panel of isolates, and tests for lot-to-lot variability and tablet stability demonstrated consistent performance. Ruggedness studies determined that none of the factors examined affect the performance of the assay. An accelerated shelf life study determined an initial 36 month shelf life for the test kit.

Nutrient analysis of the Beef Alternative Merchandising cuts.

PubMed

Desimone, T L; Acheson, R A; Woerner, D R; Engle, T E; Douglass, L W; Belk, K E

2013-03-01

The objective of this study was to generate raw and cooked nutrient composition data to identify Quality Grade differences in proximate values for eight Beef Alternative Merchandising (BAM) cuts. The data generated will be used to update the nutrient data in the USDA National Nutrient Database for Standard Reference (SR). Beef Rib, Oven-Prepared, Beef Loin, Strip Loin, and Beef Loin, Top Sirloin Butt subprimals were collected from a total of 24 carcasses from four packing plants. The carcasses were a combination of USDA Yield Grades 2 (n=12) and 3 (n=12), USDA Quality Grades upper two-thirds Choice (n=8), low Choice (n=8), and Select (n=8), and two genders, steer (n=16) and heifer (n=8). After aging, subprimals were fabricated into the BAM cuts, dissected, and nutrient analysis was performed. Sample homogenates from each animal were homogenized and composited for analysis of the following: proximate analysis, long chain and trans-fatty acids, conjugated linoleic acid, total cholesterol, vitamin B-12, and selenium. This study identified seven BAM cuts from all three Quality Grades that qualify for USDA Lean; seven Select cuts that qualify for USDA Extra Lean; and three Select cuts that qualify for the American Heart Association's Heart Healthy Check. Copyright © 2012 Elsevier Ltd. All rights reserved.

Maternal expectations and postpartum emotional adjustment in first-time mothers: results of a questionnaire survey.

PubMed

Henshaw, Erin J; Fried, Rachel; Teeters, Jenni Beth; Siskind, Emily E

2014-09-01

Several predictors of postpartum mood have been identified in the literature, but the role of maternal expectations in postpartum mental health remains unclear. The aim of this study was to identify whether maternal expectations during the postpartum hospital stay predict adjustment and depressive symptoms at 6 weeks postpartum. The sample included 233 first-time mothers recruited from the postpartum unit of a Midwestern hospital. Participants completed measures of maternal expectations and depressive symptoms (EPDS) at Time 1 (2 d postpartum) and completed EPDS and an Emotional Adjustment Scale (BaM-13) at Time 2 (6 weeks postpartum). A conditional relationship between the expectation that an infant's behavior will reflect maternal skill and Time 2 outcomes (BaM-13 and EPDS) was found, such that endorsing this belief predicted increased depression and poorer adjustment in those with higher (but not lower) Time 1 EPDS scores. Time 2 BaM-13 scores were also negatively predicted by expectations of self-sacrifice and positively predicted by expectations that parenthood would be naturally fulfilling. The expectations that new mothers hold about parenting soon after delivery are predictive of emotional adjustment in the early postpartum period, suggesting a role for discussion of expectations in future preventive strategies.

Evaluation of BAM (butorphanol-azaperone-medetomidine) in captive African lion (Panthera leo) immobilization.

PubMed

Semjonov, Aleksandr; Andrianov, Vladimir; Raath, Jacobus P; Orro, Toomas; Venter, Derik; Laubscher, Liesel; Pfitzer, Silke

2017-07-01

The combination of butorphanol, azaperone and medetomidine (BAM) with subsequent antagonism by naltrexone-yohimbine or naltrexone-atipamezole was evaluated for reversible immobilization of captive African lions (Panthea leo). Prospective, clinical trial. Twenty lions, 11 males and nine females, weighing 38-284 kg were immobilized in South Africa. The BAM volume dose rate administered was 0.005-0.008 mL kg -1 (0.6 mL 100 kg -1 ). Physiologic variables were recorded every 5 minutes. Four arterial blood samples were collected from all animals at 20, 30, 40 and 50 minutes after immobilization for analysis of blood-gases and acid-base status. The actual doses administered were as follows: butorphanol, 0.18±0.03 mg kg -1 ; azaperone, 0.07±0.01 mg kg -1 ; and medetomidine, 0.07±0.01 mg kg -1 . The inductions were calm and smooth, and induction time ranged from 4 to 10 minutes (7±2 minutes). The amount of time needed to work with each lion was 70 minutes, and no additional drug doses were needed. Heart rate (40±8 beats minute -1 ) and respiratory frequency (15±4 breaths minute -1 ) were stable throughout immobilization. The mean arterial blood pressure of all animals was stable but elevated (142±16 mmHg). The rectal temperature slightly increased over time but remained within acceptable range. The recovery time was significantly shorter when using naltrexone and atipamezole (9±1 minutes) compared to using naltrexone and yohimbine (22±7 minutes). The BAM combination proved to be reliable for general veterinary anaesthesia in lions. During anaesthesia, minor veterinary procedures such a blood collection, intubation, vaccination and collaring could safely be performed with no additional dosing required. Copyright © 2017 Association of Veterinary Anaesthetists and American College of Veterinary Anesthesia and Analgesia. Published by Elsevier Ltd. All rights reserved.

Toxicological and biochemical characterizations of AChE in phosalone-susceptible and resistant populations of the common pistachio psyllid, Agonoscena pistaciae

PubMed Central

Alizadeh, Ali; Talebi-Jahromi, Khalil; Hosseininaveh, Vahid; Ghadamyari, Mohammad

2014-01-01

Abstract The toxicological and biochemical characteristics of acetylcholinesterases (AChE) in nine populations of the common pistachio psyllid, Agonoscena pistaciae Burckhardt and Lauterer (Hemiptera: Psyllidae), were investigated in Kerman Province, Iran. Nine A. pistaciae populations were collected from pistachio orchards, Pistacia vera L. (Sapindales: Anacardiaceae), located in Rafsanjan, Anar, Bam, Kerman, Shahrbabak, Herat, Sirjan, Pariz, and Paghaleh regions of Kerman province. The previous bioassay results showed these populations were susceptible or resistant to phosalone, and the Rafsanjan population was most resistant, with a resistance ratio of 11.3. The specific activity of AChE in the Rafsanjan population was significantly higher than in the susceptible population (Bam). The affinity ( KM ) and hydrolyzing efficiency ( Vmax ) of AChE on acetylthiocholine iodide, butyrylthiocholine iodide, and propionylthiocholine odide as artificial substrates were clearly lower in the Bam population than that in the Rafsanjan population. These results indicated that the AChE of the Rafsanjan population had lower affinity to these substrates than that of the susceptible population. The higher Vmax value in the Rafsanjan population compared to the susceptible population suggests a possible over expression of AChE in the Rafsanjan population. The in vitro inhibitory effect of several organophosphates and carbamates on AChE of the Rafsanjan and Bam populations was determined. Based on I50, the results showed that the ratios of AChE insensitivity of the resistant to susceptible populations were 23 and 21.7-fold to monocrotophos and phosphamidon, respectively. Whereas, the insensitivity ratios for Rafsanjan population were 0.86, 0.8, 0.78, 0.46, and 0.43 for carbaryl, eserine, propoxur, m-tolyl methyl carbamate, and carbofuran, respectively, suggesting negatively correlated sensitivity to organophosphate-insensitive AChE. Therefore, AChE from the Rafsanjan population showed negatively correlated sensitivity, being insensitive to phosphamidon and monocrotophos and sensitive to N -methyl carbamates. PMID:25373165

The Eighth Industrial Fluids Properties Simulation Challenge

PubMed Central

Schultz, Nathan E.; Ahmad, Riaz; Brennan, John K.; Frankel, Kevin A.; Moore, Jonathan D.; Moore, Joshua D.; Mountain, Raymond D.; Ross, Richard B.; Thommes, Matthias; Shen, Vincent K.; Siderius, Daniel W.; Smith, Kenneth D.

2016-01-01

The goal of the eighth industrial fluid properties simulation challenge was to test the ability of molecular simulation methods to predict the adsorption of organic adsorbates in activated carbon materials. In particular, the eighth challenge focused on the adsorption of perfluorohexane in the activated carbon BAM-109. Entrants were challenged to predict the adsorption in the carbon at 273 K and relative pressures of 0.1, 0.3, and 0.6. The predictions were judged by comparison to a benchmark set of experimentally determined values. Overall good agreement and consistency were found between the predictions of most entrants. PMID:27840542

The block adaptive multigrid method applied to the solution of the Euler equations

NASA Technical Reports Server (NTRS)

Pantelelis, Nikos

1993-01-01

In the present study, a scheme capable of solving very fast and robust complex nonlinear systems of equations is presented. The Block Adaptive Multigrid (BAM) solution method offers multigrid acceleration and adaptive grid refinement based on the prediction of the solution error. The proposed solution method was used with an implicit upwind Euler solver for the solution of complex transonic flows around airfoils. Very fast results were obtained (18-fold acceleration of the solution) using one fourth of the volumes of a global grid with the same solution accuracy for two test cases.

LongISLND: in silico sequencing of lengthy and noisy datatypes

PubMed Central

Lau, Bayo; Mohiyuddin, Marghoob; Mu, John C.; Fang, Li Tai; Bani Asadi, Narges; Dallett, Carolina; Lam, Hugo Y. K.

2016-01-01

Summary: LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and the latest PacBio BAM format. We demonstrate its utility by downstream processing with consensus building and variant calling. Availability and Implementation: LongISLND is implemented in Java and available at http://bioinform.github.io/longislnd Contact: hugo.lam@roche.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27667791

Molecular Beam Epitaxy Integration of Magnetic Ferrites with Wide Bandgap Semiconductor 6Hydrogen-Silicon carbide for Next-generation Microwave and Spintronic Devices

NASA Astrophysics Data System (ADS)

Cai, Zhuhua

Ferrite/ferroelectric heterostructures have attracted much attention in recent years because of their unique ability to potentially enable dual magnetic and electric field tunability. The simultaneous magnetic and electric tunability in such structures can be applied in a wide range of microwave planar devices (e.g., tunable phase shifters, resonators, and delay lines) and spintronics (e.g., magnetic tunneling junctions for magnetic sensors and nonvolatile magnetic memories). However, the attempts to engineer ferrite/ferroelectric heterostructures to operate at the frequencies higher than 5 GHz are limited. Barium hexaferrite (BaM, BaFe12O19) is an ideal candidate for high frequency microwave device applications because of its strong uniaxial anisotropy (HA ˜17 kOe) and can be tuned to ferromagnetic resonance (FMR) at frequencies higher than 40 GHz with relatively small applied magnetic fields. Spinel ferrite Fe3O4 has a high Curie temperature of 858 K and is predicted to possess ˜ 100% spin polarization, which can lead to ultrahigh tunneling magnetoresistence even at room temperature. The performance of today's ferrite-based microwave communication and spintronic devices would be enhanced and next-generation monolithic microwave integrated circuit (MMIC) would be possible if ferrite/ferroelectric heterostructures can be integrated with wide band gap semiconductors (e.g., SiC or GaN), which can function in high-temperature, high-power, and high-frequency environments. The goal of this work is to use molecular beam epitaxy (MBE) to understand nucleation and film growth mechanisms needed to integrate magnetic ferrites (BaM and Fe3O4) with SiC, and subsequently understand the material chemistry and structure influences on forming functional interfaces (i.e., interfaces that enable effective ferrite/ferroelectric coupling). The study of chemistry, structure, and magnetic properties of three generations of BaM films grown by pulsed laser deposition shows a MBE-grown single crystalline MgO template promotes the c-axis alignment through formation of an oxygen bridge at the interface and minimizes the interface mixing, which enables the effective heteroepitaxy of device quality BaM on 6H-SiC. Epitaxial single crystalline BaM film with strong c-axis perpendicular alignment, high H A (16.2 kOe) and magnetization (4.1 kG) was also successfully grown by MBE for the first time on 6H-SiC. Through MBE, further study of the chemistry and structure evolution at the BaM//SiC interface suggests the 10 nm MgO template not only functions as a diffusion barrier, but also forms a spinel transition layer that is structurally similar to BaM. The high quality BaM film on SiC is compatible with MMIC and can also function as a magnetic layer in BaM/ferroelectric multiferroic heterostructures for electrostatic FMR tuning. Through MBE, single crystalline, epitaxial Fe3O4 (111) films and Fe 3O4/BaTiO3/Fe3O4 heterostructures were successfully integrated with 6H-SiC. The Fe3O4 film exhibits high strucutrual order with sharp interfaces and an easy axis in-plane magnetization with a coercivity of 200 Oe. In the Fe3O 4/BaTiO3/Fe3O4 heterostructure, the magnetoeletric coupling is demonstrated at room-temperature by an electric field induced magnetic anisotropy field change. The Fe3O4 /BaTiO3/Fe3O4 heterostructure has the potential application in multiferroic tunneling junction used in novel information storage. Understanding the ferrite growth mechanisms and interface functions through this research, is an important contribution toward the realization of a next-generation, multifunctional device.

New exponential stability criteria for stochastic BAM neural networks with impulses

NASA Astrophysics Data System (ADS)

Sakthivel, R.; Samidurai, R.; Anthoni, S. M.

2010-10-01

In this paper, we study the global exponential stability of time-delayed stochastic bidirectional associative memory neural networks with impulses and Markovian jumping parameters. A generalized activation function is considered, and traditional assumptions on the boundedness, monotony and differentiability of activation functions are removed. We obtain a new set of sufficient conditions in terms of linear matrix inequalities, which ensures the global exponential stability of the unique equilibrium point for stochastic BAM neural networks with impulses. The Lyapunov function method with the Itô differential rule is employed for achieving the required result. Moreover, a numerical example is provided to show that the proposed result improves the allowable upper bound of delays over some existing results in the literature.

BAM/DASS: Data Analysis Software for Sub-Microarcsecond Astrometry Device

NASA Astrophysics Data System (ADS)

Gardiol, D.; Bonino, D.; Lattanzi, M. G.; Riva, A.; Russo, F.

2010-12-01

The INAF - Osservatorio Astronomico di Torino is part of the Data Processing and Analysis Consortium (DPAC) for Gaia, a cornerstone mission of the European Space Agency. Gaia will perform global astrometry by means of two telescopes looking at the sky along two different lines of sight oriented at a fixed angle, also called basic angle. Knowledge of the basic angle fluctuations at the sub-microarcsecond level over periods of the order of the minute is crucial to reach the mission goals. A specific device, the Basic Angle Monitoring, will be dedicated to this purpose. We present here the software system we are developing to analyze the BAM data and recover the basic angle variations. This tool is integrated into the whole DPAC data analysis software.

Global exponential stability and lag synchronization for delayed memristive fuzzy Cohen-Grossberg BAM neural networks with impulses.

PubMed

Yang, Wengui; Yu, Wenwu; Cao, Jinde; Alsaadi, Fuad E; Hayat, Tasawar

2018-02-01

This paper investigates the stability and lag synchronization for memristor-based fuzzy Cohen-Grossberg bidirectional associative memory (BAM) neural networks with mixed delays (asynchronous time delays and continuously distributed delays) and impulses. By applying the inequality analysis technique, homeomorphism theory and some suitable Lyapunov-Krasovskii functionals, some new sufficient conditions for the uniqueness and global exponential stability of equilibrium point are established. Furthermore, we obtain several sufficient criteria concerning globally exponential lag synchronization for the proposed system based on the framework of Filippov solution, differential inclusion theory and control theory. In addition, some examples with numerical simulations are given to illustrate the feasibility and validity of obtained results. Copyright © 2017 Elsevier Ltd. All rights reserved.

How bad is bile acid diarrhoea: an online survey of patient-reported symptoms and outcomes

PubMed Central

Bannaga, Ayman; Kelman, Lawrence; O'Connor, Michelle; Pitchford, Claire; Walters, Julian R F; Arasaradnam, Ramesh P

2017-01-01

Objectives Bile acid diarrhoea (BAD) is an underdiagnosed condition producing diarrhoea, urgency and fear of faecal incontinence. How patients experience these symptoms has not previously been studied. Bile Acid Malabsorption (BAM) Support UK was established in 2015 as a national charity with objectives including to provide details regarding how BAD affects patients, to improve earlier recognition and clinical management. Design, setting and main outcome A questionnaire was collected anonymously by BAM Support UK and the Bile Salt Malabsorption Facebook group over 4 weeks at the end of 2015. It comprised 56 questions and aimed to inform patients and clinicians about how BAD affects the respondents. Results The first 100 responses were analysed. 91% of the respondents reported a diagnosis of BAD. 58% of total respondents diagnosed following a Selenium-homocholic acid taurine scan, 69% were diagnosed by a gastroenterologist, with type 2 and 3 BAD comprising 38% and 37%, respectively, of total respondents. Symptoms had been experienced for more than 5 years before diagnosis in 44% of respondents. Following treatment, usually with bile acid sequestrants, 60% of participants reported improvement of diarrhoea and most reported their mental health has been positively impacted. Just over half of the cohort felt as though their symptoms had been dismissed during clinical consultations and 28% felt their GPs were unaware of BAD. Conclusions BAD requires more recognition by clinicians to address the current delays in diagnosis. Treatment improves physical and mental symptoms in the majority of participants. PMID:28123771

Level 2 validation of a flow cytometric method for detection of Escherichia coli O157:H7 in raw spinach.

PubMed

Williams, Anna J; Cooper, Willie M; Summage-West, Christine V; Sims, Lillie M; Woodruff, Robert; Christman, Jessica; Moskal, Ted J; Ramsaroop, Shawn; Sutherland, John B; Alusta, Pierre; Wilkes, Jon G; Buzatu, Dan A

2015-12-23

The Bacteriological Analytical Manual (BAM) method currently used by the United States Food and Drug Administration (FDA) to detect Escherichia coli O157:H7 in spinach was systematically compared to a new flow cytometry based method. This Food and Drug Administration (FDA) level 2 external laboratory validation study was designed to determine the latter method's sensitivity and speed for analysis of this pathogen in raw spinach. Detection of target cell inoculations with a low cell count is critical, since enterohemorrhagic strains of E. coli require an infective dose of as few as 10 cells (Schmid-Hempel and Frank, 2007). Although, according to the FDA, the infectious dose is unknown (Food and Drug Administration, 1993). Therefore, the inoculation level into the spinach, a total of 2.0±2.6 viable E. coli O157 cells, was specified to yield between 25% and 75% detection by the new method, out of 20 samples (10 positives and 10 negatives). This criterion was met in that the new method detected 60% of the nominally positive samples; the corresponding sensitivity of the reference method was 50%. For both methods the most likely explanation for false negatives was that no viable cells were actually introduced into the sample. In this validation study, the flow cytometry method was equal to the BAM in sensitivity and far superior in speed. Published by Elsevier B.V.

Systematic review: the prevalence of idiopathic bile acid malabsorption as diagnosed by SeHCAT scanning in patients with diarrhoea-predominant irritable bowel syndrome.

PubMed

Wedlake, L; A'Hern, R; Russell, D; Thomas, K; Walters, J R F; Andreyev, H J N

2009-10-01

Recurrent, watery diarrhoea affects one-third of patients diagnosed with irritable bowel syndrome ('IBS-D'). Idiopathic bile acid malabsorption ('I-BAM') may be the cause. To determine the prevalence of I-BAM in patients suffering from IBS-D. A systematic search was performed of publications reporting patients presenting with IBS-D type symptoms, who were subsequently confirmed as having I-BAM by SeHCAT scanning. Eighteen relevant studies, 15 prospective, comprising 1223 patients were identified. Five studies (429 patients) indicated that 10% (CI: 7-13) patients had severe bile acid malabsorption (SeHCAT 7 day retention <5% of baseline value). 17 studies (1073 patients) indicated that 32% (CI: 29-35) patients had moderate bile acid malabsorption (SeHCAT <10%). 7 studies (618 patients) indicated that 26% (CI: 23-30) patients had mild (SeHCAT <15%) bile acid malabsorption. Pooled data from 15 studies showed a dose-response relationship according to severity of malabsorption to treatment with a bile acid binder: response to colestyramine occurred in 96% of patients with <5% retention, 80% at <10% retention and 70% at <15% retention. Idiopathic adult-onset bile acid malabsorption is not rare. International guidelines for the management of irritable bowel syndrome need to be revised so that clinicians become more aware of this possibility.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Radigan, Jacqueline, E-mail: radigan@stsci.edu

Observations of variability can provide valuable information about the processes of cloud formation and dissipation in brown dwarf atmospheres. Here we report the results of an independent analysis of archival data from the Brown dwarf Atmosphere Monitoring (BAM) program. Time series data for 14 L and T dwarfs reported to be significantly variable over timescales of hours were analyzed. We confirm large-amplitude variability (amplitudes >2%) for 4 out of 13 targets and place upper limits of 0.7%-1.6% on variability in the remaining sample. For two targets we find evidence of weak variability at amplitudes of 1.3% and 1.6%. Based onmore » our revised classification of variable objects in the BAM study, we find strong variability outside the L/T transition to be rare at near infrared wavelengths. From a combined sample of 81 L0-T9 dwarfs from the revised BAM sample and the variability survey of Radigan et al., we infer an overall observed frequency for large-amplitude variability outside the L/T transition of 3.2{sub −1.8}{sup +2.8}%, in contrast to 24{sub −9}{sup +11}% for L9-T3.5 spectral types. We conclude that while strong variability is not limited to the L/T transition, it occurs more frequently in this spectral type range, indicative of larger or more highly contrasting cloud features at these spectral types.« less

Enhanced and broadband microwave absorption of flake-shaped Fe and FeNi composite with Ba ferrites

NASA Astrophysics Data System (ADS)

Li, Wangchang; Lv, Junjun; Zhou, Xiang; Zheng, Jingwu; Ying, Yao; Qiao, Liang; Yu, Jing; Che, Shenglei

2017-03-01

In order to achieve a broad bandwidth absorber at high frequency, the composites of M-type ferrite BaCo1.0Ti1.0Fe10O19 (BaM) with flaked carbonyl iron powders (CIP) and flaked Fe50Ni50 were prepared to optimize the surface impedance in broadband frequency, respectively. The diameter of the flaked carbonyl iron powders (CIP) and Fe50Ni50 is in the range of 5-10 μm and 10-20 μm and the thickness of the CIP and Fe50Ni50 is close to 200 nm and 400 nm, respectively. The complex permeability and permittivity show that the addition of BaM obviously reduces the values of real part of permittivity and imaginary part of the permeability which can enhance the matched-wave-impedance. The absorption bands less than -10 dB of CIP-BaM and FeNi-BaM absorber approach to 5.5 GHz (5.7-11.2 GHz) and 7 GHz (11-18 GHz) at 1.5 mm. However, the bands of CIP and FeNi are only 1.9 GHz (4.7-6.6 GHz) and 2.1 GHz (4.0-6.1 GHz). Hence, the electromagnetic match property is greatly improved by BaM ferrites, and this composite shows a broaden absorption band.

Innovative methodology for the synthesis of Ba-M hexaferrite BaFe{sub 12}O{sub 19} nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmed, M.A., E-mail: moala@47hotmail.com; Helmy, N.; El-Dek, S.I.

2013-09-01

Graphical abstract: Transmission electron microscope images for the BaFe12O19. - Highlights: • BaFe{sub 12}O{sub 19}nanoparticles were prepared in single-phase from organometallic precursors. • BaFe{sub 12}O{sub 19} possesses small size 65 nm, H{sub C} = 3695 Oe and M{sub s} = 58 emu/g. • This method of preparation could be extended in the synthesis of other metal oxide nanoparticles. - Abstract: In this piece of work, high quality and homogeneity, barium hexaferrite (BaM) BaFe{sub 12}O{sub 19} nanoparticles were prepared from organometallic precursors for the 1st time. This method is based on the formation of supramolecular crystal structure of Ba[Fe(H{sub 3}NCH{sub 2}CH{submore » 2}NH{sub 3})]Cl{sub 7}·8H{sub 2}O. The crystal structure, morphology and magnetic properties of BaFe{sub 12}O{sub 19} at two different annealing temperatures namely 1000 °C and 1200 °C were investigated using X-ray diffraction, transmission electron microscope TEM and vibrating sample magnetometry (VSM). The results show that monophasic nanoparticles of hexaferrites were obtained. Nanoparticles of crystallite size 40–50 nm distinguished by narrow distribution and excellent homogeneity were obtained with superior magnetic properties which suggested single-domain particles of Ba-M hexaferrite.« less

Compound-Specific Stable Isotope Fractionation of Pesticides and Pharmaceuticals in a Mesoscale Aquifer Model.

PubMed

Schürner, Heide K V; Maier, Michael P; Eckert, Dominik; Brejcha, Ramona; Neumann, Claudia-Constanze; Stumpp, Christine; Cirpka, Olaf A; Elsner, Martin

2016-06-07

Compound-specific isotope analysis (CSIA) receives increasing interest for its ability to detect natural degradation of pesticides and pharmaceuticals. Despite recent laboratory studies, CSIA investigations of such micropollutants in the environment are still rare. To explore the certainty of information obtainable by CSIA in a near-environmental setting, a pulse of the pesticide bentazone, the pesticide metabolite 2,6-dichlorobenzamide (BAM), and the pharmaceuticals diclofenac and ibuprofen was released into a mesoscale aquifer with quasi-two-dimensional flow. Concentration breakthrough curves (BTC) of BAM and ibuprofen demonstrated neither degradation nor sorption. Bentazone was transformed but did not sorb significantly, whereas diclofenac showed both degradation and sorption. Carbon and nitrogen CSIA could be accomplished in similar concentrations as for "traditional" priority pollutants (low μg/L range), however, at the cost of uncertainties (0.4-0.5‰ (carbon), 1‰ (nitrogen)). Nonetheless, invariant carbon and nitrogen isotope values confirmed that BAM was neither degraded nor sorbed, while significant enrichment of (13)C and in particular (15)N corroborated transformation of diclofenac and bentazone. Retardation of diclofenac was reflected in additional (15)N sorption isotope effects, whereas isotope fractionation of transverse dispersion could not be identified. These results provide a benchmark on the performance of CSIA to monitor the reactivity of micropollutants in aquifers and may guide future efforts to accomplish CSIA at even lower concentrations (ng/L range).

Validation of a modification to Performance-Tested Method 070601: Reveal Listeria Test for detection of Listeria spp. in selected foods and selected environmental samples.

PubMed

Alles, Susan; Peng, Linda X; Mozola, Mark A

2009-01-01

A modification to Performance-Tested Method (PTM) 070601, Reveal Listeria Test (Reveal), is described. The modified method uses a new media formulation, LESS enrichment broth, in single-step enrichment protocols for both foods and environmental sponge and swab samples. Food samples are enriched for 27-30 h at 30 degrees C and environmental samples for 24-48 h at 30 degrees C. Implementation of these abbreviated enrichment procedures allows test results to be obtained on a next-day basis. In testing of 14 food types in internal comparative studies with inoculated samples, there was a statistically significant difference in performance between the Reveal and reference culture [U.S. Food and Drug Administration's Bacteriological Analytical Manual (FDA/BAM) or U.S. Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS)] methods for only a single food in one trial (pasteurized crab meat) at the 27 h enrichment time point, with more positive results obtained with the FDA/BAM reference method. No foods showed statistically significant differences in method performance at the 30 h time point. Independent laboratory testing of 3 foods again produced a statistically significant difference in results for crab meat at the 27 h time point; otherwise results of the Reveal and reference methods were statistically equivalent. Overall, considering both internal and independent laboratory trials, sensitivity of the Reveal method relative to the reference culture procedures in testing of foods was 85.9% at 27 h and 97.1% at 30 h. Results from 5 environmental surfaces inoculated with various strains of Listeria spp. showed that the Reveal method was more productive than the reference USDA-FSIS culture procedure for 3 surfaces (stainless steel, plastic, and cast iron), whereas results were statistically equivalent to the reference method for the other 2 surfaces (ceramic tile and sealed concrete). An independent laboratory trial with ceramic tile inoculated with L. monocytogenes confirmed the effectiveness of the Reveal method at the 24 h time point. Overall, sensitivity of the Reveal method at 24 h relative to that of the USDA-FSIS method was 153%. The Reveal method exhibited extremely high specificity, with only a single false-positive result in all trials combined for overall specificity of 99.5%.

LongISLND: in silico sequencing of lengthy and noisy datatypes.

PubMed

Lau, Bayo; Mohiyuddin, Marghoob; Mu, John C; Fang, Li Tai; Bani Asadi, Narges; Dallett, Carolina; Lam, Hugo Y K

2016-12-15

LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and the latest PacBio BAM format. We demonstrate its utility by downstream processing with consensus building and variant calling. LongISLND is implemented in Java and available at http://bioinform.github.io/longislnd CONTACT: hugo.lam@roche.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Total alpha-globin gene cluster deletion has high frequency in Filipinos

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunt, J.A.; Haruyama, A.Z.; Chu, B.M.

1994-09-01

Most {alpha}-thalassemias [Thal] are due to large deletions. In Southeast Asians, the (--{sup SEA}) double {alpha}-globin gene deletion is common, 3 (--{sup Tot}) total {alpha}-globin cluster deletions are known: Filipino (--{sup Fil}), Thai (--{sup Thai}), and Chinese (--{sup Chin}). In a Hawaii Thal project, provisional diagnosis of {alpha}-Thal-1 heterozygotes was based on microcytosis, normal isoelectric focusing, and no iron deficiency. One in 10 unselected Filipinos was an {alpha}-Thal-1 heterozygote, 2/3 of these had a (--{sup Tot}) deletion: a {var_sigma}-cDNA probe consistently showed fainter intensity of the constant 5.5 kb {var_sigma}{sub 2} BamHI band, with no heterzygosity for {var_sigma}-globin region polymorphisms;more » {alpha}-cDNA or {var_sigma}-cDNA probes showed no BamHI or BglII bands diagnostic of the (--{sup SEA}) deletion; bands for the (-{alpha}) {alpha}-Thal-2 single {alpha}-globin deletions were only seen in Hb H cases. A reliable monoclonal anti-{var_sigma}-peptide antibody test for the (--{sup SEA}) deletion was always negative in (--{sup Tot}) samples. Southern digests with the Lo probe, a gift from D. Higgs of Oxford Univ., confirmed that 49 of 50 (--{sup Tot}) chromosomes in Filipinos were (--{sup Fil}). Of 20 {alpha}-Thal-1 hydrops born to Filipinos, 11 were (--{sup Fil}/--{sup SEA}) compound heterozygotes; 9 were (--{sup SEA}/--{sup SEA}) homozygotes, but none was a (--{sup Fil}/--{sup Fil}).« less

Electron crystallographic analysis of two-dimensional streptavidin crystals coordinated to metal-chelated lipid monolayers.

PubMed Central

Frey, W; Brink, J; Schief, W R; Chiu, W; Vogel, V

1998-01-01

Coordination of individual histidine residues located on a protein surface to metal-chelated lipid monolayers is a potentially general method for crystallizing proteins in two dimensions. It was shown recently by Brewster angle microscopy (BAM) that the model protein streptavidin binds via its surface histidines to Cu-DOIDA lipid monolayers, and aggregates into regularly shaped domains that have the appearance of crystals. We have used electron microscopy to confirm that the domains are indeed crystalline with lattice parameters similar to those of the same protein crystallized beneath biotinylated lipid monolayers. Although BAM demonstrates that the two-dimensional protein crystals grown via metal chelation are distinct from the biotin-bound crystals in both microscopic shape and thermodynamic behavior, the two crystal types show similar density projections and the same plane group symmetry. PMID:9591691

An Epstein-Barr virus immediate-early gene product trans-activates gene expression from the human immunodeficiency virus long terminal repeat.

PubMed

Kenney, S; Kamine, J; Markovitz, D; Fenrick, R; Pagano, J

1988-03-01

Acquired immunodeficiency syndrome patients are frequently coinfected with Epstein-Barr virus (EBV). In this report, we demonstrate that an EBV immediate-early gene product, BamHI MLF1, stimulates expression of the bacterial chloramphenicol acetyltransferase (CAT) gene linked to the human immunodeficiency virus (HIV) promoter. The HIV promoter sequences necessary for trans-activation by EBV do not include the tat-responsive sequences. In addition, in contrast to the other herpesvirus trans-activators previously studied, the EBV BamHI MLF1 gene product appears to function in part by a posttranscriptional mechanism, since it increases pHIV-CAT protein activity more than it increases HIV-CAT mRNA. This ability of an EBV gene product to activate HIV gene expression may have biologic consequences in persons coinfected with both viruses.

Brewster Angle Microscopy Study of Model Stratum Corneum Lipid Monolayers at the Air-Water Interface

NASA Astrophysics Data System (ADS)

Adams, Ellen; Champagne, Alex; William, Joseph; Allen, Heather

2012-04-01

As the first and last barrier in the body, the stratum corneum (SC) is essential to life. Understanding the interactions and organization of lipids within the SC provides insight into essential physiological processes, including water loss prevention and the adsorption of substances from the environment. Langmuir monolayers have long been used to study complex systems, such as biological membranes and marine aerosols, due to their ability to shed light on intermolecular interactions. In this study, lipid mixtures with varying cholesterol and cerebroside ratios were investigated at the air/water interface. Surface tension measurements along with Brewster angle microscopy (BAM) images were used to examine the lipid phase transitions. Results indicate that cholesterol and cerebrosides form miscible monolayers, exhibiting ideal behavior. BAM images of a singular, uniform collapse phase also suggest formation of a miscible monolayer.

The potato amylase inhibitor gene SbAI regulates cold-induced sweetening in potato tubers by modulating amylase activity.

PubMed

Zhang, Huiling; Liu, Jun; Hou, Juan; Yao, Ying; Lin, Yuan; Ou, Yongbin; Song, Botao; Xie, Conghua

2014-09-01

Potato cold-induced sweetening (CIS) is critical for the postharvest quality of potato tubers. Starch degradation is considered to be one of the key pathways in the CIS process. However, the functions of the genes that encode enzymes related to starch degradation in CIS and the activity regulation of these enzymes have received less attention. A potato amylase inhibitor gene known as SbAI was cloned from the wild potato species Solanum berthaultii. This genetic transformation confirmed that in contrast to the SbAI suppression in CIS-resistant potatoes, overexpressing SbAI in CIS-sensitive potatoes resulted in less amylase activity and a lower rate of starch degradation accompanied by a lower reducing sugar (RS) content in cold-stored tubers. This finding suggested that the SbAI gene may play crucial roles in potato CIS by modulating the amylase activity. Further investigations indicated that pairwise protein-protein interactions occurred between SbAI and α-amylase StAmy23, β-amylases StBAM1 and StBAM9. SbAI could inhibit the activities of both α-amylase and β-amylase in potato tubers primarily by repressing StAmy23 and StBAM1, respectively. These findings provide the first evidence that SbAI is a key regulator of the amylases that confer starch degradation and RS accumulation in cold-stored potato tubers. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

System dynamics modeling of nitrogen removal in a stormwater infiltration basin with biosorption-activated media.

PubMed

Xuan, Zhemin; Chang, Ni-Bin; Wanielista, Martin P; Williams, Evan Shane

2013-07-01

Stormwater infiltration basins, one of the typical stormwater best management practices, are commonly constructed for surface water pollution control, flood mitigation, and groundwater restoration in rural or residential areas. These basins have soils with better infiltration capacity than the native soil; however, the ever-increasing contribution of nutrients to groundwater from stormwater due to urban expansion makes existing infiltration basins unable to meet groundwater quality criteria related to environmental sustainability and public health. This issue requires retrofitting current infiltration basins for flood control as well as nutrient control before the stormwater enters the groundwater. An existing stormwater infiltration basin in north-central Florida was selected, retrofitted, and monitored to identify subsurface physiochemical and biological processes during 2007-2010 to investigate nutrient control processes. This implementation in the nexus of contaminant hydrology and ecological engineering adopted amended soil layers packed with biosorption activated media (BAM; tire crumb, silt, clay, and sand) to perform nutrient removal in a partitioned forebay using a berm. This study presents an infiltration basin-nitrogen removal (IBNR) model, a system dynamics model that simulates nitrogen cycling in this BAM-based stormwater infiltration basin with respect to changing hydrologic conditions and varying dissolved nitrogen concentrations. Modeling outputs of IBNR indicate that denitrification is the biogeochemical indicator in the BAM layer that accounted for a loss of about one third of the total dissolved nitrogen mass input. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Involvement of MrgprC in Electroacupuncture Analgesia for Attenuating CFA-Induced Thermal Hyperalgesia by Suppressing the TRPV1 Pathway.

PubMed

Liu, Ying-Jun; Lin, Xiao-Xi; Fang, Jian-Qiao; Fang, Fang

2018-01-01

Mas-related G-protein-coupled receptor C (MrgprC) plays an important role in modulating chronic inflammatory pain. Electroacupuncture (EA) has a satisfactory analgesic effect on chronic pain. This study aimed to investigate the involvement of MrgprC and its transient receptor potential vanilloid 1 (TRPV1) pathway in EA analgesia in chronic inflammatory pain. Chronic inflammatory pain was induced by subcutaneously injecting complete Freund's adjuvant (CFA) into the left hind paw. EA (2/100 Hz) stimulation was administered. MrgprC siRNAs were intrathecally administered to inhibit MrgprC expression, and bovine adrenal medulla 8-22 (BAM8-22) was used to activate MrgprC. The mechanical allodynia was decreased by EA significantly since day 3. The piled analgesic effect of EA was partially blocked by 6 intrathecal administrations of MrgprC siRNA. Both EA and BAM8-22 could downregulate the expression of TRPV1 and PKC in both the DRG and the SCDH. Both EA and BAM8-22 could also decrease the TRPV1 translocation and p-TRPV1 level in both the DRG and the SCDH. The effects of EA on PKC ε , TRPV1 translocation, and p-TRPV1 in both the DRG and the SCDH were reversed by MrgprC siRNA. The results indicated that MrgprC played crucial roles in chronic pain modulation and was involved in EA analgesia partially through the regulation of TRPV1 function at the DRG and SCDH levels.

StratBAM: A Discrete-Event Simulation Model to Support Strategic Hospital Bed Capacity Decisions.

PubMed

Devapriya, Priyantha; Strömblad, Christopher T B; Bailey, Matthew D; Frazier, Seth; Bulger, John; Kemberling, Sharon T; Wood, Kenneth E

2015-10-01

The ability to accurately measure and assess current and potential health care system capacities is an issue of local and national significance. Recent joint statements by the Institute of Medicine and the Agency for Healthcare Research and Quality have emphasized the need to apply industrial and systems engineering principles to improving health care quality and patient safety outcomes. To address this need, a decision support tool was developed for planning and budgeting of current and future bed capacity, and evaluating potential process improvement efforts. The Strategic Bed Analysis Model (StratBAM) is a discrete-event simulation model created after a thorough analysis of patient flow and data from Geisinger Health System's (GHS) electronic health records. Key inputs include: timing, quantity and category of patient arrivals and discharges; unit-level length of care; patient paths; and projected patient volume and length of stay. Key outputs include: admission wait time by arrival source and receiving unit, and occupancy rates. Electronic health records were used to estimate parameters for probability distributions and to build empirical distributions for unit-level length of care and for patient paths. Validation of the simulation model against GHS operational data confirmed its ability to model real-world data consistently and accurately. StratBAM was successfully used to evaluate the system impact of forecasted patient volumes and length of stay in terms of patient wait times, occupancy rates, and cost. The model is generalizable and can be appropriately scaled for larger and smaller health care settings.

Development of an optical thermal history coating sensor based on the oxidation of a divalent rare earth ion phosphor

NASA Astrophysics Data System (ADS)

Yáñez-González, Álvaro; Ruiz-Trejo, Enrique; van Wachem, Berend; Skinner, Stephen; Beyrau, Frank; Heyes, Andrew

2016-11-01

The measurement of temperatures in gas turbines, boilers, heat exchangers and other components exposed to hot gases is essential to design energy efficient systems and improve maintenance procedures. When on-line measurements, such as those performed with thermocouples and pyrometers, are not possible or inconvenient, the maximum temperatures of operation can be recorded and measured off-line after operation. Although thermal paints have been used for many years for this purpose, a novel technique based on irreversible changes in the optical properties of thermographic phosphors, can overcome some of the disadvantages of previous methods. In particular, oxidation of the divalent rare earth ion phosphor BaMgAl10O17:Eu (BAM:Eu) has shown great potential for temperature sensing between 700 °C and 1200 °C. The emission spectra of this phosphor change with temperature, which permits to define an intensity ratio between different lines in the spectra that can be used as a measurand of the temperature. In this paper, the study of the sensing capabilities of a sensor coating based on BAM:Eu phosphor material is addressed for the first time. The sensitivity of the intensity ratio is investigated in the temperature range from 800 °C to 1100 °C, and is proved to be affected by ionic diffusion of transition metals from the substrate. The use of an interlayer made of zirconia proves efficient in reducing ionic diffusion and coatings with this diffusion barrier present sensitivity comparable to that of the powder material.

Sensitivity to friction for primary explosives.

PubMed

Matyáš, Robert; Šelešovský, Jakub; Musil, Tomáš

2012-04-30

The sensitivity to friction for a selection of primary explosives has been studied using a small BAM friction apparatus. The probit analysis was used for the construction of a sensitivity curve for each primary explosive tested. Two groups of primary explosives were chosen for measurement (a) the most commonly used industrially produced primary explosives (e.g. lead azide, tetrazene, dinol, lead styphnate) and (b) the most produced improvised primary explosives (e.g. triacetone triperoxide, hexamethylenetriperoxide diamine, mercury fulminate, acetylides of heavy metals). A knowledge of friction sensitivity is very important for determining manipulation safety for primary explosives. All the primary explosives tested were carefully characterised (synthesis procedure, shape and size of crystals). The sensitivity curves obtained represent a unique set of data, which cannot be found anywhere else in the available literature. Copyright © 2012 Elsevier B.V. All rights reserved.

Bi-periodicity evoked by periodic external inputs in delayed Cohen-Grossberg-type bidirectional associative memory networks

NASA Astrophysics Data System (ADS)

Cao, Jinde; Wang, Yanyan

2010-05-01

In this paper, the bi-periodicity issue is discussed for Cohen-Grossberg-type (CG-type) bidirectional associative memory (BAM) neural networks (NNs) with time-varying delays and standard activation functions. It is shown that the model considered in this paper has two periodic orbits located in saturation regions and they are locally exponentially stable. Meanwhile, some conditions are derived to ensure that, in any designated region, the model has a locally exponentially stable or globally exponentially attractive periodic orbit located in it. As a special case of bi-periodicity, some results are also presented for the system with constant external inputs. Finally, four examples are given to illustrate the effectiveness of the obtained results.

Particle-size distribution modified effective medium theory and validation by magneto-dielectric Co-Ti substituted BaM ferrite composites

NASA Astrophysics Data System (ADS)

Li, Qifan; Chen, Yajie; Harris, Vincent G.

2018-05-01

This letter reports an extended effective medium theory (EMT) including particle-size distribution functions to maximize the magnetic properties of magneto-dielectric composites. It is experimentally verified by Co-Ti substituted barium ferrite (BaCoxTixFe12-2xO19)/wax composites with specifically designed particle-size distributions. In the form of an integral equation, the extended EMT formula essentially takes the size-dependent parameters of magnetic particle fillers into account. It predicts the effective permeability of magneto-dielectric composites with various particle-size distributions, indicating an optimal distribution for a population of magnetic particles. The improvement of the optimized effective permeability is significant concerning magnetic particles whose properties are strongly size dependent.

Control system for the 2nd generation Berkeley AutoMounters (BAM2) at GM/CA CAT macromolecular crystallography beamlines

PubMed Central

Makarov, O.; Hilgart, M.; Ogata, C.; Pothineni, S.; Cork, C.

2011-01-01

GM/CA CAT at Sector 23 of the Advanced Photon Source (APS) is an NIH funded facility for crystallographic structure determination of biological macromolecules by X-ray diffraction. A second generation Berkeley automounter is being integrated into the beamline control system at the 23-BM experimental station. This new device replaces the previous all-pneumatic gripper motions with a combination of pneumatics and XYZ motorized linear stages. The latter adds a higher degree of flexibility to the robot including auto-alignment capability, accommodation of a larger capacity sample Dewar of arbitrary shape, and support for advanced operations such as crystal washing, while preserving the overall simplicity and efficiency of the Berkeley automounter design. PMID:21822343

[Prokaryotic expression of the major antigenic domain of equine arteritis virus GL protein and the establishment of putative indirect ELISA assay].

PubMed

Liang, Cheng-Zhu; Cao, Rui-Bing; Wei, Jian-Chao; Zhu, Lai-Hua; Chen, Pu-Yan

2006-06-01

According to the antigenic analysis of equine arteritis virus (EAV) GL protein, one pair of primers were designed, with which the gene fragment coding the high antigenic domain of EAV GL protein was amplified from the EAV genome. The cloned gene was digested with BamH I and Xho I and then inserted into pET-32a and resulted pET-GL1. The pET-GL1 was transformed into the host cell BL21(DE3) and the expression was optimized including cultivation temperature and concentration of IPTG. The aim protein was highly expressed and the obtained recombinant protein manifested well reactiongenicity as was confirmed by Western blot. The recombinant GL1 protein was purified by the means of His * Bind resin protein purification procedure. Then an indirect ELISA was established to detect antibody against EAV with the purified GL1 protein as the coating antigen. The result showed that the optimal concentration of coated antigen was 9.65 microg/mL and the optimal dilution of serum was 1:80. The positive criterion of this ELISA assay is OD (the tested serum) > 0.4 and OD (the tested serum) /OD (the negative serum) > 2.0. The iGL-ELISA was evaluated versus micro-virus neutralization test. The ELISA was performed on 900 sera from which were preserved by this lab during horse entry/exit inspection, the agreement (94.1%) of these test were considered suitable for individual serological detection. In another test which 180 sera samples were detected by iGL-ELISA and INGEZIM ELISA kit respectively. The agreement ratio between the two methods is 95.6%.

Integrated Data Collection Analysis (IDCA) Program — Bullseye ® Smokeless Powder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sandstrom, Mary M.; Brown, Geoffrey W.; Preston, Daniel N.

2013-05-30

The Integrated Data Collection Analysis (IDCA) program is conducting a proficiency study for Small- Scale Safety and Thermal (SSST) testing of homemade explosives (HMEs). Described here are the results for impact, friction, electrostatic discharge, and differential scanning calorimetry analysis of Bullseye ® smokeless powder (Gunpowder). The participants found the Gunpowder: 1) to have a range of sensitivity to impact, from less than RDX to almost as sensitive as PETN, 2) to be moderately sensitive to BAM and ABL friction, 3) have a range for ESD, from insensitive to more sensitive than PETN, and 4) to have thermal sensitivity about themore » same as PETN and RDX.« less

Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

PubMed

Finney, Richard P; Chen, Qing-Rong; Nguyen, Cu V; Hsu, Chih Hao; Yan, Chunhua; Hu, Ying; Abawi, Massih; Bian, Xiaopeng; Meerzaman, Daoud M

2015-01-01

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

In Situ Airborne Instrumentation: Addressing and Solving Measurement Problems in Ice Clouds

DOE PAGES

Baumgardner, Darrel; Kok, Greg; Avallone, L.; ...

2012-02-01

A meeting of 31 international experts on in situ measurements from aircraft was held to identify unresolved questions concerning ice formation and evolution in ice clouds, assess the current state of instrumentation that can address these problems, introduce emerging technology that may overcome current measurement issues and recommend future courses of action that can improve our understanding of ice cloud microphysical processes and their impact on the environment. The meeting proceedings and outcome has been described in detail in a manuscript submitted to the Bulletin of the American Meteorological Society (BAMS) on March 24, 2011. This paper is currently undermore » review. The remainder of this summary, in the following pages, is the text of the BAMS article. A technical note that will be published by the National Center for Atmospheric Research is currently underway and is expected to be published before the end of the year.« less

An Epstein-Barr virus immediate-early gene product trans-activates gene expression from the human immunodeficiency virus long terminal repeat.

PubMed Central

Kenney, S; Kamine, J; Markovitz, D; Fenrick, R; Pagano, J

1988-01-01

Acquired immunodeficiency syndrome patients are frequently coinfected with Epstein-Barr virus (EBV). In this report, we demonstrate that an EBV immediate-early gene product, BamHI MLF1, stimulates expression of the bacterial chloramphenicol acetyltransferase (CAT) gene linked to the human immunodeficiency virus (HIV) promoter. The HIV promoter sequences necessary for trans-activation by EBV do not include the tat-responsive sequences. In addition, in contrast to the other herpesvirus trans-activators previously studied, the EBV BamHI MLF1 gene product appears to function in part by a posttranscriptional mechanism, since it increases pHIV-CAT protein activity more than it increases HIV-CAT mRNA. This ability of an EBV gene product to activate HIV gene expression may have biologic consequences in persons coinfected with both viruses. Images PMID:2830625

Epstein-Barr virus immediate-early gene product trans-activates gene expression from the human immunodeficiency virus long terminal repeat

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kenney, S.; Kamine, J.; Markovitz, D.

Acquired immunodeficiency syndrome patients are frequently coinfected with Epstein-Barr virus (EBV). In this report, the authors demonstrate that an EBV immediate-early gene product, BamHI MLF1, stimulates expression of the bacterial chloramphenicol acetyltransferase (CAT) gene linked to the human immunodeficiency virus (HIV) promoter. The HIV promoter sequences necessary for trans-activation by EBV do not include the tat-responsive sequences. In addition, in contrast to the other herpesvirus trans-activators previously studied, the EBV BamHI MLF1 gene product appears to function in part by a posttranscriptional mechanism, since it increases pHIV-CAT protein activity more than it increases HIV-CAT mRNA. This ability of an EBVmore » gene product to activate HIV gene expression may have biologic consequences in persons coinfected with both viruses.« less

Characterization of ambient aerosols at the San Francisco International Airport using BioAerosol Mass Spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steele, P T; McJimpsey, E L; Coffee, K R

2006-03-16

The BioAerosol Mass Spectrometry (BAMS) system is a rapidly fieldable, fully autonomous instrument that can perform correlated measurements of multiple orthogonal properties of individual aerosol particles. The BAMS front end uses optical techniques to nondestructively measure a particle's aerodynamic diameter and fluorescence properties. Fluorescence can be excited at 266nm or 355nm and is detected in two broad wavelength bands. Individual particles with appropriate size and fluorescence properties can then be analyzed more thoroughly in a dual-polarity time-of-flight mass spectrometer. Over the course of two deployments to the San Francisco International Airport, more than 6.5 million individual aerosol particles were fullymore » analyzed by the system. Analysis of the resulting data has provided a number of important insights relevant to rapid bioaerosol detection, which are described here.« less

Biological nano-functionalization of titanium-based biomaterial surfaces: a flexible toolbox

PubMed Central

Beutner, René; Michael, Jan; Schwenzer, Bernd; Scharnweber, Dieter

2010-01-01

Surface functionalization with bioactive molecules (BAMs) on a nanometre scale is a main field in current biomaterial research. The immobilization of a vast number of substances and molecules, ranging from inorganic calcium phosphate phases up to peptides and proteins, has been investigated throughout recent decades. However, in vitro and in vivo results are heterogeneous. This may be at least partially attributed to the limits of the applied immobilization methods. Therefore, this paper highlights, in the first part, advantages and limits of the currently applied methods for the biological nano-functionalization of titanium-based biomaterial surfaces. The second part describes a new immobilization system recently developed in our groups. It uses the nanomechanical fixation of at least partially single-stranded nucleic acids (NAs) into an anodic titanium oxide layer as an immobilization principle and their hybridization ability for the functionalization of the surface with BAMs conjugated to the respective complementary NA strands. PMID:19889692

A privacy-preserving solution for compressed storage and selective retrieval of genomic data.

PubMed

Huang, Zhicong; Ayday, Erman; Lin, Huang; Aiyar, Raeka S; Molyneaux, Adam; Xu, Zhenyu; Fellay, Jacques; Steinmetz, Lars M; Hubaux, Jean-Pierre

2016-12-01

In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients' complete aligned genomic data in addition to variant calls relative to a reference sequence. Due to the large size of human genome sequence data files (varying from 30 GB to 200 GB depending on coverage), two major challenges facing genomics laboratories are the costs of storage and the efficiency of the initial data processing. In addition, privacy of genomic data is becoming an increasingly serious concern, yet no standard data storage solutions exist that enable compression, encryption, and selective retrieval. Here we present a privacy-preserving solution named SECRAM (Selective retrieval on Encrypted and Compressed Reference-oriented Alignment Map) for the secure storage of compressed aligned genomic data. Our solution enables selective retrieval of encrypted data and improves the efficiency of downstream analysis (e.g., variant calling). Compared with BAM, the de facto standard for storing aligned genomic data, SECRAM uses 18% less storage. Compared with CRAM, one of the most compressed nonencrypted formats (using 34% less storage than BAM), SECRAM maintains efficient compression and downstream data processing, while allowing for unprecedented levels of security in genomic data storage. Compared with previous work, the distinguishing features of SECRAM are that (1) it is position-based instead of read-based, and (2) it allows random querying of a subregion from a BAM-like file in an encrypted form. Our method thus offers a space-saving, privacy-preserving, and effective solution for the storage of clinical genomic data. © 2016 Huang et al.; Published by Cold Spring Harbor Laboratory Press.

Signal-on electrochemical assay for label-free detection of TdT and BamHI activity based on grown DNA nanowire-templated copper nanoclusters.

PubMed

Hu, Yufang; Zhang, Qingqing; Xu, Lihua; Wang, Jiao; Rao, Jiajia; Guo, Zhiyong; Wang, Sui

2017-11-01

Electrochemical methods allow fast and inexpensive analysis of enzymatic activity. Here, a simple and yet efficient "signal-on" electrochemical assay for sensitive, label-free detection of DNA-related enzyme activity was established on the basis of terminal deoxynucleotidyl transferase (TdT)-mediated extension strategy. TdT, which is a template-independent DNA polymerase, can catalyze the sequential addition of deoxythymidine triphosphate (dTTP) at the 3'-OH terminus of single-stranded DNA (ssDNA); then, the TdT-yield T-rich DNA nanowires can be employed as the synthetic template of copper nanoclusters (CuNCs). Grown DNA nanowires-templated CuNCs (noted as DNA-CuNCs) were attached onto graphene oxide (GO) surface and exhibited unique electrocatalytic activity to H 2 O 2 reduction. Under optimal conditions, the proposed biosensor was utilized for quantitatively monitoring TdT activity, with the observed LOD of 0.1 U/mL. It also displayed high selectivity to TdT with excellent stability, and offered a facile, convenient electrochemical method for TdT-relevant inhibitors screening. Moreover, the proposed sensor was successfully used for BamHI activity detection, in which a new 3'-OH terminal was exposed by the digestion of a phosphate group. Ultimately, it has good prospects in DNA-related enzyme-based biochemical studies, disease diagnosis, and drug discovery. Graphical Abstract Extraordinary TdT-generated DNA-CuNCs are synthesized and act as a novel electrochemical sensing platform for sensitive detection of TdT and BamHI activity in biological environments.

Facilitators and obstacles in pre-hospital medical response to earthquakes: a qualitative study.

PubMed

Djalali, Ahmadreza; Khankeh, Hamidreza; Öhlén, Gunnar; Castrén, Maaret; Kurland, Lisa

2011-05-16

Earthquakes are renowned as being amongst the most dangerous and destructive types of natural disasters. Iran, a developing country in Asia, is prone to earthquakes and is ranked as one of the most vulnerable countries in the world in this respect. The medical response in disasters is accompanied by managerial, logistic, technical, and medical challenges being also the case in the Bam earthquake in Iran. Our objective was to explore the medical response to the Bam earthquake with specific emphasis on pre-hospital medical management during the first days. The study was performed in 2008; an interview based qualitative study using content analysis. We conducted nineteen interviews with experts and managers responsible for responding to the Bam earthquake, including pre-hospital emergency medical services, the Red Crescent, and Universities of Medical Sciences. The selection of participants was determined by using a purposeful sampling method. Sample size was given by data saturation. The pre-hospital medical service was divided into three categories; triage, emergency medical care and transportation, each category in turn was identified into facilitators and obstacles. The obstacles identified were absence of a structured disaster plan, absence of standardized medical teams, and shortage of resources. The army and skilled medical volunteers were identified as facilitators. The most compelling, and at the same time amenable obstacle, was the lack of a disaster management plan. It was evident that implementing a comprehensive plan would not only save lives but decrease suffering and enable an effective praxis of the available resources at pre-hospital and hospital levels.

Facilitators and obstacles in pre-hospital medical response to earthquakes: a qualitative study

PubMed Central

2011-01-01

Background Earthquakes are renowned as being amongst the most dangerous and destructive types of natural disasters. Iran, a developing country in Asia, is prone to earthquakes and is ranked as one of the most vulnerable countries in the world in this respect. The medical response in disasters is accompanied by managerial, logistic, technical, and medical challenges being also the case in the Bam earthquake in Iran. Our objective was to explore the medical response to the Bam earthquake with specific emphasis on pre-hospital medical management during the first days. Methods The study was performed in 2008; an interview based qualitative study using content analysis. We conducted nineteen interviews with experts and managers responsible for responding to the Bam earthquake, including pre-hospital emergency medical services, the Red Crescent, and Universities of Medical Sciences. The selection of participants was determined by using a purposeful sampling method. Sample size was given by data saturation. Results The pre-hospital medical service was divided into three categories; triage, emergency medical care and transportation, each category in turn was identified into facilitators and obstacles. The obstacles identified were absence of a structured disaster plan, absence of standardized medical teams, and shortage of resources. The army and skilled medical volunteers were identified as facilitators. Conclusions The most compelling, and at the same time amenable obstacle, was the lack of a disaster management plan. It was evident that implementing a comprehensive plan would not only save lives but decrease suffering and enable an effective praxis of the available resources at pre-hospital and hospital levels. PMID:21575233

A privacy-preserving solution for compressed storage and selective retrieval of genomic data

PubMed Central

Huang, Zhicong; Ayday, Erman; Lin, Huang; Aiyar, Raeka S.; Molyneaux, Adam; Xu, Zhenyu; Hubaux, Jean-Pierre

2016-01-01

In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients’ complete aligned genomic data in addition to variant calls relative to a reference sequence. Due to the large size of human genome sequence data files (varying from 30 GB to 200 GB depending on coverage), two major challenges facing genomics laboratories are the costs of storage and the efficiency of the initial data processing. In addition, privacy of genomic data is becoming an increasingly serious concern, yet no standard data storage solutions exist that enable compression, encryption, and selective retrieval. Here we present a privacy-preserving solution named SECRAM (Selective retrieval on Encrypted and Compressed Reference-oriented Alignment Map) for the secure storage of compressed aligned genomic data. Our solution enables selective retrieval of encrypted data and improves the efficiency of downstream analysis (e.g., variant calling). Compared with BAM, the de facto standard for storing aligned genomic data, SECRAM uses 18% less storage. Compared with CRAM, one of the most compressed nonencrypted formats (using 34% less storage than BAM), SECRAM maintains efficient compression and downstream data processing, while allowing for unprecedented levels of security in genomic data storage. Compared with previous work, the distinguishing features of SECRAM are that (1) it is position-based instead of read-based, and (2) it allows random querying of a subregion from a BAM-like file in an encrypted form. Our method thus offers a space-saving, privacy-preserving, and effective solution for the storage of clinical genomic data. PMID:27789525

Ultra-hard amorphous AlMgB14 films RF sputtered onto curved substrates

NASA Astrophysics Data System (ADS)

Grishin, A. M.; Putrolaynen, V. V.; Yuzvyuk, M. H.

2017-03-01

Recently, hard AlMgB14 (BAM) coatings were deposited for the first time by RF magnetron sputtering using a single stoichiometric ceramic target. High target sputtering power and sufficiently short target-to-substrate distance were found to be critical processing conditions. They enabled fabrication of stoichiometric in-depth compositionally homogeneous films with the peak values of nanohardness 88 GPa and Young’s modulus 517 GPa at the penetration depth of 26 nm and, respectively, 35 GPa and 275 GPa at 200 nm depth in 2 µm thick film (Grishin et al 2014 JETP Lett. 100 680). The narrow range of sufficiently short target-to-substrate distance makes impossible to coat non flat specimens. To achieve ultimate BAM films’ characteristics onto curved surfaces we developed two-step sputtering process. The first thin layer is deposited as a template at low RF power that facilitates a layered Frank van der Merwe mode growth of smooth film occurs. The next layer is grown at high RF target sputtering power. The affinity of subsequent flow of sputtered atoms to already evenly condensed template fosters the development of smooth film surface. As an example, we made BAM coating onto hemispherical 5 mm in diameter ball made from a hard tool steel and used as a head of a special gauge. Very smooth (6.6 nm RMS surface roughness) and hard AlMgB14 films fabricated onto commercial ball-shaped items enhance hardness of tool steel specimens by a factor of four.

Integrating smoking cessation into substance use disorder treatment for military veterans: measurement and treatment engagement efforts.

PubMed

Shealy, Suzanne E; Winn, Jaime L

2014-02-01

Military personnel and veterans smoke at higher rates than the general population, compromising physical performance readiness and health (Committee on Smoking Cessation in Military and Veteran Populations & Institute of Medicine, 2009). While efforts are being made within both the Department of Defense and the Veterans' Administration (VA) hospitals to prevent onset, change the smoking culture, and promote smoking cessation; smoking rates are increasing among combat deployed service members, and smoking rates are particularly high among veterans with mental health and other substance use disorders (McFall, 2006). Recent research supports making smoking cessation widely available and integrated with other forms of care (Gierisch et al., 2012; McFall et al., 2010). This paper describes the efforts of one VA substance use disorder (SUD) treatment program to integrate smoking cessation in routine care, including assessment of tobacco use and motivation and intention to quit via the proposed Nic-BAM assessment. Our team was 100% successful in incorporating the Nic-BAM into our regular assessment of treatment program participants. This suggests that staff members are amenable to assessing for tobacco addiction alongside other substance addictions. Although smoking did not decrease according to the Nic-BAM, an increase in the use of nicotine-replacement products suggests that participants are willing to initiate a quit attempt during SUD treatment. The availability of new evidence-based approaches for integration of tobacco cessation with mental health and SUD treatment may help to enhance programmatic efforts. Environmental changes are needed to fully incorporate tobacco recovery into SUD programming, and additional resources may include peer support specialists. © 2013.

Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters.

PubMed

Barr, Jeremy J; Auro, Rita; Sam-Soon, Nicholas; Kassegne, Sam; Peters, Gregory; Bonilla, Natasha; Hatay, Mark; Mourtada, Sarah; Bailey, Barbara; Youle, Merry; Felts, Ben; Baljon, Arlette; Nulton, Jim; Salamon, Peter; Rohwer, Forest

2015-11-03

Bacteriophages (phages) defend mucosal surfaces against bacterial infections. However, their complex interactions with their bacterial hosts and with the mucus-covered epithelium remain mostly unexplored. Our previous work demonstrated that T4 phage with Hoc proteins exposed on their capsid adhered to mucin glycoproteins and protected mucus-producing tissue culture cells in vitro. On this basis, we proposed our bacteriophage adherence to mucus (BAM) model of immunity. Here, to test this model, we developed a microfluidic device (chip) that emulates a mucosal surface experiencing constant fluid flow and mucin secretion dynamics. Using mucus-producing human cells and Escherichia coli in the chip, we observed similar accumulation and persistence of mucus-adherent T4 phage and nonadherent T4∆hoc phage in the mucus. Nevertheless, T4 phage reduced bacterial colonization of the epithelium >4,000-fold compared with T4∆hoc phage. This suggests that phage adherence to mucus increases encounters with bacterial hosts by some other mechanism. Phages are traditionally thought to be completely dependent on normal diffusion, driven by random Brownian motion, for host contact. We demonstrated that T4 phage particles displayed subdiffusive motion in mucus, whereas T4∆hoc particles displayed normal diffusion. Experiments and modeling indicate that subdiffusive motion increases phage-host encounters when bacterial concentration is low. By concentrating phages in an optimal mucus zone, subdiffusion increases their host encounters and antimicrobial action. Our revised BAM model proposes that the fundamental mechanism of mucosal immunity is subdiffusion resulting from adherence to mucus. These findings suggest intriguing possibilities for engineering phages to manipulate and personalize the mucosal microbiome.

Rapid Identification of Shiga Toxin-Producing Escherichia coli O Serogroups from Fresh Produce and Raw Milk Enrichment Cultures by Luminex Bead-Based Suspension Array.

PubMed

Kase, Julie A; Maounounen-Laasri, Anna; Lin, Andrew

2016-09-01

The U.S. Food and Drug Administration's Bacteriological Analytical Manual (BAM) Chapter 4a describes a Luminex microbead-based suspension array used to screen colonies for 11 clinically relevant Shiga toxin-producing Escherichia coli (STEC) serogroups: O26, O45, O91, O103, O104, O111, O113, O121, O128, O145, and O157. We evaluated the usefulness of this method to identify STEC-positive enrichment samples before agar plating. Twelve E. coli strains were added to three types of fresh produce (bagged baby spinach, alfalfa sprouts, and cilantro) at levels near the detection limit of the test. A subset of these strains (six O serogroups) was similarly evaluated in raw milk. For comparison, portions of each of the 168 enrichment cultures were analyzed for serogroup by a real-time PCR assay and a Bio-Plex 200 assay with the bead-based suspensions. No false-positive results were obtained. Of the 112 samples with a reported cycle threshold (C T ) value, 101 undiluted, diluted, or extracted enrichment cultures also produced ratios above 5.0 in the Bio-Plex assay. When PCR C T values approached or were greater than 35, Bio-Plex detection became less reliable. Using undiluted or extracted enrichment cultures resulted in a significantly larger number of positive results. With the same enrichment material prepared for real-time PCR analysis as described in the BAM Chapter 4a, the STEC microbead-based suspension array can accurately screen food enrichment cultures.

Randomised clinical trial: colestyramine vs. hydroxypropyl cellulose in patients with functional chronic watery diarrhoea.

PubMed

Fernández-Bañares, F; Rosinach, M; Piqueras, M; Ruiz-Cerulla, A; Modolell, I; Zabana, Y; Guardiola, J; Esteve, M

2015-06-01

Idiopathic bile acid malabsorption (BAM) has been suggested as a cause of chronic watery diarrhoea, with a response to colestyramine in 70% of patients. However, the efficacy of this drug has never been investigated in placebo-controlled trials. To evaluate the efficacy of colestyramine as compared with hydroxypropyl cellulose in the treatment of functional chronic watery diarrhoea. Patients with chronic watery diarrhoea were randomly assigned to groups given colestyramine sachets 4 g twice daily (n = 13) or identical hydroxypropyl cellulose sachets (n = 13) for 8 weeks. The primary end-point was clinical remission defined as a mean of 3 or fewer stools per day during the week before the visit, with less than 1 watery stool per day. A secondary end-point was the reduction in daily watery stool number. SeHCAT test was performed in all patients, but an abnormal test was not a prerequisite to be included. All included patients had a SeHCAT 7-day retention ≤20%. There were no statistical differences in the percentage of patients in clinical remission at week 8 between colestyramine and hydroxypropyl cellulose with either intention-to-treat (53.8% vs. 38.4%; P = 0.43) or per-protocol (63.6% vs. 38.4%; P = 0.22) analyses. However, the mean per cent decrease in watery stool number was significantly higher with colestyramine than with hydroxypropyl cellulose (-92.4 ± 3.5% vs. -75.8 ± 7.1%; P = 0.048). The rate of adverse events related to study drugs did not differ between groups. Colestyramine (4 g twice daily) is effective and safe for short-term treatment of patients with chronic watery diarrhoea presumably secondary to BAM. Clinical Trials Register number EudraCT 2009-011149-14. © 2015 John Wiley & Sons Ltd.

Data-driven discovery of energy materials: efficient BaM2Si3O10 : Eu2+ (M = Sc, Lu) phosphors for application in solid state white lighting.

PubMed

Brgoch, Jakoah; Hasz, Kathryn; Denault, Kristin A; Borg, Christopher K H; Mikhailovsky, Alexander A; Seshadri, Ram

2014-01-01

In developing phosphors for application in solid state lighting, it is advantageous to target structures from databases with highly condensed polyhedral networks that produce rigid host compounds. Rigidity limits channels for non-radiative decay that will decrease the luminescence quantum yield. BaM(2)Si(3)O(10) (M = Sc, Lu) follows this design criterion and is studied here as an efficient Eu(2+)-based phosphor. M = Sc(3+) and Lu(3+) compounds with Eu(2+) substitution were prepared and characterized using synchrotron X-ray powder diffraction and photoluminescence spectroscopy. Substitution with Eu(2+) according to Ba(1-x)Eu(x)Sc(2)Si(3)O(10) and Ba(1-x)Eu(x)Lu(2)Si(3)O(10) results in UV-to-blue and UV-to-blue-green phosphors, respectively. Interestingly, substitution with Eu(2+) in the Lu(3+) containing material produces two emission peaks at low temperature and with 365 nm excitation, as allowed by the two substitution sites. The photoluminescence of the Sc(3+) compound is robust at high temperature, decreasing by only 25% of its room temperature intensity at 503 K, while the Lu-analogue suffers a large drop (75%) from its room temperature intensity. The decrease in emission intensity is explained as stemming from charge transfer quenching due to the short distances separating the luminescent centers on the Lu(3+) substitution site. The correlation between structure and optical response in these two compounds indicates that even though the structures are three-dimensionally connected, high symmetry is required to prevent structural distortions that could impact photoluminescence.

Tissue-engineered human bioartificial muscles expressing a foreign recombinant protein for gene therapy

NASA Technical Reports Server (NTRS)

Powell, C.; Shansky, J.; Del Tatto, M.; Forman, D. E.; Hennessey, J.; Sullivan, K.; Zielinski, B. A.; Vandenburgh, H. H.

1999-01-01

Murine skeletal muscle cells transduced with foreign genes and tissue engineered in vitro into bioartificial muscles (BAMs) are capable of long-term delivery of soluble growth factors when implanted into syngeneic mice (Vandenburgh et al., 1996b). With the goal of developing a therapeutic cell-based protein delivery system for humans, similar genetic tissue-engineering techniques were designed for human skeletal muscle stem cells. Stem cell myoblasts were isolated, cloned, and expanded in vitro from biopsied healthy adult (mean age, 42 +/- 2 years), and elderly congestive heart failure patient (mean age, 76 +/- 1 years) skeletal muscle. Total cell yield varied widely between biopsies (50 to 672 per 100 mg of tissue, N = 10), but was not significantly different between the two patient groups. Percent myoblasts per biopsy (73 +/- 6%), number of myoblast doublings prior to senescence in vitro (37 +/- 2), and myoblast doubling time (27 +/- 1 hr) were also not significantly different between the two patient groups. Fusion kinetics of the myoblasts were similar for the two groups after 20-22 doublings (74 +/- 2% myoblast fusion) when the biopsy samples had been expanded to 1 to 2 billion muscle cells, a number acceptable for human gene therapy use. The myoblasts from the two groups could be equally transduced ex vivo with replication-deficient retroviral expression vectors to secrete 0.5 to 2 microg of a foreign protein (recombinant human growth hormone, rhGH)/10(6) cells/day, and tissue engineered into human BAMs containing parallel arrays of differentiated, postmitotic myofibers. This work suggests that autologous human skeletal myoblasts from a potential patient population can be isolated, genetically modified to secrete foreign proteins, and tissue engineered into implantable living protein secretory devices for therapeutic use.

Cryotherapy Reinvented: Application of Phase Change Material for Recovery in Elite Soccer.

PubMed

Clifford, Tom; Abbott, Will; Kwiecien, Susan Y; Howatson, Glyn; McHugh, Malachy P

2018-05-01

To examine whether donning lower-body garments fitted with cooled phase change material (PCM) would enhance recovery after a soccer match. In a randomized, crossover design, 11 elite soccer players from the reserve squad of a team in the second-highest league in England wore PCM cooled to 15°C (PCM cold ) or left at ambient temperature (PCM amb ; sham control) for 3 h after a soccer match. To assess recovery, countermovement jump height, maximal isometric voluntary contraction (MIVC), muscle soreness, and the adapted Brief Assessment of Mood Questionnaire (BAM+) were measured before 12, 36, and 60 h after each match. A belief questionnaire was completed preintervention and postintervention to determine the perceived effectiveness of each garment. Results are comparisons between the 2 conditions at each time point postmatch. MIVC at 36 h postmatch was greater with PCM cold versus PCM warm (P = .01; ES = 1.59; 95% CI, 3.9-17.1%). MIVC also tended to be higher at 60 h postmatch (P = .05; ES = 0.85; 95% CI, -0.4% to 11.1%). Muscle soreness was 26.5% lower in PCM cold versus PCM warm at 36 h (P = .02; ES = 1.7; 95% CI, -50.4 to -16.1 mm) and 24.3% lower at 60 h (P = .04; ES = 1.1; 95% CI, -26.9 to -0.874 mm). There were no between-conditions differences in postmatch countermovement jump height or BAM+ (P > .05). The belief questionnaire revealed that players felt the PCM cold was more effective than the PCM amb after the intervention (P = .004). PCM cooling garments provide a practical means of delivering prolonged postexercise cooling and thereby accelerate recovery in elite soccer players.

RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy

PubMed Central

Lo, Kitty K.; Boustred, Christopher; Chitty, Lyn S.; Plagnol, Vincent

2014-01-01

Non-invasive prenatal testing (NIPT) of fetal aneuploidy using cell-free fetal DNA is becoming part of routine clinical practice. RAPIDR (Reliable Accurate Prenatal non-Invasive Diagnosis R package) is an easy-to-use open-source R package that implements several published NIPT analysis methods. The input to RAPIDR is a set of sequence alignment files in the BAM format, and the outputs are calls for aneuploidy, including trisomies 13, 18, 21 and monosomy X as well as fetal sex. RAPIDR has been extensively tested with a large sample set as part of the RAPID project in the UK. The package contains quality control steps to make it robust for use in the clinical setting. Availability and implementation: RAPIDR is implemented in R and can be freely downloaded via CRAN from here: http://cran.r-project.org/web/packages/RAPIDR/index.html. Contact: kitty.lo@ucl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24990604

Dinucleotide repeat polymorphisms in waterfowl (family Anatidae): Characterization of a sex-linked (Z-specific) and 14 autosomal loci

USGS Publications Warehouse

Buchholz, W.G.; Pearce, J.M.; Pierson, B.J.; Scribner, K.T.

1998-01-01

Canada goose (Branta Canadensis) and harlequin duck (Histrionicus histrionicus) DNAs were digested with Sau3AI, and size selected (300-700 bp) fragments were ligated into BamHI-digested pBluscriptII KS+. The enrichment protocol of Ostrander et al.1 was followed. The resulting libraries were screened using a [ƴ-32P]ATP end-labelled (CA)20 oligonucleotides as a hybridization probe. Positive clones were sequenced using cycle-sequencing protocols (Epicentre Technologies, Madison, WI) and primers flanking the inserts. PCR primers were designed to amplify the repeat and yield amplification products of ≈100-200 bp. DNA  samples were screened for variation at these loci using [ƴ-32P]ATP end-labelled primers. The products were resolved using 6% denaturing polyacrylamide gels and autoradiography.

Innovative instrumentation for mineralogical and elemental analyses of solid extraterrestrial surfaces: The Backscatter Moessbauer Spectrometer/X Ray Fluorescence analyzer (BaMS/XRF)

NASA Technical Reports Server (NTRS)

Shelfer, T. D.; Morris, Richard V.; Nguyen, T.; Agresti, D. G.; Wills, E. L.

1994-01-01

We have developed a four-detector research-grade backscatter Moessbauer spectrometer (BaMS) instrument with low resolution x-ray fluorescence analysis (XRF) capability. A flight-qualified instrument based on this design would be suitable for use on missions to the surfaces of solid solar-system objects (Moon, Mars, asteroids, etc.). Target specifications for the flight instrument are as follows: mass less than 500 g; volumes less than 300 cu cm; and power less than 2 W. The BaMS/XRF instrument would provide data on the oxidation state of iron and its distribution among iron-bearing mineralogies and elemental composition information. This data is a primary concern for the characterization of extraterrestrial surface materials.

Crew Earth Observations (CEO) taken during Expedition 8

NASA Image and Video Library

2004-02-15

ISS008-E-16328 (15 February 2004) --- A major dust storm in the Kerman Desert, just east of the city of Bam in Southeastern Iran, was featured in this image photographed by an Expedition 8 crewmember onboard the International Space Station (ISS).

A Wavefield Imaging Technique for Delamination Detection in Composite Structures

DTIC Science & Technology

2010-08-01

YANG1, M. P. DESIMIO3, S. E. OLSON3 AND E. D. SWENSON4 Joachim Schneider -Gloetzl, Gloetzl GmbH...Rheinste ten, Germany Rainer Gloetzl, RG Research, Ettling n, Germany Katerina Krebber, Sascha Liehr, Mario Wendt, Aleksander Wosniok, BAM, Federal

Zap! Bam! Flop!

ERIC Educational Resources Information Center

Case, Doug

1976-01-01

Too many teachers have misguided ideas about the principles of the oral approach to teaching EFL. They are either too sure of themselves and of the theory and become complacent, or their confidence is shaken by the failure of a technique they thought to be infallible. (SCC)

Optimal exponential synchronization of general chaotic delayed neural networks: an LMI approach.

PubMed

Liu, Meiqin

2009-09-01

This paper investigates the optimal exponential synchronization problem of general chaotic neural networks with or without time delays by virtue of Lyapunov-Krasovskii stability theory and the linear matrix inequality (LMI) technique. This general model, which is the interconnection of a linear delayed dynamic system and a bounded static nonlinear operator, covers several well-known neural networks, such as Hopfield neural networks, cellular neural networks (CNNs), bidirectional associative memory (BAM) networks, and recurrent multilayer perceptrons (RMLPs) with or without delays. Using the drive-response concept, time-delay feedback controllers are designed to synchronize two identical chaotic neural networks as quickly as possible. The control design equations are shown to be a generalized eigenvalue problem (GEVP) which can be easily solved by various convex optimization algorithms to determine the optimal control law and the optimal exponential synchronization rate. Detailed comparisons with existing results are made and numerical simulations are carried out to demonstrate the effectiveness of the established synchronization laws.

Differentiation of canine distemper virus isolates in fur animals from various vaccine strains by reverse transcription-polymerase chain reaction-restriction fragment length polymorphism according to phylogenetic relations in china

PubMed Central

2011-01-01

In order to effectively identify the vaccine and field strains of Canine distemper virus (CDV), a new differential diagnostic test has been developed based on reverse transcription-polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP). We selected an 829 bp fragment of the nucleoprotein (N) gene of CDV. By RFLP analysis using BamHI, field isolates were distinguishable from the vaccine strains. Two fragments were obtained from the vaccine strains by RT-PCR-RFLP analysis while three were observed in the field strains. An 829 nucleotide region of the CDV N gene was analyzed in 19 CDV field strains isolated from minks, raccoon dogs and foxes in China between 2005 and 2007. The results suggest this method is precise, accurate and efficient. It was also determined that three different genotypes exist in CDV field strains in fur animal herds of the north of China, most of which belong to Asian type. Mutated field strains, JSY06-R1, JSY06-R2 and JDH07-F1 also exist in Northern China, but are most closely related to the standard virulent strain A75/17, designated in Arctic and America-2 genetype in the present study, respectively. PMID:21352564

Performance analysis and comparison of a minimum interconnections direct storage model with traditional neural bidirectional memories.

PubMed

Bhatti, A Aziz

2009-12-01

This study proposes an efficient and improved model of a direct storage bidirectional memory, improved bidirectional associative memory (IBAM), and emphasises the use of nanotechnology for efficient implementation of such large-scale neural network structures at a considerable lower cost reduced complexity, and less area required for implementation. This memory model directly stores the X and Y associated sets of M bipolar binary vectors in the form of (MxN(x)) and (MxN(y)) memory matrices, requires O(N) or about 30% of interconnections with weight strength ranging between +/-1, and is computationally very efficient as compared to sequential, intraconnected and other bidirectional associative memory (BAM) models of outer-product type that require O(N(2)) complex interconnections with weight strength ranging between +/-M. It is shown that it is functionally equivalent to and possesses all attributes of a BAM of outer-product type, and yet it is simple and robust in structure, very large scale integration (VLSI), optical and nanotechnology realisable, modular and expandable neural network bidirectional associative memory model in which the addition or deletion of a pair of vectors does not require changes in the strength of interconnections of the entire memory matrix. The analysis of retrieval process, signal-to-noise ratio, storage capacity and stability of the proposed model as well as of the traditional BAM has been carried out. Constraints on and characteristics of unipolar and bipolar binaries for improved storage and retrieval are discussed. The simulation results show that it has log(e) N times higher storage capacity, superior performance, faster convergence and retrieval time, when compared to traditional sequential and intraconnected bidirectional memories.

Insights about α-tocopherol and Trolox interaction with phosphatidylcholine monolayers under peroxidation conditions through Brewster angle microscopy.

PubMed

Castro, Carla M; Pinheiro, Marina; Lúcio, Marlene; Giner-Casares, Juan J; Camacho, Luis; Lima, José L F C; Reis, Salette; Segundo, Marcela A

2013-11-01

Membranes are major targets to oxidative damage, particularly due to lipid oxidation, which has been associated to aging. The role, efficacy and membrane interaction of antioxidants is still unclear, requiring further understanding of molecular interaction. Hence, the objective of this work was to evaluate the interaction between antioxidants (α-tocopherol and its aqueous soluble analog Trolox) and the monolayer formed by phosphatidylcholine molecules at air/liquid interface upon peroxidation conditions, promoted by peroxyl radicals from thermal decomposition of 2,2'-azobis(2-methylpropionamidine) (AAPH). The interaction with three different monolayers, containing (i) 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine (DPPC), (ii) DDPC+α-linolenic acid, or (iii) egg yolk l-α-phosphatidylcholine (EPC), was ascertain by surface pressure (π)-molecular area (A) isotherms and by monitoring monolayer features through Brewster angle microscopy (BAM). The interaction of antioxidants with DPPC monolayers was confirmed by modifications on DPPC domain shape for α-tocopherol and through the maintenance of typical multilobed domain shape during an extended surface pressure interval for Trolox. Under peroxidation conditions, BAM images showed a clear interaction between components of AAPH subphase with the monolayer through changes on DPPC domain shape and appearance of white dots, located mainly at the frontier between the condensed and expanded liquid phases. White branched structures were also observed whenever both α-linolenic acid and α-tocopherol were present, indicating the segregation of these components within the monolayer, which is highly significant in biological systems. For EPC monolayers, no information from BAM was obtained but π-A isotherms confirmed the existence of the same interactions observed within the other two monolayers. Copyright © 2013 Elsevier B.V. All rights reserved.

Identification and characterization of the tungsten-containing class of benzoyl-coenzyme A reductases

PubMed Central

Kung, Johannes W.; Löffler, Claudia; Dörner, Katerina; Heintz, Dimitri; Gallien, Sébastien; Van Dorsselaer, Alain; Friedrich, Thorsten; Boll, Matthias

2009-01-01

Aromatic compounds are widely distributed in nature and can only be biomineralized by microorganisms. In anaerobic bacteria, benzoyl-CoA (BCoA) is a central intermediate of aromatic degradation, and serves as substrate for dearomatizing BCoA reductases (BCRs). In facultative anaerobes, the mechanistically difficult reduction of BCoA to cyclohexa-1,5-dienoyl-1-carboxyl-CoA (dienoyl-CoA) is driven by a stoichiometric ATP hydrolysis, catalyzed by a soluble, three [4Fe-4S] cluster-containing BCR. In this work, an in vitro assay for BCR from the obligately anaerobic Geobacter metallireducens was established. It followed the reverse reaction, the formation of BCoA from dienoyl-CoA in the presence of various electron acceptors. The benzoate-induced activity was highly specific for dienoyl-CoA (Km = 24 ± 4 μM). The corresponding oxygen-sensitive enzyme was purified by several chromatographic steps with a 115-fold enrichment and a yield of 18%. The 185-kDa enzyme comprised 73- and 20-kDa subunits, suggesting an α2β2-composition. MS analysis revealed the subunits as products of the benzoate-induced bamBC genes. The αβ unit contained 0.9 W, 15 Fe, and 12.5 acid-labile sulfur. Results from EPR spectroscopy suggest the presence of one [3Fe-4S]0/+1 and three [4Fe-4S]+1/+2 clusters per αβ unit; oxidized BamBC exhibited an EPR signal typical for a W(V) species. The FeS clusters and the W- cofactor could only be fully reduced by dienoyl-CoA. BamBC represents the prototype of a previously undescribed class of dearomatizing BCRs that differ completely from the ATP-dependent enzymes from facultative anaerobes. PMID:19815533

Unsupervised Segmentation of Head Tissues from Multi-modal MR Images for EEG Source Localization.

PubMed

Mahmood, Qaiser; Chodorowski, Artur; Mehnert, Andrew; Gellermann, Johanna; Persson, Mikael

2015-08-01

In this paper, we present and evaluate an automatic unsupervised segmentation method, hierarchical segmentation approach (HSA)-Bayesian-based adaptive mean shift (BAMS), for use in the construction of a patient-specific head conductivity model for electroencephalography (EEG) source localization. It is based on a HSA and BAMS for segmenting the tissues from multi-modal magnetic resonance (MR) head images. The evaluation of the proposed method was done both directly in terms of segmentation accuracy and indirectly in terms of source localization accuracy. The direct evaluation was performed relative to a commonly used reference method brain extraction tool (BET)-FMRIB's automated segmentation tool (FAST) and four variants of the HSA using both synthetic data and real data from ten subjects. The synthetic data includes multiple realizations of four different noise levels and several realizations of typical noise with a 20% bias field level. The Dice index and Hausdorff distance were used to measure the segmentation accuracy. The indirect evaluation was performed relative to the reference method BET-FAST using synthetic two-dimensional (2D) multimodal magnetic resonance (MR) data with 3% noise and synthetic EEG (generated for a prescribed source). The source localization accuracy was determined in terms of localization error and relative error of potential. The experimental results demonstrate the efficacy of HSA-BAMS, its robustness to noise and the bias field, and that it provides better segmentation accuracy than the reference method and variants of the HSA. They also show that it leads to a more accurate localization accuracy than the commonly used reference method and suggest that it has potential as a surrogate for expert manual segmentation for the EEG source localization problem.

Effective factors on menstrual health among female students in Bam city: a qualitative study

PubMed Central

Morowatisharifabad, Mohammad Ali; Vaezi, Aliakbar

2018-01-01

Background Menarche is an independent puberty event in a girl’s life, and is associated with physical growth, ability in marriage and fertility. Therefore, poor menstrual health can be a major determinant of morbidity, as well as physical, mental and social problems in this age group. Objective The aim of this study was to explore the effective factors on menstrual health among female students in Bam city. Methods The qualitative study was conducted using content analysis approach in 2017. The participants were 32 individuals consisting of 13 students, 10 mothers of the same students, 9 school associates and health educators of 5 secondary schools in Bam city, who were selected based on an objective-oriented approach. The sampling was done until data saturation. Data collection methods were semi-structured and in-depth interview. Data analysis was performed using the steps suggested by Graneheim and Landman. Results There were two categories (easy interaction and inappropriate adaptation to changes in health behavior), 13 sub-categories and 52 initial codes. The positive factors included easy access to sanitary pads, appropriate school education, easy access to health and therapeutic services and school flexibility on menstrual issues, while the negative factors included inadequate facilities for sanitary pad disposal, lack of access to informed people about menstrual issues, insufficient attention to menstrual problems, feeling ashamed, the high cost of menstrual health, self-medication with traditional medicines, inadequate self-directed education, lack of awareness and trust in health center staff, and following family and teachers in menstrual problems. Conclusion Overall, this study indicated that economic, social, cultural and educational factors affect menstrual health. Therefore, the identification of each of these factors helps planners to apply the most appropriate methods and strategies for menstrual health improvement. PMID:29629053

Pax gene diversity in the basal cnidarian Acropora millepora (Cnidaria, Anthozoa): Implications for the evolution of the Pax gene family

PubMed Central

Miller, David J.; Hayward, David C.; Reece-Hoyes, John S.; Scholten, Ingo; Catmull, Julian; Gehring, Walter J.; Callaerts, Patrick; Larsen, Jill E.; Ball, Eldon E.

2000-01-01

Pax genes encode a family of transcription factors, many of which play key roles in animal embryonic development but whose evolutionary relationships and ancestral functions are unclear. To address these issues, we are characterizing the Pax gene complement of the coral Acropora millepora, an anthozoan cnidarian. As the simplest animals at the tissue level of organization, cnidarians occupy a key position in animal evolution, and the Anthozoa are the basal class within this diverse phylum. We have identified four Pax genes in Acropora: two (Pax-Aam and Pax-Bam) are orthologs of genes identified in other cnidarians; the others (Pax-Cam and Pax-Dam) are unique to Acropora. Pax-Aam may be orthologous with Drosophila Pox neuro, and Pax-Bam clearly belongs to the Pax-2/5/8 class. The Pax-Bam Paired domain binds specifically and preferentially to Pax-2/5/8 binding sites. The recently identified Acropora gene Pax-Dam belongs to the Pax-3/7 class. Clearly, substantial diversification of the Pax family occurred before the Cnidaria/higher Metazoa split. The fourth Acropora Pax gene, Pax-Cam, may correspond to the ancestral vertebrate Pax gene and most closely resembles Pax-6. The expression pattern of Pax-Cam, in putative neurons, is consistent with an ancestral role of the Pax family in neural differentiation and patterning. We have determined the genomic structure of each Acropora Pax gene and show that some splice sites are shared both between the coral genes and between these and Pax genes in triploblastic metazoans. Together, these data support the monophyly of the Pax family and indicate ancient origins of several introns. PMID:10781047

Eddy current testing of composite pressure vessels

NASA Astrophysics Data System (ADS)

Casperson, R.; Pohl, R.; Munzke, D.; Becker, B.; Pelkner, M.

2018-04-01

The use of composite pressure vessels instead of conventional vessels made of steel or aluminum grew strongly over the last decade. The reason for this trend is the tremendous weight saving in the case of composite vessels. However, the long-time behavior is not fully understood for filling and discharging cycles and creep strength and their influence on the CFRP coating (carbon fiber reinforced plastics) and the internal liner (steel, aluminum, or plastics). The CFRP ensures the pressure resistance while the inner liner is used as a container for liquid or gas. To overcome the missing knowledge of aging, BAM started an internal project to investigate degradation of these material systems. Therefore, applicable testing methods like eddy current testing are needed. Normally, high-frequency eddy current testing (HF-ET, f > 10 MHz) is deployed for CFRP due to its low conductivity of the fiber, which is in the order of 0.01 MS/s, and the capacitive coupling between the fibers. Nevertheless, in some cases conventional ET can be applied. We show a concise summary of studies on the application of conventional ET of composite pressure vessels.

Study of structural, electrical, magnetic and optical properties of BaFe12O19 and its modified systems with Ni and Ti

NASA Astrophysics Data System (ADS)

Nayak, Debabrata; Pattanayak, Ranjit; Raut, Subhajit; Panigrahi, Simanchalo

2018-02-01

In this work, BaFe12O19 (BaM) and its modified systems (by substitution of Ni and Ti) have been synthesized by solid-state reaction method. From Rietveld refinement of X-ray diffraction pattern, it is found that volume of unit cell increased slightly in case of modified systems. SEM images provided the information about the microstructure of BaM and its modified systems. The electric, magnetic and optical properties have been carried out with the help of complex impedance spectroscopy, VSM and UV spectrum, respectively. From electrical analysis, it is perceived that Ni-substitution system has shown co-contribution of grain and grain boundary effect due to increases of grain size. The M- H loops are explored that, with substitution of Ni and Ti both M s and H c are decreased. From the variation of band gap ( E g), it is observed that E g has been significantly decreased with substitution (least for Ni-substitution).

Effect of Powder Grain Size on Microstructure and Magnetic Properties of Hexagonal Barium Ferrite Ceramic

NASA Astrophysics Data System (ADS)

Shao, Li-Huan; Shen, Si-Yun; Zheng, Hui; Zheng, Peng; Wu, Qiong; Zheng, Liang

2018-05-01

Compact hexagonal barium ferrite (BaFe12O19, BaM) ceramics with excellent magnetic properties have been prepared from powder with the optimal grain size. The dependence of the microstructure and magnetic properties of the ceramics on powder grain size was studied in detail. Single-phase hexagonal barium ferrite powder with grain size of 177 nm, 256 nm, 327 nm, and 454 nm was obtained by calcination under different conditions. Scanning electron microscopy revealed that 327-nm powder was beneficial for obtaining homogeneous grain size and compact ceramic. In addition, magnetic hysteresis loops and complex permeability spectra demonstrated that the highest saturation magnetization (67.2 emu/g) and real part of the permeability (1.11) at 1 GHz were also obtained using powder with grain size of 327 nm. This relationship between the powder grain size and the properties of the resulting BaM ceramic could be significant for development of microwave devices.

The neuron classification problem

PubMed Central

Bota, Mihail; Swanson, Larry W.

2007-01-01

A systematic account of neuron cell types is a basic prerequisite for determining the vertebrate nervous system global wiring diagram. With comprehensive lineage and phylogenetic information unavailable, a general ontology based on structure-function taxonomy is proposed and implemented in a knowledge management system, and a prototype analysis of select regions (including retina, cerebellum, and hypothalamus) presented. The supporting Brain Architecture Knowledge Management System (BAMS) Neuron ontology is online and its user interface allows queries about terms and their definitions, classification criteria based on the original literature and “Petilla Convention” guidelines, hierarchies, and relations—with annotations documenting each ontology entry. Combined with three BAMS modules for neural regions, connections between regions and neuron types, and molecules, the Neuron ontology provides a general framework for physical descriptions and computational modeling of neural systems. The knowledge management system interacts with other web resources, is accessible in both XML and RDF/OWL, is extendible to the whole body, and awaits large-scale data population requiring community participation for timely implementation. PMID:17582506

An investigation into the socioeconomic aspects of two major earthquakes in Iran.

PubMed

Amini Hosseini, Kambod; Hosseinioon, Solmaz; Pooyan, Zhila

2013-07-01

An evaluation of the socioeconomic consequences of earthquakes is an essential part of the development of risk reduction and disaster management plans. However, these variables are not normally addressed sufficiently after strong earthquakes; researchers and relevant stakeholders focus primarily on the physical damage and casualties. The importance of the socioeconomic consequences of seismic events became clearer in Iran after the Bam earthquake on 26 December 2003, as demonstrated by the formulation and approval of various laws and ordinances. This paper reviews the country's regulatory framework in the light of the socioeconomic aspects of two major and destructive earthquakes: in Manjil-Rudbar in 1990, and in Bam in 2003. The results take the form of recommendations and practical strategies for incorporating the socioeconomic dimensions of earthquakes in disaster risk management planning. The results presented here can be applied in other countries with similar conditions to those of Iran in order to improve public preparedness and risk reduction. © 2013 The Author(s). Journal compilation © Overseas Development Institute, 2013.

An insight into the isolation, enumeration, and molecular detection of Listeria monocytogenes in food

PubMed Central

Law, Jodi Woan-Fei; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan; Lee, Learn-Han

2015-01-01

Listeria monocytogenes, a foodborne pathogen that can cause listeriosis through the consumption of food contaminated with this pathogen. The ability of L. monocytogenes to survive in extreme conditions and cause food contaminations have become a major concern. Hence, routine microbiological food testing is necessary to prevent food contamination and outbreaks of foodborne illness. This review provides insight into the methods for cultural detection, enumeration, and molecular identification of L. monocytogenes in various food samples. There are a number of enrichment and plating media that can be used for the isolation of L. monocytogenes from food samples. Enrichment media such as buffered Listeria enrichment broth, Fraser broth, and University of Vermont Medium (UVM) Listeria enrichment broth are recommended by regulatory agencies such as Food and Drug Administration-bacteriological and analytical method (FDA-BAM), US Department of Agriculture-Food and Safety (USDA-FSIS), and International Organization for Standardization (ISO). Many plating media are available for the isolation of L. monocytogenes, for instance, polymyxin acriflavin lithium-chloride ceftazidime aesculin mannitol, Oxford, and other chromogenic media. Besides, reference methods like FDA-BAM, ISO 11290 method, and USDA-FSIS method are usually applied for the cultural detection or enumeration of L. monocytogenes. most probable number technique is applied for the enumeration of L. monocytogenes in the case of low level contamination. Molecular methods including polymerase chain reaction, multiplex polymerase chain reaction, real-time/quantitative polymerase chain reaction, nucleic acid sequence-based amplification, loop-mediated isothermal amplification, DNA microarray, and next generation sequencing technology for the detection and identification of L. monocytogenes are discussed in this review. Overall, molecular methods are rapid, sensitive, specific, time- and labor-saving. In future, there are chances for the development of new techniques for the detection and identification of foodborne with improved features. PMID:26579116

Porphyromonas endodontalis reactivates latent Epstein-Barr virus.

PubMed

Makino, K; Takeichi, O; Imai, K; Inoue, H; Hatori, K; Himi, K; Saito, I; Ochiai, K; Ogiso, B

2018-06-01

To determine whether Porphyromonas endodontalis can reactivate latent Epstein-Barr virus (EBV). The concentrations of short-chain fatty acids (SCFAs) in P. endodontalis culture supernatants were determined using high-performance liquid chromatography. A promoter region of BamHI fragment Z leftward open reading frame 1 (BZLF-1), which is a transcription factor that controls the EBV lytic cycle, was cloned into luciferase expression vectors. Then, the luciferase assay was performed using P. endodontalis culture supernatants. Histone acetylation using Daudi cells treated with P. endodontalis culture supernatants was examined using Western blotting. BZLF-1 mRNA and BamHI fragment Z EB replication activator (ZEBRA) protein were also detected quantitatively using real-time polymerase chain reaction (PCR) and Western blotting. Surgically removed periapical granulomas were examined to detect P. endodontalis, EBV DNA, and BZLF-1 mRNA expression using quantitative real-time PCR. Statistical analysis using Steel tests was performed. The concentrations of n-butyric acid in P. endodontalis culture supernatants were significantly higher than those of other SCFAs (P=0.0173). Using B-95-8-221 Luc cells treated with P. endodontalis culture supernatants, the luciferase assay demonstrated that P. endodontalis induced BZLF-1 expression. Hyperacetylation of histones was also observed with the culture supernatants. BZLF-1 mRNA and ZEBRA protein were expressed by Daudi cells in a dose-dependent manner after the treatment with P. endodontalis culture supernatants. P. endodontalis and BZLF-1 in periapical granulomas were also detected. The expression levels of BZLF-1 mRNA were similar to the numbers of P. endodontalis cells in each specimen. n-butyric acid produced by P. endodontalis reactivated latent EBV. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

An insight into the isolation, enumeration, and molecular detection of Listeria monocytogenes in food.

PubMed

Law, Jodi Woan-Fei; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan; Lee, Learn-Han

2015-01-01

Listeria monocytogenes, a foodborne pathogen that can cause listeriosis through the consumption of food contaminated with this pathogen. The ability of L. monocytogenes to survive in extreme conditions and cause food contaminations have become a major concern. Hence, routine microbiological food testing is necessary to prevent food contamination and outbreaks of foodborne illness. This review provides insight into the methods for cultural detection, enumeration, and molecular identification of L. monocytogenes in various food samples. There are a number of enrichment and plating media that can be used for the isolation of L. monocytogenes from food samples. Enrichment media such as buffered Listeria enrichment broth, Fraser broth, and University of Vermont Medium (UVM) Listeria enrichment broth are recommended by regulatory agencies such as Food and Drug Administration-bacteriological and analytical method (FDA-BAM), US Department of Agriculture-Food and Safety (USDA-FSIS), and International Organization for Standardization (ISO). Many plating media are available for the isolation of L. monocytogenes, for instance, polymyxin acriflavin lithium-chloride ceftazidime aesculin mannitol, Oxford, and other chromogenic media. Besides, reference methods like FDA-BAM, ISO 11290 method, and USDA-FSIS method are usually applied for the cultural detection or enumeration of L. monocytogenes. most probable number technique is applied for the enumeration of L. monocytogenes in the case of low level contamination. Molecular methods including polymerase chain reaction, multiplex polymerase chain reaction, real-time/quantitative polymerase chain reaction, nucleic acid sequence-based amplification, loop-mediated isothermal amplification, DNA microarray, and next generation sequencing technology for the detection and identification of L. monocytogenes are discussed in this review. Overall, molecular methods are rapid, sensitive, specific, time- and labor-saving. In future, there are chances for the development of new techniques for the detection and identification of foodborne with improved features.

Effect of sample preparation and preenrichment media on the recovery of Salmonella from cantaloupes, mangoes, and tomatoes.

PubMed

Hammack, Thomas S; Johnson, Mildred L; Jacobson, Andrew P; Andrews, Wallace H

2006-01-01

Studies were conducted to determine the relative effectiveness of buffered peptone water (BPW), lactose (LAC) broth, and Universal Preenrichment (UP) broth for the recovery of Salmonella organisms from fruit rinses, whole fruit, and comminuted fruit. In the first phase, the relative effectiveness of the rinse and soak methods for the recovery of Salmonella from surface-contaminated mangoes and tomatoes was examined. Fruits were spot inoculated with single Salmonella serovars and held for 4 days at 2-6 degrees C before analysis was initiated. The contaminated fruit was rinsed in portions of BPW, LAC broth, or UP broth. Portions from each rinse were added to its respective broth (e.g., BPW to BPW). Individual whole fruit, in their remaining broth rinses (soak method), and the fruit rinse/broths (rinse method) were incubated for 24 h at 35 degrees C. The Bacteriological Analytical Manual (BAM) Salmonella culture method was followed thereafter. The soak method produced significantly greater numbers (P < 0.05) of positive test portions than did the rinse method for the analysis of mangoes (93 versus 12) and tomatoes (85 versus 34). The 3 broths were comparable for the recovery of Salmonella for both the soak and the rinse methods for mangoes. For tomatoes, there were no significant differences among the broths for the soak method, but BPW and UP broth were significantly more productive (P < 0.05) than LAC broth by the rinse method. In the second phase, the relative effectiveness of LAC broth, BPW, and UP broth for the recovery of Salmonella from comminuted fruit was examined. Fruits were contaminated with single Salmonella serovars and aged for 4 days at 2-6 degrees C. Twenty 25 g test portions were preenriched in each of the following broths: BPW, LAC broth, and UP broth. The BAM Salmonella culture method was followed thereafter. For cantaloupes, significantly more (P < 0.05) Salmonella-positive test portions were recovered with UP broth (96 Salmonella-positive test portions) and BPW (87 Salmonella-positive test portions) than with LAC broth (57 Salmonella-positive test portions). For mangoes, BPW recovered an arithmetically larger number of Salmonella-positive test portions (27 Salmonella-positive test portions) than did either LAC broth (14 Salmonella-positive test portions) or UP broth (18 Salmonella-positive test portions). For tomatoes, there were no significant differences among the broths: BPW recovered 65 Salmonella-positive test portions, UP broth recovered 62 Salmonella-positive test portions, and LAC broth recovered 60 Salmonella-positive test portions. For the analysis of whole fruit, it is recommended that the soak method be used. For whole fruit analyzed with the soak method, UP broth should be used for tomatoes and BPW should be used for mangoes. It is further recommended that UP broth be used for the analysis of comminuted cantaloupes and that BPW be used for the analysis of comminuted mangoes and tomatoes.

77 FR 54927 - Comment Request for Information Collection for Unemployment Insurance (UI) Benefit Accuracy...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-06

... Collection for Unemployment Insurance (UI) Benefit Accuracy Measurement (BAM), Extension Without Revisions... Andrew Spisak, Office of Unemployment Insurance, Room S-4524, Employment and Training Administration, U.S... payments in three programs: State UI, Unemployment Compensation for Federal Employees (UCFE), and...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sandstrom, Mary M.; Brown, Geoffrey W.; Preston, Daniel N.

The Integrated Data Collection Analysis (IDCA) program is conducting a proficiency study for Small- Scale Safety and Thermal (SSST) testing of homemade explosives (HMEs). Described here are the results for impact, friction, electrostatic discharge, and differential scanning calorimetry analysis of PETN Class 4. The PETN was found to have: 1) an impact sensitivity (DH 50) range of 6 to 12 cm, 2) a BAM friction sensitivity (F 50) range 7 to 11 kg, TIL (0/10) of 3.7 to 7.2 kg, 3) a ABL friction sensitivity threshold of 5 or less psig at 8 fps, 4) an ABL ESD sensitivity thresholdmore » of 0.031 to 0.326 j/g, and 5) a thermal sensitivity of an endothermic feature with T min = ~ 141 °C, and a exothermic feature with a T max = ~205°C.« less

Temporal trend in dementia incidence since 2002 and projections for prevalence in England and Wales to 2040: modelling study

PubMed Central

Guzman-Castillo, Maria; Bandosz, Piotr; Shipley, Martin J; Muniz-Terrera, Graciela; Singh-Manoux, Archana; Kivimäki, Mika; Steptoe, Andrew; Capewell, Simon; O’Flaherty, Martin; Brunner, Eric J

2017-01-01

Objective To forecast dementia prevalence with a dynamic modelling approach that integrates calendar trends in dementia incidence with those for mortality and cardiovascular disease. Design Modelling study. Setting General adult population of England and Wales. Participants The English Longitudinal Study of Ageing (ELSA) is a representative panel study with six waves of data across 2002-13. Men and women aged 50 or more years, selected randomly, and their cohabiting partners were recruited to the first wave of ELSA (2002-03). 11392 adults participated (response rate 67%). To maintain representativeness, refreshment participants were recruited to the study at subsequent waves. The total analytical sample constituted 17 906 people. Constant objective criteria based on cognitive and functional impairment were used to ascertain dementia cases at each wave. Main outcome measures To estimate calendar trends in dementia incidence, correcting for bias due to loss to follow-up of study participants, a joint model of longitudinal and time-to-event data was fitted to ELSA data. To forecast future dementia prevalence, the probabilistic Markov model IMPACT-BAM (IMPACT-Better Ageing Model) was developed. IMPACT-BAM models transitions of the population aged 35 or more years through states of cardiovascular disease, cognitive and functional impairment, and dementia, to death. It enables prediction of dementia prevalence while accounting for the growing pool of susceptible people as a result of increased life expectancy and the competing effects due to changes in mortality, and incidence of cardiovascular disease. Results In ELSA, dementia incidence was estimated at 14.3 per 1000 person years in men and 17.0/1000 person years in women aged 50 or more in 2010. Dementia incidence declined at a relative rate of 2.7% (95% confidence interval 2.4% to 2.9%) for each year during 2002-13. Using IMPACT-BAM, we estimated there were approximately 767 000 (95% uncertainty interval 735 000 to 797 000) people with dementia in England and Wales in 2016. Despite the decrease in incidence and age specific prevalence, the number of people with dementia is projected to increase to 872 000, 1 092 000, and 1 205 000 in 2020, 2030, and 2040, respectively. A sensitivity analysis without the incidence decline gave a much larger projected growth, of more than 1.9 million people with dementia in 2040. Conclusions Age specific dementia incidence is declining. The number of people with dementia in England and Wales is likely to increase by 57% from 2016 to 2040. This increase is mainly driven by improved life expectancy. PMID:28679494

Randomised vaccine trial of single dose of killed Leishmania major plus BCG against anthroponotic cutaneous leishmaniasis in Bam, Iran.

PubMed

Sharifi, I; FeKri, A R; Aflatonian, M R; Khamesipour, A; Nadim, A; Mousavi, M R; Momeni, A Z; Dowlati, Y; Godal, T; Zicker, F; Smith, P G; Modabber, F

1998-05-23

A vaccine consisting of a single dose of whole-cell autoclave-killed Leishmania major (ALM) mixed with BCG was assessed in comparison with BCG alone against anthroponotic (human to human transmission) cutaneous leishmaniasis in a randomised double-blind trial in Bam, Iran. 3637 schoolchildren, aged 6-15 years, with no history of cutaneous leishmaniasis and no response to a leishmanin skin test, were randomly assigned to receive 1 mg ALM mixed with BCG (n = 1839), or BCG alone (n = 1798). Safety of the vaccine and the incidence of confirmed cases of cutaneous leishmaniasis were followed up for 2 years. Side-effects were those usually associated with BCG vaccination, but tended to persist longer in the ALM + BCG group. After exclusion of four cases occurring within 80 days of vaccination (one in the ALM + BCG group and three in the BCG group), the 2-year incidence of cutaneous leishmaniasis did not differ significantly between vaccine and BCG groups: 2.8% vs 3.3%, respectively (total cases 112). A sex-stratified analysis showed that in boys the vaccine conferred a protective efficacy of 18% and 78% for the first and second years, respectively--a crude 2-year overall protection of 55% (95% CI 19-75%, p < 0.01). In the first 9 months after vaccination, there was a non-significant excess of cases in the ALM + BCG group (25 vs 16), whereas the incidence of cutaneous leishmaniasis thereafter was significantly reduced in the ALM + BCG group (27 vs 44, p < 0.05). A single dose of ALM + BCG was safe and more immunogenic than BCG alone, as measured by leishmanin skin test. The exact reason for the apparent protective effect of the vaccine in boys is unknown, and may be a chance finding. However, since boys are more exposed to the infection, which is indicated by higher disease prevalence in boys in this study population, the preferential protective effect in boys may have resulted from a greater booster effect produced by repeated exposure to infected sandflies. Booster injections or alternative adjuvants should be tried to improve the potential efficacy of this vaccine.

Recycling rate of bile acids in the enterohepatic recirculation as a major determinant of whole body 75SeHCAT retention.

PubMed

Peters, A Michael; Walters, Julian R F

2013-10-01

Measurement of the whole body retention of orally administered (75)SeHCAT is used to investigate patients with unexplained diarrhoea. Retention values of <15 % at 7 days post-administration are taken to indicate bile acid malabsorption (BAM). Whilst idiopathic BAM is frequently diagnosed with (75)SeHCAT, functional and morphological studies of the terminal ileum rarely show any abnormality, so the disorder may be more appropriately termed bile acid diarrhoea (BAD). In addition to malabsorption, excess bile acid may reach the colon, where the events leading to diarrhoea take place, as a result firstly of increased bile acid synthesis and secondly of an increased recycling rate of bile acids. Increased recycling has been largely ignored as a cause of BAD, but, as shown in this study, can readily result in excess bile acids reaching the colon even when ileal absorption efficiency is normal (i.e. 95-97 %). There needs to be a re-evaluation of the causes of BAD in patients without a history of previous intestinal resection or evidence of ileal pathology, such as Crohn's disease.

Synthesis and photoluminescence properties of a cyan-emitting phosphor Ca3(PO4)2:Eu2+ for white light-emitting diodes

NASA Astrophysics Data System (ADS)

Zhou, Wenli; Han, Jin; Zhang, Xuejie; Qiu, Zhongxian; Xie, Qingji; Liang, Hongbin; Lian, Shixun; Wang, Jing

2015-01-01

In this paper, a cyan-emitting phosphor Ca3(PO4)2:Eu2+ (TCP:Eu2+) was synthesized and evaluated as a candidate for white light emitting diodes (WLEDs). This phosphor shows strong and broad absorption in 250-450 nm region, but the emission spectrum is prominent at around 480 nm. The emission intensity of the TCP:Eu2+ was found to be 60% and 82% of that of the commercial BaMgAl10O17:Eu2+ (BAM) under excitation at 340 nm and 370 nm, respectively. Upon excitation at 370 nm, the absolute internal and external quantum efficiencies of the Ca3(PO4)2:1.5%Eu2+ are 60% and 42%, respectively. Moreover, a white LED lamp was fabricated by coating TCP:Eu2+ with a blue-emitting BAM and a red-emitting CaAlSiN3:Eu2+ on a near-ultraviolet (375 nm) LED chip, driven by a 350 mA forward bias current, and it produces an intense white light with a color rendering index of 75.

svviz: a read viewer for validating structural variants.

PubMed

Spies, Noah; Zook, Justin M; Salit, Marc; Sidow, Arend

2015-12-15

Visualizing read alignments is the most effective way to validate candidate structural variants (SVs) with existing data. We present svviz, a sequencing read visualizer for SVs that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads, realigning them against the inferred sequence of the putative variant allele as well as the reference allele and identifying reads that match one allele better than the other. Separate views of the two alleles are then displayed in a scrollable web browser view, enabling a more intuitive visualization of each allele, compared with the single reference genome-based view common to most current read browsers. The browser view facilitates examining the evidence for or against a putative variant, estimating zygosity, visualizing affected genomic annotations and manual refinement of breakpoints. svviz supports data from most modern sequencing platforms. svviz is implemented in python and freely available from http://svviz.github.io/. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

Modification of structure and pattern of lipid monolayer on water and solid surfaces in presence of globular protein

NASA Astrophysics Data System (ADS)

Sah, Bijay Kumar; Kundu, Sarathi

2017-05-01

Langmuir monolayers of phospholipids at the air-water interface are well-established model systems for mimicking biological membranes and hence are useful for studying lipid-protein interactions. In the present work, phases and phase transformations occurring in the lipid (DMPA) monolayer in the presence of globular protein (BSA) at neutral subphase pH (≈7.0) are highlighted and the corresponding in-plane pattern and morphology are explored from the surface pressure (π) - specific molecular area (A) isotherm, Brewster angle microscopy (BAM) and atomic force microscopy (AFM) both at air-water and air-solid interfaces. Films of pure lipid and lipid-protein complexes are deposited on solid surfaces by Langmuir-Blodgett method. Due to the presence of BSA molecules, phases and domain pattern changes in comparison with that of the pure DMPA. Moreover, accumulations of globular proteins in between lipid domains are also visible through BAM. AFM shows that the mixed film has relatively bigger globular-like morphology in comparison with that of pure DMPA domains. Combination of electrostatic and hydrophobic interactions between protein and lipid are responsible for such modifications.

Epitaxial growth of 100-μm thick M-type hexaferrite crystals on wide bandgap semiconductor GaN/Al{sub 2}O{sub 3} substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Bolin; Su, Zhijuan; Bennett, Steve

2014-05-07

Thick barium hexaferrite BaFe{sub 12}O{sub 19} (BaM) films having thicknesses of ∼100 μm were epitaxially grown on GaN/Al{sub 2}O{sub 3} substrates from a molten-salt solution by vaporizing the solvent. X-ray diffraction measurement verified the growth of BaM (001) textured growth of thick films. Saturation magnetization, 4πM{sub s}, was measured for as-grown films to be 4.6 ± 0.2 kG and ferromagnetic resonance measurements revealed a microwave linewidth of ∼100 Oe at X-band. Scanning electron microscopy indicated clear hexagonal crystals distributed on the semiconductor substrate. These results demonstrate feasibility of growing M-type hexaferrite crystal films on wide bandgap semiconductor substrates by using a simplemore » powder melting method. It also presents a potential pathway for the integration of ferrite microwave passive devices with active semiconductor circuit elements creating system-on-a-wafer architectures.« less

Mechanisms of Molecular Mimicry of Plant CLE Peptide Ligands by the Parasitic Nematode Globodera rostochiensis1[C][W

PubMed Central

Guo, Yongfeng; Ni, Jun; Denver, Robert; Wang, Xiaohong; Clark, Steven E.

2011-01-01

Nematodes that parasitize plant roots cause huge economic losses and have few mechanisms for control. Many parasitic nematodes infect plants by reprogramming root development to drive the formation of feeding structures. How nematodes take control of plant development is largely unknown. Here, we identify two host factors involved in the function of a receptor ligand mimic, GrCLE1, secreted by the potato cyst nematode Globodera rostochiensis. GrCLE1 is correctly processed to an active form by host plant proteases. Processed GrCLE1 peptides bind directly to the plant CLE receptors CLV2, BAM1, and BAM2. Involvement of these receptors in the ligand-mimicking process is also supported by the fact that the ability of GrCLE1 peptides to alter plant root development in Arabidopsis (Arabidopsis thaliana) is dependent on these receptors. Critically, we also demonstrate that GrCLE1 maturation can be entirely carried out by plant factors and that the availability of CLE processing activity may be essential for successful ligand mimicry. PMID:21750229

Pathobiologic Roles of Epstein–Barr Virus-Encoded MicroRNAs in Human Lymphomas

PubMed Central

Navari, Mohsen; Etebari, Maryam; Ibrahimi, Mostafa; Leoncini, Lorenzo

2018-01-01

Epstein–Barr virus (EBV) is a human γ-herpesvirus implicated in several human malignancies, including a wide range of lymphomas. Several molecules encoded by EBV in its latent state are believed to be related to EBV-induced lymphomagenesis, among which microRNAs—small RNAs with a posttranscriptional regulating role—are of great importance. The genome of EBV encodes 44 mature microRNAs belonging to two different classes, including BamHI-A rightward transcript (BART) and Bam HI fragment H rightward open reading frame 1 (BHRF1), with different expression levels in different EBV latency types. These microRNAs might contribute to the pathogenetic effects exerted by EBV through targeting self mRNAs and host mRNAs and interfering with several important cellular mechanisms such as immunosurveillance, cell proliferation, and apoptosis. In addition, EBV microRNAs can regulate the surrounding microenvironment of the infected cells through exosomal transportation. Moreover, these small molecules could be potentially used as molecular markers. In this review, we try to present an updated and extensive view of the role of EBV-encoded miRNAs in human lymphomas. PMID:29649101

Mechanisms of molecular mimicry of plant CLE peptide ligands by the parasitic nematode Globodera rostochiensis.

PubMed

Guo, Yongfeng; Ni, Jun; Denver, Robert; Wang, Xiaohong; Clark, Steven E

2011-09-01

Nematodes that parasitize plant roots cause huge economic losses and have few mechanisms for control. Many parasitic nematodes infect plants by reprogramming root development to drive the formation of feeding structures. How nematodes take control of plant development is largely unknown. Here, we identify two host factors involved in the function of a receptor ligand mimic, GrCLE1, secreted by the potato cyst nematode Globodera rostochiensis. GrCLE1 is correctly processed to an active form by host plant proteases. Processed GrCLE1 peptides bind directly to the plant CLE receptors CLV2, BAM1, and BAM2. Involvement of these receptors in the ligand-mimicking process is also supported by the fact that the ability of GrCLE1 peptides to alter plant root development in Arabidopsis (Arabidopsis thaliana) is dependent on these receptors. Critically, we also demonstrate that GrCLE1 maturation can be entirely carried out by plant factors and that the availability of CLE processing activity may be essential for successful ligand mimicry.

Determination of psychostimulants and their metabolites by electrochemistry linked on-line to flowing atmospheric pressure afterglow mass spectrometry.

PubMed

Smoluch, Marek; Mielczarek, Przemyslaw; Reszke, Edward; Hieftje, Gary M; Silberring, Jerzy

2014-09-07

The flowing atmospheric pressure afterglow (FAPA) ion source operates in the ambient atmosphere and has been proven to be a promising tool for direct and rapid determination of numerous compounds. Here we linked a FAPA-MS system to an electrochemical flow cell for the identification of drug metabolites generated electrochemically in order to study simulated metabolic pathways. Psychostimulants and their metabolites produced by electrochemistry (EC) were detected on-line by FAPA-MS. The FAPA source has never been used before for an on-line connection with liquid flow, neither for identification of products generated in an electrochemical flow cell. The system was optimized to achieve the highest ionization efficiency by adjusting several parameters, including distances and angles between the ion source and the outlet of the EC system, the high voltage for plasma generation, flow-rates, and EC parameters. Simulated metabolites from tested compounds [methamphetamine (MAF), para-methoxy-N-methylamphetamine (PMMA), dextromethorphan (DXM), and benzydamine (BAM)] were formed in the EC cell at various pH levels. In all cases the main products were oxidized substrates and compounds after N-demethylation. Generation of such products and their thorough on-line identification confirm that the cytochrome P450 - driven metabolism of pharmaceuticals can be efficiently simulated in an electrochemical cell; this approach may serve as a step towards predictive pharmacology using a fast and robust design.

Development of a real-time PCR assay for rapid detection and quantification of Photobacterium damselae subsp. piscicida in fish tissues.

PubMed

Carraro, R; Dalla Rovere, G; Ferraresso, S; Carraro, L; Franch, R; Toffan, A; Pascoli, F; Patarnello, T; Bargelloni, L

2018-02-01

The availability of a rapid and accurate method for the diagnosis of Photobacterium damselae subsp. piscicida (Phdp), able to discriminate its strictly correlated subsp. damselae (Phdd), formally known as Vibrio damsela, is essential for managing fish pasteurellosis outbreaks in farmed fish. A single-step, high-sensitivity real-time PCR assay for simultaneous detection and quantification of P. damselae was designed targeting partial of the sequence of the bamB gene and tested for specificity and sensitivity on laboratory-generated samples as well as on experimentally infected seabream tissue samples. With a limit of detection (LOD) of one copy in pure bacterial DNA, the sensitivity was higher than all methods previously reported. Validation in target and non-target bacterial species proved the assay was able to discriminate Phdd-Phdp subspecies from diverse hosts/geographical origins and between non-target species. In addition, two SNPs in the target amplicon region determine two distinctive qPCR dissociation curves distinguishing between Phdp-Phdd. This is the first time that a molecular method for P. damselae diagnosis combines detection, quantification and subspecies identification in one step. The assay holds the potential to improve the knowledge of infection dynamics and the development of better strategies to control an important fish disease. © 2017 John Wiley & Sons Ltd.

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

PubMed

Samadian, Soroush; Bruce, Jeff P; Pugh, Trevor J

2018-03-01

Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format), lists of non-overlapping genome coordinates for introduction of gains and losses (bed file), and an optional file defining known haplotypes (vcf format). To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total). To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01%) while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

Mineralogical Controls over Carbon Storage and Residence Times in Grassland Soils

NASA Astrophysics Data System (ADS)

Dwivedi, D.; Riley, W. J.; Torn, M. S.; Spycher, N.

2014-12-01

Globally, soil organic matter (SOM) contains approximately three times more carbon than the atmosphere and terrestrial vegetation contain combined. However, it is not well understood why some SOM persists for a long time while other SOM decomposes quickly. For future climate predictions, representing soil organic matter (SOM) dynamics accurately in Earth system models is essential. Soil minerals stabilize organic carbon in soil; however, there are gaps in our understanding of how soil mineralogy controls the quantity and turnover of long-residence-time organic carbon. To investigate the impact of soil mineralogy on SOM dynamics, we used a new model (Biotic and Abiotic Model of SOM—BAMS1 [Riley et al., 2014]) integrated with a three-dimensional, multiphase reactive transport solver (TOUGHREACT). The model represents bacterial and fungal activity, archetypal polymer and monomer carbon substrate groups, aqueous chemistry, gaseous diffusion, aqueous advection and diffusion, and adsorption and desorption processes. BAMS1 can predict bulk SOM and radiocarbon signatures without resorting to an arbitrary depth-dependent decline in SOM turnover rates. Results show a reasonable match between observed and simulated depth-resolved SOM and Δ14C in grassland ecosystems (soils formed on terraces south of Eureka, California, and the Central Chernozem Region of Russia) and were consistent with expectations of depth-resolved profiles of lignin content and fungi:aerobic bacteria ratios. Results also suggest that clay-mineral surface area and soil sorption coefficients constitute dominant controls over organic carbon stocks and residence times, respectively. Bibliography: Riley, W.J., F.M. Maggi, M. Kleber, M.S. Torn, J.Y. Tang, D. Dwivedi, and N. Guerry (2014), Long residence times of rapidly decomposable soil organic matter: application of a multi-phase, multi-component, and vertically resolved model (BAMS1) to soil carbon dynamics, Geoscientific Model Development, vol. 7, 1335-2014, doi:10.5194/gmd-7-1335-2014.

Genetic and isotope ratio mass spectrometric evidence for the occurrence of starch degradation and cycling in illuminated Arabidopsis leaves

PubMed Central

Baslam, Marouane; Baroja-Fernández, Edurne; Ricarte-Bermejo, Adriana; Sánchez-López, Ángela María; Aranjuelo, Iker; Bahaji, Abdellatif; Muñoz, Francisco José; Almagro, Goizeder; Pujol, Pablo; Galarza, Regina; Teixidor, Pilar; Pozueta-Romero, Javier

2017-01-01

Although there is a great wealth of data supporting the occurrence of simultaneous synthesis and breakdown of storage carbohydrate in many organisms, previous 13CO2 pulse-chase based studies indicated that starch degradation does not operate in illuminated Arabidopsis leaves. Here we show that leaves of gwd, sex4, bam4, bam1/bam3 and amy3/isa3/lda starch breakdown mutants accumulate higher levels of starch than wild type (WT) leaves when cultured under continuous light (CL) conditions. We also show that leaves of CL grown dpe1 plants impaired in the plastidic disproportionating enzyme accumulate higher levels of maltotriose than WT leaves, the overall data providing evidence for the occurrence of extensive starch degradation in illuminated leaves. Moreover, we show that leaves of CL grown mex1/pglct plants impaired in the chloroplastic maltose and glucose transporters display a severe dwarf phenotype and accumulate high levels of maltose, strongly indicating that the MEX1 and pGlcT transporters are involved in the export of starch breakdown products to the cytosol to support growth during illumination. To investigate whether starch breakdown products can be recycled back to starch during illumination through a mechanism involving ADP-glucose pyrophosphorylase (AGP) we conducted kinetic analyses of the stable isotope carbon composition (δ13C) in starch of leaves of 13CO2 pulsed-chased WT and AGP lacking aps1 plants. Notably, the rate of increase of δ13C in starch of aps1 leaves during the pulse was exceedingly higher than that of WT leaves. Furthermore, δ13C decline in starch of aps1 leaves during the chase was much faster than that of WT leaves, which provides strong evidence for the occurrence of AGP-mediated cycling of starch breakdown products in illuminated Arabidopsis leaves. PMID:28152100

The Epstein-Barr virus (EBV) nuclear antigen 1 BamHI F promoter is activated on entry of EBV-transformed B cells into the lytic cycle.

PubMed Central

Lear, A L; Rowe, M; Kurilla, M G; Lee, S; Henderson, S; Kieff, E; Rickinson, A B

1992-01-01

In Epstein-Barr virus (EBV)-positive Burkitt's lymphoma cell lines exhibiting the latency I form of infection (i.e., EBV nuclear antigen 1 [EBNA1] positive in the absence of other latent proteins), the EBNA1 mRNA has a unique BamHI Q/U/K splice structure and is expressed from a novel promoter, Fp, located near the BamHI FQ boundary. This contrasts with the situation in EBV-transformed lymphoblastoid cell lines (LCLs) exhibiting the latency III form of infection (i.e., positive for all latent proteins), in which transcription from the upstream Cp or Wp promoters is the principal source of EBNA mRNAs. We carried out cDNA amplifications with oligonucleotide primer-probe combinations to determine whether Fp is ever active in an LCL environment. The results clearly showed that some LCLs express a Q/U/K-spliced EBNA1 mRNA in addition to the expected Cp/Wp-initiated transcripts; this seemed inconsistent with the concept of Cp/Wp and Fp as mutually exclusive promoters. Here we show that Fp is indeed silent in latency III cells but is activated at an early stage following the switch from latency III into the virus lytic cycle. Four pieces of evidence support this conclusion: (i) examples of coincident Cp/Wp and Fp usage in LCLs are restricted to those lines in which a small subpopulation of cells have spontaneously entered the lytic cycle; (ii) transcripts initiating from Fp can readily be demonstrated in spontaneously productive lines by S1 nuclease protection; (iii) the presence of Fp-initiated transcripts is not affected by acyclovir blockade of the late lytic cycle; and (iv) infection of latently infected LCLs with a recombinant vaccinia virus encoding the EBV immediate-early protein BZLF1, a transcriptional transactivator which normally initiates the lytic cycle, results in the appearance of the diagnostic Q/U/K-spliced transcripts. Images PMID:1331531

Breaking Benzene Aromaticity-Computational Insights into the Mechanism of the Tungsten-Containing Benzoyl-CoA Reductase.

PubMed

Culka, Martin; Huwiler, Simona G; Boll, Matthias; Ullmann, G Matthias

2017-10-18

Aromatic compounds are environmental pollutants with toxic and carcinogenic properties. Despite the stability of aromatic rings, bacteria are able to degrade the aromatic compounds into simple metabolites and use them as growth substrates under oxic or even under anoxic conditions. In anaerobic microorganisms, most monocyclic aromatic growth substrates are converted to the central intermediate benzoyl-coenzyme A, which is enzymatically reduced to cyclohexa-1,5-dienoyl-CoA. The strictly anaerobic bacterium Geobacter metallireducens uses the class II benzoyl-CoA reductase complex for this reaction. The catalytic BamB subunit of this complex harbors an active site tungsten-bis-pyranopterin cofactor with the metal being coordinated by five protein/cofactor-derived sulfur atoms and a sixth, so far unknown, ligand. Although BamB has been biochemically and structurally characterized, its mechanism still remains elusive. Here we use continuum electrostatic and QM/MM calculations to model benzoyl-CoA reduction by BamB. We aim to elucidate the identity of the sixth ligand of the active-site tungsten ion together with the interplay of the electron and proton transfer events during the aromatic ring reduction. On the basis of our calculations, we propose that benzoyl-CoA reduction is initiated by a hydrogen atom transfer from a W(IV) species with an aqua ligand, yielding W(V)-[OH - ] and a substrate radical intermediate. In the next step, a proton-assisted second electron transfer takes place with a conserved active-site histidine serving as the second proton donor. Interestingly, our calculations suggest that the electron for the second reduction step is taken from the pyranopterin cofactors rather than from the tungsten ion. The resulting cationic radical, which is distributed over both pyranopterins, is stabilized by conserved anionic amino acid residues. The stepwise mechanism of the reduction shows similarities to the Birch reduction known from organic chemistry. However, the strict coupling of protons and electrons allows the reaction to proceed under milder conditions.

Control of photosynthetic membrane assembly in Rhodobacter sphaeroides mediated by puhA and flanking sequences.

PubMed Central

Sockett, R E; Donohue, T J; Varga, A R; Kaplan, S

1989-01-01

A reaction center H- strain (RCH-) of Rhodobacter sphaeroides, PUHA1, was made by in vitro deletion of an XhoI restriction endonuclease fragment from the puhA gene coupled with insertion of a kanamycin resistance gene cartridge. The resulting construct was delivered to R. sphaeroides wild-type 2.4.1, with the defective puhA gene replacing the wild-type copy by recombination, followed by selection for kanamycin resistance. When grown under conditions known to induce intracytoplasmic membrane development, PUHA1 synthesized a pigmented intracytoplasmic membrane. Spectral analysis of this membrane showed that it was deficient in B875 spectral complexes as well as functional reaction centers and that the level of B800-850 spectral complexes was greater than in the wild type. The RCH- strain was photosythetically incompetent, but photosynthetic growth was restored by complementation with a 1.45-kilobase (kb) BamHI restriction endonuclease fragment containing the puhA gene carried in trans on plasmid pRK404. B875 spectral complexes were not restored by complementation with the 1.45-kb BamHI restriction endonuclease fragment containing the puhA gene but were restored along with photosynthetic competence by complementation with DNA from a cosmid carrying the puhA gene, as well as a flanking DNA sequence. Interestingly, B875 spectral complexes, but not photosynthetic competence, were restored to PUHA1 by introduction in trans of a 13-kb BamHI restriction endonuclease fragment carrying genes encoding the puf operon region of the DNA. The effect of the puhA deletion was further investigated by an examination of the levels of specific mRNA species derived from the puf and puc operons, as well as by determinations of the relative abundances of polypeptides associated with various spectral complexes by immunological methods. The roles of puhA and other genetic components in photosynthetic gene expression and membrane assembly are discussed. Images PMID:2644200

Histone H3K9 Trimethylase Eggless Controls Germline Stem Cell Maintenance and Differentiation

PubMed Central

Zhou, Jian; McDowell, William; Park, Jungeun; Haug, Jeff; Staehling, Karen; Tang, Hong; Xie, Ting

2011-01-01

Epigenetic regulation plays critical roles in the regulation of cell proliferation, fate determination, and survival. It has been shown to control self-renewal and lineage differentiation of embryonic stem cells. However, epigenetic regulation of adult stem cell function remains poorly defined. Drosophila ovarian germline stem cells (GSCs) are a productive adult stem cell system for revealing regulatory mechanisms controlling self-renewal and differentiation. In this study, we show that Eggless (Egg), a H3K9 methyltransferase in Drosophila, is required in GSCs for controlling self-renewal and in escort cells for regulating germ cell differentiation. egg mutant ovaries primarily exhibit germ cell differentiation defects in young females and gradually lose GSCs with time, indicating that Egg regulates both germ cell maintenance and differentiation. Marked mutant egg GSCs lack expression of trimethylated H3K9 (H3k9me3) and are rapidly lost from the niche, but their mutant progeny can still differentiate into 16-cell cysts, indicating that Egg is required intrinsically to control GSC self-renewal but not differentiation. Interestingly, BMP-mediated transcriptional repression of differentiation factor bam in marked egg mutant GSCs remains normal, indicating that Egg is dispensable for BMP signaling in GSCs. Normally, Bam and Bgcn interact with each other to promote GSC differentiation. Interestingly, marked double mutant egg bgcn GSCs are still lost, but their progeny are able to differentiate into 16-cell cysts though bgcn mutant GSCs normally do not differentiate, indicating that Egg intrinsically controls GSC self-renewal through repressing a Bam/Bgcn-independent pathway. Surprisingly, RNAi-mediated egg knockdown in escort cells leads to their gradual loss and a germ cell differentiation defect. The germ cell differentiation defect is at least in part attributed to an increase in BMP signaling in the germ cell differentiation niche. Therefore, this study has revealed the essential roles of histone H3K9 trimethylation in controlling stem cell maintenance and differentiation through distinct mechanisms. PMID:22216012

IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data.

PubMed

Baez-Ortega, Adrian; Lorenzo-Diaz, Fabian; Hernandez, Mariano; Gonzalez-Vila, Carlos Ignacio; Roda-Garcia, Jose Luis; Colebrook, Marcos; Flores, Carlos

2015-09-01

We introduce IonGAP, a publicly available Web platform designed for the analysis of whole bacterial genomes using Ion Torrent sequence data. Besides assembly, it integrates a variety of comparative genomics, annotation and bacterial classification routines, based on the widely used FASTQ, BAM and SRA file formats. Benchmarking with different datasets evidenced that IonGAP is a fast, powerful and simple-to-use bioinformatics tool. By releasing this platform, we aim to translate low-cost bacterial genome analysis for microbiological prevention and control in healthcare, agroalimentary and pharmaceutical industry applications. IonGAP is hosted by the ITER's Teide-HPC supercomputer and is freely available on the Web for non-commercial use at http://iongap.hpc.iter.es. mcolesan@ull.edu.es or cflores@ull.edu.es Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The impact of photovoltaic (PV) installations on downwind particulate matter concentrations: Results from field observations at a 550-MWAC utility-scale PV plant.

PubMed

Ravikumar, Dwarakanath; Sinha, Parikhit

2017-10-01

With utility-scale photovoltaic (PV) projects increasingly developed in dry and dust-prone geographies with high solar insolation, there is a critical need to analyze the impacts of PV installations on the resulting particulate matter (PM) concentrations, which have environmental and health impacts. This study is the first to quantify the impact of a utility-scale PV plant on PM concentrations downwind of the project site. Background, construction, and post-construction PM 2.5 and PM 10 (PM with aerodynamic diameters <2.5 and <10 μm, respectively) concentration data were collected from four beta attenuation monitor (BAM) stations over 3 yr. Based on these data, the authors evaluate the hypothesis that PM emissions from land occupied by a utility-scale PV installation are reduced after project construction through a wind-shielding effect. The results show that the (1) confidence intervals of the mean PM concentrations during construction overlap with or are lower than background concentrations for three of the four BAM stations; and (2) post-construction PM 2.5 and PM 10 concentrations downwind of the PV installation are significantly lower than the background concentrations at three of the four BAM stations. At the fourth BAM station, downwind post-construction PM 2.5 and PM 10 concentrations increased marginally by 5.7% and 2.6% of the 24-hr ambient air quality standards defined by the U.S. Environmental Protection Agency, respectively, when compared with background concentrations, with the PM 2.5 increase being statistically insignificant. This increase may be due to vehicular emissions from an access road near the southwest corner of the site or a drainage berm near the south station. The findings demonstrate the overall environmental benefit of downwind PM emission abatement from a utility-scale PV installation in desert conditions due to wind shielding. With PM emission reductions observed within 10 months of completion of construction, post-construction monitoring of downwind PM levels may be reduced to a 1-yr period for other projects with similar soil and weather conditions. This study is the first to analyze impact of a utility photovoltaic (PV) project on downwind particulate matter (PM) concentration in desert conditions. The PM data were collected at four beta attenuation monitor stations over a 3-yr period. The post-construction PM concentrations are lower than background concentrations at three of four stations, therefore supporting the hypothesis of post-construction wind shielding from PV installations. With PM emission reductions observed within 10 months of completion of construction, postconstruction monitoring of downwind PM levels may be reduced to a 1-yr period for other PV projects with similar soil and weather conditions.

Restriction Fragment Length Polymorphisms of Virulence Plasmids in Rhodococcus equi

PubMed Central

Takai, Shinji; Shoda, Masato; Sasaki, Yukako; Tsubaki, Shiro; Fortier, Guillaume; Pronost, Stephane; Rahal, Karim; Becu, Teotimo; Begg, Angela; Browning, Glenn; Nicholson, Vivian M.; Prescott, John F.

1999-01-01

Virulent Rhodococcus equi, which is a well-known cause of pyogranulomatous pneumonia in foals, possesses a large plasmid encoding virulence-associated 15- to 17-kDa antigens. Foal and soil isolates from five countries—Argentina, Australia, Canada, France, and Japan—were investigated for the presence of 15- to 17-kDa antigens by colony blotting, using the monoclonal antibody 10G5, and the gene coding for 15- to 17-kDa antigens by PCR. Plasmid DNAs extracted from positive isolates were digested with restriction endonucleases BamHI, EcoRI, EcoT22I, and HindIII, and the digestion patterns that resulted divided the plasmids of virulent isolates into five closely related types. Three of the five types had already been reported in Canadian and Japanese isolates, and the two new types had been found in French and Japanese isolates. Therefore, we tentatively designated these five types 85-kb type I (pREAT701), 85-kb type II (a new type), 87-kb type I (EcoRI and BamHI type 2 [V. M. Nicholson and J. F. Prescott, J. Clin. Microbiol. 35:738–740, 1997]), 87-kb type II (a new type), and 90-kb (pREL1) plasmids. The 85-kb type I plasmid was found in isolates from Argentina, Australia, Canada, and France. Plasmid 87-kb type I was isolated in specimens from Argentina, Canada, and France. The 85-kb type II plasmid appeared in isolates from France. On the other hand, plasmids 87-kb type II and 90-kb were found only in isolates from Japan. These results revealed geographic differences in the distribution of the virulence plasmids found in the five countries and suggested that the restriction fragment length polymorphism of virulence plasmids might be useful to elucidate the molecular epidemiology of virulent R. equi in the world. PMID:10488224

Construction and characterization of a bacterial artificial chromosome library for hexaploid wheat line 92R137

USDA-ARS?s Scientific Manuscript database

For map-based cloning of genes conferring important traits in the hexaploid wheat line 92R137, a bacterial artificial chromosome (BAC) library, including two sub libraries, was constructed using the genomic DNA of 92R137 digested with restriction enzymes HindIII and BamHI. The BAC library was compos...

Re-Configuring Inclusion, Decolonising Practice: Digital Participation and Learning in Black Women's Community-Led Heritage

ERIC Educational Resources Information Center

Clarke, Rachel; Lewis, Rosie M.

2016-01-01

This article explores an innovative model of adult education within museums developed from a Black feminist approach. BAM! Sistahood! is a community-led project with regional heritage organisations, universities and women's centres in the UK, that offers a holistic approach to heritage development. The ethos is to challenge the perpetuation of…

The Acceptance of Microblogging in the Learning Process: The µBAM Model

ERIC Educational Resources Information Center

Rejón-Guardia, Francisco; Sánchez-Fernández, Juan; Muñoz-Leiva, Francisco

2013-01-01

Microblogging social networks (µBSNs) provide the opportunity to communicate worldwide while using a small number of characters; this is an apparent limitation that forces users to share only essential information when linking to the world with which they interact. These platforms can serve to motivate students by narrowing the physical and…

Temporal trend in dementia incidence since 2002 and projections for prevalence in England and Wales to 2040: modelling study.

PubMed

Ahmadi-Abhari, Sara; Guzman-Castillo, Maria; Bandosz, Piotr; Shipley, Martin J; Muniz-Terrera, Graciela; Singh-Manoux, Archana; Kivimäki, Mika; Steptoe, Andrew; Capewell, Simon; O'Flaherty, Martin; Brunner, Eric J

2017-07-05

Objective  To forecast dementia prevalence with a dynamic modelling approach that integrates calendar trends in dementia incidence with those for mortality and cardiovascular disease. Design  Modelling study. Setting  General adult population of England and Wales. Participants  The English Longitudinal Study of Ageing (ELSA) is a representative panel study with six waves of data across 2002-13. Men and women aged 50 or more years, selected randomly, and their cohabiting partners were recruited to the first wave of ELSA (2002-03). 11392 adults participated (response rate 67%). To maintain representativeness, refreshment participants were recruited to the study at subsequent waves. The total analytical sample constituted 17 906 people. Constant objective criteria based on cognitive and functional impairment were used to ascertain dementia cases at each wave. Main outcome measures  To estimate calendar trends in dementia incidence, correcting for bias due to loss to follow-up of study participants, a joint model of longitudinal and time-to-event data was fitted to ELSA data. To forecast future dementia prevalence, the probabilistic Markov model IMPACT-BAM (IMPACT-Better Ageing Model) was developed. IMPACT-BAM models transitions of the population aged 35 or more years through states of cardiovascular disease, cognitive and functional impairment, and dementia, to death. It enables prediction of dementia prevalence while accounting for the growing pool of susceptible people as a result of increased life expectancy and the competing effects due to changes in mortality, and incidence of cardiovascular disease. Results  In ELSA, dementia incidence was estimated at 14.3 per 1000 person years in men and 17.0/1000 person years in women aged 50 or more in 2010. Dementia incidence declined at a relative rate of 2.7% (95% confidence interval 2.4% to 2.9%) for each year during 2002-13. Using IMPACT-BAM, we estimated there were approximately 767 000 (95% uncertainty interval 735 000 to 797 000) people with dementia in England and Wales in 2016. Despite the decrease in incidence and age specific prevalence, the number of people with dementia is projected to increase to 872 000, 1 092 000, and 1 205 000 in 2020, 2030, and 2040, respectively. A sensitivity analysis without the incidence decline gave a much larger projected growth, of more than 1.9 million people with dementia in 2040. Conclusions  Age specific dementia incidence is declining. The number of people with dementia in England and Wales is likely to increase by 57% from 2016 to 2040. This increase is mainly driven by improved life expectancy. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Diversity and antimicrobial resistance of Salmonella enterica isolates from surface water in Southeastern United States.

PubMed

Li, Baoguang; Vellidis, George; Liu, Huanli; Jay-Russell, Michele; Zhao, Shaohua; Hu, Zonglin; Wright, Anita; Elkins, Christopher A

2014-10-01

A study of prevalence, diversity, and antimicrobial resistance of Salmonella enterica in surface water in the southeastern United States was conducted. A new scheme was developed for recovery of Salmonella from irrigation pond water and compared with the FDA's Bacteriological Analytical Manual (8th ed., 2014) (BAM) method. Fifty-one isolates were recovered from 10 irrigation ponds in produce farms over a 2-year period; nine Salmonella serovars were identified by pulsed-field gel electrophoresis analysis, and the major serovar was Salmonella enterica serovar Newport (S. Newport, n = 29), followed by S. enterica serovar Enteritidis (n = 6), S. enterica serovar Muenchen (n = 4), S. enterica serovar Javiana (n = 3), S. enterica serovar Thompson (n = 2), and other serovars. It is noteworthy that the PulseNet patterns of some of the isolates were identical to those of the strains that were associated with the S. Thompson outbreaks in 2010, 2012, and 2013, S. Enteritidis outbreaks in 2011 and 2013, and an S. Javiana outbreak in 2012. Antimicrobial susceptibility testing confirmed 16 S. Newport isolates of the multidrug resistant-AmpC (MDR-AmpC) phenotype, which exhibited resistance to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (ACSSuT), and to the 1st, 2nd, and 3rd generations of cephalosporins (cephalothin, amoxicillin-clavulanic acid, and ceftriaxone). Moreover, the S. Newport MDR-AmpC isolates had a PFGE pattern indistinguishable from the patterns of the isolates from clinical settings. These findings suggest that the irrigation water may be a potential source of contamination of Salmonella in fresh produce. The new Salmonella isolation scheme significantly increased recovery efficiency from 21.2 (36/170) to 29.4% (50/170) (P = 0.0002) and streamlined the turnaround time from 5 to 9 days with the BAM method to 4 days and thus may facilitate microbiological analysis of environmental water. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Invasion biology in non-free-living species: interactions between abiotic (climatic) and biotic (host availability) factors in geographical space in crayfish commensals (Ostracoda, Entocytheridae)

PubMed Central

Mestre, Alexandre; Aguilar-Alberola, Josep A; Baldry, David; Balkis, Husamettin; Ellis, Adam; Gil-Delgado, Jose A; Grabow, Karsten; Klobučar, Göran; Kouba, Antonín; Maguire, Ivana; Martens, Andreas; Mülayim, Ayşegül; Rueda, Juan; Scharf, Burkhard; Soes, Menno; S Monrós, Juan; Mesquita-Joanes, Francesc

2013-01-01

In invasion processes, both abiotic and biotic factors are considered essential, but the latter are usually disregarded when modeling the potential spread of exotic species. In the framework of set theory, interactions between biotic (B), abiotic (A), and movement-related (M) factors in the geographical space can be hypothesized with BAM diagrams and tested using ecological niche models (ENMs) to estimate A and B areas. The main aim of our survey was to evaluate the interactions between abiotic (climatic) and biotic (host availability) factors in geographical space for exotic symbionts (i.e., non-free-living species), using ENM techniques combined with a BAM framework and using exotic Entocytheridae (Ostracoda) found in Europe as model organisms. We carried out an extensive survey to evaluate the distribution of entocytherids hosted by crayfish in Europe by checking 94 European localities and 12 crayfish species. Both exotic entocytherid species found, Ankylocythere sinuosa and Uncinocythere occidentalis, were widely distributed in W Europe living on the exotic crayfish species Procambarus clarkii and Pacifastacus leniusculus, respectively. No entocytherids were observed in the remaining crayfish species. The suitable area for A. sinuosa was mainly restricted by its own limitations to minimum temperatures in W and N Europe and precipitation seasonality in circum-Mediterranean areas. Uncinocythere occidentalis was mostly restricted by host availability in circum-Mediterranean regions due to limitations of P. leniusculus to higher precipitation seasonality and maximum temperatures. The combination of ENMs with set theory allows studying the invasive biology of symbionts and provides clues about biogeographic barriers due to abiotic or biotic factors limiting the expansion of the symbiont in different regions of the invasive range. The relative importance of abiotic and biotic factors on geographical space can then be assessed and applied in conservation plans. This approach can also be implemented in other systems where the target species is closely interacting with other taxa. PMID:24455152

Invasion biology in non-free-living species: interactions between abiotic (climatic) and biotic (host availability) factors in geographical space in crayfish commensals (Ostracoda, Entocytheridae).

PubMed

Mestre, Alexandre; Aguilar-Alberola, Josep A; Baldry, David; Balkis, Husamettin; Ellis, Adam; Gil-Delgado, Jose A; Grabow, Karsten; Klobučar, Göran; Kouba, Antonín; Maguire, Ivana; Martens, Andreas; Mülayim, Ayşegül; Rueda, Juan; Scharf, Burkhard; Soes, Menno; S Monrós, Juan; Mesquita-Joanes, Francesc

2013-12-01

In invasion processes, both abiotic and biotic factors are considered essential, but the latter are usually disregarded when modeling the potential spread of exotic species. In the framework of set theory, interactions between biotic (B), abiotic (A), and movement-related (M) factors in the geographical space can be hypothesized with BAM diagrams and tested using ecological niche models (ENMs) to estimate A and B areas. The main aim of our survey was to evaluate the interactions between abiotic (climatic) and biotic (host availability) factors in geographical space for exotic symbionts (i.e., non-free-living species), using ENM techniques combined with a BAM framework and using exotic Entocytheridae (Ostracoda) found in Europe as model organisms. We carried out an extensive survey to evaluate the distribution of entocytherids hosted by crayfish in Europe by checking 94 European localities and 12 crayfish species. Both exotic entocytherid species found, Ankylocythere sinuosa and Uncinocythere occidentalis, were widely distributed in W Europe living on the exotic crayfish species Procambarus clarkii and Pacifastacus leniusculus, respectively. No entocytherids were observed in the remaining crayfish species. The suitable area for A. sinuosa was mainly restricted by its own limitations to minimum temperatures in W and N Europe and precipitation seasonality in circum-Mediterranean areas. Uncinocythere occidentalis was mostly restricted by host availability in circum-Mediterranean regions due to limitations of P. leniusculus to higher precipitation seasonality and maximum temperatures. The combination of ENMs with set theory allows studying the invasive biology of symbionts and provides clues about biogeographic barriers due to abiotic or biotic factors limiting the expansion of the symbiont in different regions of the invasive range. The relative importance of abiotic and biotic factors on geographical space can then be assessed and applied in conservation plans. This approach can also be implemented in other systems where the target species is closely interacting with other taxa.

Convergence analysis of stochastic hybrid bidirectional associative memory neural networks with delays

NASA Astrophysics Data System (ADS)

Wan, Li; Zhou, Qinghua

2007-10-01

The stability property of stochastic hybrid bidirectional associate memory (BAM) neural networks with discrete delays is considered. Without assuming the symmetry of synaptic connection weights and the monotonicity and differentiability of activation functions, the delay-independent sufficient conditions to guarantee the exponential stability of the equilibrium solution for such networks are given by using the nonnegative semimartingale convergence theorem.

Non-Reciprocal on Wafer Microwave Devices

DTIC Science & Technology

2015-05-27

filter uses a barium hexagonal ferrite film incorporated into the dielectric layer of a microstrip transmission line. The zero-field operational...Fal,, Robert E. Camley. Millimeter wave phase shifter based on ferromagnetic resonancein a hexagonal barium ferrite thin film, Applied Physics...materials for on-wafer microwave devices concentrated on barium hexagonal ferrite (BaM) films grown on Si because these material is a good candidate

Human Factors Feedback: Brain Acoustic Monitor

DTIC Science & Technology

2012-02-01

Microsoft Office Excel .................................................................12  iv 4.  Conclusions 13  5.  References 15  Appendix A...Panasonic Toughbook system. †Toughbook is registered trademark of Panasonic Corporation. ‡Windows is a registered trademark of Microsoft Corporation. 4...was preloaded with Microsoft Windows XP service pack 2 OS. This OS is widely used on IBM-style personal computers, and the BAM system did not

Profiling Teachers Based on Their Professional Attitudes towards Teaching Responsible Research and Innovation

ERIC Educational Resources Information Center

de Vocht, Miikka; Laherto, Antti

2017-01-01

In order to facilitate policy-driven reforms in science education, it is important to understand how teaching innovations diffuse among teachers and how that adoption process can be catalysed. Little is known about the set of attitudes that makes teachers early or late adopters. In this study, the Concerns-Based Adoption Model (C-BAM) was employed…

Differences in photoluminescence properties and thermal degradation between nanoparticle and bulk particle BaMgAl10O17:Eu2+ phosphors under UV?VUV irradiation.

PubMed

Liu, Bitao; Xin, Shuangyu; Li, Fenghua; Zhang, Jiachi; Wang, Yuhua

2014-05-01

BaMgAl10O17:Eu2+ (BAM) phosphors used for plasma display panels and three-band fluorescence lamps are exposed to an oxidizing environment at about 500 degrees C, which is currently unavoidable in actual applications. We investigated the mechanism of the luminance degradation of BAM caused by annealing at 500 degrees C based on the difference in luminance degradation of bulk particle and nanoparticle samples under various excitation source irradiations. When the samples were excited by the different light sources, more than 30% degradation of luminance occurred under 147 nm while less than 10% degradation occurred under 254 nm both for nanoparticle and bulk particle samples. In addition, the luminescence degradation of nanophosphors shows a different tendency compared to the bulk phosphors. With a model based on the particle size and excitation light penetration depth, we demonstrate that the degradation is still mainly ascribed to the oxidized of divalent Eu. The differences in luminescence properties between nanophosphors and bulk phosphors are also illustrated by this model. As a result, the potential industrial applications of nanophosphors are evaluated.

Consed: a graphical editor for next-generation sequencing.

PubMed

Gordon, David; Green, Phil

2013-11-15

The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions of interest and automate as many tasks as possible. We have adapted consed to reflect this. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for user review and launches the consed graphical editor on user-selected regions, allowing, in addition to longstanding consed capabilities such as assembly editing, a variety of new features including direct editing of the reference sequence, variant and error detection, display of annotation tracks and the ability to simultaneously process a group of reads. Many batch processing capabilities have been added. The consed package is free to academic, government and non-profit users, and licensed to others for a fee by the University of Washington. The current version (26.0) is available for linux, macosx and solaris systems or as C++ source code. It includes a user's manual (with exercises) and example datasets. http://www.phrap.org/consed/consed.html dgordon@uw.edu .

BamHI-A rightward frame 1, an Epstein–Barr virus-encoded oncogene and immune modulator

PubMed Central

Hoebe, Eveline K; Le Large, Tessa Y S; Greijer, Astrid E; Middeldorp, Jaap M

2013-01-01

Epstein–Barr virus (EBV) causes several benign and malignant disorders of lymphoid and epithelial origin. EBV-related tumors display distinct patterns of viral latent gene expression, of which the BamHI-A rightward frame 1 (BARF1) is selectively expressed in carcinomas, regulated by cellular differentiation factors including ΔNp63α. BARF1 functions as a viral oncogene, immortalizing and transforming epithelial cells of different origin by acting as a mitogenic growth factor, inducing cyclin-D expression, and up-regulating antiapoptotic Bcl-2, stimulating host cell growth and survival. In addition, secreted hexameric BARF1 has immune evasive properties, functionally corrupting macrophage colony stimulating factor, as supported by recent functional and structural data. Therefore, BARF1, an intracellular and secreted protein, not only has multiple pathogenic functions but also can function as a target for immune responses. Deciphering the role of BARF1 in EBV biology will contribute to novel diagnostic and treatment options for EBV-driven carcinomas. Herein, we discuss recent insights on the regulation of BARF1 expression and aspects of structure-function relating to its oncogenic and immune suppressive properties. © 2013 The Authors. Reviews in Medical Virology published by John Wiley & Sons, Ltd. PMID:23996634

Electrochemical detection of the MT-ND6 gene and its enzymatic digestion: application in human genomic sample.

PubMed

Mazloum-Ardakani, Mohammad; Ahmadi, Roya; Heidari, Mohammad Mehdi; Sheikh-Mohseni, Mohammad Ali

2014-06-15

A simple electrochemical biosensor was developed for the detection of the mitochondrial NADH dehydrogenase 6 gene (MT-ND6) and its enzymatic digestion by BamHI enzyme. This biosensor was fabricated by modification of a glassy carbon electrode with gold nanoparticles (AuNPs/GCE) and a probe oligonucleotide (ssDNA/AuNPs/GCE). The probe, which is a thiolated segment of the MT-ND6 gene, was deposited by self-assembling immobilization on AuNPs/GCE. Two indicators including methylene blue (MB) and neutral red (NR) were used as the electroactive indicators and the electrochemical response of the modified electrode was measured by differential pulse voltammetry. The proposed biosensor can detect the complementary sequences of the MT-ND6 gene. Also the modified electrode was used for the detection of an enzymatic digestion process by BamHI enzyme. The electrochemical biosensor can detect the MT-ND6 gene and its enzymatic digestion in polymerase chain reaction (PCR)-amplified DNA extracted from human blood. Also the biosensor was used directly for detection of the MT-ND6 gene in all of the human genome. Copyright © 2014 Elsevier Inc. All rights reserved.

Comparison of 17 genome types of adenovirus type 3 identified among strains recovered from six continents.

PubMed Central

Li, Q G; Wadell, G

1988-01-01

Restriction endonucleases BamHI, BclI, BglI, BglII, BstEII, EcoRI, HindIII, HpaI, SalI, SmalI, XbalI, and XholI were used to analyze 61 selected strains of adenovirus type 3 (Ad3) isolated from Africa, Asia, Australia, Europe, North America, and South America. It was noted that the use of BamHI, BclI, BglII, HpaI, SalI, and SmaI was sufficient to distinguish 17 genome types; 13 of them were newly identified. All 17 Ad3 genome types could be divided into three genomic clusters. Genome types of Ad3 cluster 1 occurred in Africa, Europe, South America, and North America. Genomic cluster 2 was identified in Africa; genomic cluster 3 was identified in Africa, Asia, Australia, Europe (a few), and North America. This was of interest because 15 identified genome types of Ad7 could also be divided into three genomic clusters. The degree of genetic relatedness between the 17 Ad3 and the 15 Ad7 genome types was analyzed and was expressed in a three-dimensional model. Images PMID:2838500

Molecular cloning and expression in Saccharomyces cerevisiae and Neurospora crassa of the invertase gene from Neurospora crassa.

PubMed

Carú, M; Cifuentes, V; Pincheira, G; Jiménez, A

1989-10-01

A plasmid (named pCN2) carrying a 7.6 kb BamHI DNA insert was isolated from a Neurospora crassa genomic library raised in the yeast vector YRp7. Saccharomyces cerevisiae suco and N. crassa inv strains transformed with pNC2 were able to grow on sucrose-based media and expressed invertase activity. Saccharomyces cerevisiae suco (pNC2) expressed a product which immunoreacted with antibody raised against purified invertase from wild type N. crassa, although S. cerevisiae suc+ did not. The cloned DNA hybridized with a 7.6 kb DNA fragment from BamHI-restricted wild type N. crassa DNA. Plasmid pNC2 transformed N. crassa Inv- to Inv+ by integration either near to the endogenous inv locus (40% events) or at other genomic sites (60% events). It appears therefore that the cloned DNA piece encodes the N. crassa invertase enzyme. A 3.8 kb XhoI DNA fragment, derived from pNC2, inserted in YRp7, in both orientation, was able to express invertase activity in yeast, suggesting that it contains an intact invertase gene which is not expressed from a vector promoter.

Construction of a food-grade cloning vector for Lactobacillus plantarum and its utilization in a food model.

PubMed

Rattanachaikunsopon, Pongsak; Phumkhachorn, Parichat

2012-01-01

The development of Lactobacillus plantarum to be used in starter cultures in the food industry has been limited because of the lack of a food-grade cloning vector for the bacterium. In this study, the plasmid pFLP1 was constructed by joining 2 DNA fragments derived from food-approved organisms. The 5.2-kb BamHI/KpnI DNA fragment of pRV566 containing the theta-type replicon of Lactobacillus sakei was ligated to the BamHI/KpnI DNA fragment of a 2.9-kb lactococcal cadmium resistance determinant amplified from pND918. The 8.1-kb newly constructed plasmid could transform L. plantarum N014, a bacteriocin-producing bacteria originally isolated from nham, a traditional Thai fermented sausage. The resulting transformant, L. plantarum N014-FLP, and its parent strain were shown to be very similar in growth rate and bacteriocin activity. In addition, the plasmid was very stable in its host bacteria under nonselective pressure for 100 generations in MRS medium and for 5 days in a nham model. These results suggest that pFLP1 is a potential food-grade cloning vector for L. plantarum.

A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution

PubMed Central

Heinz, Eva; Lithgow, Trevor

2014-01-01

Members of the Omp85/TpsB protein superfamily are ubiquitously distributed in Gram-negative bacteria, and function in protein translocation (e.g., FhaC) or the assembly of outer membrane proteins (e.g., BamA). Several recent findings are suggestive of a further level of variation in the superfamily, including the identification of the novel membrane protein assembly factor TamA and protein translocase PlpD. To investigate the diversity and the causal evolutionary events, we undertook a comprehensive comparative sequence analysis of the Omp85/TpsB proteins. A total of 10 protein subfamilies were apparent, distinguished in their domain structure and sequence signatures. In addition to the proteins FhaC, BamA, and TamA, for which structural and functional information is available, are families of proteins with so far undescribed domain architectures linked to the Omp85 β-barrel domain. This study brings a classification structure to a dynamic protein superfamily of high interest given its essential function for Gram-negative bacteria as well as its diverse domain architecture, and we discuss several scenarios of putative functions of these so far undescribed proteins. PMID:25101071

Advances in understanding of bile acid diarrhea

PubMed Central

Camilleri, Michael

2014-01-01

Bile acids (BA) are actively reabsorbed in the terminal ileum by the apical Na+-dependent bile salt transporter. This review addresses the epidemiology, pathophysiology, diagnosis and treatment of BA diarrhea (BAD). BAD is typically caused by ileal resection or disease; 25–33% of patients with chronic functional diarrhea or irritable bowel syndrome-diarrhea (IBS-D) have BAD, possibly from deficiency in the ileal hormone, FGF-19, which normally provides feedback inhibition of BA synthesis. Diagnosis of BAD is typically based on reduced BA retention of radiolabeled BA (75SeHCAT), increased BA synthesis (serum C4) or increased fecal BA loss. In clinical practice, diagnosis is often based on response to BA sequestrants (e.g., cholestyramine or colesevelam). Diagnostic tests for BA malabsorption (BAM) need to be used more extensively in clinical practice. In the future, farnesoid X receptor agonists that stimulate ileal production of FGF-19 may be alternative treatments of BAD. PMID:24410472

Simulation supported POD for RT test case-concept and modeling

NASA Astrophysics Data System (ADS)

Gollwitzer, C.; Bellon, C.; Deresch, A.; Ewert, U.; Jaenisch, G.-R.; Zscherpel, U.; Mistral, Q.

2012-05-01

Within the framework of the European project PICASSO, the radiographic simulator aRTist (analytical Radiographic Testing inspection simulation tool) developed by BAM has been extended for reliability assessment of film and digital radiography. NDT of safety relevant components of aerospace industry requires the proof of probability of detection (POD) of the inspection. Modeling tools can reduce the expense of such extended, time consuming NDT trials, if the result of simulation fits to the experiment. Our analytic simulation tool consists of three modules for the description of the radiation source, the interaction of radiation with test pieces and flaws, and the detection process with special focus on film and digital industrial radiography. It features high processing speed with near-interactive frame rates and a high level of realism. A concept has been developed as well as a software extension for reliability investigations, completed by a user interface for planning automatic simulations with varying parameters and defects. Furthermore, an automatic image analysis procedure is included to evaluate the defect visibility. The radiographic modeling from 3D CAD of aero engine components and quality test samples are compared as a precondition for real trials. This enables the evaluation and optimization of film replacement for application of modern digital equipment for economical NDT and defined POD.

OSSE Evaluation of Aircraft Reconnaissance Observations and their Impact on Hurricane Analyses and Forecasts

NASA Astrophysics Data System (ADS)

Ryan, K. E.; Bucci, L. R.; Delgado, J.; Atlas, R. M.; Murillo, S.; Dodge, P.

2016-12-01

NOAA/AOML's Hurricane Research Division (HRD) annually conducts its Hurricane Field Program during which observations are collected via NOAA aircraft to improve the understanding and prediction of hurricanes. Mission experiments suggest a variety of flight patterns and sampling strategies aimed towards their respective goals described by the Intensity Forecasting Experiment (IFEX; Rogers et al., BAMS, 2006, 2013), a collaborative effort among HRD, NHC, and EMC. Evaluating the potential impact of various trade-offs in track design is valuable for determining the optimal air reconnaissance flight pattern for a prospective mission. AOML's HRD has developed a system for performing regional Observing System Simulation Experiments (OSSEs) to assess the potential impact of proposed observing systems on hurricane track and intensity forecasts and analyses. This study focuses on investigating the potential impact of proposed aircraft reconnaissance observing system designs. Aircraft instrument and flight level retrievals were simulated from a regional WRF ARW Nature Run (Nolan et al., 2013) spanning 13 days, covering the life cycle of a rapidly intensifying Atlantic tropical cyclone. The aircraft trajectories of NOAA aircraft are simulated in a variety of ways and are evaluated to examine the potential impact of aircraft reconnaissance observations on hurricane track and intensity forecasts.

OSSE Evaluation of Prospective Aircraft Reconnaissance Flight Patterns and their Impact on Hurricane Forecasts

NASA Astrophysics Data System (ADS)

Ryan, K. E.; Bucci, L. R.; Christophersen, H.; Atlas, R. M.; Murillo, S.; Dodge, P.

2015-12-01

Each year, NOAA/AOML's Hurricane Research Division (HRD) conducts its Hurricane field Program in which observations are collected via NOAA aircraft to improve the understanding and prediction of hurricanes. Mission experiments suggest a variety of flight patterns and sampling strategies aimed towards their respective goals described by the Intensity Forecasting Experiment (IFEX; Rogers et al., BAMS, 2006, 2013), a collaborative effort among HRD, NHC, and EMC. Evaluating the potential impact of various trade-offs in design is valuable for determining the optimal air reconnaissance flight pattern for a given prospective mission. AOML's HRD has developed a system for performing regional Observing System Simulation Experiments (OSSEs) to assess the potential impact of proposed observing systems on hurricane track and intensity forecasts and analyses. This study focuses on investigating the potential impact of proposed aircraft reconnaissance observing system designs. Aircraft instrument and flight level retrievals were simulated from a regional WRF ARW Nature Run (Nolan et al., 2013) spanning 13 days, covering the life cycle of a rapidly intensifying Atlantic tropical cyclone. The aircraft trajectories are simulated in a variety of ways and are evaluated to investigate the potential impact of aircraft reconnaissance observations on hurricane track and intensity forecasts.

Building Toward an Unmanned Aircraft System Training Strategy

DTIC Science & Technology

2014-01-01

37 4.7. Global Hawk UAS...either trained into a new career field or cross-trained from another Air Force Specialty Code. Those for Global Hawk come from the imagery analyst...Service(s) Capability/Mission rQ-4A Global hawk/ BAMS-D Block 10 9 3 USAF navy ISr Maritime domain awareness (navy) rQ-4B Global hawk Block 20/30 15 3

Measuring Recovery in Elite Rugby Players: The Brief Assessment of Mood, Endocrine Changes, and Power

ERIC Educational Resources Information Center

Shearer, David A.; Kilduff, Liam P.; Finn, Charlotte; Jones, Rhys M.; Bracken, Richard M.; Mellalieu, Stephen D.; Owen, Nic; Crewther, Blair T.; Cook, Christian J.

2015-01-01

Purpose: There is demand in applied sport settings to measure recovery briefly and accurately. Research indicates mood disturbance as the strongest psychological predictor of mental and physical recovery. The Brief Assessment of Mood (BAM) is a shortened version of the Profile of Mood States that can be completed in less than 30 s. The purpose of…

Physical mapping of the genomic DNA of the Oryctes rhinoceros baculovirus, KI.

PubMed

Mohan, K S; Gopinathan, K P

1991-11-15

A non-occluded baculovirus, OBV-KI has been isolated from the insect pest, Oryctes rhinoceros. The viral genome is estimated to be 123 kb, with a G + C content of 43 mol% and no detectible methylated bases. A restriction map of the OBV-KI genome for BamHI, EcoRI, HindIII, PstI, SalI and XbaI has been constructed.

Defense Acquisitions: Assessments of Selected Major Weapon Programs

DTIC Science & Technology

2006-03-01

also continue to reduce DOD’s buying power, as less capability will be provided for the money invested. In the larger context, DOD needs to make...Brilliant Antiarmor Submunition BAMS Broad Area Maritime Surveillance CDA Commander’s Digital Assistant CEC Cooperative Engagement Capability CMUP...Defense (DOD) maximize its return on investment and provide the warfighter with needed capabilities at the best value for the taxpayer. Since 1990

Development and field validation of a community-engaged particulate matter air quality monitoring network in Imperial, California, USA.

PubMed

Carvlin, Graeme N; Lugo, Humberto; Olmedo, Luis; Bejarano, Ester; Wilkie, Alexa; Meltzer, Dan; Wong, Michelle; King, Galatea; Northcross, Amanda; Jerrett, Michael; English, Paul B; Hammond, Donald; Seto, Edmund

2017-12-01

The Imperial County Community Air Monitoring Network was developed as part of a community-engaged research study to provide real-time particulate matter (PM) air quality information at a high spatial resolution in Imperial County, California. The network augmented the few existing regulatory monitors and increased monitoring near susceptible populations. Monitors were both calibrated and field validated, a key component of evaluating the quality of the data produced by the community monitoring network. This paper examines the performance of a customized version of the low-cost Dylos optical particle counter used in the community air monitors compared with both PM 2.5 and PM 10 (particulate matter with aerodynamic diameters <2.5 and <10 μm, respectively) federal equivalent method (FEM) beta-attenuation monitors (BAMs) and federal reference method (FRM) gravimetric filters at a collocation site in the study area. A conversion equation was developed that estimates particle mass concentrations from the native Dylos particle counts, taking into account relative humidity. The R 2 for converted hourly averaged Dylos mass measurements versus a PM 2.5 BAM was 0.79 and that versus a PM 10 BAM was 0.78. The performance of the conversion equation was evaluated at six other sites with collocated PM 2.5 environmental beta-attenuation monitors (EBAMs) located throughout Imperial County. The agreement of the Dylos with the EBAMs was moderate to high (R 2 = 0.35-0.81). The performance of low-cost air quality sensors in community networks is currently not well documented. This paper provides a methodology for quantifying the performance of a next-generation Dylos PM sensor used in the Imperial County Community Air Monitoring Network. This air quality network provides data at a much finer spatial and temporal resolution than has previously been possible with government monitoring efforts. Once calibrated and validated, these high-resolution data may provide more information on susceptible populations, assist in the identification of air pollution hotspots, and increase community awareness of air pollution.

Characterization of a New Type of Human Papillomavirus That Causes Skin Warts

PubMed Central

Orth, Gérard; Favre, Michel; Croissant, Odile

1977-01-01

A human papillomavirus (HPV) was isolated from the lesions of a patient (ML) bearing numerous hand common warts. This virus was compared with the well-characterized HPV found in typical plantar warts (plantar HPV). ML and plantar HPV DNAs have similar molecular weights (5.26 × 106 and 5.23 × 106, respectively) but were shown to be different by restriction enzyme analysis. When the cleavage products of both DNAs by endonuclease EcoRI, BamI, HpaI, or Hind were analyzed by electron microscopy, one, two, one, and four fragments were detected for ML HPV DNA instead of the two, one, two, and six fragments, respectively, detected for plantar HPV DNA. In contrast to plantar HPV DNA, a high proportion of ML HPV DNA molecules were resistant to these restriction enzymes. Most, if not all, of the molecules were either resistant to BamI and sensitive to EcoRI or sensitive to BamI and resistant to EcoRI. After denaturation and renaturation of the cleavage products of ML HPV DNA by a mixture of the two enzymes, the circular “heteroduplexes” formed showed one to three heterology loops corresponding to about 4 to 8% of the genome length. No sequence homology was detected between ML and plantar HPV DNAs by cRNA-DNA filter hybridization, by measuring the reassociation kinetics of an iodinated plantar HPV DNA in the presence of a 25-fold excess of ML HPV DNA, or by the heteroduplex technique. The two viruses had distinct electrophoretic polypeptide patterns and showed no antigenic cross-reaction by immunodiffusion or immunofluorescence techniques. Preliminary cRNA-DNA hybridization experiments, using viral DNAs from single or pooled plantar or hand warts, suggest that hand common warts are associated with viruses similar or related to ML HPV. The existence of at least two distinct types of HPVs that cause skin warts was demonstrated; they were provisionally called HPV type 1 and HPV type 2, with plantar HPV and ML HPV as prototypical viruses, respectively. Images PMID:198572

Spin-Orbit Torque-Assisted Switching in Magnetic Insulator Thin Films with Perpendicular Magnetic Anisotropy

NASA Astrophysics Data System (ADS)

Wu, Mingzhong

As an in-plane charge current flows in a heavy metal film with spin-orbit coupling, it produces a torque that can induce magnetization switching in a neighboring ferromagnetic metal film. Such spin-orbit torque (SOT)-induced switching has been studied extensively in recent years and has shown higher efficiency than switching using conventional spin-transfer torque. This presentation reports the SOT-assisted switching in heavy metal/magnetic insulator systems.1 The experiments made use of Pt/BaFe12O19 bi-layered structures. Thanks to its strong spin-orbit coupling, Pt has been widely used to produce pure spin currents in previous studies. BaFe12O19 is an M-type barium hexagonal ferrite and is often referred as BaM. It is one of the few magnetic insulators with strong magneto-crystalline anisotropy and shows an effective uniaxial anisotropy field of about 17 kOe. It's found that the switching response in the BaM film strongly depends on the charge current applied to the Pt film. When a constant magnetic field is applied in the film plane, the charge current in the Pt film can switch the normal component of the magnetization (M⊥) in the BaM film between the up and down states. The current also dictates the up and down states of the remnant magnetization when the in-plane field is reduced to zero. When M⊥ is measured by sweeping an in-plane field, the response manifests itself as a hysteresis loop, which evolves in a completely opposite manner if the sign of the charge current is flipped. When the coercivity is measured by sweeping an out-of-plane field, its value can be reduced or increased by as much as about 500 Oe if an appropriate charge current is applied. 1. P. Li, T. Liu, H. Chang, A. Kalitsov, W. Zhang, G. Csaba, W. Li, D. Richardson, A. Demann, G. Rimal, H. Dey, J. S. Jiang, W. Porod, S. Field, J. Tang, M. C. Marconi, A. Hoffmann, O. Mryasov, and M. Wu, Nature Commun. 7:12688 doi: 10.1038/ncomms12688 (2016).

Fate of herbicides in a shallow aerobic aquifer: A continuous field injection experiment (Vejen, Denmark)

NASA Astrophysics Data System (ADS)

Broholm, Mette M.; Rügge, Kirsten; Tuxen, Nina; HøJberg, Anker L.; MosbæK, Hans; Bjerg, Poul L.

2001-12-01

A continuous, natural gradient, field injection experiment, involving six herbicides and a tracer, was performed in a shallow aerobic aquifer near Vejen, Denmark. Bentazone, (±)-2-(4-chloro-2-methylphenoxy) propanoic acid (MCPP), dichlorprop, isoproturon, and the dichlobenil metabolite 2,6-dichlor-benzamide (BAM) were injected along with 2-methyl-4,6-dinitrophenol (not discussed in this paper) and the tracer bromide. The injection lasted for 216 days and created a continuous plume in the aquifer. The plume was monitored in three dimensions in 96 multilevel samplers of 6-9 points each for 230 days, with selected individual points for a longer period. The bromide plume followed a complex path through the monitoring network downgradient of the injection wells. The plume movement was controlled by spatially varied hydraulic conductivities of the sand deposit and influenced by asynchronous seasonal variation in groundwater potentials. An average flow velocity of 0.5 m/d was observed, as depicted by bromide. Bentazone, BAM, MCPP, and dichlorprop retardation was negligible, and only slight retardation of isoproturon was observed in the continuous injection experiment and a preceding pulse experiment. No degradation of bentazone was observed in the aerobic aquifer during the monitoring period. BAM and isoproturon were not degraded within 5 m downgradient of the injection. The two phenoxy acids MCPP and dichlorprop were both degraded in the aerobic aquifer. Near the source a lag phase was observed followed by fast degradation of the phenoxy acids, indicating growth kinetics. The phenoxy acids were completely degraded within l m downgradient of the injection wells, resulting in the plumes being divided into small plumes at the injection wells and pulses farther downgradient. During the lag phase, phenoxy acids had spread beyond the 25 m long monitoring network. However, the mass of the phenoxy acids passing the 10-25 m fences never matched the corresponding bentazone or bromide masses, and the pulse was observed to shrink in size. This indicates that this pulse of phenoxy acids was being partially degraded at a low rate as it traveled through the aquifer.

Nitrogen-rich salts based on the energetic [monoaquabis(N,N-bis(1H-tetrazol-5-yl)amine)-zinc(II)] anion: a promising design in the development of new energetic materials.

PubMed

Li, Fugang; Bi, Yangang; Zhao, Wenyuan; Zhang, Tonglai; Zhou, Zunning; Yang, Li

2015-02-16

Nitrogen-rich energetic salts involving various cations (lithium, 1; ammonium, 2; hydrazinium, 3; hydroxylammonium, 4; guanidinium, 5; aminoguanidinium, 6; diaminoguanidinium, 7; and triaminoguanidinium, 8) based on nitrogen-rich anion [Zn(BTA)2(H2O)](2-) (N% = 65.37, BTA = N,N-bis[1H-tetrazol-5-yl]amine anion) were synthesized with a simple method. The crystal structures of all compounds except 1, 2, and 6 were determined by single-crystal X-ray diffraction and fully characterized by elemental analysis and FT-IR spectroscopy. The thermal stabilities were investigated by differential scanning calorimetry (DSC). The DSC results show that all compounds exhibit high thermal stabilities (decomposition temperature >200 °C). Additionally, the heats of formation were calculated on the basis of the experimental constant-volume energies of combustion measured by using bomb calorimetry. Lastly, the sensitivities toward impact and friction were assessed according to Bundesamt für Materialforschung (BAM) standard methods.

A Massively Parallel Computational Method of Reading Index Files for SOAPsnv.

PubMed

Zhu, Xiaoqian; Peng, Shaoliang; Liu, Shaojie; Cui, Yingbo; Gu, Xiang; Gao, Ming; Fang, Lin; Fang, Xiaodong

2015-12-01

SOAPsnv is the software used for identifying the single nucleotide variation in cancer genes. However, its performance is yet to match the massive amount of data to be processed. Experiments reveal that the main performance bottleneck of SOAPsnv software is the pileup algorithm. The original pileup algorithm's I/O process is time-consuming and inefficient to read input files. Moreover, the scalability of the pileup algorithm is also poor. Therefore, we designed a new algorithm, named BamPileup, aiming to improve the performance of sequential read, and the new pileup algorithm implemented a parallel read mode based on index. Using this method, each thread can directly read the data start from a specific position. The results of experiments on the Tianhe-2 supercomputer show that, when reading data in a multi-threaded parallel I/O way, the processing time of algorithm is reduced to 3.9 s and the application program can achieve a speedup up to 100×. Moreover, the scalability of the new algorithm is also satisfying.

Friction Sensitivity of Primary Explosives

DTIC Science & Technology

1982-09-01

diffeomI from. Report) ISI. SUPPLEMENTARY NOTES It. KEY WORDS (Contflnuo on rvotr.. oldo. it nec~oaoty and Identify by block ri,uobr) Friction...friction senisitivity. Primary explosives RD 1333 lead azide, dextrinated lead azide, polyvinyl-alcohol (PVA)-lead a~.ide, colloidal lead azide, nocrnal lead...results for dextrinated lead azide duPont 52-127 13 4 A comparison of friction data at 10% probability of initiation 14 FIGURES 1 Working surfaces of BAM

Assembly of the β-Barrel Outer Membrane Proteins in Gram-Negative Bacteria, Mitochondria, and Chloroplasts

PubMed Central

Misra, Rajeev

2012-01-01

In the last decade, there has been an explosion of publications on the assembly of β-barrel outer membrane proteins (OMPs), which carry out diverse cellular functions, including solute transport, protein secretion, and assembly of protein and lipid components of the outer membrane. Of the three outer membrane model systems—Gram-negative bacteria, mitochondria and chloroplasts—research on bacterial and mitochondrial systems has so far led the way in dissecting the β-barrel OMP assembly pathways. Many exciting discoveries have been made, including the identification of β-barrel OMP assembly machineries in bacteria and mitochondria, and potentially the core assembly component in chloroplasts. The atomic structures of all five components of the bacterial β-barrel assembly machinery (BAM) complex, except the β-barrel domain of the core BamA protein, have been solved. Structures reveal that these proteins contain domains/motifs known to facilitate protein-protein interactions, which are at the heart of the assembly pathways. While structural information has been valuable, most of our current understanding of the β-barrel OMP assembly pathways has come from genetic, molecular biology, and biochemical analyses. This paper provides a comparative account of the β-barrel OMP assembly pathways in Gram-negative bacteria, mitochondria, and chloroplasts. PMID:27335668

The Klebsiella pneumoniae YfgL (BamB) lipoprotein contributes to outer membrane protein biogenesis, type-1 fimbriae expression, anti-phagocytosis, and in vivo virulence

PubMed Central

Hsieh, Pei-Fang; Hsu, Chun-Ru; Chen, Chun-Tang; Lin, Tzu-Lung; Wang, Jin-Town

2016-01-01

ABSTRACT Klebsiella pneumoniae is an opportunistic pathogen that causes several kinds of infections, including pneumonia, bacteremia, urinary tract infection and community-acquired pyogenic liver abscess (PLA). Adhesion is the critical first step in the infection process. Our previous work demonstrated that the transcellular translocation is exploited by K. pneumoniae strains to migrate from the gut flora into other tissues, resulting in systemic infections. However, the initial stages of K. pneumoniae infection remain unclear. In this study, we demonstrated that a K. pneumoniae strain deleted for yfgL (bamB) exhibited reduced adherence to and invasion of host cells; changed biogenesis of major β-barrel outer membrane proteins; decreased transcriptional expression of type-1 fimbriae; and increased susceptibility to vancomycin and erythromycin. The yfgL deletion mutant also had reduced ability to against neutrophil phagocytosis; exhibited decreased induction of host IL-6 production; and was profoundly attenuated for virulence in a K. pneumoniae model of bacteremia. Thus, the K. pneumoniae YfgL lipoprotein mediates in outer membrane proteins biogenesis and is crucial for anti-phagocytosis and survival in vivo. These data provide a new insight for K. pneumoniae attachment and such knowledge could facilitate preventive therapies or alternative therapies against K. pneumoniae. PMID:27029012

Nanoparticles: Nanoscale Systems for Medical Applications

NASA Astrophysics Data System (ADS)

Wadkins, David Allen

The goal of this project was to develop a series of nano platforms for single cell analysis and drug delivery. Nanoparticles are a promising option to improve our medical therapies by controlling biodistribution and pharmacokinetics of therapeutics. Nanosystems also offer significant opportunity to improve current imaging modalities. The systems developed during this thesis work can be foundations for developing advanced therapies for obesity and improving our fundamental understandings of single cell behavior. The first of the two systems we attempt to create was a drug delivery system that could selectively target adipose tissue to deliver uncoupling agents and drive browning of adipose tissue and associated weight loss. Protonophores have a history of significant toxic side effects in cardiac and neuronal tissues a recently discovered protonophore, but BAM-15, has been shown to have reduced cytotoxicity. We hypothesized that the altered biodistribution of BAM-15 encapsulated in a nanoparticle could provide systemic weight loss with minimized side effects. The second system developed utilized quantum dots to create a fluorescent barcode that could be repeatedly identified using quantitative fluorescent emission readings. This platform would allow for the tracking of individual cells, allowing repeat interrogation across time and space in complex multicellular environments. Ultimately this work demonstrates the process and complexity involved in developing nanoparticulate systems meant to interact with incredibly complex intracellular environments.

A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane in Escherichia coli*

PubMed Central

Urfer, Matthias; Bogdanovic, Jasmina; Lo Monte, Fabio; Moehle, Kerstin; Zerbe, Katja; Omasits, Ulrich; Ahrens, Christian H.; Pessi, Gabriella; Eberl, Leo; Robinson, John A.

2016-01-01

Increasing antibacterial resistance presents a major challenge in antibiotic discovery. One attractive target in Gram-negative bacteria is the unique asymmetric outer membrane (OM), which acts as a permeability barrier that protects the cell from external stresses, such as the presence of antibiotics. We describe a novel β-hairpin macrocyclic peptide JB-95 with potent antimicrobial activity against Escherichia coli. This peptide exhibits no cellular lytic activity, but electron microscopy and fluorescence studies reveal an ability to selectively disrupt the OM but not the inner membrane of E. coli. The selective targeting of the OM probably occurs through interactions of JB-95 with selected β-barrel OM proteins, including BamA and LptD as shown by photolabeling experiments. Membrane proteomic studies reveal rapid depletion of many β-barrel OM proteins from JB-95-treated E. coli, consistent with induction of a membrane stress response and/or direct inhibition of the Bam folding machine. The results suggest that lethal disruption of the OM by JB-95 occurs through a novel mechanism of action at key interaction sites within clusters of β-barrel proteins in the OM. These findings open new avenues for developing antibiotics that specifically target β-barrel proteins and the integrity of the Gram-negative OM. PMID:26627837

Governance of Offshore IT Outsourcing at Shell Global Functions IT-BAM Development and Application of a Governance Framework to Improve Outsourcing Relationships

NASA Astrophysics Data System (ADS)

de Jong, Floor; van Hillegersberg, Jos; van Eck, Pascal; van der Kolk, Feiko; Jorissen, Rene

The lack of effective IT governance is widely recognized as a key inhibitor to successful global IT outsourcing relationships. In this study we present the development and application of a governance framework to improve outsourcing relationships. The approach used to developing an IT governance framework includes a meta model and a customization process to fit the framework to the target organization. The IT governance framework consists of four different elements (1) organisational structures, (2) joint processes between in- and outsourcer, (3) responsibilities that link roles to processes and (4) a diverse set of control indicators to measure the success of the relationship. The IT governance framework is put in practice in Shell GFIT BAM, a part of Shell that concluded to have a lack of management control over at least one of their outsourcing relationships. In a workshop the governance framework was used to perform a gap analysis between the current and desired governance. Several gaps were identified in the way roles and responsibilities are assigned and joint processes are set-up. Moreover, this workshop also showed the usefulness and usability of the IT governance framework in structuring, providing input and managing stakeholders in the discussions around IT governance.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kasparek, Eva M.; Voelzke, Holger; Scheidemann, Robert

Rigid, closed-cell polyurethane foams are frequently used as cask impact limiters in nuclear materials and hazardous waste transport due to their high energy-absorption potential. When assessing the cask integrity in accidental scenarios based on numerical simulations, a description of the foam damping properties is required for different strain rates and for a wide temperature range with respect to waste heat generation in conjunction with critical operating and environmental conditions. Implementation and adaption of a respective finite element material model strongly relies on an appropriate experimental data base. Even though extensive impact experiments were conducted e.g. in Sandia National Laboratories, Savannahmore » River National Laboratory and by Rolls Royce plc, not all relevant factors were taken into account. Hence, BAM who is in charge of the mechanical evaluation of such packages within the approval procedure in Germany, incorporated systematic test series into a comprehensive research project aimed to develop numerical methods for a couple of damping materials. In a first step, displacement driven compression tests have been performed on confined, cubic specimens at five loading rates ranging from 0.02 mm/s to 3 m/s at temperatures between +90 deg. C and -40 deg. C. Materials include two different polyurethane foam types called FR3718 and FR3730 having densities of 280 kg/m{sup 3} and 488 kg/m{sup 3} from the product line-up of General Plastics Manufacturing Company. Their data was used to adapt an advanced plasticity model allowing for reliably simulating cellular materials under multi-axial compression states. Therefore, an automated parameter identification procedure had been established by combining an artificial neural network with local optimization techniques. Currently, the selected numerical material input values are validated and optimized by means of more complex loading configurations with the prospect of establishing methods applicable to impact limiters under severe accidental conditions. The reference data base is provided by experiments, where weights between 212 kg and 1200 kg have been dropped from heights between 1.25 m and 7 m on confined 10 cm cubic foam specimens. By presenting the deviations between experimental values and the corresponding output of finite element simulations, the potentials and restrictions of the resulting models are highlighted. Systematic compression tests on polyurethane foams had been performed at BAM test site within the framework of a research project on impact limiters for handling casks for radioactive waste. The experimental results had been used to adapt numerical models for simulating the behaviour of different foam types at different temperatures. The loading speed, however, turned out to have a major influence on their flow curves that can not be captured by simple strain-rate dependent multipliers. Especially for guided drop tests that come close to real accidental scenarios there is a significant gap between experimental and numerical results even when applying such advanced material models. Hence, the extensive data base is currently deployed for expanding the standard algorithms to include adequate dynamic hardening factors. (authors)« less

Building the Ferretome

PubMed Central

Sukhinin, Dmitrii I.; Engel, Andreas K.; Manger, Paul; Hilgetag, Claus C.

2016-01-01

Databases of structural connections of the mammalian brain, such as CoCoMac (cocomac.g-node.org) or BAMS (https://bams1.org), are valuable resources for the analysis of brain connectivity and the modeling of brain dynamics in species such as the non-human primate or the rodent, and have also contributed to the computational modeling of the human brain. Another animal model that is widely used in electrophysiological or developmental studies is the ferret; however, no systematic compilation of brain connectivity is currently available for this species. Thus, we have started developing a database of anatomical connections and architectonic features of the ferret brain, the Ferret(connect)ome, www.Ferretome.org. The Ferretome database has adapted essential features of the CoCoMac methodology and legacy, such as the CoCoMac data model. This data model was simplified and extended in order to accommodate new data modalities that were not represented previously, such as the cytoarchitecture of brain areas. The Ferretome uses a semantic parcellation of brain regions as well as a logical brain map transformation algorithm (objective relational transformation, ORT). The ORT algorithm was also adopted for the transformation of architecture data. The database is being developed in MySQL and has been populated with literature reports on tract-tracing observations in the ferret brain using a custom-designed web interface that allows efficient and validated simultaneous input and proofreading by multiple curators. The database is equipped with a non-specialist web interface. This interface can be extended to produce connectivity matrices in several formats, including a graphical representation superimposed on established ferret brain maps. An important feature of the Ferretome database is the possibility to trace back entries in connectivity matrices to the original studies archived in the system. Currently, the Ferretome contains 50 reports on connections comprising 20 injection reports with more than 150 labeled source and target areas, the majority reflecting connectivity of subcortical nuclei and 15 descriptions of regional brain architecture. We hope that the Ferretome database will become a useful resource for neuroinformatics and neural modeling, and will support studies of the ferret brain as well as facilitate advances in comparative studies of mesoscopic brain connectivity. PMID:27242503

Building the Ferretome.

PubMed

Sukhinin, Dmitrii I; Engel, Andreas K; Manger, Paul; Hilgetag, Claus C

2016-01-01

Databases of structural connections of the mammalian brain, such as CoCoMac (cocomac.g-node.org) or BAMS (https://bams1.org), are valuable resources for the analysis of brain connectivity and the modeling of brain dynamics in species such as the non-human primate or the rodent, and have also contributed to the computational modeling of the human brain. Another animal model that is widely used in electrophysiological or developmental studies is the ferret; however, no systematic compilation of brain connectivity is currently available for this species. Thus, we have started developing a database of anatomical connections and architectonic features of the ferret brain, the Ferret(connect)ome, www.Ferretome.org. The Ferretome database has adapted essential features of the CoCoMac methodology and legacy, such as the CoCoMac data model. This data model was simplified and extended in order to accommodate new data modalities that were not represented previously, such as the cytoarchitecture of brain areas. The Ferretome uses a semantic parcellation of brain regions as well as a logical brain map transformation algorithm (objective relational transformation, ORT). The ORT algorithm was also adopted for the transformation of architecture data. The database is being developed in MySQL and has been populated with literature reports on tract-tracing observations in the ferret brain using a custom-designed web interface that allows efficient and validated simultaneous input and proofreading by multiple curators. The database is equipped with a non-specialist web interface. This interface can be extended to produce connectivity matrices in several formats, including a graphical representation superimposed on established ferret brain maps. An important feature of the Ferretome database is the possibility to trace back entries in connectivity matrices to the original studies archived in the system. Currently, the Ferretome contains 50 reports on connections comprising 20 injection reports with more than 150 labeled source and target areas, the majority reflecting connectivity of subcortical nuclei and 15 descriptions of regional brain architecture. We hope that the Ferretome database will become a useful resource for neuroinformatics and neural modeling, and will support studies of the ferret brain as well as facilitate advances in comparative studies of mesoscopic brain connectivity.

Passivity of memristive BAM neural networks with leakage and additive time-varying delays

NASA Astrophysics Data System (ADS)

Wang, Weiping; Wang, Meiqi; Luo, Xiong; Li, Lixiang; Zhao, Wenbing; Liu, Linlin; Ping, Yuan

2018-02-01

This paper investigates the passivity of memristive bidirectional associate memory neural networks (MBAMNNs) with leakage and additive time-varying delays. Based on some useful inequalities and appropriate Lyapunov-Krasovskii functionals (LKFs), several delay-dependent conditions for passivity performance are obtained in linear matrix inequalities (LMIs). Moreover, the leakage delays as well as additive delays are considered separately. Finally, numerical simulations are provided to demonstrate the feasibility of the theoretical results.

Morphogenesis of the Bacillus anthracis Spore

DTIC Science & Technology

2007-02-01

product and plasmid pEO-3 (53) with BamHI and HindIII and ligated the resulting DNA fragments to build pRG23. We passaged pRG23 through E. coli GM1684...to remove debris. The removal of the exosporium was confirmed by elec- tron microscopy (data not shown). Antibody production . To produce a...O. Henriques, and S. M. Cutting (ed.), Bacterial spore formers: probiotics and emerging applications. Horizon Bioscience, Norfolk, United Kingdom

Cloning and Partial Characterization of an Aniline Metabolic Pathway (Preprint)

DTIC Science & Technology

1995-08-03

of aniline to organic acids. The pathway resides on a 20.66 kb BamH1 fragment, and is induced by a broad range of substituted anilines, with para ...methyl substitutions, with preference to additions in the meta and para positions. Metabolism of aniline in CIT1 is initiated by aniline, 1,2...metabolism in E.coli, expressing the cloned pathway was confirmed using HPLC . Cloning, Partial Characterization, Aniline Metabolic Pathway U U

Further Development of a Tissue Engineered Muscle Repair Construct In Vitro for Enhanced Functional Recovery Following Implantation In Vivo in a Murine Model of Volumetric Muscle Loss Injury

DTIC Science & Technology

2012-01-01

ence ( LSD ) correction. Statistical significance was set at an aɘ.05. Statistical analyses were performed using SPSS 18.0. Results BAM...Tissue Eng Part A 16, 1395, 2010. 15. Page, R.L., Malcuit, C., Vilner, L., Vojtic, I., Shaw , S., Hed- blom, E., Hu, J., Pins, G.D., Rolle, M.W., and

Military Climate Resilience Planning and Contemporary Urban Systems Thinking

DTIC Science & Technology

2017-12-11

2011), a partnership that in- cludes military-related organizations such as the Society of American Mili- tary Engineers (SAME). The guide serves to...the American Meteorological Society 93(12):1879–1900. https://doi.org/10.1175/BAMS-D-11-00019.1. TISP. 2011. “2011 Regional Disaster Resilience...authorized documents. DESTROY THIS REPORT WHEN NO LONGER NEEDED. DO NOT RETURN IT TO THE ORIGINATOR. ERDC/CERL MP-17-4 iii Contents Abstract

Managing bile acid diarrhoea

PubMed Central

Walters, Julian R. F.; Pattni, Sanjeev S.

2010-01-01

Bowel symptoms including diarrhoea can be produced when excess bile acids (BA) are present in the colon. This condition, known as bile acid or bile salt malabsorption, has been under recognized, as the best diagnostic method, the 75Se-homocholic acid taurine (SeHCAT) test, is not available in many countries and is not fully utilized in others. Reduced SeHCAT retention establishes that this is a complication of many other gastrointestinal diseases. Repeated studies show SeHCAT tests are abnormal in about 30% of patients otherwise diagnosed as diarrhoea-predominant irritable bowel syndrome or functional diarrhoea, with an estimated population prevalence of around 1%. Recent work suggests that the condition previously called idiopathic bile acid malabsorption (BAM) is not in fact due to a defect in absorption, but results from an overproduction of BA because of defective feedback inhibition of hepatic bile acid synthesis, a function of the ileal hormone fibroblast growth factor 19 (FGF19). The approach to treatment currently depends on binding excess BA, to reduce their secretory actions, using colestyramine, colestipol and, most recently, colesevelam. Colesevelam has a number of potential advantages that merit further investigation in trials directed at patients with bile acid diarrhoea. PMID:21180614

Managing bile acid diarrhoea.

PubMed

Walters, Julian R F; Pattni, Sanjeev S

2010-11-01

Bowel symptoms including diarrhoea can be produced when excess bile acids (BA) are present in the colon. This condition, known as bile acid or bile salt malabsorption, has been under recognized, as the best diagnostic method, the (75)Se-homocholic acid taurine (SeHCAT) test, is not available in many countries and is not fully utilized in others. Reduced SeHCAT retention establishes that this is a complication of many other gastrointestinal diseases. Repeated studies show SeHCAT tests are abnormal in about 30% of patients otherwise diagnosed as diarrhoea-predominant irritable bowel syndrome or functional diarrhoea, with an estimated population prevalence of around 1%. Recent work suggests that the condition previously called idiopathic bile acid malabsorption (BAM) is not in fact due to a defect in absorption, but results from an overproduction of BA because of defective feedback inhibition of hepatic bile acid synthesis, a function of the ileal hormone fibroblast growth factor 19 (FGF19). The approach to treatment currently depends on binding excess BA, to reduce their secretory actions, using colestyramine, colestipol and, most recently, colesevelam. Colesevelam has a number of potential advantages that merit further investigation in trials directed at patients with bile acid diarrhoea.

Certified ion implantation fluence by high accuracy RBS.

PubMed

Colaux, Julien L; Jeynes, Chris; Heasman, Keith C; Gwilliam, Russell M

2015-05-07

From measurements over the last two years we have demonstrated that the charge collection system based on Faraday cups can robustly give near-1% absolute implantation fluence accuracy for our electrostatically scanned 200 kV Danfysik ion implanter, using four-point-probe mapping with a demonstrated accuracy of 2%, and accurate Rutherford backscattering spectrometry (RBS) of test implants from our quality assurance programme. The RBS is traceable to the certified reference material IRMM-ERM-EG001/BAM-L001, and involves convenient calibrations both of the electronic gain of the spectrometry system (at about 0.1% accuracy) and of the RBS beam energy (at 0.06% accuracy). We demonstrate that accurate RBS is a definitive method to determine quantity of material. It is therefore useful for certifying high quality reference standards, and is also extensible to other kinds of samples such as thin self-supporting films of pure elements. The more powerful technique of Total-IBA may inherit the accuracy of RBS.

Distributed acoustic fibre optic sensors for condition monitoring of pipelines

NASA Astrophysics Data System (ADS)

Hussels, Maria-Teresa; Chruscicki, Sebastian; Habib, Abdelkarim; Krebber, Katerina

2016-05-01

Industrial piping systems are particularly relevant to public safety and the continuous availability of infrastructure. However, condition monitoring systems based on many discrete sensors are generally not well-suited for widespread piping systems due to considerable installation effort, while use of distributed fibre-optic sensors would reduce this effort to a minimum. Specifically distributed acoustic sensing (DAS) is employed for detection of third-party threats and leaks in oil and gas pipelines in recent years and can in principle also be applied to industrial plants. Further possible detection routes amenable by DAS that could identify damage prior to emission of medium are subject of a current project at BAM, which aims at qualifying distributed fibre optic methods such as DAS as a means for spatially continuous monitoring of industrial piping systems. Here, first tests on a short pipe are presented, where optical fibres were applied directly to the surface. An artificial signal was used to define suitable parameters of the measurement system and compare different ways of applying the sensor.

Phases, line tension and pattern formation in molecularly thin films at the air-water interface

NASA Astrophysics Data System (ADS)

Mandal, Pritam

A Langmuir film, which is a molecularly thin insoluble film on a liquid substrate, is one practical realization of a quasi-two dimensional matter. The major advantages of this system for the study of phase separation and phase co-existence are (a) it allows accurate control of the components and molecular area of the film and (b) it can be studied by various methods that require very flat films. Phase separation in molecularly thin films plays an important role in a range of systems from biomembranes to biosensors. For example, phase-separated lipid nano-domains in biomembranes are thought to play crucial roles in membrane function. I use Brewster Angel Microscopy (BAM) coupled with Fluorescence Microscopy (FM) and static Light Scattering Microscopy (LSM) to image phases and patterns within Langmuir films. The three microscopic techniques --- BAM, FM and LSM --- are complimentary to each other, providing distinct sets of information. They allow direct comparison with literature results in lipid systems. I have quantitatively validated the use of detailed hydrodynamic simulations to determine line tension in monolayers. Line tension decreases as temperature rises. This decrease gives us information on the entropy associated with the line, and thus about line structure. I carefully consider the thermodynamics of line energy and entropy to make this connection. In the longer run, LSM will be exploited to give us further information about line structure. I have also extended the technique by testing it on domains within the curved surface of a bilayer vesicle. I also note that in the same way that the presence of surface-active agents, known as surfactants, affects surface energy, the addiction of line active agents alters the inter-phase line energy. Thus my results set to stage to systematically study the influence of line active agents ---'linactants' --- on the inter-phase line energy. Hierarchal self-assembled chiral patterns were observed as a function of temperature. I found that the appearance of these domains could be explained with a simple uniaxial optical axis in the underlying structure, which is the first critical step to understanding the origin of these patterns.

Investigating the role of MRGPRC11 and capsaicin-sensitive afferent nerves in the anti-influenza effects exerted by SLIGRL-amide in murine airways.

PubMed

Chang, Amy Y; Mann, Tracy S; McFawn, Peter K; Han, Liang; Dong, Xinzhong; Henry, Peter J

2016-05-23

The hexapeptide SLIGRL-amide activates protease-activated receptor-2 (PAR-2) and mas-related G protein-coupled receptor C11 (MRGPRC11), both of which are known to be expressed on populations of sensory nerves. SLIGRL-amide has recently been reported to inhibit influenza A (IAV) infection in mice independently of PAR-2 activation, however the explicit roles of MRGPRC11 and sensory nerves in this process are unknown. Thus, the principal aim of this study was to determine whether SLIGRL-amide-induced inhibition of influenza infection is mediated by MRGPRC11 and/or by capsaicin-sensitive sensory nerves. The inhibitory effect of SLIGRL-amide on IAV infection observed in control mice in vivo was compared to effects produced in mice that did not express MRGPRC11 (mrgpr-cluster∆ (-/-) mice) or had impaired sensory nerve function (induced by chronic pre-treatment with capsaicin). Complementary mechanistic studies using both in vivo and ex vivo approaches investigated whether the anti-IAV activity of SLIGRL-amide was (1) mimicked by either activators of MRGPRC11 (BAM8-22) or by activators (acute capsaicin) or selected mediators (substance P, CGRP) of sensory nerve function, or (2) suppressed by inhibitors of sensory nerve function (e.g. NK1 receptor antagonists). SLIGRL-amide and BAM8-22 dose-dependently inhibited IAV infection in mrgpr-cluster∆ (-/-) mice that do not express MRGPRC11. In addition, SLIGRL-amide and BAM8-22 each inhibited IAV infection in capsaicin-pre-treated mice that lack functional sensory nerves. Furthermore, the anti-IAV activity of SLIGRL-amide was not mimicked by the sensory neuropeptides substance P or CGRP, nor blocked by either NK1 (L-703,606, RP67580) and CGRP receptor (CGRP8-37) antagonists. Direct stimulation of airway sensory nerves through acute exposure to the TRPV1 activator capsaicin also failed to mimic SLIGRL-amide-induced inhibition of IAV infectivity. The anti-IAV activity of SLIGRL-amide was mimicked by the purinoceptor agonist ATP, a direct activator of mucus secretion from airway epithelial cells. Additionally, both SLIGRL-amide and ATP stimulated mucus secretion and inhibited IAV infectivity in mouse isolated tracheal segments. SLIGRL-amide inhibits IAV infection independently of MRGPRC11 and independently of capsaicin-sensitive, neuropeptide-releasing sensory nerves, and its secretory action on epithelial cells warrants further investigation.

A reassessment and review of the Bam earthquake five years onward: what was done wrong?

PubMed

Motamedi, Mohammad Hosein Kalantar; Saghafinia, Masound; Bararani, Azadeh Hassani; Panahi, Farzad

2009-01-01

An earthquake measuring 6.6 on the Richter scale on 23 December 2003 devastated the city of Bam in southeastern Iran. During the response and recovery phases, considerable shortcomings were discovered. The dire situation in the affected area, a variety of urgently required interventions, and the large number of aid organizations involved brought about difficulties in management, coordination, and communication among authorities and aid organizations. This article highlights flaws in management in the various aspects of this disaster in order to assess what was done, and what should be done to overcome these shortcomings in future disasters. A retrospective review of the various aspects of management related to the Bam disaster was done via the assessment of files, multi-center studies, governmental data, and available literature from 2003-2008. A review of the available data relevant to search and rescue operations and short-term aid provision revealed flaws in different aspects of disaster management including personnel, the transfer of the injured, availability medical supplies, treatment planning, problems concerning the composition of treatment forces dispatched to the region, distribution of tasks among treatment workers, transferring of equipment, availability of facilities, and lack of coordination among the organizations responsible for the management of the disaster. Most of the aforementioned issues have been addressed. A comprehensive disaster management plan must not be limited only to the response phase, but rather must include: preparedness, recovery with optimal legislation and budgeting, improvement of healthcare facilities, and organized communication channels between the different governmental departments. This important issue has been addressed, and a disaster management organization under the supervision of the President has been established, developing a national search and rescue strategy and protocol for unified managerial organization, an alert system, an international disaster command system (under which search and rescue and emergency medical service teams can be deployed, increasing the efficacy and coordination of the arrival of foreign teams and the construction field hospitals), and developing a flowchart to coordinate international agencies and the domestic authorities in charge. Continuous education, training of the general population, conducting periodic exercise drills, and provision for prepared task force mobilization in disaster management all are important aspects of the management of disasters due to natural hazards.

New restriction enzymes discovered from Escherichia coli clinical strains using a plasmid transformation method

PubMed Central

Kasarjian, Julie K. A.; Iida, Masatake; Ryu, Junichi

2003-01-01

The presence of restriction enzymes in bacterial cells has been predicted by either classical phage restriction-modification (R-M) tests, direct in vitro enzyme assays or more recently from bacterial genome sequence analysis. We have applied phage R-M test principles to the transformation of plasmid DNA and established a plasmid R-M test. To validate this test, six plasmids that contain BamHI fragments of phage lambda DNA were constructed and transformed into Escherichia coli strains containing known R-M systems including: type I (EcoBI, EcoAI, Eco124I), type II (HindIII) and type III (EcoP1I). Plasmid DNA with a single recognition site showed a reduction of relative efficiency of transformation (EOT = 10–1–10–2). When multiple recognition sites were present, greater reductions in EOT values were observed. Once established in the cell, the plasmids were subjected to modification (EOT = 1.0). We applied this test to screen E.coli clinical strains and detected the presence of restriction enzymes in 93% (14/15) of cells. Using additional subclones and the computer program, RM Search, we identified four new restriction enzymes, Eco377I, Eco585I, Eco646I and Eco777I, along with their recognition sequences, GGA(8N)ATGC, GCC(6N)TGCG, CCA(7N)CTTC, and GGA(6N)TATC, respectively. Eco1158I, an isoschizomer of EcoBI, was also found in this study. PMID:12595571

Global asymptotic stability of hybrid bidirectional associative memory neural networks with time delays

NASA Astrophysics Data System (ADS)

Arik, Sabri

2006-02-01

This Letter presents a sufficient condition for the existence, uniqueness and global asymptotic stability of the equilibrium point for bidirectional associative memory (BAM) neural networks with distributed time delays. The results impose constraint conditions on the network parameters of neural system independently of the delay parameter, and they are applicable to all bounded continuous non-monotonic neuron activation functions. The results are also compared with the previous results derived in the literature.

Advanced Microwave Ferrite Research (AMFeR): Phase Two

DTIC Science & Technology

2006-12-31

motion for the single crystal LPE films were a qualitative success, but a complete set of parameters for these films has not yet been achieved. Key...biasing field. In order to address these issues, we investigated and optimized a new LPE flux system to grow high quality thick films and bulk single...self-biased circulators. III. Methodology: BaM thick film and bulk single crystal growth by LPE process BaFe 120 19 flux melt was prepared from a

In Vivo Imaging of mdrla Gene Expression

DTIC Science & Technology

2005-06-01

svImJ mouse strain, compatible with the ES cells used in our Transgenic Mouse Facility. b. Engineer PGK-neo and Renilla luciferase cassettes...inserted between the two loxP sites, upstream of the Neo cassette. A cloning strategy was then devised to fuse Renilla luciferase in-frame with the...sites: B, BamHI; E, EcoRI; S, ScaI. PGK-neo: neo under the control of the PGK promoter. Luc: Renilla luciferase fused in- frame with the translated

Molecular organization of a water-insoluble iridium(III) complex in mixed monolayers.

PubMed

Giner-Casares, Juan J; Pérez-Morales, Marta; Bolink, Henk J; Muñoz, Eulogia; de Miguel, Gustavo; Martín-Romero, María T; Camacho, Luis

2007-11-01

In this work, organized mixed monolayers containing a cationic water-insoluble iridium(III) complex, Ir-dye, [Ir(ppy)(2)(tmphen)]PF(6), (tmphen = 3,4,7,8-tetramethyl-1,10-phenanthroline, and ppy = 2-phenylpyridine), and an anionic lipid matrix, DMPA, dimyristoyl-phosphatidic acid, with different molar proportions, were formed by the co-spreading method at the air-water interface. The presence of the dye at the interface, as well as the molecular organization of the mixed films, is deduced from surface techniques such as pi-A isotherms, Brewster angle microscopy (BAM) and reflection spectroscopy. The results obtained remark the formation of an equimolar mixed film, Ir-dye/DMPA = 1:1. BAM images reveal a whole homogeneous monolayer, with gradually increasing reflectivity along the compression process up to reaching the collapse of this equimolecular monolayer at pi approximately equal to 37 mNm(-1). Increasing the molar ratio of DMPA in the mixture, the excess of lipid molecules organizes themselves forming dark flower-like domains of pure DMPA at high surface pressures, coexisting with the mixed Ir-dye/DMPA = 1:1 monolayer. On the other hand, unstable mixed monolayers are obtained by using an initial dye surface concentration higher than the equimolecular one. These mixed Langmuir monolayers have been successfully transferred onto solid substrates by the LB (Langmuir-Blodgett) technique.

FASTdoop: a versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications.

PubMed

Ferraro Petrillo, Umberto; Roscigno, Gianluca; Cattaneo, Giuseppe; Giancarlo, Raffaele

2017-05-15

MapReduce Hadoop bioinformatics applications require the availability of special-purpose routines to manage the input of sequence files. Unfortunately, the Hadoop framework does not provide any built-in support for the most popular sequence file formats like FASTA or BAM. Moreover, the development of these routines is not easy, both because of the diversity of these formats and the need for managing efficiently sequence datasets that may count up to billions of characters. We present FASTdoop, a generic Hadoop library for the management of FASTA and FASTQ files. We show that, with respect to analogous input management routines that have appeared in the Literature, it offers versatility and efficiency. That is, it can handle collections of reads, with or without quality scores, as well as long genomic sequences while the existing routines concentrate mainly on NGS sequence data. Moreover, in the domain where a comparison is possible, the routines proposed here are faster than the available ones. In conclusion, FASTdoop is a much needed addition to Hadoop-BAM. The software and the datasets are available at http://www.di.unisa.it/FASTdoop/ . umberto.ferraro@uniroma1.it. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Elderly peoples’ experiences of nursing homes in Bam city: A qualitative study

PubMed Central

Mohammadinia, Neda; Rezaei, Mohammad Ali; Atashzadeh-Shoorideh, Foroozan

2017-01-01

Background With the increasing number of elderly, especially in recent decades, transfer to nursing homes and the number of centers has also increased but experiences and problems of elders in these centers is less considered. So, the goal of this study is to explore the Elderly peoples’ experiences of nursing homes. Methods The current research was performed using a phenomenological approach in 2016. Participation in the study is comprised of the elderly residents in a nursing home in Bam city who were selected based on an objective-oriented approach. The sampling was done until data saturation. Data collection methods were observation and an unstructured and in-depth interview. Data were analyzed using seven-stage Colaizzi process. Results In total, fifteen 68 – 82 years old people participated in our study and 52 primary and conceptual codes that were eventually categorized in five main themes (sense of rejection, sense of daily routine, impaired of communications, sense of hardship and mental obsession) and ten sub-themes emerged. Conclusion Overall, most of the elders were not satisfied with the conditions. It seems that helpful, community and family education to acculturate respect for the elderly in the community, teach proper coping strategies, use the elderly’s experiences, and consultation with them could be a way to maintain a sense of usefulness, independence and to prevent them from sensing monotonous and routine rhythm of life. PMID:28979736

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

PubMed Central

2012-01-01

Background Next-generation sequencing technologies have become important tools for genome-wide studies. However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores are used in downstream analyses, these inaccuracies can have a significant impact on the results. Results Here we present ReQON, a tool that recalibrates the base quality scores from an input BAM file of aligned sequencing data using logistic regression. ReQON also generates diagnostic plots showing the effectiveness of the recalibration. We show that ReQON produces quality scores that are both more accurate, in the sense that they more closely correspond to the probability of a sequencing error, and do a better job of discriminating between sequencing errors and non-errors than the original quality scores. We also compare ReQON to other available recalibration tools and show that ReQON is less biased and performs favorably in terms of quality score accuracy. Conclusion ReQON is an open source software package, written in R and available through Bioconductor, for recalibrating base quality scores for next-generation sequencing data. ReQON produces a new BAM file with more accurate quality scores, which can improve the results of downstream analysis, and produces several diagnostic plots showing the effectiveness of the recalibration. PMID:22946927

Factor IX gene haplotypes in Amerindians.

PubMed

Franco, R F; Araújo, A G; Zago, M A; Guerreiro, J F; Figueiredo, M S

1997-02-01

We have determined the haplotypes of the factor IX gene for 95 Indians from 5 Brazilian Amazon tribes: Wayampí, Wayana-Apalaí, Kayapó, Arára, and Yanomámi. Eight polymorphisms linked to the factor IX gene were investigated: MseI (at 5', nt -698), BamHI (at 5', nt -561), DdeI (intron 1), BamHI (intron 2), XmnI (intron 3), TaqI (intron 4), MspI (intron 4), and HhaI (at 3', approximately 8 kb). The results of the haplotype distribution and the allele frequencies for each of the factor IX gene polymorphisms in Amerindians were similar to the results reported for Asian populations but differed from results for other ethnic groups. Only five haplotypes were identified within the entire Amerindian study population, and the haplotype distribution was significantly different among the five tribes, with one (Arára) to four (Wayampí) haplotypes being found per tribe. These findings indicate a significant heterogeneity among the Indian tribes and contrast with the homogeneous distribution of the beta-globin gene cluster haplotypes but agree with our recent findings on the distribution of alpha-globin gene cluster haplotypes and the allele frequencies for six VNTRs in the same Amerindian tribes. Our data represent the first study of factor IX-associated polymorphisms in Amerindian populations and emphasizes the applicability of these genetic markers for population and human evolution studies.

An Independent Assessment of Anthropogenic Attribution Statements for Recent Extreme Temperature and Rainfall Events

DOE Office of Scientific and Technical Information (OSTI.GOV)

Angélil, Oliver; Stone, Dáithí; Wehner, Michael

The annual "State of the Climate" report, published in the Bulletin of the American Meteorological Society (BAMS), has included a supplement since 2011 composed of brief analyses of the human influence on recent major extreme weather events. There are now several dozen extreme weather events examined in these supplements, but these studies have all differed in their data sources as well as their approaches to defining the events, analyzing the events, and the consideration of the role of anthropogenic emissions. This study reexamines most of these events using a single analytical approach and a single set of climate model andmore » observational data sources. In response to recent studies recommending the importance of using multiple methods for extreme weather event attribution, results are compared from these analyses to those reported in the BAMS supplements collectively, with the aim of characterizing the degree to which the lack of a common methodological framework may or may not influence overall conclusions. Results are broadly similar to those reported earlier for extreme temperature events but disagree for a number of extreme precipitation events. Based on this, it is advised that the lack of comprehensive uncertainty analysis in recent extreme weather attribution studies is important and should be considered when interpreting results, but as yet it has not introduced a systematic bias across these studies.« less

An Independent Assessment of Anthropogenic Attribution Statements for Recent Extreme Temperature and Rainfall Events

DOE PAGES

Angélil, Oliver; Stone, Dáithí; Wehner, Michael; ...

2016-12-16

The annual "State of the Climate" report, published in the Bulletin of the American Meteorological Society (BAMS), has included a supplement since 2011 composed of brief analyses of the human influence on recent major extreme weather events. There are now several dozen extreme weather events examined in these supplements, but these studies have all differed in their data sources as well as their approaches to defining the events, analyzing the events, and the consideration of the role of anthropogenic emissions. This study reexamines most of these events using a single analytical approach and a single set of climate model andmore » observational data sources. In response to recent studies recommending the importance of using multiple methods for extreme weather event attribution, results are compared from these analyses to those reported in the BAMS supplements collectively, with the aim of characterizing the degree to which the lack of a common methodological framework may or may not influence overall conclusions. Results are broadly similar to those reported earlier for extreme temperature events but disagree for a number of extreme precipitation events. Based on this, it is advised that the lack of comprehensive uncertainty analysis in recent extreme weather attribution studies is important and should be considered when interpreting results, but as yet it has not introduced a systematic bias across these studies.« less

The histidine permease gene (HIP1) of Saccharomyces cerevisiae.

PubMed

Tanaka, J; Fink, G R

1985-01-01

The histidine-specific permease gene (HIP1) of Saccharomyces cerevisiae has been mapped, cloned, and sequenced. The HIP1 gene maps to the right arm of chromosome VII, approx. 11 cM distal to the ADE3 gene. The gene was isolated as an 8.6-kb BamHI-Sau3A fragment by complementation of the histidine-specific permease deficiency in recipient yeast cells. We sequenced a 2.4-kb subfragment of this BamHI-Sau3A fragment containing the HIP1 gene and identified a 1596-bp open reading frame (ORF). We confirmed the assignment of the 1596-bp ORF as the HIP1 coding sequence by sequencing a hip1 nonsense mutation. Analysis of the amino acid (aa) sequence of the HIP1 gene reveals several hydrophobic stretches, but shows no obvious N-terminal signal peptide. We have constructed a deletion of the HIP1 gene in vitro and replaced the wild-type copy of the gene with this deletion. The hip1 deletion mutant can grow when it is supplemented with 30 mM histidine, 50 times the amount required for the growth of HIP1 cells. Revertants of this deletion mutant able to grow on a normal level of histidine arise by mutation in unlinked genes. Both these observations suggest that there are additional, low-affinity pathways for histidine uptake.

The SPARC_LAB femtosecond synchronization for electron and photon pulsed beams

NASA Astrophysics Data System (ADS)

Bellaveglia, M.; Gallo, A.; Piersanti, L.; Pompili, R.; Gatti, G.; Anania, M. P.; Petrarca, M.; Villa, F.; Chiadroni, E.; Biagioni, A.; Mostacci, A.

2015-05-01

The SPARC LAB complex hosts a 150 MeV electron photo-injector equipped with an undulator for FEL production (SPARC) together with a high power TW laser (FLAME). Recently the synchronization system reached the performance of < 100 fsRMS relative jitter between lasers, electron beam and RF accelerating fields. This matches the requirements for next future experiments: (i) the production of X-rays by means of Thomson scattering (first collisions achieved in 2014) and (ii) the particle driven PWFA experiment by means of multiple electron bunches. We report about the measurements taken during the machine operation using BAMs (Bunch Arrival Monitors) and EOS (Electro-Optical Sampling) system. A new R and D activity concerning the LWFA using the external injection of electron bunches in a plasma generated by the FLAME laser pulse is under design. The upgrade of the synchronization system is under way to guarantee the < 30 fs RMS jitter required specification. It foresees the transition from electrical to optical architecture that mainly affects the reference signal distribution and the time of arrival detection performances. The new system architecture is presented together with the related experimental data.

Destabilizing Effects of Impulse in Delayed Bam Neural Networks

NASA Astrophysics Data System (ADS)

Li, Chuandong; Li, Chaojie; Liu, Chao

This paper further studies the global exponential stability of the equilibrium point of the delayed bidirectional associative memory (DBAM) neural networks with impulse effects. Several results characterizing the aggregated effects of impulse and dynamical property of the impulse-free DBAM on the exponential stability of the considered DBAM have been established. It is shown that the impulsive DBAM will preserve the global exponential stability of the impulse-free DBAM even if the impulses have enlarging effects on the states of neurons.

Delay-Dependent Stability Criterion for Bidirectional Associative Memory Neural Networks with Interval Time-Varying Delays

NASA Astrophysics Data System (ADS)

Park, Ju H.; Kwon, O. M.

In the letter, the global asymptotic stability of bidirectional associative memory (BAM) neural networks with delays is investigated. The delay is assumed to be time-varying and belongs to a given interval. A novel stability criterion for the stability is presented based on the Lyapunov method. The criterion is represented in terms of linear matrix inequality (LMI), which can be solved easily by various optimization algorithms. Two numerical examples are illustrated to show the effectiveness of our new result.

[Morbidity with temporary disability in railway tunnel workers].

PubMed

Kudrin, V A; Prokhorov, A A

2003-01-01

The paper presents data on the health status of a large professional group of transport building workers--those who build BAM railway tunnels and those who build Moscow and Saint Petersburg underground stations. Major factors that are associated with underground work and that form the level of morbidity with temporary disability are identified. Respiratory, osteomuscular, digestive diseases, accidents, intoxications, and injuries are predominant in the structure of temporary disability. Lines of better organization of therapeutical-and-prophylactic aid to this contingent are defined.

Homology between genes for aromatic hydrocarbon degradation in surface and deep-subsurface sphingomonas strains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, E.; Aversano, P.J.; Zylstra, G.J.

The cloned genes for aromatic hydrocarbon degradation from Sphingomonas yanoikuyae B1 were utilized in Southern hybridization experiments with Sphingomonas strains from the surface and deep-subsurface environments. One hybridization pattern was obtained with BamHI-digested genomic DNAs for two surface strains, while a differing pattern was seen for five deep-subsurface strains. The cross-hybridizing genes were located in the chromosomes of the surface strains and on plasmids in the deep-subsurface strains. 31 refs., 3 figs., 1 tab.

DEFTEST. Defence Technological and Scientific Thesaurus. Volume 1. A - L.

DTIC Science & Technology

1988-05-01

bombin ____a atrasbriioRdus(ins Strategic bombing Deiirtttiasbnn ai bns Tactic! bombing Ribs (bones) Tos bomnbing Bonded costinge Skauls NT Ares...As R? bams WY Combustia - 0 jeium, Engne -4IN Business .ea Enlft*v~A UP Coution kwb A"ob F 01ne Cciu&.fpb Flame luldCobusio Cost omtpson Jaucl UMim...Err CoypWa CUmiamcelons isum Eharrie Inteligence CommiWarie kuaaen IT _ Mltr d communledeon busy . Thdelglc lipence Er &op. Comods" .~w"ETMum"~u ums0

Function of the SpoVAEa and SpoVAF Proteins of Bacillus subtilis Spores

DTIC Science & Technology

2014-06-01

outer surface of the spore’s inner membrane, as SpoVAEa was accessible to an external biotinylation agent in spores and SpoVAEa disappeared in parallel...codon was PCR amplified from PS832 chromosomal DNA with primers that inserted BamHI and PstI restriction sites upstream and downstream, respectively... chromosomal structure, and this strain was termed PS4348 (spoVAEa mutant). A B. subtilis strain with a deletion of the spoVF gene was constructed by a two

Transitions Towards Operational Space-Based Ocean Observations: From Single Research Missions into Series and Constellations

DTIC Science & Technology

2011-02-16

Meleorol. Soc... 88 (8). 1197-121.1. 2007 . (DOI: 10.1175/ BAMS-88-8-1197) 4. GCOS Implementation Plan for the Global Observing System for Climate...21-25 September 2009, Hall, J.. Harrison 1) 1 and Stammer . D., Eds., ESA Publication WPP-306, 2010. 6. Le Traon, P.-Y.. and Co-Authors (2010...Information for Society" Conference (Vol. 2), Venice, Italy, 21-25 September 2009, Hall, J., Harrison D.E. and Stammer , D., Eds., ESA Publication WPP

Novel Immune Modulating Cellular Vaccine for Prostate Cancer

DTIC Science & Technology

2014-10-01

restriction sites. Murine PSMA : The cDNA encoding mPSMA was purchased from Sino Biologicals and was cloned into the HindIII and BamHI sites of pSP73-Sph/A64...sequence) and reverse primer 5’-TATATAGAGCTCTCAGATGTTCCGATACACATCTC-3’ Murine PSMA no signal sequence (mPSMA-SS): Murine PSMA minus the signal sequence...contains a HindIII site for cloning and utilizes an ATG that lies downstream of the signal sequence as the start codon in PSMA -SS ( PSMA without signal

Translations on USSR Science and Technology, Biomedical and Behavioral Sciences, Number 33

DTIC Science & Technology

1978-07-05

7.6, 6.6 mM MgCl2, 6.6 mM 2-ß- mercaptoethanol, 2 y£ BamHI. Restriction was performed at 37°C for 15 min. We used, as marker DNA, EcoRI restrictor...linear DNA as function of molecular weight, plotted according to marker DNA to determine the molecular weights of DNA restrictors. Electron...according to the amp marker ; 3) reaction to agents that eliminate plasmids (acridine orange, ethidium bromide, sodium dodecylsulfate). The obtained

Third International Meeting on Esterases Reacting with Organophosphorus Compounds

DTIC Science & Technology

1998-01-01

cassette for negative selection, 884 bp of ACHE including exon 1, 1.6 kb of a Neor gene cassette for positive selection, 5.2 kb of the ACHE Bam HI...fragment including exon 6, and 3 kb of Bluescript. Deletion of exons 2-5 removed 80% of the ACHE coding sequence. The gene targeting vector was...expression due to environmental influences on CYP3A4 and the presence or absence of CYP3A5 which may be under genetic control in man. Plasma

Experimental study on the minimum ignition temperature of coal dust clouds in oxy-fuel combustion atmospheres.

PubMed

Wu, Dejian; Norman, Frederik; Verplaetsen, Filip; Van den Bulck, Eric

2016-04-15

BAM furnace apparatus tests were conducted to investigate the minimum ignition temperature of coal dusts (MITC) in O2/CO2 atmospheres with an O2 mole fraction from 20 to 50%. Three coal dusts: Indonesian Sebuku coal, Pittsburgh No.8 coal and South African coal were tested. Experimental results showed that the dust explosion risk increases significantly with increasing O2 mole fraction by reducing the minimum ignition temperature for the three tested coal dust clouds dramatically (even by 100°C). Compared with conventional combustion, the inhibiting effect of CO2 was found to be comparatively large in dust clouds, particularly for the coal dusts with high volatile content. The retardation effect of the moisture content on the ignition of dust clouds was also found to be pronounced. In addition, a modified steady-state mathematical model based on heterogeneous reaction was proposed to interpret the observed experimental phenomena and to estimate the ignition mechanism of coal dust clouds under minimum ignition temperature conditions. The analysis revealed that heterogeneous ignition dominates the ignition mechanism for sub-/bituminous coal dusts under minimum ignition temperature conditions, but the decrease of coal maturity facilitates homogeneous ignition. These results improve our understanding of the ignition behaviour and the explosion risk of coal dust clouds in oxy-fuel combustion atmospheres. Copyright © 2015 Elsevier B.V. All rights reserved.

Sequence analysis of Epstein-Barr virus (EBV) early genes BARF1 and BHRF1 in NK/T cell lymphoma from Northern China.

PubMed

Sun, Lingling; Che, Kui; Zhao, Zhenzhen; Liu, Song; Xing, Xiaoming; Luo, Bing

2015-09-04

NK/T cell lymphoma is an aggressive lymphoma almost always associated with EBV. BamHI-A rightward open reading frame 1 (BARF1) and BamHI-H rightward open reading frame 1 (BHRF1) are two EBV early genes, which may be involved in the oncogenicity of EBV. It has been found that V29A strains, a BARF1 mutant subtype, showed higher prevalence in NPC, which may suggest the association between this variation and nasopharyngeal carcinoma (NPC). To characterize the sequence variation patterns of the Epstein-Barr virus (EBV) early genes and to elucidate their association with NK/T cell lymphoma, we analyzed the sequences of BARF1 and BHRF1 in EBV-positive NK/T cell lymphoma samples from Northern China. In situ hybridization (ISH) performed for EBV-encoded small RNA1 (EBER1) with specific digoxigenin-labeled probes was used to select the EBV positive lymphoma samples. Nested-polymerase chain reaction (nested-PCR) and DNA sequence analysis technique were used to obtain the sequences of BARF1 and BHRF1. The polymorphisms of these two genes were classified according to the signature changes and compared with the known corresponding EBV gene variation data. Two major subtypes of BARF1 gene, designated as B95-8 and V29A subtype, were identified. B95-8 subtype was the dominant subtype. The V29A subtype had one consistent amino acid change at amino acid residue 29 (V → A). Compared with B95-8, AA change at 88 (L → V) of BHRF1 was found in the majority of the isolates, and AA79 (V → L) mutation in a few isolates. Functional domains of BARF1 and BHRF1 were highly conserved. The distributions of BARF1 and BHRF1 subtypes had no significant differences among different EBV-associated malignancies and healthy donors. The sequences of BARF1 and BHRF1 are highly conserved which may contribute to maintain the biological function of these two genes. There is no evidence that particular EBV substrains of BARF1 or BHRF1 is region-restricted or disease-specific.

Neural coding in graphs of bidirectional associative memories.

PubMed

Bouchain, A David; Palm, Günther

2012-01-24

In the last years we have developed large neural network models for the realization of complex cognitive tasks in a neural network architecture that resembles the network of the cerebral cortex. We have used networks of several cortical modules that contain two populations of neurons (one excitatory, one inhibitory). The excitatory populations in these so-called "cortical networks" are organized as a graph of Bidirectional Associative Memories (BAMs), where edges of the graph correspond to BAMs connecting two neural modules and nodes of the graph correspond to excitatory populations with associative feedback connections (and inhibitory interneurons). The neural code in each of these modules consists essentially of the firing pattern of the excitatory population, where mainly it is the subset of active neurons that codes the contents to be represented. The overall activity can be used to distinguish different properties of the patterns that are represented which we need to distinguish and control when performing complex tasks like language understanding with these cortical networks. The most important pattern properties or situations are: exactly fitting or matching input, incomplete information or partially matching pattern, superposition of several patterns, conflicting information, and new information that is to be learned. We show simple simulations of these situations in one area or module and discuss how to distinguish these situations based on the overall internal activation of the module. This article is part of a Special Issue entitled "Neural Coding". Copyright © 2011 Elsevier B.V. All rights reserved.

Effect of Lipid-Based Nanostructure on Protein Encapsulation within the Membrane Bilayer Mimetic Lipidic Cubic Phase Using Transmembrane and Lipo-proteins from the Beta-Barrel Assembly Machinery.

PubMed

van 't Hag, Leonie; Shen, Hsin-Hui; Lin, Tsung-Wu; Gras, Sally L; Drummond, Calum J; Conn, Charlotte E

2016-11-29

A fundamental understanding of the effect of amphiphilic protein encapsulation on the nanostructure of the bicontinuous cubic phase is crucial to progressing biomedical and biological applications of these hybrid protein-lipid materials, including as drug delivery vehicles, as biosensors, biofuel cells and for in meso crystallization. The relationship between the lipid nanomaterial and the encapsulated protein, however, remains poorly understood. In this study, we investigated the effect of incorporating the five transmembrane and lipo-proteins which make up the β-barrel assembly machinery from Gram-negative bacteria within a series of bicontinuous cubic phases. The transmembrane β-barrel BamA caused an increase in lattice parameter of the cubic phase upon encapsulation. By contrast, the mainly hydrophilic lipo-proteins BamB-E caused the cubic phase lattice parameters to decrease, despite their large size relative to the diameter of the cubic phase water channels. Analysis of the primary amino acid sequence was used to rationalize this effect, based on specific interactions between aromatic amino acids within the proteins and the polar-apolar interface. Other factors that were found to have an effect were lateral bilayer pressure and rigidity within the lipid bilayer, water channel diameter, and size and structure of the lipo-proteins. The data presented suggest that hydrophilic bioactive molecules can be selectively encapsulated within the cubic phase by using a lipid anchor or aromatic amino acids, for drug delivery or biosensing applications.

Therapeutic implications of Epstein–Barr virus infection for the treatment of nasopharyngeal carcinoma

PubMed Central

Hutajulu, Susanna Hilda; Kurnianda, Johan; Tan, I Bing; Middeldorp, Jaap M

2014-01-01

Nasopharyngeal carcinoma (NPC) is highly endemic in certain regions including the People’s Republic of China and Southeast Asia. Its etiology is unique and multifactorial, involving genetic background, epigenetic, and environment factors, including Epstein–Barr virus (EBV) infection. The presence of EBV in all tumor cells, aberrant pattern of antibodies against EBV antigens in patient sera, and elevated viral DNA in patient circulation as well as nasopharyngeal site underline the role of EBV during NPC development. In NPC tumors, EBV expresses latency type II, where three EBV-encoded proteins, Epstein–Barr nuclear antigen 1, latent membrane protein 1 and 2 (LMP1, 2), are expressed along with BamH1-A rightward reading frame 1, Epstein–Barr virus-encoded small nuclear RNAs, and BamH1-A rightward transcripts. Among all encoded proteins, LMP1 plays a central role in the propagation of NPC. Standard treatment of NPC consists of radiotherapy with or without chemotherapy for early stage, concurrent chemoradiotherapy in locally advanced tumors, and palliative systemic chemotherapy in metastatic disease. However, this standard care has limitations, allowing recurrences and disease progression in a certain proportion of cases. Although the pathophysiological link and molecular process of EBV-induced oncogenesis are not fully understood, therapeutic approaches targeting the virus may increase the cure rate and add clinical benefit. The promising results of early phase clinical trials on EBV-specific immunotherapy, epigenetic therapy, and treatment with viral lytic induction offer new options for treating NPC. PMID:25228810

Do lipids retard the evaporation of the tear fluid?

PubMed

Rantamäki, Antti H; Javanainen, Matti; Vattulainen, Ilpo; Holopainen, Juha M

2012-09-21

We examined in vitro the potential evaporation-retarding effect of the tear film lipid layer (TFLL). The artificial TFLL compositions used here were based on the present knowledge of TFLL composition. A custom-built system was developed to measure evaporation rates at 35°C. Lipids were applied to an air-water interface, and the evaporation rate through the lipid layer was defined as water loss from the interface. A thick layer of olive oil and a monolayer of long-chain alcohol were used as controls. The artificial TFLLs were composed of 1 to 4 lipid species: polar phosphatidylcholine (PC), nonpolar cholesteryl ester, triglycerides, and wax ester (WE). Brewster angle microscopy (BAM) and interfacial shear rheometry (ISR) were used to assess the lateral structure and shear stress response of the lipid layers, respectively. Olive oil and long-chain alcohol decreased evaporation by 54% and 45%, respectively. The PC monolayer and the four-component mixtures did not retard evaporation. WE was the most important evaporation-retardant TFLL lipid (∼20% decrease). In PC/WE mixtures, an ∼90% proportion of WE was required for evaporation retardation. Based on BAM and ISR, WE resulted in more condensed layers than the non-retardant layers. Highly condensed, solid-like lipid layers, such as those containing high proportions of WEs, are evaporation-retardant. In multi-component lipid layers, the evaporation-retardant interactions between carbon chains decrease and, therefore, these lipid layers do not retard evaporation.

Tannerella forsythia and the HLA-DQB1 allele are associated with susceptibility to periodontal disease in Japanese adolescents.

PubMed

Shimomura-Kuroki, Junko; Yamashita, Kie; Shimooka, Shohachi

2009-01-01

Periodontal disease is a multiple factor disease caused by genetic factors, environmental factors, and periodontal bacteria (periodontal pathogens). The present study aimed to elucidate the risk factors for periodontal disease in Japanese adolescents. Subjects (11-16 years old) were classified into three groups: localized aggressive periodontitis (LAP), periodontal attachment loss (PAL), and periodontally healthy (PH) groups. Genomic DNA isolated from the buccal mucosa was used for single-nucleotide polymorphism analyses of the candidate genes (interleukin-1alpha-889; interleukin-1alpha +4845; interleukin-1beta +3954; an immunoglobulin G Fc gamma receptor, FcgammaRIIa-R/H131; and a human leukocyte antigen class II allele, HLA-DQB1) of aggressive periodontitis. Subgingival plaque samples obtained from the same subjects were used for 16S rRNAbased polymerase chain reaction analysis of five important periodontal pathogens (Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Treponema denticola, and Tannerella forsythia). Tannerella forsythia was detected in the deepest periodontal pockets in all subjects in the LAP and PAL groups. The prevalence of an atypical BamHI restriction site in HLA-DQB1 of the LAP group was significantly higher than that in the PH and PAL groups. Furthermore, all subjects who had the atypical BamHI restriction site in HLA-DQB1 had T. forsythia infection. These results suggested that T. forsythia is associated with periodontal disease in Japanese adolescents and also suggested that HLA-DQB1 is related to LAP and is associated with T. forsythia infection.

Approach to knowledge of the interaction between the constituents of contact lenses and ocular tears: mixed monolayers of poly(methyl methacrylate) and dipalmitoyl phosphatidyl choline.

PubMed

Miñones Conde, M; Conde, O; Trillo, J M; Miñones, J

2011-04-05

Mixed monolayers of poly(methyl methacrylate) (PMMA), the main component of hard contact lenses, and dipalmitoyl phosphatidyl choline (DPPC), a characteristic phospholipidic constituent of ocular tear films, were selected as an in vitro model in order to observe the behavior of contact lenses on the eye. Using Langmuir monolayer and Brewster angle microscopy (BAM) techniques, the interaction between both components was analyzed from the data of surface pressure-area isotherms, compressional modulus-surface pressure, and relative film thickness versus time elapsed from the beginning of compression, together with BAM images. Regardless of the surface pressure at which the molecular/monomer areas (A(m)) were recorded, the A(m) mole fractions of PMMA (X(PMMA)) plots show that the experimental results match the theoretical values calculated from additivity rule A(m) = X(PMMA)A(PMMA) + X(DPPC)A(DPPC). The application of the Crisp phase rule to the phase diagram of the PMMA-DPPC system can explain the existence of a mixed monolayer made up of miscible components with ideal behavior at surface pressures below 25 mN/m. However, at very high surface pressures, when collapse is reached (at 60 mN/m), the single collapsed components are segregated into two independent phases. These results allows us to argue that PMMA hard contact lenses in the eye do not alter the structural characteristics of the phospholipid (DPPC) in tears.

How bad is bile acid diarrhoea: an online survey of patient-reported symptoms and outcomes.

PubMed

Bannaga, Ayman; Kelman, Lawrence; O'Connor, Michelle; Pitchford, Claire; Walters, Julian R F; Arasaradnam, Ramesh P

2017-01-01

Bile acid diarrhoea (BAD) is an underdiagnosed condition producing diarrhoea, urgency and fear of faecal incontinence. How patients experience these symptoms has not previously been studied. Bile Acid Malabsorption (BAM) Support UK was established in 2015 as a national charity with objectives including to provide details regarding how BAD affects patients, to improve earlier recognition and clinical management. A questionnaire was collected anonymously by BAM Support UK and the Bile Salt Malabsorption Facebook group over 4 weeks at the end of 2015. It comprised 56 questions and aimed to inform patients and clinicians about how BAD affects the respondents. The first 100 responses were analysed. 91% of the respondents reported a diagnosis of BAD. 58% of total respondents diagnosed following a Selenium-homocholic acid taurine scan, 69% were diagnosed by a gastroenterologist, with type 2 and 3 BAD comprising 38% and 37%, respectively, of total respondents. Symptoms had been experienced for more than 5 years before diagnosis in 44% of respondents. Following treatment, usually with bile acid sequestrants, 60% of participants reported improvement of diarrhoea and most reported their mental health has been positively impacted. Just over half of the cohort felt as though their symptoms had been dismissed during clinical consultations and 28% felt their GPs were unaware of BAD. BAD requires more recognition by clinicians to address the current delays in diagnosis. Treatment improves physical and mental symptoms in the majority of participants.

Investigating the effect of multiple grain-grain interfaces on electric transport behavior of [50 wt% BaFe12O19-50 wt% Na0.5Bi0.5TiO3] magnetoelectric nanocomposite system

NASA Astrophysics Data System (ADS)

Pattanayak, Ranjit; Raut, Subhajit; Dash, Tapan; Mohapatra, Soumyaranjan; Muduli, Rakesh; Panigrahi, Simanchala

2017-05-01

Polycrystalline [50 wt% BaFe12O19 (BaM)-50 wt% Na0.5Bi0.5TiO3 (NBT)] particulate novel magnetoelectric nanocomposite system was successfully fabricated by solid state reaction technique. The Rietveld refinement of X-ray diffraction pattern was provided the evidence about the pure phase formation of desired nanocomposite system as well as the presence of both ferrimagnetic (FM) BaM & ferroelectric (FE) NBT phases separately. The Field Scanning Electron Micrograph (FESEM) and Scanning Tunneling Electron Micrograph (STEM) explored the information about grain size and connectivity of the composite system. The XPS study was helped to examine the presence of oxygen vacancy (Ov) as well as multi oxidation states of transition metal ions for nanocomposite system. In this report we have systematically examined the conduction mechanism of different interfaces (BaM-BaM, BaM-NBT and NBT-NBT) by the help of complex impedance spectroscopy technique. From our investigation it was observed that, different interfaces activates at different temperature ranges. Due to absence of OV, BaM-NBT interfaces conduction dominants over BaM-BaM interfaces conduction even at room temperature (RT). The mechanism behind the appeared high dielectric loss (tanδ) at RT which was reduced when NBT-NBT interfaces were activates at higher temperature was explained by Maxwell-Wagner type interfacial polarization concept.

Microbial diversity and anaerobic hydrocarbon degradation potential in an oil-contaminated mangrove sediment

PubMed Central

2012-01-01

Background Mangrove forests are coastal wetlands that provide vital ecosystem services and serve as barriers against natural disasters like tsunamis, hurricanes and tropical storms. Mangroves harbour a large diversity of organisms, including microorganisms with important roles in nutrient cycling and availability. Due to tidal influence, mangroves are sites where crude oil from spills farther away can accumulate. The relationship between mangrove bacterial diversity and oil degradation in mangrove sediments remains poorly understood. Results Mangrove sediment was sampled from 0–5, 15–20 and 35–40 cm depth intervals from the Suruí River mangrove (Rio de Janeiro, Brazil), which has a history of oil contamination. DGGE fingerprinting for bamA, dsr and 16S rRNA encoding fragment genes, and qPCR analysis using dsr and 16S rRNA gene fragment revealed differences with sediment depth. Conclusions Analysis of bacterial 16S rRNA gene diversity revealed changes with depth. DGGE for bamA and dsr genes shows that the anaerobic hydrocarbon-degrading community profile also changed between 5 and 15 cm depth, and is similar in the two deeper sediments, indicating that below 15 cm the anaerobic hydrocarbon-degrading community appears to be well established and homogeneous in this mangrove sediment. qPCR analysis revealed differences with sediment depth, with general bacterial abundance in the top layer (0–5 cm) being greater than in both deeper sediment layers (15–20 and 35–40 cm), which were similar to each other. PMID:22935169

Microbial diversity and anaerobic hydrocarbon degradation potential in an oil-contaminated mangrove sediment.

PubMed

Andrade, Luiza L; Leite, Deborah C A; Ferreira, Edir M; Ferreira, Lívia Q; Paula, Geraldo R; Maguire, Michael J; Hubert, Casey R J; Peixoto, Raquel S; Domingues, Regina M C P; Rosado, Alexandre S

2012-08-30

Mangrove forests are coastal wetlands that provide vital ecosystem services and serve as barriers against natural disasters like tsunamis, hurricanes and tropical storms. Mangroves harbour a large diversity of organisms, including microorganisms with important roles in nutrient cycling and availability. Due to tidal influence, mangroves are sites where crude oil from spills farther away can accumulate. The relationship between mangrove bacterial diversity and oil degradation in mangrove sediments remains poorly understood. Mangrove sediment was sampled from 0-5, 15-20 and 35-40 cm depth intervals from the Suruí River mangrove (Rio de Janeiro, Brazil), which has a history of oil contamination. DGGE fingerprinting for bamA, dsr and 16S rRNA encoding fragment genes, and qPCR analysis using dsr and 16S rRNA gene fragment revealed differences with sediment depth. Analysis of bacterial 16S rRNA gene diversity revealed changes with depth. DGGE for bamA and dsr genes shows that the anaerobic hydrocarbon-degrading community profile also changed between 5 and 15 cm depth, and is similar in the two deeper sediments, indicating that below 15 cm the anaerobic hydrocarbon-degrading community appears to be well established and homogeneous in this mangrove sediment. qPCR analysis revealed differences with sediment depth, with general bacterial abundance in the top layer (0-5 cm) being greater than in both deeper sediment layers (15-20 and 35-40 cm), which were similar to each other.

Integrated Data Collection Analysis (IDCA) Program - AN and Bullseye Smokeless Powder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sandstrom, Mary M.; Brown, Geoffrey W.; Preston, Daniel N.

The Integrated Data Collection Analysis (IDCA) program is conducting a proficiency study for Small- Scale Safety and Thermal (SSST) testing of homemade explosives (HMEs). Described here are the results for impact, friction, electrostatic discharge, and differential scanning calorimetry analysis of ammonium nitrate (AN) mixed with Bullseye® smokeless powder (Gunpowder). The participants found the AN/Gunpowder to: 1) have a range of sensitivity to impact, comparable to or less than RDX, 2) be fairly insensitive to friction as measured by BAM and ABL, 3) have a range for ESD, from insensitive to more sensitive than PETN, and 4) have thermal sensitivity aboutmore » the same as PETN and Gunpowder. This effort, funded by the Department of Homeland Security (DHS), is putting the issues of safe handling of these materials in perspective with standard military explosives. The study is adding SSST testing results for a broad suite of different HMEs to the literature. Ultimately the study has the potential to suggest new guidelines and methods and possibly establish the SSST testing accuracies needed when developing safe handling practices for HMEs. Each participating testing laboratory uses identical test materials and preparation methods. Note, however, the test procedures differ among the laboratories. The testing performers involved are Lawrence Livermore National Laboratory (LLNL), Los Alamos National Laboratory (LANL), Indian Head Division, Naval Surface Warfare Center, (NSWC IHD), Sandia National Laboratories (SNL), and Air Force Research Laboratory (AFRL/RXQL). These tests are conducted as a proficiency study in order to establish some consistency in test protocols, procedures, and experiments and to compare results when these testing variables cannot be made consistent. Keywords: Small-scale safety testing, proficiency test, impact-, friction-, spark discharge-, thermal testing, round-robin test, safety testing protocols, HME, RDX, potassium perchlorate, potassium chlorate, sodium chlorate, sugar, dodecane, PETN, carbon, ammonium nitrate, Gunpowder, Bullseye® smokeless powder.« less

Final report on CCQM-K70: Determination of Hg in natural water at a concentration level required by the European environmental quality standard (EQS)

NASA Astrophysics Data System (ADS)

Schiel, Detlef; Rienitz, Olaf

2011-01-01

This comparison 'Hg in natural water' was a follow-up to the pilot studies CCQM-P100.1 and CCQM-P100.2. The aim of this comparison was to demonstrate the capability of national metrology institutes to measure the Hg mass concentration in a natural water sample at the very low concentration level of γ(Hg) ≈ 70 ng/L as required by the EQS. In this way it served to help implement the European Water Framework Directive (WFD). This comparison was an activity of the Inorganic Analysis Working Group (IAWG) of CCQM and was piloted by Physikalisch-Technische Bundesanstalt (PTB, Braunschweig, Germany) with the help of the co-organizers Bundesanstalt für Materialforschung und -prüfung (BAM, Berlin, Germany), Laboratoire National de Métrologie et d'Essais (LNE, Paris, France), and the Joint Research Centre-Institute for Reference Materials and Measurements (EC-JRC-IRMM, Geel, Belgium). The following laboratories participated in this key comparison (in alphabetical order): BAM (Germany) EC-JRC-IRMM (European Union) KRISS (Republic of Korea) LGC (United Kingdom) LNE (France) NIST (United States of America) NMIA (Australia) NRC (Canada) PTB (Germany) SP (Sweden) The majority of participants applied isotope dilution mass spectrometry (IDMS) using sector field or quadrupole inductively coupled plasma MS (ICP-MS) in combination with cold vapour (CV) generation as the analytical technique. NRC reported a combined result of ID-CV-ICP-MS and CV atomic absorption spectrometry (CV-AAS). SP applied a standard addition method on a sector field ICP-MS, while BAM made use of an external 5-point calibration on a CV atomic fluorescence spectrometer (AFS). The key comparison reference value (KCRV) was agreed upon during the IAWG meeting in April 2010 at BIPM as the sum of the added Hg content calculated from the gravimetric sample preparation and the Hg matrix content of the water used for sample preparation (determined and validated on two independent pathways). Accordingly the degrees of equivalence were calculated. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

Major Earthquakes of the Past Decade (2000-2010): A Comparative Review of Various Aspects of Management

PubMed Central

Kalantar Motamedi, Mohammad Hosein; Sagafinia, Masoud; Ebrahimi, Ali; Shams, Ehsan; Kalantar Motamedi, Mostafa

2012-01-01

Objectives: This article sought to review and compare data of major earthquakes of the past decade and their aftermath in order to compare the magnitude, death toll, type of injuries, management procedures, extent of destruction and effectiveness of relief efforts. Materials and Methods: A retrospective study of the various aspects of management and aftermath of 5 major earthquakes of the past decade (2000–2010) was undertaken. This included earthquakes occurring in Bam Iran, Sichuan China, Port-au-Prince Haiti, Kashmir Pakistan and Ica Peru. A literature search was done via computer of published articles (indexed in Pubmed). The issues assessed included: 1)Local magnitude,2)Type of building structure 3)Time of the earthquake (day/time/season), 4)Time to rescue, 5)Triage, Transfer, and Treatment 6) Distribution of casualties (dead/ injured), 7)Degree of city damage, 8)Degree of damage to health facilities, 9)Field hospital availability, 10)International aid, 11)Air transfer, 12) Telecommunication systems availability, 13) PTSD prevalence, 14) Most common injury and 15) Most common disease outbreak. Results: The Bam earthquake had the lowest (6.6 Richter’s) and the Sichuan earthquake had the greatest magnitude (8.0 Richter’s). Mortality in Haiti was 212,000 and it was the deadliest earthquake of the past decade. Collapse of heavy clay roofing structures was a major cause of death in Iran and Pakistan. Earthquakes occurring at night and nonworking days carried a high death toll. The time to rescue and treat was the lengthiest in Haiti (possibly contributing to the death to injured ratio). However, the worst dead to injured ratios were in Bam (51%) and in Pakistan (47%); the best ratio was in China (15%). Iran and Pakistan suffered the highest percentage of damage to the health facilities (90%). Field hospital availability, international aid and air transfer were important issues. Telecommunication systems were best in China and worst in Pakistan. PTSD prevalence was highest in Iran. Respiratory infection was the most common infection following all 5 earthquakes. Conclusions: Earthquake damage, death toll, managerial protocols etc. vary in different countries and are influenced by many factors including the hour the earthquake hits and the day of the week. Additionally, social, structural and geographic factors as well as the medical, governmental and NGO respondents are influential. Engineered residential construction remains to be of importance in reducing mortality in developing countries. It is essential that hospitals, fire departments and police stations, water, telephone and electrical facilities be made earthquake proof. PMID:24829886

Major earthquakes of the past decade (2000-2010): a comparative review of various aspects of management.

PubMed

Kalantar Motamedi, Mohammad Hosein; Sagafinia, Masoud; Ebrahimi, Ali; Shams, Ehsan; Kalantar Motamedi, Mostafa

2012-01-01

This article sought to review and compare data of major earthquakes of the past decade and their aftermath in order to compare the magnitude, death toll, type of injuries, management procedures, extent of destruction and effectiveness of relief efforts. A retrospective study of the various aspects of management and aftermath of 5 major earthquakes of the past decade (2000-2010) was undertaken. This included earthquakes occurring in Bam Iran, Sichuan China, Port-au-Prince Haiti, Kashmir Pakistan and Ica Peru. A literature search was done via computer of published articles (indexed in Pubmed). The issues assessed included: 1)Local magnitude,2)Type of building structure 3)Time of the earthquake (day/time/season), 4)Time to rescue, 5)Triage, Transfer, and Treatment 6) Distribution of casualties (dead/ injured), 7)Degree of city damage, 8)Degree of damage to health facilities, 9)Field hospital availability, 10)International aid, 11)Air transfer, 12) Telecommunication systems availability, 13) PTSD prevalence, 14) Most common injury and 15) Most common disease outbreak. The Bam earthquake had the lowest (6.6 Richter's) and the Sichuan earthquake had the greatest magnitude (8.0 Richter's). Mortality in Haiti was 212,000 and it was the deadliest earthquake of the past decade. Collapse of heavy clay roofing structures was a major cause of death in Iran and Pakistan. Earthquakes occurring at night and nonworking days carried a high death toll. The time to rescue and treat was the lengthiest in Haiti (possibly contributing to the death to injured ratio). However, the worst dead to injured ratios were in Bam (51%) and in Pakistan (47%); the best ratio was in China (15%). Iran and Pakistan suffered the highest percentage of damage to the health facilities (90%). Field hospital availability, international aid and air transfer were important issues. Telecommunication systems were best in China and worst in Pakistan. PTSD prevalence was highest in Iran. Respiratory infection was the most common infection following all 5 earthquakes. Earthquake damage, death toll, managerial protocols etc. vary in different countries and are influenced by many factors including the hour the earthquake hits and the day of the week. Additionally, social, structural and geographic factors as well as the medical, governmental and NGO respondents are influential. Engineered residential construction remains to be of importance in reducing mortality in developing countries. It is essential that hospitals, fire departments and police stations, water, telephone and electrical facilities be made earthquake proof.

Open reading frames in a 4556 nucleotide sequence within MDV-1 BamHI-D DNA fragment: evidence for splicing of mRNA from a new viral glycoprotein gene.

PubMed

Becker, Y; Asher, Y; Tabor, E; Davidson, I; Malkinson, M

1994-01-01

A DNA segment of the MDV-1 BamHI-D fragment was sequenced, and the open reading frames (ORFs) present in the 4556 nucleotide fragment were analyzed by computer programs. Computer analysis identified 19 putative ORFs in the sequence ranging from a coding capacity of 37 amino acids (aa) (ORF-1a) to 684aa (ORF-1). The special properties of four ORFs (1a, 1, 2, and 3) were investigated. Two adjacent ORFs, ORF-1a and ORF-1, were found by computer analysis to have the properties of two introns encoding a glycoprotein: ORF-1a encodes an aa sequence with the properties of a signal peptide, and ORF-1 encodes a polypeptide with a membrane anchor domain and putative N-glycosylation sites in the aa sequence. ORF-1a and ORF-1 were found to be transcribed in MDV-1-infected cells. Two RNA transcripts were detected: a precursor RNA and its spliced form. Both are transcribed from a promoter located 5' to ORF-1a, and splice donor and acceptor sites are used to splice the mRNA after cleavage of a 71-nucleotide sequence. This finding suggest that ORF-1a and ORF-1 are two introns of a new MDV-1 glycoprotein gene. The DNA sequence containing ORF-1 was transiently expressed in COS-1 cells, and the viral protein produced in these cells was found to react with anti-MDV serotype-1 Antigen B-specific monoclonal antibodies. These studies indicate that the protein encoded by ORF-1 has antigenic properties resembling Antigen B of MDV-1. A gene homologous to ORF-1 was detected in the genome of both MDV-2(SB1) and MDV-3(HVT), which serve as commercial vaccine strains. Two additional ORFs were noted in the 4556 nucleotide sequence: ORF-2, which encodes a 333 aa polypeptide initiating in the UL and terminating in the TRL prior to the putative origin of replication, and ORF-3, which encodes a 155 aa polypeptide that is partly homologous to the phosphoprotein pp38 encoded by the BamHI-H sequence. The 65 N-terminal aa of the two gene products are identical, both being derived from the nucleotide sequences in the TRL and IRL, respectively. Additional homologous aa sequences are the hydrophobic aa domain in the middle of both proteins. The functions of ORF-2, ORF-3, and additional ORFs are under study.

Simulations of inspiraling and merging double neutron stars using the Spectral Einstein Code

NASA Astrophysics Data System (ADS)

Haas, Roland; Ott, Christian D.; Szilagyi, Bela; Kaplan, Jeffrey D.; Lippuner, Jonas; Scheel, Mark A.; Barkett, Kevin; Muhlberger, Curran D.; Dietrich, Tim; Duez, Matthew D.; Foucart, Francois; Pfeiffer, Harald P.; Kidder, Lawrence E.; Teukolsky, Saul A.

2016-06-01

We present results on the inspiral, merger, and postmerger evolution of a neutron star-neutron star (NSNS) system. Our results are obtained using the hybrid pseudospectral-finite volume Spectral Einstein Code (SpEC). To test our numerical methods, we evolve an equal-mass system for ≈22 orbits before merger. This waveform is the longest waveform obtained from fully general-relativistic simulations for NSNSs to date. Such long (and accurate) numerical waveforms are required to further improve semianalytical models used in gravitational wave data analysis, for example, the effective one body models. We discuss in detail the improvements to SpEC's ability to simulate NSNS mergers, in particular mesh refined grids to better resolve the merger and postmerger phases. We provide a set of consistency checks and compare our results to NSNS merger simulations with the independent bam code. We find agreement between them, which increases confidence in results obtained with either code. This work paves the way for future studies using long waveforms and more complex microphysical descriptions of neutron star matter in SpEC.

mod_bio: Apache modules for Next-Generation sequencing data.

PubMed

Lindenbaum, Pierre; Redon, Richard

2015-01-01

We describe mod_bio, a set of modules for the Apache HTTP server that allows the users to access and query fastq, tabix, fasta and bam files through a Web browser. Those data are made available in plain text, HTML, XML, JSON and JSON-P. A javascript-based genome browser using the JSON-P communication technique is provided as an example of cross-domain Web service. https://github.com/lindenb/mod_bio. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Langmuir-Blodgett Films of Supported Polyester Dendrimers

PubMed Central

Redón, Rocío; Carreón-Castro, M. Pilar; Mendoza-Martínez, F. J.

2012-01-01

Amphiphiles with a dendritic structure are attractive materials as they combine the features of dendrimers with the self-assembling properties and interfacial behavior of water-air affinities. We have synthesized three generations of polyester dendrimers and studied their interfacial properties on the Langmuir films. The behavior obtained was, as a rule, the lowest generation dendrimers behaving like traditional amphiphiles and the larger molecules presenting complicated isotherms. The Langmuir films of these compounds have been characterized by their surface pressure versus molecular area (π/A) and Brewster angle microscopy (BAM) observations. PMID:24052855

Potential microbial risk factors related to soil amendments and irrigation water of potato crops.

PubMed

Selma, M V; Allende, A; López-Gálvez, F; Elizaquível, P; Aznar, R; Gil, M I

2007-12-01

This study assesses the potential microbial risk factors related to the use of soil amendments and irrigation water on potato crops, cultivated in one traditional and two intensive farms during two harvest seasons. The natural microbiota and potentially pathogenic micro-organisms were evaluated in the soil amendment, irrigation water, soil and produce. Uncomposted amendments and residual and creek water samples showed the highest microbial counts. The microbial load of potatoes harvested in spring was similar among the tested farms despite the diverse microbial levels of Listeria spp. and faecal coliforms in the potential risk sources. However, differences in total coliform load of potato were found between farms cultivated in the autumn. Immunochromatographic rapid tests and the BAM's reference method (Bacteriological Analytical Manual; AOAC International) were used to detect Escherichia coli O157:H7 from the potential risk sources and produce. Confirmation of the positive results by polymerase chain reaction procedures showed that the immunochromatographic assay was not reliable as it led to false-positive results. The potentially pathogenic micro-organisms of soil amendment, irrigation water and soil samples changed with the harvest seasons and the use of different agricultural practices. However, the microbial load of the produce was not always influenced by these risk sources. Improvements in environmental sample preparation are needed to avoid interferences in the use of immunochromatographic rapid tests. The potential microbial risk sources of fresh produce should be regularly controlled using reliable detection methods to guarantee their microbial safety.

Atypical myxomatosis--virus isolation, experimental infection of rabbits and restriction endonuclease analysis of the isolate.

PubMed

Psikal, I; Smíd, B; Rodák, L; Valícek, L; Bendová, J

2003-08-01

Atypical form of myxomatosis, which caused non-lethal and clinically mild disease in domestic rabbits 1 month after immunization with a commercially available vaccine MXT, is described. The isolated myxoma virus designated as Litovel 2 (Li-2) did not induce systemic disease following subcutaneous and intradermal applications in susceptible experimental rabbits but led to the immune response demonstrated by ELISA. No severe disease was induced in those Li-2 inoculated rabbits by challenge with the virulent strains Lausanne (Lu) or Sanar (SA), while the control animals showed nodular form of myxomatosis with lethal course of the illness. Restriction fragment length polymorphism (RFLP) of genomic DNA with KpnI and BamHI endonucleases was used for genetic characterization of the Li-2 isolate, the vaccine strain MXT and both virulent strains Lu and SA, respectively. In general, RFLP analysis has shown to be informative for inferring genetic relatedness between myxoma viruses. Based on restriction endonuclease DNA fragment size distribution, it was evident that the pathogenic strain SA is genetically related to the reference strain Lu and the isolate Li-2 is more related, but not identical, to the vaccination strain MXT.

The interaction of an antiparasitic peptide active against African sleeping sickness with cell membrane models.

PubMed

Pascholati, Cauê P; Lopera, Esteban Parra; Pavinatto, Felippe J; Caseli, Luciano; Nobre, Thatyane M; Zaniquelli, Maria E D; Viitala, Tapani; D'Silva, Claudius; Oliveira, Osvaldo N

2009-12-01

Zwitterionic peptides with trypanocidal activity are promising lead compounds for the treatment of African Sleeping Sickness, and have motivated research into the design of compounds capable of disrupting the protozoan membrane. In this study, we use the Langmuir monolayer technique to investigate the surface properties of an antiparasitic peptide, namely S-(2,4-dinitrophenyl)glutathione di-2-propyl ester, and its interaction with a model membrane comprising a phospholipid monolayer. The drug formed stable Langmuir monolayers, whose main feature was a phase transition accompanied by a negative surface elasticity. This was attributed to aggregation upon compression due to intermolecular bond associations of the molecules, inferred from surface pressure and surface potential isotherms, Brewster angle microscopy (BAM) images, infrared spectroscopy and dynamic elasticity measurements. When co-spread with dipalmitoyl phosphatidyl choline (DPPC), the drug affected both the surface pressure and the monolayer morphology, even at high surface pressures and with low amounts of the drug. The results were interpreted by assuming a repulsive, cooperative interaction between the drug and DPPC molecules. Such repulsive interaction and the large changes in fluidity arising from drug aggregation may be related to the disruption of the membrane, which is key for the parasite killing property.

Amination of nitroazoles--a comparative study of structural and energetic properties.

PubMed

Zhao, Xiuxiu; Qi, Cai; Zhang, Lubo; Wang, Yuan; Li, Shenghua; Zhao, Fengqi; Pang, Siping

2014-01-14

In this work, 3-nitro-1H-1,2,4-triazole (1) and 3,5-dinitro-1H-pyrazole (2) were C-aminated and N-aminated using different amination agents, yielding their respective C-amino and N-amino products. All compounds were fully characterized by NMR (1H, 13C, 15N), IR spectroscopy, differential scanning calorimetry (DSC). X-ray crystallographic measurements were performed and delivered insight into structural characteristics as well as inter- and intramolecular interactions of the products. Their impact sensitivities were measured by using standard BAM fallhammer techniques and their explosive performances were computed using the EXPLO 5.05 program. A comparative study on the influence of those different amino substituents on the structural and energetic properties (such as density, stability, heat of formation, detonation performance) is presented. The results showed that the incorporation of an N-amino group into a nitroazole ring can improve nitrogen content, heat of formation and impact sensitivity, while the introduction of a C-amino group can enhance density, detonation velocity and pressure. The potential of N-amino and C-amino moieties for the design of next generation energetic materials is explored.

Sucrose esters as biocompatible surfactants for penetration enhancement: An insight into the mechanism of penetration enhancement studied using stratumcorneum model lipids and Langmuir monolayers.

PubMed

Todosijević, Marija N; Brezesinski, Gerald; Savić, Snežana D; Neubert, Reinhard H H

2017-03-01

Up to now, the molecular mechanism of the penetration enhancing effect of sucrose esters (SEs) on stratumcorneum (SC) has not been explained in details. In this study, variety of surface sensitive techniques, including surface pressure-area (π-A) isotherms, infrared reflection-absorption spectroscopy (IRRAS), and Brewster angle microscopy (BAM), have been used to investigate interactions between SEs and SC intercellular lipids. A monolayer of the mixture of ceramide AS C18:18, stearic acid and cholesterol in the molar ratio of 1:1:0.7 on an aqueous subphase is a good model to mimic a single layer of intercellular SC lipids. The π-A isotherms of mixed monolayers and parameters derived from the curves demonstrated the interaction between nonionic surfactants such as SEs and SC lipids. With increasing SE concentration, the resultant monolayer films became more fluid and better compressible. IRRAS measurements showed that SEs disordered the acyl chains of SC lipids, and the BAM images demonstrated the modification of the domain structures in SC monolayers. Longer chain-SE has a stronger disordering effect and is better miscible with ceramides in comparison to SE with a shorter hydrophobic part. In conclusion, this study demonstrates the disordering effect of SEs on the biomimetic SC model, pointing out that small changes in the structure of surfactant may have a strong influence on a penetration enhancement of lipophilic drugs through intercellular lipids of skin. Copyright © 2016 Elsevier B.V. All rights reserved.

Biophysical characterization of monofilm model systems composed of selected tear film phospholipids.

PubMed

Patterson, Matthew; Vogel, Hans J; Prenner, Elmar J

2016-02-01

The tear film protects the eye from foreign particles and pathogens, prevents excess evaporation, provides lubrication, and maintains a high quality optical surface necessary for vision. The anterior layer of tear film consists of polar and non-polar lipid layers. The polar lipids form a monolayer on the aqueous subphase, acting as surfactants for the non-polar lipid multilayer. A tear film polar lipid biomimetic consisting of dipalmitoyl phosphatidylcholine (DPPC), dipalmitoyl phosphatidylethanolamine (DPPE), palmitoyl glucosylceramide (PGC), and palmitoyl sphingomyelin (PSM) was characterized using Langmuir monolayers and Brewster angle microscopy (BAM). Lipid combinations formed very stable monolayers, especially those containing DPPC or PSM. Surface experiments and elasticity analyses revealed that PGC resulted in more condensed and rigid mixed monolayers. DPPE provided resistance to large changes in lipid ordering over a wide surface pressure range. Ternary mixtures containing DPPE and PGC with either DPPC or PSM experienced the greatest lipid ordering within the natural tear film surface pressure range suggesting that these lipids are important to maintain tear film integrity during the inter-blink period. Finally, BAM images revealed unique structures within monolayers of DPPC, DPPE, and PGC at the natural tear film surface pressure. 3D analysis of these domains suggested either the formation of multilayers or outward protrusions at surface pressures far below the point of irreversible collapse as seen on the isotherm. This entails that the polar lipids of tear film may be capable of multilayer formation or outward folding as a mechanism to prevent rupture of the tear film during a blink. Copyright © 2015 Elsevier B.V. All rights reserved.

Stress induced magnetic-domain evolution in magnetoelectric composites

NASA Astrophysics Data System (ADS)

Trivedi, Harsh; Shvartsman, Vladimir V.; Lupascu, Doru C.; Medeiros, Marco S. A.; Pullar, Robert C.

2018-06-01

Local observation of the stress mediated magnetoelectric (ME) effect in composites has gained a great deal of interest over the last decades. However, there is an apparent lack of rigorous methods for a quantitative characterization of the ME effect at the local scale, especially in polycrystalline microstructures. In the present work, we address this issue by locally probing the surface magnetic state of barium titante–hexagonal barium ferrite (BaTiO3–BaFe12O19) ceramic composites using magnetic force microscopy (MFM). The effect of the piezoelectrically induced local stress on the magnetostrictive component (BaFe12O19, BaM) was observed in the form of the evolution of the magnetic domains. The local piezoelectric stress was induced by applying a voltage to the neighboring BaTiO3 grains, using a conductive atomic force microscopy tip. The resulting stochastic evolution of magnetic domains was studied in the context of the induced magnetoelastic anisotropy. In order to overcome the ambiguity in the domain changes observed by MFM, certain generalizations about the observed MFM contrast are put forward, followed by application of an algorithm for extracting the average micromagnetic changes. An average change in domain wall thickness of 50 nm was extracted, giving a lower limit on the corresponding induced magnetoelastic anisotropy energy. Furthermore, we demonstrate that this induced magnetomechanical energy is approximately equal to the K1 magnetocrystalline anisotropy constant of BaM, and compare it with a modeled value of applied elastic energy density. The comparison allowed us to judge the quality of the interfaces in the composite system, by roughly gauging the energy conversion ratio.

Influence of organic matter, nutrients, and cyclodextrin on microbial and chemical herbicide and degradate dissipation in subsurface sediment slurries.

PubMed

Kerminen, Kaisa; Le Moël, Romain; Harju, Vilhelmiina; Kontro, Merja H

2018-03-15

Pesticides leaching from soil to surface and groundwater are a global threat for drinking water safety, as no cleaning methods occur for groundwater environment. We examined whether peat, compost-peat-sand (CPS) mixture, NH 4 NO 3 , NH 4 NO 3 with sodium citrate (Na-citrate), and the surfactant methyl-β-cyclodextrin additions enhance atrazine, simazine, hexazinone, dichlobenil, and the degradate 2,6-dichlorobenzamide (BAM) dissipations in sediment slurries under aerobic and anaerobic conditions, with sterilized controls. The vadose zone sediment cores were drilled from a depth of 11.3-14.6m in an herbicide-contaminated groundwater area. The peat and CPS enhanced chemical atrazine and simazine dissipation, and the peat enhanced chemical hexazinone dissipation, all oxygen-independently. Dichlobenil dissipated under all conditions, while BAM dissipation was fairly slow and half-lives could not be calculated. The chemical dissipation rates could be associated with the chemical structures and properties of the herbicides, and additive compositions, not with pH. Microbial atrazine degradation was only observed in the Pseudomonas sp. ADP amended slurries, although the sediment slurries were known to contain atrazine-degrading microorganisms. The bioavailability of atrazine in the water phase seemed to be limited, which could be due to complex formation with organic and inorganic colloids. Atrazine degradation by indigenous microbes could not be stimulated by the surfactant methyl-β-cyclodextrin, or by the additives NH 4 NO 3 and NH 4 NO 3 with Na-citrate, although the nitrogen additives increased microbial growth. Copyright © 2017 Elsevier B.V. All rights reserved.

Refractive index and thickness determination in Langmuir monolayers of myelin lipids.

PubMed

Pusterla, Julio M; Malfatti-Gasperini, Antonio A; Puentes-Martinez, Ximena E; Cavalcanti, Leide P; Oliveira, Rafael G

2017-05-01

Langmuir monolayers at the air/water interface are widely used as biomembrane models and for amphiphilic molecules studies in general. Under controlled intermolecular organization (lateral molecular area), surface pressure, surface potential, reflectivity (R) and other magnitudes can be precisely determined on these planar monomolecular films. However, some physical parameters such as the refractive index of the monolayer (n) still remain elusive. The refractive index is very relevant because (in combination with R) it allows for the determination of the thickness of the film. The uncertainties of n determine important errors that propagate non-linearly into the calculation of monolayers thickness. Here we present an analytical method for the determination of n in monolayers based on refractive index matching. By using a Brewster angle microscopy (BAM) setup and monolayers spread over subphases with variable refractive index (n 2 ), a minimum in R is search as a function of n 2 . In these conditions, n equals n 2 . The results shown correspond to monolayers of myelin lipids. The n values remain constant at 1.46 upon compression and equals the obtained value for myelin lipid bilayers in suspension. The values for n and R allow for the determination of thickness. We establish comparisons between these thicknesses for the monolayer and those obtained from two X-ray scattering techniques: 1) GIXOS for monolayers at the air/water interface and 2) SAXS for bilayers in bulk suspension. This allows us to conclude that the thickness that we measure by BAM includes the apolar and polar headgroup regions of the monolayer. Copyright © 2017 Elsevier B.V. All rights reserved.

Whole-genome mapping reveals a large chromosomal inversion on Iberian Brucella suis biovar 2 strains.

PubMed

Ferreira, Ana Cristina; Dias, Ricardo; de Sá, Maria Inácia Corrêa; Tenreiro, Rogério

2016-08-30

Optical mapping is a technology able to quickly generate high resolution ordered whole-genome restriction maps of bacteria, being a proven approach to search for diversity among bacterial isolates. In this work, optical whole-genome maps were used to compare closely-related Brucella suis biovar 2 strains. This biovar is the unique isolated in domestic pigs and wild boars in Portugal and Spain and most of the strains share specific molecular characteristics establishing an Iberian clonal lineage that can be differentiated from another lineage mainly isolated in several Central European countries. We performed the BamHI whole-genome optical maps of five B. suis biovar 2 field strains, isolated from wild boars in Portugal and Spain (three from the Iberian lineage and two from the Central European one) as well as of the reference strain B. suis biovar 2 ATCC 23445 (Central European lineage, Denmark). Each strain showed a distinct, highly individual configuration of 228-231 BamHI fragments. Nevertheless, a low divergence was globally observed in chromosome II (1.6%) relatively to chromosome I (2.4%). Optical mapping also disclosed genomic events associated with B. suis strains in chromosome I, namely one indel (3.5kb) and one large inversion (944kb). By using targeted-PCR in a set of 176 B. suis strains, including all biovars and haplotypes, the indel was found to be specific of the reference strain ATCC 23445 and the large inversion was shown to be an exclusive genomic marker of the Iberian clonal lineage of biovar 2. Copyright © 2016 Elsevier B.V. All rights reserved.

Stability and Hopf bifurcation in a simplified BAM neural network with two time delays.

PubMed

Cao, Jinde; Xiao, Min

2007-03-01

Various local periodic solutions may represent different classes of storage patterns or memory patterns, and arise from the different equilibrium points of neural networks (NNs) by applying Hopf bifurcation technique. In this paper, a bidirectional associative memory NN with four neurons and multiple delays is considered. By applying the normal form theory and the center manifold theorem, analysis of its linear stability and Hopf bifurcation is performed. An algorithm is worked out for determining the direction and stability of the bifurcated periodic solutions. Numerical simulation results supporting the theoretical analysis are also given.

Global asymptotic stability analysis of bidirectional associative memory neural networks with time delays.

PubMed

Arik, Sabri

2005-05-01

This paper presents a sufficient condition for the existence, uniqueness and global asymptotic stability of the equilibrium point for bidirectional associative memory (BAM) neural networks with distributed time delays. The results impose constraint conditions on the network parameters of neural system independently of the delay parameter, and they are applicable to all continuous nonmonotonic neuron activation functions. It is shown that in some special cases of the results, the stability criteria can be easily checked. Some examples are also given to compare the results with the previous results derived in the literature.

Economic manufacturing of bulk metallic glass compositions by microalloying

DOEpatents

Liu, Chain T.

2003-05-13

A method of making a bulk metallic glass composition includes the steps of:a. providing a starting material suitable for making a bulk metallic glass composition, for example, BAM-11; b. adding at least one impurity-mitigating dopant, for example, Pb, Si, B, Sn, P, to the starting material to form a doped starting material; and c. converting the doped starting material to a bulk metallic glass composition so that the impurity-mitigating dopant reacts with impurities in the starting material to neutralize deleterious effects of the impurities on the formation of the bulk metallic glass composition.

Observation of grain size effect on multiferroism and magnetoelectric coupling of Na0.5Bi0.5TiO3 - BaFe12O19 novel composite system

NASA Astrophysics Data System (ADS)

Pattanayak, Ranjit; Kuila, Sourav; Raut, Subhajit; Ghosh, Surya Prakash; Dhal, Satyanarayan; Panigrahi, Simanchalo

2017-12-01

Four novel polycrystalline magnetoelectric composite systems: S1, S2, S3 and S4 having composition [90 wt% Na0.5Bi0.5TiO3 (NBT) - 10 wt% BaFe12O19 (BaM)] considering the variation of grain size of both the phases [NBT(Lg)-BaM(Lg)-[S1], NBT(Lg)-BaM(Sg)-[S2], NBT(Sg)-BaM(Lg)-[S3] and NBT(Sg)-BaM(Sg)-[S4

Pleiotrophin as a Growth Factor and Therapeutic Target in Breast Cancer

DTIC Science & Technology

1997-10-01

novel phospholipase A2 related gene. Nucl Acid Res 21:135-143. 11. Gattoni-Celli, S., K . Kirsch, S. Kalled , and K . J. Isselbacher. 1986. Expression...clone (G11-F7) is enlarged. Genomic Southern blot probes (a,b,c) and restriction sites are shown (B=BamHI, H=HindIII, Sc=ScaI, K =KpnI). 10WJ 3fr 4&V...otherwise in 25 mM Tris pH8.3/200 mM glycine/20% methanol. The membrane was blocked in PBS (phospate-buffered saline )/0.1% Tween 20/5% powdered milk and

Proton clouds to measure long-range contacts between nonexchangeable side chain protons in solid-state NMR.

PubMed

Sinnige, Tessa; Daniëls, Mark; Baldus, Marc; Weingarth, Markus

2014-03-26

We show that selective labeling of proteins with protonated amino acids embedded in a perdeuterated matrix, dubbed 'proton clouds', provides general access to long-range contacts between nonexchangeable side chain protons in proton-detected solid-state NMR, which is important to study protein tertiary structure. Proton-cloud labeling significantly improves spectral resolution by simultaneously reducing proton line width and spectral crowding despite a high local proton density in clouds. The approach is amenable to almost all canonical amino acids. Our method is demonstrated on ubiquitin and the β-barrel membrane protein BamA.

Development of adapted GMR-probes for automated detection of hidden defects in thin steel sheets

NASA Astrophysics Data System (ADS)

Pelkner, Matthias; Pohl, Rainer; Kreutzbruck, Marc; Commandeur, Colin

2016-02-01

Thin steel sheets with a thickness of 0.3 mm and less are the base materials of many everyday life products (cans, batteries, etc.). Potential inhomogeneities such as non-metallic inclusions inside the steel can lead to a rupture of the sheets when it is formed into a product such as a beverage can. Therefore, there is a need to develop automated NDT techniques to detect hidden defects and inclusions in thin sheets during production. For this purpose Tata Steel Europe and BAM, the Federal Institute for Materials Research and Testing (Germany), collaborate in order to develop an automated NDT-system. Defect detection systems have to be robust against external influences, especially when used in an industrial environment. In addition, such a facility has to achieve a high sensitivity and a high spatial resolution in terms of detecting small inclusions in the μm-regime. In a first step, we carried out a feasibility study to determine which testing method is promising for detecting hidden defects and inclusions inside ferrous thin steel sheets. Therefore, two methods were investigated in more detail - magnetic flux leakage testing (MFL) using giant magneto resistance sensor arrays (GMR) as receivers [1,2] and eddy current testing (ET). The capabilities of both methods were tested with 0.2 mm-thick steel samples containing small defects with depths ranging from 5 µm up to 60 µm. Only in case of GMR-MFL-testing, we were able to detect parts of the hidden defects with a depth of 10 µm trustworthily with a SNR better than 10 dB. Here, the lift off between sensor and surface was 250 µm. On this basis, we investigated different testing scenarios including velocity tests and different lift offs. In this contribution we present the results of the feasibility study leading to first prototypes of GMR-probes which are now installed as part of a demonstrator inside a production line.

Optimized Next-Generation Sequencing Genotype-Haplotype Calling for Genome Variability Analysis

PubMed Central

Navarro, Javier; Nevado, Bruno; Hernández, Porfidio; Vera, Gonzalo; Ramos-Onsins, Sebastián E

2017-01-01

The accurate estimation of nucleotide variability using next-generation sequencing data is challenged by the high number of sequencing errors produced by new sequencing technologies, especially for nonmodel species, where reference sequences may not be available and the read depth may be low due to limited budgets. The most popular single-nucleotide polymorphism (SNP) callers are designed to obtain a high SNP recovery and low false discovery rate but are not designed to account appropriately the frequency of the variants. Instead, algorithms designed to account for the frequency of SNPs give precise results for estimating the levels and the patterns of variability. These algorithms are focused on the unbiased estimation of the variability and not on the high recovery of SNPs. Here, we implemented a fast and optimized parallel algorithm that includes the method developed by Roesti et al and Lynch, which estimates the genotype of each individual at each site, considering the possibility to call both bases from the genotype, a single one or none. This algorithm does not consider the reference and therefore is independent of biases related to the reference nucleotide specified. The pipeline starts from a BAM file converted to pileup or mpileup format and the software outputs a FASTA file. The new program not only reduces the running times but also, given the improved use of resources, it allows its usage with smaller computers and large parallel computers, expanding its benefits to a wider range of researchers. The output file can be analyzed using software for population genetics analysis, such as the R library PopGenome, the software VariScan, and the program mstatspop for analysis considering positions with missing data. PMID:28894353

[The forensic medical characteristics of the entrance bullet holes created by the shots from pneumatic rifles].

PubMed

Legin, G A; Bondarchuk, A O; Perebetjuk, A N

2015-01-01

The objective of the present study was to compare the injurious action of three types of the bullets for the pneumatic weapons shot from different distances using the Gamo pump air pistol and the BAM B22-1 pneumatic rifle. The following four kinds of the bullets were tested: "the fireball", "Luman cap 0.3", "Luman Field Target 0.68" and "DIABOLO". It was experimentally shown that the injurious action of the bullets fired from the same distance from the pneumatic weapons depends on the type of both the bullet and the weapon, as well as the properties of the target material. Specifically, the action of bullets fired from the piston pneumatic rifle remained stable whereas that of the bullets shot from the gas-balloon air pistol decreased as the gas was exhausted. The studies by the contact-diffusion method have demonstrated that the entrance bullet holes created by the shots from pneumatic weapons are surrounded by dispersed metal particles which makes it possible to estimate the shooting distance. Moreover, the bullets fired from the pneumatic weapons leave the muzzle face imprint on certain target materials.

Haplotype-Based Genotyping in Polyploids.

PubMed

Clevenger, Josh P; Korani, Walid; Ozias-Akins, Peggy; Jackson, Scott

2018-01-01

Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs) are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads. Implementing a haplotype-based method in contrasting subgenome-specific sequences leads to higher accuracy of SNP identification in polyploids. To test this method, a large-scale 48K SNP array (Axiom Arachis2) was developed for Arachis hypogaea (peanut), an allotetraploid, in which 1,674 haplotype-based SNPs were included. Results of the array show that 74% of the haplotype-based SNP markers could be validated, which is considerably higher than previous methods used for peanut. The haplotype method has been implemented in a standalone program, HAPLOSWEEP, which takes as input bam files and a vcf file and identifies haplotype-based markers. Haplotype discovery can be made within single reads or span paired reads, and can leverage long read technology by targeting any length of haplotype. Haplotype-based genotyping is applicable in all allopolyploid genomes and provides confidence in marker identification and in silico-based genotyping for polyploid genomics.

Self-Presentation Strategies, Fear of Success and Anticipation of Future Success among University and High School Students.

PubMed

Kosakowska-Berezecka, Natasza; Jurek, Paweł; Besta, Tomasz; Badowska, Sylwia

2017-01-01

The backlash avoidance model (BAM) suggests women insufficiently self-promote because they fear backlash for behavior which is incongruent with traditional gender roles. Avoiding self-promoting behavior is also potentially related to associating success with negative consequences. In two studies we tested whether self-promotion and fear of success will be predictors of lower salaries and anticipation of lower chances of success in an exam. In study 1, prior to the exam they were about to take, we asked 234 students about their predictions concerning exam results and their future earnings. They also filled scales measuring their associations with success (fear of success) and tendency for self-promotion. The tested model proved that in comparison to men, women expect lower salaries in the future, anticipate lower test performance and associate success with more negative consequences. Both tendency for self-promotion and fear of success are related to anticipation of success in test performance and expectations concerning future earnings. In study 2 we repeated the procedure on a sample of younger female and male high school pupils ( N = 100) to verify whether associating success with negative consequences and differences in self-promotion strategies are observable in a younger demographic. Our results show that girls and boys in high school do not differ with regard to fear of success, self-promotion or agency levels. Girls and boys anticipated to obtain similar results in math exam results, but girls expected to have higher results in language exams. Nevertheless, school pupils also differed regarding their future earnings but only in the short term. Fear of success and agency self-ratings were significant predictors of expectations concerning future earnings, but only among high school boys and with regard to earnings expected just after graduation.

Self-Presentation Strategies, Fear of Success and Anticipation of Future Success among University and High School Students

PubMed Central

Kosakowska-Berezecka, Natasza; Jurek, Paweł; Besta, Tomasz; Badowska, Sylwia

2017-01-01

The backlash avoidance model (BAM) suggests women insufficiently self-promote because they fear backlash for behavior which is incongruent with traditional gender roles. Avoiding self-promoting behavior is also potentially related to associating success with negative consequences. In two studies we tested whether self-promotion and fear of success will be predictors of lower salaries and anticipation of lower chances of success in an exam. In study 1, prior to the exam they were about to take, we asked 234 students about their predictions concerning exam results and their future earnings. They also filled scales measuring their associations with success (fear of success) and tendency for self-promotion. The tested model proved that in comparison to men, women expect lower salaries in the future, anticipate lower test performance and associate success with more negative consequences. Both tendency for self-promotion and fear of success are related to anticipation of success in test performance and expectations concerning future earnings. In study 2 we repeated the procedure on a sample of younger female and male high school pupils (N = 100) to verify whether associating success with negative consequences and differences in self-promotion strategies are observable in a younger demographic. Our results show that girls and boys in high school do not differ with regard to fear of success, self-promotion or agency levels. Girls and boys anticipated to obtain similar results in math exam results, but girls expected to have higher results in language exams. Nevertheless, school pupils also differed regarding their future earnings but only in the short term. Fear of success and agency self-ratings were significant predictors of expectations concerning future earnings, but only among high school boys and with regard to earnings expected just after graduation. PMID:29163271

Emergency skills learning on video (ESLOV): A single-blinded randomized control trial of teaching common emergency skills using self-instruction video (SIV) versus traditional face-to-face (FTF) methods.

PubMed

Mohd Saiboon, Ismail; Jaafar, Mohd Johar; Ahmad, Nurul Saadah; Nasarudin, Nazhatul Muna Ahmad; Mohamad, Nabishah; Ahmad, Mohd Radhi; Gilbert, John H V

2014-03-01

Self-instruction video (SIV) has been widely explored as a teaching mode for cardiopulmonary resuscitation (CPR) and automated external defibrillation (AED), but not with other basic emergency skills. To evaluate the effectiveness of SIV in teaching other basic emergency skill in comparison with traditional face-to-face (FTF) methods. Participants were randomized into SIV and FTF groups. Each group was assigned to learn basic airway management (BAM), cervical collar application (CCA), manual cardiac defibrillation (MCD), and emergency extremity splinting (EES) skills. Confidence level was assessed using questionnaires, and skills performances were assessed using calibrated-blinded assessors through an Objective Structured Clinical Examination (OSCE). Forty-five participants took part in the assessment exercises. There were no significant differences between both groups, on all four skill categories. The mean OSCE-score of an individual category between the FTF-group vs. the SIV-group were as follows: BAM (10.23 ± 1.04 vs. 10.04 ± 1.49; p = 0.62); CCA (7.86 ± 4.39 vs. 7.13 ± 4.12; p = 0.57); MCD (8.24 ± 0.89 vs. 7.58 ± 1.14; p = 0.39); EES (5.43 ± 2.11 vs. 4.63 ± 2.30; p = 0.23). The composite mean score for the FTF-group was 6.85, and for the SIV-group was 6.20 (p < 0.05). There was no significant different in the level of confidence for both groups. SIV is as effective as FTF in teaching and learning basic emergency skills.

Profiling of EBV-Encoded microRNAs in EBV-Associated Hemophagocytic Lymphohistiocytosis.

PubMed

Zhou, Chen; Xie, Zhengde; Gao, Liwei; Liu, Chunyan; Ai, Junhong; Zhang, Li; Shen, Kunling

2015-10-01

Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis (EBV-HLH) is a life-threatening complication of EBV infection. MicroRNAs (miRNAs) were small non-coding RNA, and EBV could encode miRNAs that are involved in the progression of infection. However, the profiles of EBV-miRNAs in EBV-HLH were unknown. Here, we aimed to profile the expression of EBV-miRNAs in children with EBV-HLH by analyzing 44 known EBV-miRNAs, encoded within the BamHI fragment H rightward open reading frame 1 (BHRF1) and the BamHI-A region rightward transcript (BART), in plasma and cellular targets by real-time quantitative PCR. The study included 15 children with EBV-HLH, 15 children with infectious mononucleosis (IM), and 15 healthy controls. CD8(+) T cells were found to be the cellular target of EBV infection in EBV-HLH, while CD19(+) B cells were infected with EBV in IM. We also found the greater levels of several miRNAs encoded by BART in EBV-HLH, compared to those in IM and healthy controls, whereas the levels of BHRF1 miRNAs were lower than those in IM. The profile and pattern of EBV-miRNAs in EBV-HLH indicated that EBV could display type II latency in EBV-HLH. Importantly, the level of plasma miR-BART16-1 continued decreasing during the whole chemotherapy, suggesting that plasma miR-BART16-1 could be a potential biomarker for monitoring EBV-HLH progression. The pathogenesis of EBV-HLH might be attributed to the abundance of EBV-miRNAs in EBV-HLH. These findings help elucidate the roles of EBV miRNAs in EBV-HLH, enabling the understanding of the basis of this disease and providing clues for its treatment.

Novel variants of the 5S rRNA genes in Eruca sativa.

PubMed

Singh, K; Bhatia, S; Lakshmikumaran, M

1994-02-01

The 5S ribosomal RNA (rRNA) genes of Eruca sativa were cloned and characterized. They are organized into clusters of tandemly repeated units. Each repeat unit consists of a 119-bp coding region followed by a noncoding spacer region that separates it from the coding region of the next repeat unit. Our study reports novel gene variants of the 5S rRNA genes in plants. Two families of the 5S rDNA, the 0.5-kb size family and the 1-kb size family, coexist in the E. sativa genome. The 0.5-kb size family consists of the 5S rRNA genes (S4) that have coding regions similar to those of other reported plant 5S rDNA sequences, whereas the 1-kb size family consists of the 5S rRNA gene variants (S1) that exist as 1-kb BamHI tandem repeats. S1 is made up of two variant units (V1 and V2) of 5S rDNA where the BamHI site between the two units is mutated. Sequence heterogeneity among S4, V1, and V2 units exists throughout the sequence and is not limited to the noncoding spacer region only. The coding regions of V1 and V2 show approximately 20% dissimilarity to the coding regions of S4 and other reported plant 5S rDNA sequences. Such a large variation in the coding regions of the 5S rDNA units within the same plant species has been observed for the first time. Restriction site variation is observed between the two size classes of 5S rDNA in E. sativa.(ABSTRACT TRUNCATED AT 250 WORDS)