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Sample records for volumes 20-40 ml

  1. Impact of increasing sample volume from 4 ml to 8 ml on bacterial detection rates in apheresis platelets: a meta-analysis.

    PubMed

    Bruhn, R; Custer, B; Vanderpool, S; Townsend, M; Kamel, H; Tomasulo, P

    2015-04-01

    Some blood centres have increased sample volume of in-process cultures to improve detection of bacterial contamination when screening apheresis platelet units. We performed a meta-analysis to evaluate extant published North American data comparing apheresis platelet bacterial contamination rates from 4 ml and 8 ml sample volume. Pooled results indicate an 8 ml sample volume yields higher true-positive rates than 4 ml resulting in a significant increase in the detection rate and interdiction of contaminated units, which should contribute to reduced risk of adverse transfusion outcomes.

  2. Microwave Ablation of Symptomatic Benign Thyroid Nodules: Energy Requirement per ml Volume Reduction.

    PubMed

    Korkusuz, Y; Kohlhase, K; Gröner, D; Erbelding, C; Luboldt, W; Happel, C; Ahmad, S; Vogl, T J; Gruenwald, F

    2016-11-01

    Purpose: Microwave ablation (MWA) represents a novel thermal ablative treatment of benign thyroid nodules. The aim was to determine the energy required per ml volume reduction in order to match the required energy to the volume-of-interest (VOI). Materials and Methods: 25 patients with 25 nodules (6 solid, 13 complex and 6 cystic) were treated by microwave ablation (MWA). The transmitted energy (E) was correlated with the volume change (∆ V) after 3 months. The energy required per ml volume reduction after 3 months was calculated by E/∆ V. Results: MWA resulted in a significant (p < 0.0001) volume reduction (∆ V) with a mean of 12.4 ± 13.0 ml (range: 1.5 - 63.2 ml) and relative reduction of 52 ± 16 % (range: 22 - 77 %). There was a positive correlation between E and ∆ V (r = 0.82; p < 0.05). The mean E/∆ V was 1.52 ± 1.08 (range: 0.4 - 4.6) kJ/ml for all nodules and 2.30 ± 1.5 (0.9 - 4.6), 1.5 ± 0.9 (0.4 - 3.6), 0.75 ± 0.25 (0.4 - 1.2) kJ/ml, respectively, for solid, complex and cystic nodules with a significant difference in E/∆ V for solid and cystic (p < 0.03). Conclusion: The energy required per volume depends on the nodule consistency. Solid nodules require more energy than cystic ones. The estimation of the energy needed per volume-of-interest as an additional parameter should help to avoid under- or overtreatment. Key Points: • The estimated required energy for a volume-of-interest depends on the nodule consistency• In solid nodules a higher energy transmission than in cystic nodules is recommended• The energy transmission as an additional marker to ultrasound is helpful for improving periprocedural monitoring Citation Format: • Korkusuz Y, Kohlhase K, Gröner D et al. Microwave Ablation of Symptomatic Benign Thyroid Nodules: Energy Requirement per ml Volume Reduction. Fortschr Röntgenstr 2016; 188: 1054 - 1060.

  3. Method for the Thermal Characterization of PCM Systems in the Volume Range from 100 ml to 1000 ml

    NASA Astrophysics Data System (ADS)

    Göbel, A.; Vidi, S.; Klinker, F.; Hemberger, F.; Brütting, M.; Ebert, H.-P.; Mehling, H.

    2017-05-01

    The storage of latent heat in phase change materials (PCM) is of great interest in many applications, for example in building applications. However, there is no standard method for the determination of the thermophysical properties of application-sized PCM specimens, i.e., specimens with sizes around 100 ml to 1000 ml. In order to close this metrological gap, a commercially available heat flow meter was modified to perform enthalpy measurements. The feasibility of this method was proven by performing comparative measurements on a stainless steel specimen using both the standard method DSC and the modified heat flow meter. Furthermore, measurements on a gypsum board with microencapsulated PCM were performed with the heat flow meter in order to determine the enthalpy. The coincidence with literature values is within ±4% which demonstrates that this method is a good choice for performing measurements on application-sized PCM specimens.

  4. [The effect of cerebrolysin in dosage 50 ml on the volume of lesion in ischemic stroke].

    PubMed

    Shamalov, N A; Stakhovskaia, L V; Burenchev, D V; Kichuk, I V; Tvorogova, T V; Botsina, A Iu; Smychkov, A S; Kerbikov, O B; Moessler, H; Novak, P; Skvortsova, V I

    2010-01-01

    The purpose of this randomized, double-blind, placebo-controlled study was to assess safety and efficacy of cerebrolysin used in dosage 50 ml in acute ischemic stroke. Forty-seven patients with ischemic stroke, aged 45-85 years, who were admitted to a clinical unit within the first 12 h after stroke onset were included in the study. A quantitative time-related MRI analysis of the dynamics of neurological deficit revealed the more rapid decrease of stroke volume to the 28th day in the group treated with cerebrolysin (45.4% versus 43.6% in the placebo-group (p < 0.05)). No side-effects of treatment with cerebrolysin was found. The results of this prospective, randomized, placebo-controlled study suggest the positive effect of cerebrolysin on the dynamics of volume lesion in patients with ischemic stroke.

  5. Frequency of early remodeling of left ventricle and its comparison between patients with stroke volume ≥97 Ml versus patients with stroke volume <97 Ml after aortic valve replacement for severe aortic regurgitation

    PubMed Central

    Ali Rizvi, Hafiz Muhammad Farhan; Khalid, Zaigham Rasool; Baksh, Allah; Raza Baig, Mirza Ahmad

    2016-01-01

    Objectives: To evaluate the frequency of early remodeling in patients of severe aortic regurgitation after aortic valve replacement and to see the incidence of early remodeling in patients with stroke volume >97 ml versus < 97 ml before aortic valve replacement. Method: This was a prospective comparative study conducted from August 2013 to December 2014 in a tertiary care hospital. Fifty seven (57) patients of isolated chronic aortic regurgitation were included in this study. SPSS v23 was used for data analysis. Independent sample t-test was used for analysis of continuous variables and chi-square test for qualitative variables. Results: Out of fifty seven patients, early remodeling occurred in 34 (59.64%) patients after surgery. The mean pre-operative stroke volume of patient in whom remodeling occurred was 110.3+9.66 ml while mean pre-operative stroke volume of patients who did not undergo remodeling was 86.65+7.63 ml. There were 28 (82.4%) patients with stroke volume >97 ml in whom Remodeling occurred where as in patients with stroke volume <97 ml remodeling occurred only in 6 (17.6%) patients (p value 0.004). There was no in-hospital mortality. Conclusion: There is an association between stroke volume and early LV remodeling after Aortic valve replacement. Stroke volume >97 ml is a good predictor of early LV remodeling. PMID:28083026

  6. Does Diffusion Lesion Volume Above 70 mL Preclude Favorable Outcome Despite Post-Thrombolysis Recanalization?

    PubMed

    Tisserand, Marie; Turc, Guillaume; Charron, Sylvain; Legrand, Laurence; Edjlali, Myriam; Seners, Pierre; Roca, Pauline; Lion, Stéphanie; Naggara, Olivier; Mas, Jean-Louis; Méder, Jean-François; Baron, Jean-Claude; Oppenheim, Catherine

    2016-04-01

    Whether to withhold recanalization treatment when the diffusion-weighted imaging (DWI) lesion exceeds a given volume is unsettled. Our aim was to assess the impact of recanalization on outcome in patients with baseline DWI lesion ≥70 mL (DWI≥70 mL) treated ≤4.5 hours from onset. We hypothesized that recanalization is beneficial in a sizeable fraction of these patients and that this is associated with a larger DWI lesion reversal. We analyzed 267 consecutive patients treated with intravenous recombinant tissue-type plasminogen activator for middle cerebral artery territory stroke in whom an occlusion was present on magnetic resonance angiography and 24-hour recanalization and 90-day clinical outcome could be assessed. After stratification relative to the 70-mL DWI lesion cut point, we calculated the odds ratio for recanalization of the primary arterial occlusive lesion (AOL score ≥2) to predict favorable outcome (modified Rankin scale score ≤2). DWI lesion reversal was compared between recanalizers with DWI≥70 mL with favorable and unfavorable outcomes. Median (interquartile range) DWI lesion volume was 22 mL (10-60), and median onset time to imaging was 116 minutes (86-151). Twelve (22%) of the 54 patients with DWI≥70 mL experienced favorable outcome, of which 9 had recanalized. In patients with DWI≥70 mL, recanalization was significantly associated with favorable outcome after adjustment for age and National Institutes of Health Stroke Scale (odds ratio =4.72 [1.09-20.32]; P=0.0375). Among recanalizers with DWI≥70 mL, absolute and relative DWI reversal volumes were larger in those with favorable as compared with unfavorable outcome (18.8 mL [12.2-47.6] versus 8.5 mL [4.3-31.1]; P=0.17; and 19.6% [10.9-62.8] versus 8.7% [3.9-16.5], respectively; P=0.049). Patients with DWI lesion volume ≥70 mL can benefit from recanalization after intravenous recombinant tissue-type plasminogen activator. This may partly reflect a larger amount of DWI lesion

  7. Tolerability of Vidaza (azacitidine) subcutaneous administration using a maximum volume of 3 ml per injection.

    PubMed

    Ferruccio, Lauren F; Murray, Cindy; Yee, Karen W; Incekol, Diana; Lee, Roy; Paisley, Emma; Ng, Pamela

    2016-08-01

    The azacitidine (Vidaza®) product monograph indicates that doses greater than 4 ml should be divided equally into two syringes and injected into different sites. Although 2 ml is a more commonly used maximum volume for subcutaneous injections, there is a lack of evidence to support the use of any given maximum volume with azacitidine. Applying the status quo of 2 ml to azacitidine results in patients receiving 3-4 injections per visit. This prospective study evaluated the frequency and type of injection site reactions when the maximum subcutaneous injection volume was increased from 2 to 3 ml per injection site. Among 30 patients, 309 doses were administered, and injection site reactions were noted in 92.9% of all doses, with the majority (82.2%) being grade 1; only 10.7% of doses resulted in grade 2 reactions, and there were no grade 3 or 4 reactions. There was no increase in frequency or severity of injection site reactions when the maximum volume was increased to 3 ml. The median number of injections that patients received per visit decreased from 3 to 2 after the volume was increased, and there was a statistically significant reduction in the incidence of pain. Decreasing the number of injections also facilitates ease of rotation of injection sites and decreases pharmacy preparation time. This is the first time that injection site reaction data relating to injection volume have been reported for azacitidine. © The Author(s) 2015.

  8. Low-temperature volume radiation annealing of cold-worked bands of Al-Li-Cu-Mg alloy by 20-40 keV Ar+ ion

    NASA Astrophysics Data System (ADS)

    Ovchinnikov, V. V.; Gushchina, N. V.; Mozharovsky, S. M.; Kaigorodova, L. I.

    2017-01-01

    The processes of radiation-dynamic nature (in contrast to the thermally-activated processes) in the course of short-term irradiation of 1 mm thick bands of cold-worked aluminum alloy 1441 (of system Al-Li-Cu-Mg) with Ar+ 20-40 keV were studied. An effect of in-the-bulk (throughout the whole of metal bands thickness) low-temperature radiation annealing of the named alloy, multiply accelerated as compared with common thermal annealing processes was registered (with projected ranges of ions of considered energies definitely not exceeding 0.1 μm). The processes of recrystallization and intermetallic structure changes (occurring within a few seconds of Ar+ irradiation) have the common features as well as the differences in comparison with the results of two hour standard thermal annealing.

  9. Final report on regional supplementary comparison SIM.M.FF-S5: Volume of liquids at 50 mL

    NASA Astrophysics Data System (ADS)

    Morales, Abed; Malta, Dalni; Kornblit, Fernando; Ramírez, Ruben R.; Arias, Roberto; Trujillo, Sonia

    2012-01-01

    A regional supplementary comparison for the volume of liquid at 50 mL was conducted during October 2009 to June 2010 between the SIM members CENAM, INTI, INMETRO, INDECOPI and INTN. The transfer standard consisted of two 50 mL glass pycnometers, of the Gay Lussac type. CENAM acted as the pilot, collected the measurement results, analyzed the data and produced the comparison report. The median of all participants' results was used to calculate the regional comparison reference value because the result for one of the two pycnometers in one laboratory failed the chi-squared test at the 0.05 probability level. The measurements reported by the participants show an excellent overlap in four out of the five NMIs (-34×10-6 < Di < 29×10-6). The degree of equivalence obtained herein will be taken into account for the preparation of calibration and measurement capabilities claims from the participants. 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 SIM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

  10. [Transurethral resection of the prostate combined with 2-micron continuous-wave laser vaporesection for benign prostatic hyperplasia with the prostate volume > 80 ml].

    PubMed

    Ren, Xiao-lei; Gao, Zhi-ming; Xia, Hai-bo; Bao, Guo-chang; Li, Chun-sheng; Zhang, Hao

    2015-02-01

    To sum up the clinical experience in the management of benign prostatic hyperplasia (BPH) with the prostate weighing over 80 ml by transurethral resection of the prostate (TURP) combined with 2 μm continuous-wave laser vaporesection (LVR). We retrospectively analyzed the clinical effects of TURP combined with 2 μm LVR in the treatment of 46 cases of BPH with the prostate volume > 80 ml. All the operations were successfully accomplished. The operation time and intraoperative blood loss were (112.0 ± 20.0) min (range 86-176 min) and (77.9 ± 25.9) ml (range 50-200 ml), respectively. The catheters were withdrawn at 7 days after surgery. Transient urinary incontinence occurred in 6 cases and secondary hemorrhage was found in 2 postoperatively. Six-month follow-up revealed no urethral stricture or other complications. Compared with the baseline, the international prostate symptom score (IPSS) was significantly decreased at 6 months after operation (26.3 ± 1.8 vs 11.6 ± 1.7, P <0.05), and so were the quality of life (QOL) score (5.3 ± 0.7 vs 1.3 ± 1.1, P <0.05) and post-void residual urine (PVR) ([115.5 ± 55.6] ml vs [19.9 ± 11.6] ml, P <0.05). However, the maximum urinary flow rate (Qmax) was remarkably increased from (4.1 ± 2.6) ml/s to (16.2 ± 1.7) ml/s (P <0.05). TURP combined with 2 μm LVR is safe and effective for the treatment of BPH with the prostate volume >80 ml.

  11. Lower tidal volume strategy (≈3 ml/kg) combined with extracorporeal CO2 removal versus 'conventional' protective ventilation (6 ml/kg) in severe ARDS: the prospective randomized Xtravent-study.

    PubMed

    Bein, Thomas; Weber-Carstens, Steffen; Goldmann, Anton; Müller, Thomas; Staudinger, Thomas; Brederlau, Jörg; Muellenbach, Ralf; Dembinski, Rolf; Graf, Bernhard M; Wewalka, Marlene; Philipp, Alois; Wernecke, Klaus-Dieter; Lubnow, Matthias; Slutsky, Arthur S

    2013-05-01

    Acute respiratory distress syndrome is characterized by damage to the lung caused by various insults, including ventilation itself, and tidal hyperinflation can lead to ventilator induced lung injury (VILI). We investigated the effects of a low tidal volume (V(T)) strategy (V(T) ≈ 3 ml/kg/predicted body weight [PBW]) using pumpless extracorporeal lung assist in established ARDS. Seventy-nine patients were enrolled after a 'stabilization period' (24 h with optimized therapy and high PEEP). They were randomly assigned to receive a low V(T) ventilation (≈3 ml/kg) combined with extracorporeal CO2 elimination, or to a ARDSNet strategy (≈6 ml/kg) without the extracorporeal device. The primary outcome was the 28-days and 60-days ventilator-free days (VFD). Secondary outcome parameters were respiratory mechanics, gas exchange, analgesic/sedation use, complications and hospital mortality. Ventilation with very low V(T)'s was easy to implement with extracorporeal CO2-removal. VFD's within 60 days were not different between the study group (33.2 ± 20) and the control group (29.2 ± 21, p = 0.469), but in more hypoxemic patients (PaO2/FIO2 ≤150) a post hoc analysis demonstrated significant improved VFD-60 in study patients (40.9 ± 12.8) compared to control (28.2 ± 16.4, p = 0.033). The mortality rate was low (16.5%) and did not differ between groups. The use of very low V(T) combined with extracorporeal CO2 removal has the potential to further reduce VILI compared with a 'normal' lung protective management. Whether this strategy will improve survival in ARDS patients remains to be determined (Clinical trials NCT 00538928).

  12. KEY COMPARISON: Results of the key comparison CCM.FF-K4 for volume of liquids at 20 L and 100 mL

    NASA Astrophysics Data System (ADS)

    Arias, Roberto; Maldonado, Manuel; Wright, John; Jacques, Claude; Lachance, Christian; Lau, Peter; Többen, Helmut; Cignolo, Giorgio; Lorefice, Salvatore; Man, John; Aibe, Valter Y.

    2006-01-01

    A key comparison was performed in order to compare national measurement systems to determine volume of liquids, particularly at fixed volumes of 20 L and 100 mL. The participants were CENAM (Mexico), NIST (United States of America), NRC/MC (Canada), SP (Sweden), PTB (Germany), INRIM (former IMGC, Italy), NMIA (Australia) and INMETRO (Brazil). CENAM acted as pilot laboratory. The measurements were carried out from December 2003 to March 2005. The chosen values of volume (20 L and 100 mL) are both representatives of the Calibration and Measurement Capabilities (CMCs) declared by most of the participating national metrology institutes. The transfer standards (TSs) were three stainless steel pipettes for volume at 20 L and six commercially available glass pycnometers for volume at 100 mL. Prior to the beginning of the key comparison, the 20 L TSs were tested by CENAM, SP and NMIA The results of the test phase showed excellent values for both repeatability and reproducibility. During the CCM.FF-K4, the results of most of the laboratories showed good agreement with the reference values. The best estimation of the measurands, as reported by the participants showed a general agreement better than ±0.0025% for volume of liquids at 100 mL and 20 L. 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 CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

  13. KEY COMPARISON: Final report on regional key comparison SIM.M.FF-K4: Volume of liquids at 20 L and 100 mL

    NASA Astrophysics Data System (ADS)

    Arias, Roberto; Maldonado, Manuel; Wright, John; Wallace, Tanisha; Rodríguez, Sandra; Pinzón, Orlando; Morales, Abed; Vega, Maria; Santo, Claudia; Kornblit, Fernando; Malta, Dalni

    2010-01-01

    At its meeting in October 2006 in Querétaro, Mexico, the Interamerican Metrology System (SIM) Technical Committee for Fluid Flow (TCFF) approved a Regional Key Comparison for Volume of Liquids at 20 L and 100 mL, to be piloted by the national metrology institute of Mexico (CENAM). The objective of this comparison was to demonstrate the degree of equivalence of the volume measurement standards held at national measurement institutes (NMIs) and to provide supporting evidence for the Calibration and Measurement Capabilities (CMCs) claimed by the participating laboratories in the Americas. During the comparison, one of the pycnometers suffered irreversible damage, and degrees of equivalence for volume at 100 mL were calculated using the results obtained with one single pycnometer (TS 03.04.04). Conclusions are as follows: The transfer standards for SIM.M.FF-K4 exhibited global good performance all the way along, both in terms of stability and repeatability. Degrees of equivalence have been produced for volumes at 20 L and at 100 mL. The best estimation of the measurands, as reported by the participants, shows a general agreement better than +/-0.0070% for volume of liquids at 100 mL and 20 L. It is advisable to review the uncertainty analysis of some participants. New CMC entries for some NMIs should take into account the information presented in this Report. 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 CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

  14. Final report on APMP key comparison of volume of liquids at 20 L and 100 mL: APMP.M.FF-K4

    NASA Astrophysics Data System (ADS)

    Man, John; Arias, Roberto; Terao, Yoshiya; Lee, Yong Jae; Ligong, Guo; Tulasombut, Verra; Chan, Tak Kin; Thai, Nguyen Hong; Steyn, Ronel; Sampath, H. L. I. S.

    2011-01-01

    This report presents the results of a key comparison of liquid volume measurement conducted between ten participating institutes during the period July 2006 to August 2008 within the framework of the Asia Pacifica Metrology Program (APMP). The transfer standards comprised one 20 L volume measure and two 100 mL glass pycnometers. These transfer standards had been used in a similar CIPM key comparison CCM.FF-K4 in 2003 to 2005. The pilot institute was the National Measurement Institute, Australia (NMIA), which together with CENAM act as link laboratories to the CCM.FF-K4 comparison. 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 CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

  15. SIM.M.FF-S7: Final report on SIM/ANDIMET supplementary comparison for volume of liquids at 100 mL and 100 μL

    NASA Astrophysics Data System (ADS)

    Trujillo, S.; Maldonado, J. M.; Vega, M. C.; Santalla, E.; Sica, A.; Cantero, D.; Salazar, M.; Morales, A.; Solano, P.; Rodríguez, L. D.

    2016-01-01

    A SIM/ANDIMET comparison for liquid volume using two 100 mL pycnometers and two 100 μL piston pipettes was performed between January 2012 and October 2013. The National Metrology Institute (NMI) of Bolivia was the coordinating laboratory and the Mexican NMI provided technical assistance. The participating labs were IBMETRO (Bolivia), INM (Colombia), INEN (Ecuador), INDECOPI (Peru), LACOMET (Costa Rica), LATU (Uruguay), INTN (Paraguay), and CENAM (Mexico). Based on measurements made by CENAM at the beginning and end of the comparison, the transfer standards were stable during the comparison within 0.0001 mL for the 100 mL pycnometers and 0.03 μL for the 100 μL pipettes. For 100 mL, six of the eight participants agreed within ± 0.003 % and had standardized degrees of equivalence (EN) less than 1. Two participants (INEN and INM) had EN values greater than 1. For the 100 μL pipettes, the results were corrected for the influence of altitude and seven of the eight participants agreed within ± 0.3 %. Results from INEN and some from INM and IBMETRO had EN values greater than 1 for the 100 μL pipettes. Uncertainties recommended by Guideline DKD-R 8-1 for micropipettes were included. 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 CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).

  16. KEY COMPARISON: Final report on EUROMET key comparison EUROMET.M.FF-K4 for volume intercomparison of 100 ml Gay-Lussac pycnometer

    NASA Astrophysics Data System (ADS)

    Batista, Elsa

    2006-01-01

    Pycnometers are currently used for the measurement of the density of different liquids (from water to high viscosity inks). In order to have a correct density measurement the volume of the pycnometer must be obtained by calibration. Usually the calibration method is a gravimetric method. In 2002 a project for the comparison of the volume of 100 ml Gay-Lussac pycnometer was initially proposed in the EUROMET TC Flow. Fourteen NMIs agreed to participate and the EUROMET 692 project started officially in September 2002 and was concluded in March 2004. The main purpose of the project was to compare the experimental method and the uncertainty calculation in the pycnometer volume determination and it was expected to be representative for all types of laboratory glassware. In the EUROMET TC Flow 2006 in Lisbon it was decided to propose this project as a EUROMET Key Comparison due to the good overall agreement found. It was therefore necessary to link the EUROMET 692 results with the Key Comparison CCM.FF-K4. Because the pycnometers were not identical in both intercomparisons, some calculations on equivalence were performed based on BIPM rules. The results of all laboratories participating in EUROMET project 692 are presented in this report as well as their equivalence with the reference value of the key comparison CCM.FF-K4. 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 CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

  17. 46 CFR 42.20-40 - Standard height of superstructure.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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  18. 46 CFR 42.20-40 - Standard height of superstructure.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

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  19. Efficacy of Adding Dutasteride to α-Blocker Therapy Treated Benign Prostatic Hyperplasia Patients with Small Volume Prostate (<30 mL).

    PubMed

    Hashimoto, Mamoru; Shimizu, Nobutaka; Sugimoto, Koichi; Hongoh, Sachiko; Minami, Takafumi; Nozawa, Masahiro; Yoshimura, Kazuhiro; Hirayama, Akihide; Tahara, Hideo; Uemura, Hirotsugu

    2017-09-01

    To assess the efficacy of dutasteride add-on therapy for patients with benign prostatic hyperplasia (BPH) and lower urinary tract symptoms (LUTS) with small prostates who have been treated with α-blocker therapy for >3 months. A total of 110 men with clinical BPH were enrolled. There were 17 and 93 subjects with a prostate volume (PV) <30 and ≥30 mL, respectively. All subjects had been treated with α-blocker therapy for >3 months. Subjective and objective clinical variables were assessed using the total International Prostate Symptom Score (IPSS-T), IPSS quality of life (IPSS-QoL), IPSS voiding subscore (IPSS-V), IPSS storage subscore (IPSS-S), overactive bladder symptom score (OABSS), PV, prostate specific antigen (PSA) level, post-void residual (PVR), and maximum flow rate (Qmax). These variables were assessed at baseline and every 3 months for 1 year. In the small prostate group, IPSS-T and IPSS-V showed improvements from baseline at 6 and 9 months, storage subscore at 6 months, and OABSS at 3 months, but no sustained improvements were observed. During the study period, only the IPSS QoL scores did not show any improvement. Conversly, dutasteride was significantly effective at improving IPSS-T, IPSS-V, IPSS-S, and IPSS-QoL scores throughout the study period in the large prostate BPH group. PSA levels and PV significantly decreased in both groups throughout the study. Benign prostatic hyperplasia in LUTS patients with small prostates did not show a sustainable benefit from the addition of dutasteride to α-blocker therapy. © 2016 John Wiley & Sons Australia, Ltd.

  20. 46 CFR 2.20-40 - Chief engineer's reports.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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  1. 46 CFR 92.20-40 - Other spaces.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

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  2. 46 CFR 72.20-40 - Other spaces.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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  3. 46 CFR 72.20-40 - Other spaces.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 3 2014-10-01 2014-10-01 false Other spaces. 72.20-40 Section 72.20-40 Shipping COAST... Accommodations for Officers and Crew § 72.20-40 Other spaces. Each vessel must have— (a) Sufficient facilities... fresh water; (b) Recreation spaces; and (c) A space or spaces of adequate size on an open deck to which...

  4. 46 CFR 190.20-40 - Other spaces.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

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  5. 46 CFR 92.20-40 - Other spaces.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 4 2012-10-01 2012-10-01 false Other spaces. 92.20-40 Section 92.20-40 Shipping COAST... ARRANGEMENT Accommodations for Officers and Crew § 92.20-40 Other spaces. Each vessel must have— (a... with hot and cold fresh water; (b) Recreation spaces; and (c) A space or spaces of adequate size on an...

  6. 46 CFR 190.20-40 - Other spaces.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 7 2014-10-01 2014-10-01 false Other spaces. 190.20-40 Section 190.20-40 Shipping COAST... ARRANGEMENT Accomodations for Officers, Crew, and Scientific Personnel § 190.20-40 Other spaces. Each vessel... least 1 sink supplied with hot and cold fresh water; (b) Recreation spaces; and (c) A space or spaces of...

  7. 46 CFR 190.20-40 - Other spaces.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 7 2013-10-01 2013-10-01 false Other spaces. 190.20-40 Section 190.20-40 Shipping COAST... ARRANGEMENT Accomodations for Officers, Crew, and Scientific Personnel § 190.20-40 Other spaces. Each vessel... least 1 sink supplied with hot and cold fresh water; (b) Recreation spaces; and (c) A space or spaces of...

  8. 46 CFR 72.20-40 - Other spaces.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 3 2013-10-01 2013-10-01 false Other spaces. 72.20-40 Section 72.20-40 Shipping COAST... Accommodations for Officers and Crew § 72.20-40 Other spaces. Each vessel must have— (a) Sufficient facilities... fresh water; (b) Recreation spaces; and (c) A space or spaces of adequate size on an open deck to which...

  9. 46 CFR 92.20-40 - Other spaces.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 4 2013-10-01 2013-10-01 false Other spaces. 92.20-40 Section 92.20-40 Shipping COAST... ARRANGEMENT Accommodations for Officers and Crew § 92.20-40 Other spaces. Each vessel must have— (a... with hot and cold fresh water; (b) Recreation spaces; and (c) A space or spaces of adequate size on an...

  10. 46 CFR 2.20-40 - Chief engineer's reports.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Chief engineer's reports. 2.20-40 Section 2.20-40... INSPECTIONS Reports and Forms § 2.20-40 Chief engineer's reports. (a) Repairs to boilers and pressure vessels. The chief engineer is required to report any repairs to boilers or unfired pressure vessels in...

  11. 46 CFR 2.20-40 - Chief engineer's reports.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 1 2012-10-01 2012-10-01 false Chief engineer's reports. 2.20-40 Section 2.20-40... INSPECTIONS Reports and Forms § 2.20-40 Chief engineer's reports. (a) Repairs to boilers and pressure vessels. The chief engineer is required to report any repairs to boilers or unfired pressure vessels in...

  12. 46 CFR 2.20-40 - Chief engineer's reports.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 1 2013-10-01 2013-10-01 false Chief engineer's reports. 2.20-40 Section 2.20-40... INSPECTIONS Reports and Forms § 2.20-40 Chief engineer's reports. (a) Repairs to boilers and pressure vessels. The chief engineer is required to report any repairs to boilers or unfired pressure vessels in...

  13. 46 CFR 2.20-40 - Chief engineer's reports.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 1 2014-10-01 2014-10-01 false Chief engineer's reports. 2.20-40 Section 2.20-40... INSPECTIONS Reports and Forms § 2.20-40 Chief engineer's reports. (a) Repairs to boilers and pressure vessels. The chief engineer is required to report any repairs to boilers or unfired pressure vessels in...

  14. 46 CFR 92.20-40 - Other spaces.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 4 2011-10-01 2011-10-01 false Other spaces. 92.20-40 Section 92.20-40 Shipping COAST... ARRANGEMENT Accommodations for Officers and Crew § 92.20-40 Other spaces. Each vessel must have— (a... with hot and cold fresh water; (b) Recreation spaces; and (c) A space or spaces of adequate size on...

  15. 46 CFR 190.20-40 - Other spaces.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 7 2011-10-01 2011-10-01 false Other spaces. 190.20-40 Section 190.20-40 Shipping COAST... ARRANGEMENT Accomodations for Officers, Crew, and Scientific Personnel § 190.20-40 Other spaces. Each vessel... least 1 sink supplied with hot and cold fresh water; (b) Recreation spaces; and (c) A space or spaces...

  16. 46 CFR 72.20-40 - Other spaces.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 3 2011-10-01 2011-10-01 false Other spaces. 72.20-40 Section 72.20-40 Shipping COAST... Accommodations for Officers and Crew § 72.20-40 Other spaces. Each vessel must have— (a) Sufficient facilities... fresh water; (b) Recreation spaces; and (c) A space or spaces of adequate size on an open deck to...

  17. 46 CFR 190.20-40 - Other spaces.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Other spaces. 190.20-40 Section 190.20-40 Shipping COAST... ARRANGEMENT Accomodations for Officers, Crew, and Scientific Personnel § 190.20-40 Other spaces. Each vessel... least 1 sink supplied with hot and cold fresh water; (b) Recreation spaces; and (c) A space or spaces...

  18. 46 CFR 72.20-40 - Other spaces.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false Other spaces. 72.20-40 Section 72.20-40 Shipping COAST... Accommodations for Officers and Crew § 72.20-40 Other spaces. Each vessel must have— (a) Sufficient facilities... fresh water; (b) Recreation spaces; and (c) A space or spaces of adequate size on an open deck to...

  19. 46 CFR 92.20-40 - Other spaces.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Other spaces. 92.20-40 Section 92.20-40 Shipping COAST... ARRANGEMENT Accommodations for Officers and Crew § 92.20-40 Other spaces. Each vessel must have— (a... with hot and cold fresh water; (b) Recreation spaces; and (c) A space or spaces of adequate size on...

  20. ML Construction Progress

    NASA Image and Video Library

    2014-11-17

    Modifications continue on the Mobile Launcher, or ML, at the Mobile Launcher Park Site at NASA’s Kennedy Space Center in Florida. The haunch, a structure that will support the launch vehicle on the ML, arrives by flatbed truck at the park site. The ML is being modified and strengthened to accommodate the weight, size and thrust at launch of NASA's Space Launch System, or SLS, and Orion spacecraft. In 2013, the agency awarded a contract to J.P. Donovan Construction Inc. of Rockledge, Fla., to modify the ML, which is one of the key elements of ground support equipment that is being upgraded by the Ground Systems Development and Operations Program at Kennedy. The existing 24-foot exhaust hole is being enlarged and strengthened for the larger, heavier SLS rocket. The ML will carry the SLS rocket and Orion spacecraft to Launch Pad 39B for its first uncrewed mission, Exploration Mission-1, in 2018.

  1. ML Construction Progress

    NASA Image and Video Library

    2014-12-17

    Modifications continue on the Mobile Launcher, or ML, at the Mobile Launcher Park Site at NASA’s Kennedy Space Center in Florida. A crane is being used to move scaffolding, or work platforms, around the base of the tower on the ML to continue upgrades and modifications to the structure. The ML is being modified and strengthened to accommodate the weight, size and thrust at launch of NASA's Space Launch System, or SLS, and Orion spacecraft. The ML is one of the key elements of ground support equipment that is being upgraded by the Ground Systems Development and Operations Program at Kennedy. The ML will carry the SLS rocket and Orion spacecraft to Launch Pad 39B for its first uncrewed mission, Exploration Mission-1, in 2018.

  2. ML Construction Progress

    NASA Image and Video Library

    2014-12-17

    Modifications continue on the Mobile Launcher, or ML, at the Mobile Launcher Park Site at NASA’s Kennedy Space Center in Florida. Scaffolding, or work platforms, have been installed around the base of the tower on the ML to continue upgrades and modifications to the structure. The ML is being modified and strengthened to accommodate the weight, size and thrust at launch of NASA's Space Launch System, or SLS, and Orion spacecraft. The ML is one of the key elements of ground support equipment that is being upgraded by the Ground Systems Development and Operations Program at Kennedy. The ML will carry the SLS rocket and Orion spacecraft to Launch Pad 39B for its first uncrewed mission, Exploration Mission-1, in 2018.

  3. Workers Welding on ML

    NASA Image and Video Library

    2014-02-24

    CAPE CANAVERAL, Fla. – Modifications continue on the Mobile Launcher, or ML, at the Mobile Launcher Park Site at NASA’s Kennedy Space Center in Florida. A construction worker prepares a metal beam that will be attached to the ML. In 2013, the agency awarded a contract to J.P. Donovan Construction Inc. of Rockledge, Fla., to modify the ML, which is one of the key elements of ground support equipment that is being upgraded by the Ground Systems Development and Operations Program office at Kennedy. The ML will carry the SLS rocket and Orion spacecraft to Launch Pad 39B for its first mission, Exploration Mission 1, in 2017. Photo credit: NASA/Dimitri Gerondidakis

  4. 50 CFR 20.40 - Gift of migratory game birds.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 9 2013-10-01 2013-10-01 false Gift of migratory game birds. 20.40... WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD HUNTING Possession § 20.40 Gift of migratory game birds. No person may receive, possess, or give to another, any freshly killed migratory game birds as a gift...

  5. 50 CFR 20.40 - Gift of migratory game birds.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 9 2014-10-01 2014-10-01 false Gift of migratory game birds. 20.40... WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD HUNTING Possession § 20.40 Gift of migratory game birds. No person may receive, possess, or give to another, any freshly killed migratory game birds as a gift...

  6. 50 CFR 20.40 - Gift of migratory game birds.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 9 2012-10-01 2012-10-01 false Gift of migratory game birds. 20.40... WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD HUNTING Possession § 20.40 Gift of migratory game birds. No person may receive, possess, or give to another, any freshly killed migratory game birds as a gift...

  7. 50 CFR 20.40 - Gift of migratory game birds.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 8 2011-10-01 2011-10-01 false Gift of migratory game birds. 20.40... WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD HUNTING Possession § 20.40 Gift of migratory game birds. No person may receive, possess, or give to another, any freshly killed migratory game birds as a gift...

  8. ML Construction Progress

    NASA Image and Video Library

    2014-11-17

    A water moccasin snake travels across the gravel surface near the Mobile Launcher, or ML, at the Mobile Launcher Park Site at NASA’s Kennedy Space Center in Florida. Nearby, the haunch, a structure that will support the launch vehicle on the ML, arrives by flatbed truck at the park site. The ML is being modified and strengthened to accommodate the weight, size and thrust at launch of NASA's Space Launch System, or SLS, and Orion spacecraft. In 2013, the agency awarded a contract to J.P. Donovan Construction Inc. of Rockledge, Fla., to modify the ML, which is one of the key elements of ground support equipment that is being upgraded by the Ground Systems Development and Operations Program at Kennedy. The existing 24-foot exhaust hole is being enlarged and strengthened for the larger, heavier SLS rocket. The ML will carry the SLS rocket and Orion spacecraft to Launch Pad 39B for its first uncrewed mission, Exploration Mission-1, in 2018.

  9. MPS and ML

    MedlinePlus

    ... individuals about MPS and ML, the National MPS Society has created a central location for more information on MPS. Click here to go to the MPS Library. Share Tweet Our Mission The National MPS Society exists to cure, support and advocate for MPS ...

  10. 50 CFR 20.40 - Gift of migratory game birds.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... WILDLIFE AND PLANTS (CONTINUED) MIGRATORY BIRD HUNTING Possession § 20.40 Gift of migratory game birds. No... hunter who took the birds, stating such hunter's address, the total number and species of birds and the...

  11. Reliability of blood test results in samples obtained using a 2-mL discard volume from the proximal lumen of a triple-lumen central venous catheter in the critically ill patient.

    PubMed

    Villalta-García, Pedro; López-Herránz, Marta; Mazo-Pascual, Salvador; Honrubia-Fernández, Teresa; Jáñez-Escalada, Luis; Fernández-Pérez, Cristina

    2017-09-01

    Intensive care patients require a high frequency of blood testing, which results in a significant amount of blood loss. When blood is obtained from a central venous catheter (CVC), a large volume is usually discarded to obtain an unaltered sample for testing. To determine the reliability of complete blood test results in blood samples obtained from the proximal lumen of a triple-lumen CVC using a 2-mL discard volume DESIGN: Observational study with the prospective collection of data METHODS: The subjects enrolled were all patients with a subclavian triple-lumen CVC, older than 17 years and consecutively admitted to intensive care over a 2-year period. In each of the 54 participants, one blood sample was drawn from the proximal lumen of the catheter, discarding 1·61 mL of blood plus 0·39 mL of catheter deadspace (2 mL) and without interrupting infusion in the middle and distal lumens. A second sample was then obtained by direct venous puncture. The reliability of blood test results was determined by comparing sets of variables recorded for the two sampling methods through intraclass correlation coefficients in the Bland-Altman method. Inter-method reliability for the variables examined was excellent, >0·75; range (0·868-0·998). Mean differences between the two sample types for the variables most often determined in critically ill patients were leukocytes: 0·200 × 10(3) /µL, 95% confidence interval (CI) (0·025 to 0·375); erythrocytes: 0·045 × 10(6) /uL, 95% CI (-0·003 to 0·094); sodium: 0·074 mEq/L, 95% CI (-0·369 to 0·517); potassium: -0·002mEq/L, 95% CI (-0·065 to 0·061) and glucose: 2·426 mg/dL, 95% CI (0·498-4·354). The sampling method proposed minimizes blood loss while offering reliable blood test results. The main benefit of the method proposed is reduced blood loss, improving the care of a critically ill patient. © 2015 British Association of Critical Care Nurses.

  12. Determination of dioxin-like polychlorinated biphenyls in 1 mL whole blood using programmable temperature vaporization large volume injection coupled to gas chromatogram and high-resolution mass spectrometry.

    PubMed

    Shen, Haitao; Guan, Rongfa; Li, Jingguang; Zhang, Lei; Ren, Yiping; Xu, Xiaomin; Song, Yang; Zhao, Yunfeng; Han, Jianlong; Wu, Yongning

    2013-03-12

    A sensitive method based on programmable temperature vaporization large volume injection coupled to gas chromatogram and high-resolution mass spectrometry (PTV-GC-HRMS) has been developed for the determination of ultra trace levels of dioxin-like polychlorinated biphenyls (DL PCBs) in small amounts of human blood. Blood samples (1mL) were first extracted by column extraction and then purified with column chromatorgraphies. Final extracts (20μL) were introduced to the PTV injector under the solvent vent mode and detected by GC-HRMS (SIM mode). PTV parameters were observed by changing one factor at a time (practical conditions: vent flow: 50mLmin(-1), vent pressure: 0kPa and vent time: 0.1min), recoveries of most PCB congeners ranged from 55.1% to 108%, and method detection limits were in the range of 0.11-1.63pgg(-1).

  13. The Hard X-ray 20-40 keV AGN Luminosity Function

    NASA Technical Reports Server (NTRS)

    Beckmann, V.; Soldi, S.; Shrader, C. R.; Gehrels, N.; Produit, N.

    2006-01-01

    We have compiled a complete, significance limited extragalactic sample based on approximately 25,000 deg(sup 2) to a limiting flux of 3 x 10(exp -11) ergs per square centimeter per second. (approximately 7,000 deg(sup 2)) to a flux limit of 10(exp -11) ergs per square centimeter per second)) in the 20 - 40 keV band with INTEGRAL. We have constructed a detailed exposure map to compensate for effects of non-uniform exposure. The flux-number relation is best described by a power-law with a slope of alpha = 1.66 plus or minus 0.11. The integration of the cumulative flux per unit area leads to f(sub 20-40 keV) = 2.6 x 10(exp -10) ergs per square centimeter per second per sr(sup -1) which is about 1% of the known 20-40 keV X-ray background. We present the first luminosity function of AGN in the 20-40 keV energy range, based on 68 extragalactic objects detected by the imager IBIS/ISGRI on-board INTEGRAL. The luminosity function shows a smoothly connected two power-law form, with an index of gamma (sub 1) = 0.9 below, and gamma (sub 2) = 2.2 above the turn-over luminosity of L(sub *), = 4.6 x 10(sup 43) ergs per second. The emissivity of all INTEGRAL AGNs per unit volume is W(sub 20-40keV)(greater than 10(sup 41) ergs per second) = 2.8 x 10(sup 38) ergs per second h(sup 3)(sub 70) Mpc(sup -3). These results are consistent with those derived in the 2-20keV energy band and do not show a significant contribution by Compton-thick objects. Because the sample used in this study is truly local (z(raised bar) = 0.022)), only limited conclusions can be drawn for the evolution of AGNs in this energy band. But the objects explaining the peak in the cosmic X-ray background are likely to be either low luminosity AGN (L(sub x) less than 10(sup 41) ergs per second) or of other type, such as intermediate mass black holes, clusters, and star forming regions.

  14. DAVE-ML Utility Programs

    NASA Technical Reports Server (NTRS)

    Jackson, Bruce

    2006-01-01

    DAVEtools is a set of Java archives that embodies tools for manipulating flight-dynamics models that have been encoded in dynamic aerospace vehicle exchange markup language (DAVE-ML). [DAVE-ML is an application program, written in Extensible Markup Language (XML), for encoding complete computational models of the dynamics of aircraft and spacecraft.

  15. 46 CFR 35.20-40 - Maneuvering characteristics-T/OC.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Maneuvering characteristics-T/OC. 35.20-40 Section 35.20-40 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY TANK VESSELS OPERATIONS Navigation § 35.20-40 Maneuvering characteristics—T/OC. For each ocean and coastwise tankship of 1,600 gross tons...

  16. Vascular Disease in Young Indians (20-40 years): Role of Hypertension

    PubMed Central

    Sethi, Kamal Kumar; Kerkar, Prafulla Gopinath; Ray, Saumitra; Guha, Santanu; Hiremath, Murugesh Shantaveeraya

    2016-01-01

    Hypertension (HTN) being one of the important risk factors for cardiovascular disease (CVD) is a significant health concern, especially in India. With age, prevalence of HTN, especially systolic HTN increases. Special attention needs to be directed to HTN in young ages (20-40 years) due to lower awareness, need for early treatment and better control of HTN. HTN in the age group of 20-40 years needs critical reappraisal. Given the high prevalence of HTN in the general population in India, in this review we attempt to provide current evidence and expert opinion on epidemiology, aetiopathogenesis and treatment of HTN in young (20-40 years) Indians. PMID:27656492

  17. ML 3.1 developer's guide.

    SciTech Connect

    Sala, Marzio; Hu, Jonathan Joseph; Tuminaro, Raymond Stephen

    2004-05-01

    ML development was started in 1997 by Ray Tuminaro and Charles Tong. Currently, there are several full- and part-time developers. The kernel of ML is written in ANSI C, and there is a rich C++ interface for Trilinos users and developers. ML can be customized to run geometric and algebraic multigrid; it can solve a scalar or a vector equation (with constant number of equations per grid node), and it can solve a form of Maxwell's equations. For a general introduction to ML and its applications, we refer to the Users Guide [SHT04], and to the ML web site, http://software.sandia.gov/ml.

  18. Economic Impact of Converting from Pen and 10-mL Vial to 3-mL Vial for Insulin Delivery in a Hospital Setting.

    PubMed

    Elizabeth, Eby; Smolen, Lee; Pitts, Amber; Krueger, Linda A; Grimm, Doneen

    2014-12-01

    To compare the impact on acquisition cost and purchased volume of rapid- and short-acting insulins following conversion from 3-mL disposable pens and 10-mL vials to 3-mL vials for individual patient supply (IPS) in a hospital setting. On February 1, 2010, St. Joseph's Hospital and Medical Center of Dignity Health in Phoenix, Arizona, converted from pens to 3-mL vials for IPS subcutaneous (SC) injection and from 10-mL short-acting insulin vials to 3-mL vials for intravenous (IV) preparation. Pharmacy purchasing data were analyzed over 6-month periods before and after conversion (March 1 through August 31, 2009, and March 1 through August 31, 2010). Before conversion, acquisition costs were $27,866 for 5,335 mL of rapid-acting insulins and $53,336 for 26,310 mL of short-acting insulins. After conversion, insulin acquisition costs were $24,211 for 5,850 mL of rapid-acting insulins (13.1% decrease in costs, 9.7% rise in volume), with cost reduction attributable to the lower cost of 3-mL vials. Acquisition costs were $17,395 for 14,700 mL of short-acting insulins after conversion (67.4% decrease in costs, 44.1% reduction in volume), with cost reduction attributable to lower cost of 3-mL vials versus pens for IPS SC injections and 10-mL vials for IV preparation. The reduction in purchased volumes of short-acting insulins may be partly due to decreased insulin use in IV preparation. Conversion from pens and 10-mL vials to 3-mL vials for rapid-and short-acting insulins resulted in reduced acquisition costs and decreased use of short-acting insulin in IV preparations.

  19. Note on Conditional Compilation in Standard ML

    DTIC Science & Technology

    1993-06-01

    eOmputer-Science No-te on Coridhitiom Cominliati"I~n Standard ML1 Nicholas Haines Edoardo Biagioni Robert Hiarper mom Brian G. Mimnes June 1993 CMU...CS-93. 11 TIC ELECTE f 00..7733 %goo~~OO Note on Conditioual Compilation in Standard ML Nicholas Haines Edoardo Biagioni Robert Harper Brian G. Milnes

  20. Comparing Multitarget Multisensor ML-PMHT with ML-PDA for VLO Targets

    DTIC Science & Technology

    2013-07-01

    closely spaced with similar motion dynamics. Keywords: ML-PDA, ML-PMHT, multitarget ML-PMHT, maximum likelihood, multistatic, bistatic , sonar, tracking...motion dynamics. 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report ( SAR ) 18. NUMBER OF PAGES 8 19a

  1. Vascular Disease in Young Indians (20-40 years): Role of Ischemic Heart Disease

    PubMed Central

    Hiremath, Murugesh Shantaveeraya; Das, Mrinal Kanti; Desai, Devangkumar M; Chopra, Vijay Kumar; Biswas, Arup Das

    2016-01-01

    Coronary Artery Disease (CAD) occurs at a younger age in Indians with over 50% of Cardiovascular Disease (CVD) mortality occurring in individuals aged less than 50 years. Although several risk factors have been suggested; smoking, dyslipidemia and hypertension are major risk factors in the young. In this review, we have pooled the current evidence on Ischemic Heart Disease (IHD) in young (20-40 years) and provided an opinion for the effective management of IHD in young Indians. PMID:27790504

  2. morePhyML: improving the phylogenetic tree space exploration with PhyML 3.

    PubMed

    Criscuolo, Alexis

    2011-12-01

    PhyML is a widely used Maximum Likelihood (ML) phylogenetic tree inference software based on a standard hill-climbing method. Starting from an initial tree, the version 3 of PhyML explores the tree space by using "Nearest Neighbor Interchange" (NNI) or "Subtree Pruning and Regrafting" (SPR) tree swapping techniques in order to find the ML phylogenetic tree. NNI-based local searches are fast but can often get trapped in local optima, whereas it is expected that the larger (but slower to cover) SPR-based neighborhoods will lead to trees with higher likelihood. Here, I verify that PhyML infers more likely trees with SPRs than with NNIs in almost all cases. However, I also show that the SPR-based local search of PhyML often does not succeed at locating the ML tree. To improve the tree space exploration, I deliver a script, named morePhyML, which allows escaping from local optima by performing character reweighting. This ML tree search strategy, named ratchet, often leads to higher likelihood estimates. Based on the analysis of a large number of amino acid and nucleotide data, I show that morePhyML allows inferring more accurate phylogenetic trees than several other recently developed ML tree inference softwares in many cases. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Economic Impact of Converting from Pen and 10-mL Vial to 3-mL Vial for Insulin Delivery in a Hospital Setting

    PubMed Central

    Elizabeth, Eby; Smolen, Lee; Pitts, Amber; Krueger, Linda A.

    2014-01-01

    Purpose: To compare the impact on acquisition cost and purchased volume of rapid- and short-acting insulins following conversion from 3-mL disposable pens and 10-mL vials to 3-mL vials for individual patient supply (IPS) in a hospital setting. Methods: On February 1, 2010, St. Joseph’s Hospital and Medical Center of Dignity Health in Phoenix, Arizona, converted from pens to 3-mL vials for IPS subcutaneous (SC) injection and from 10-mL short-acting insulin vials to 3-mL vials for intravenous (IV) preparation. Pharmacy purchasing data were analyzed over 6-month periods before and after conversion (March 1 through August 31, 2009, and March 1 through August 31, 2010). Results: Before conversion, acquisition costs were $27,866 for 5,335 mL of rapid-acting insulins and $53,336 for 26,310 mL of short-acting insulins. After conversion, insulin acquisition costs were $24,211 for 5,850 mL of rapid-acting insulins (13.1% decrease in costs, 9.7% rise in volume), with cost reduction attributable to the lower cost of 3-mL vials. Acquisition costs were $17,395 for 14,700 mL of short-acting insulins after conversion (67.4% decrease in costs, 44.1% reduction in volume), with cost reduction attributable to lower cost of 3-mL vials versus pens for IPS SC injections and 10-mL vials for IV preparation. The reduction in purchased volumes of short-acting insulins may be partly due to decreased insulin use in IV preparation. Conclusion: Conversion from pens and 10-mL vials to 3-mL vials for rapid-and short-acting insulins resulted in reduced acquisition costs and decreased use of short-acting insulin in IV preparations. PMID:25673892

  4. FieldML: concepts and implementation

    PubMed Central

    Christie, G. Richard; Nielsen, Poul M.F.; Blackett, Shane A.; Bradley, Chris P.; Hunter, Peter J.

    2009-01-01

    The field modelling language FieldML is being developed as a standard for modelling and interchanging field descriptions in software, suitable for a wide range of computation techniques. It comprises a rich set of operators for defining generalized fields as functions of other fields, starting with basic domain fields including sets of discrete objects and coordinate systems. It is extensible by adding new operators and by their arbitrary combination in expressions, making it well suited for describing the inherent complexity of biological materials and organ systems. This paper describes the concepts behind FieldML, including a simple example of a spatially varying finite-element field. It outlines current implementations in established, open source computation and visualization software, both drawing on decades of bioengineering modelling software development experience. PMID:19380316

  5. CytometryML and other data formats

    NASA Astrophysics Data System (ADS)

    Leif, Robert C.

    2006-02-01

    Cytology automation and research will be enhanced by the creation of a common data format. This data format would provide the pathology and research communities with a uniform way for annotating and exchanging images, flow cytometry, and associated data. This specification and/or standard will include descriptions of the acquisition device, staining, the binary representations of the image and list-mode data, the measurements derived from the image and/or the list-mode data, and descriptors for clinical/pathology and research. An international, vendor-supported, non-proprietary specification will allow pathologists, researchers, and companies to develop and use image capture/analysis software, as well as list-mode analysis software, without worrying about incompatibilities between proprietary vendor formats. Presently, efforts to create specifications and/or descriptions of these formats include the Laboratory Digital Imaging Project (LDIP) Data Exchange Specification; extensions to the Digital Imaging and Communications in Medicine (DICOM); Open Microscopy Environment (OME); Flowcyt, an extension to the present Flow Cytometry Standard (FCS); and CytometryML. The feasibility of creating a common data specification for digital microscopy and flow cytometry in a manner consistent with its use for medical devices and interoperability with both hospital information and picture archiving systems has been demonstrated by the creation of the CytometryML schemas. The feasibility of creating a software system for digital microscopy has been demonstrated by the OME. CytometryML consists of schemas that describe instruments and their measurements. These instruments include digital microscopes and flow cytometers. Optical components including the instruments' excitation and emission parts are described. The description of the measurements made by these instruments includes the tagged molecule, data acquisition subsystem, and the format of the list-mode and/or image data. Many

  6. Assessing Quality in SysML Models

    DTIC Science & Technology

    2011-05-01

    nature of something. – 3. A feature of personality. – 4. Degree or standard of excellence. – 5. High social status. – 6. Musical tone color. – 7...Analysis Test Specifications Changes in Systems Engineering Practice 11© 2010 Atego. All rights reserved. The Four Pillars of SysML (ABS Example) ibd...copy, trace, and refinement relationships. – Relate requirements to − one another − system design model elements − test cases. – The «rationale

  7. A Structured TCP in Standard ML

    DTIC Science & Technology

    1994-07-01

    U.S. Government. Keywords: Standard ML, Transmission Control Protocol, computer networks, schedulers, modules 1 Introduction The design of programming ...much of the common practice of systems programming . In this paper, we concentrate on the design of our implementation of the TCP protocol and on its...the lines of existing protocols, others using ideas from the functional programming world to design interesting and useful network protocols. 15 8

  8. Raman Spectrum of Methane in the Range 20-40oC

    NASA Astrophysics Data System (ADS)

    Petrov, D. V.

    2017-07-01

    The influence of temperature in the range 20-40oC on the main vibrational-rotational Raman bands (ν1, ν2, ν3, 2ν2, and 2ν4) of methane was investigated. An increase of temperature caused the frequencies of the Q-branches to shift differently and the relative intensities of the 2ν2 and 2ν4 overtones that were in Fermi resonance with ν1 to decrease. A method for determining the temperature of a methane-containing gaseous medium was proposed. The impact of temperature fluctuations on results from Raman analyses of natural-gas compositions was estimated.

  9. Vascular Disease in Young Indians (20-40 years): Role of Dyslipidemia

    PubMed Central

    Deb, Pradeep Kumar; Shrivastava, Sameer; Rao, Maddury Srinivas; Mohan, Jagdish Chander; Kumar, Arramraju Sreenivas

    2016-01-01

    Dyslipidemia is an established risk factor for cardiovascular disease (CVD). Atherosclerosis begins early in life as suggested by “fatty streaks” observed in coronaries of healthy organ donors aged 20-29 years. Premature occurrence of coronary heart disease (CHD) in Indians, increases the risk for young individuals. Management of Dyslipidemia in the young Indian poses several challenges. In this article we provide in-depth review of prevalence, guidelines’ perspective and expert comments on management of Dyslipidemia in the young (20-40 years) Indian. PMID:27630892

  10. AllerML: markup language for allergens.

    PubMed

    Ivanciuc, Ovidiu; Gendel, Steven M; Power, Trevor D; Schein, Catherine H; Braun, Werner

    2011-06-01

    Many concerns have been raised about the potential allergenicity of novel, recombinant proteins into food crops. Guidelines, proposed by WHO/FAO and EFSA, include the use of bioinformatics screening to assess the risk of potential allergenicity or cross-reactivities of all proteins introduced, for example, to improve nutritional value or promote crop resistance. However, there are no universally accepted standards that can be used to encode data on the biology of allergens to facilitate using data from multiple databases in this screening. Therefore, we developed AllerML a markup language for allergens to assist in the automated exchange of information between databases and in the integration of the bioinformatics tools that are used to investigate allergenicity and cross-reactivity. As proof of concept, AllerML was implemented using the Structural Database of Allergenic Proteins (SDAP; http://fermi.utmb.edu/SDAP/) database. General implementation of AllerML will promote automatic flow of validated data that will aid in allergy research and regulatory analysis.

  11. AllerML: Markup Language for Allergens

    PubMed Central

    Ivanciuc, Ovidiu; Gendel, Steven M.; Power, Trevor D.; Schein, Catherine H.; Braun, Werner

    2011-01-01

    Many concerns have been raised about the potential allergenicity of novel, recombinant proteins into food crops. Guidelines, proposed by WHO/FAO and EFSA, include the use of bioinformatics screening to assess the risk of potential allergenicity or cross-reactivities of all proteins introduced, for example, to improve nutritional value or promote crop resistance. However, there are no universally accepted standards that can be used to encode data on the biology of allergens to facilitate using data from multiple databases in this screening. Therefore, we developed AllerML a markup language for allergens to assist in the automated exchange of information between databases and in the integration of the bioinformatics tools that are used to investigate allergenicity and cross-reactivity. As proof of concept, AllerML was implemented using the Structural Database of Allergenic Proteins (SDAP; http://fermi.utmb.edu/SDAP/) database. General implementation of AllerML will promote automatic flow of validated data that will aid in allergy research and regulatory analysis. PMID:21420460

  12. GeoSciML and EarthResourceML Update, 2012

    NASA Astrophysics Data System (ADS)

    Richard, S. M.; Commissionthe Management; Application Inte, I.

    2012-12-01

    CGI Interoperability Working Group activities during 2012 include deployment of services using the GeoSciML-Portrayal schema, addition of new vocabularies to support properties added in version 3.0, improvements to server software for deploying services, introduction of EarthResourceML v.2 for mineral resources, and collaboration with the IUSS on a markup language for soils information. GeoSciML and EarthResourceML have been used as the basis for the INSPIRE Geology and Mineral Resources specifications respectively. GeoSciML-Portrayal is an OGC GML simple-feature application schema for presentation of geologic map unit, contact, and shear displacement structure (fault and ductile shear zone) descriptions in web map services. Use of standard vocabularies for geologic age and lithology enables map services using shared legends to achieve visual harmonization of maps provided by different services. New vocabularies have been added to the collection of CGI vocabularies provided to support interoperable GeoSciML services, and can be accessed through http://resource.geosciml.org. Concept URIs can be dereferenced to obtain SKOS rdf or html representations using the SISSVoc vocabulary service. New releases of the FOSS GeoServer application greatly improve support for complex XML feature schemas like GeoSciML, and the ArcGIS for INSPIRE extension implements similar complex feature support for ArcGIS Server. These improved server implementations greatly facilitate deploying GeoSciML services. EarthResourceML v2 adds features for information related to mining activities. SoilML provides an interchange format for soil material, soil profile, and terrain information. Work is underway to add GeoSciML to the portfolio of Open Geospatial Consortium (OGC) specifications.

  13. Ubiquitin ligase RNF20/40 facilitates spindle assembly and promotes breast carcinogenesis through stabilizing motor protein Eg5

    PubMed Central

    Duan, Yang; Huo, Dawei; Gao, Jie; Wu, Heng; Ye, Zheng; Liu, Zhe; Zhang, Kai; Shan, Lin; Zhou, Xing; Wang, Yue; Su, Dongxue; Ding, Xiang; Shi, Lei; Wang, Yan; Shang, Yongfeng; Xuan, Chenghao

    2016-01-01

    Whether transcriptional regulators are functionally involved in mitosis is a fundamental question in cell biology. Here we report that the RNF20/40 complex, a major ubiquitin ligase catalysing histone H2B monoubiquitination, interacts with the motor protein Eg5 during mitosis and participates in spindle assembly. We show that the RNF20/40 complex monoubiquitinates and stabilizes Eg5. Loss of RNF20/40 results in spindle assembly defects, cell cycle arrest and apoptosis. Consistently, depletion of either RNF20/40 or Eg5 suppresses breast cancer in vivo. Significantly, RNF20/40 and Eg5 are concurrently upregulated in human breast carcinomas and high Eg5 expression is associated with poorer overall survival of patients with luminal A, or B, breast cancer. Our study uncovers an important spindle assembly role of the RNF20/40 complex, and implicates the RNF20/40-Eg5 axis in breast carcinogenesis, supporting the pursuit of these proteins as potential targets for breast cancer therapeutic interventions. PMID:27557628

  14. CytometryML binary data standards

    NASA Astrophysics Data System (ADS)

    Leif, Robert C.

    2005-03-01

    CytometryML is a proposed new Analytical Cytology (Cytomics) data standard, which is based on a common set of XML schemas for encoding flow cytometry and digital microscopy text based data types (metadata). CytometryML schemas reference both DICOM (Digital Imaging and Communications in Medicine) codes and FCS keywords. Flow Cytometry Standard (FCS) list-mode has been mapped to the DICOM Waveform Information Object. The separation of the large binary data objects (list mode and image data) from the XML description of the metadata permits the metadata to be directly displayed, analyzed, and reported with standard commercial software packages; the direct use of XML languages; and direct interfacing with clinical information systems. The separation of the binary data into its own files simplifies parsing because all extraneous header data has been eliminated. The storage of images as two-dimensional arrays without any extraneous data, such as in the Adobe Photoshop RAW format, facilitates the development by scientists of their own analysis and visualization software. Adobe Photoshop provided the display infrastructure and the translation facility to interconvert between the image data from commercial formats and RAW format. Similarly, the storage and parsing of list mode binary data type with a group of parameters that are specified at compilation time is straight forward. However when the user is permitted at run-time to select a subset of the parameters and/or specify results of mathematical manipulations, the development of special software was required. The use of CytometryML will permit investigators to be able to create their own interoperable data analysis software and to employ commercially available software to disseminate their data.

  15. The Ml Magnitude Scale In Italy

    NASA Astrophysics Data System (ADS)

    Gasperini, P.; Lolli, B.; Filippucci, M.; de Simoni, B.

    To improve the reliability of Ml magnitude estimates in Italy, we have updated the database of real Wood-Anderson (WA) and of simulated Wood Anderson (SWA) am- plitudes recently revised by Gasperini (2002). This was done by the re-reading of orig- inal WA seismograms, made available by the SISMOS Project of the Istituto Nazionale di Geofisica (INGV), as well as by the analysis of further Very Broad Band (VBB) recordings of the MEDNET network of INGV for the period from 1996 to 1998. The full operability, in the last five years, of a VBB station located exactly at the same site (TRI) of a former WA instrument allowed us to reliably infer a new attenuation function from the joined WA and SWA dataset. We found a significant deviation of the attenuation law from the standard Richter table at distances larger than 400 km where the latter overestimates the magnitude up to about 0.3 units. We also computed regionalized attenuation functions accounting for the differences in the propagation properties of seismic waves between the Adriatic (less attenuating) and Tyrrhenian (more attenuating) sides of the Italian peninsula. Using this improved Ml magnitude database we were also able to further improve the computation of duration (Md) and amplitude (Ma) magnitudes computed from short period vertical seismometers of the INGV as well as to analyze the time variation of the station calibrations. We found that the absolute amplification of INGV stations is underestimated almost exactly by a factor 2 starting from the entering upon in operation of the digital acquisition system at INGV in middle 1984.

  16. dc-40 GHz and 20-40 GHz MMIC SPDT switches

    NASA Astrophysics Data System (ADS)

    Schindler, Manfred J.; Morris, Annamarie

    1987-12-01

    Direct current to 40 GHz and 20 to 40 GHz monolithic GaAs SPDT (single pole-double throw) switches have been demonstrated. Both the measured and the modeled small-signal performance are presented. Measured power handling performance and switching speed data are also presented. The 20-40 GHz switch uses a combination of shunt FETs and quarter-wave transformers. Better than 2 dB insertion loss and 25 dB isolation have been achieved. The dc-40 GHz switch uses a combination of series and shunt FETs. Better than 3 dB insertion loss and 23 dB isolation have been achieved. A simplified switching FET model is used to adequately model switch performance. It is demonstrated that parasitic 'off' state resistance is an important FET characteristic for broad-band switch design. The switches use MESFETs with the same characteristics as an existing millimeter-wave amplifier to allow for ease of future integration.

  17. Comparison of the bonding between ML(+) and ML2(+) (M = metal, L = noble gas)

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.

    1990-01-01

    Ab initio calculations are reported of the spectroscopic constants for the low-lying states of the molecular ions ML2(+), where M = Li, Na, Mg, V, Fe, Co, Ni and Cu, and where L is usually Ar. Comparison with existing analogous calculations on the ML(+) ions shows how the bonding and binding energy change with the addition of a second noble gas atom. The second binding energy is predicted to be essentially the same as the first for the Li, Na, Mg, and V ions, but larger for the Fe, Co, Ni and Cu ions. The binding energies of the transition metal noble gas ions are not accurately predicted at the SCF level, because correlation is required to describe their M(0)Ln(+) character. All trends can be explained in terms of promotion and hybridization on the metal ion.

  18. Comparison of the bonding between ML(+) and ML2(+) (M = metal, L = noble gas)

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.

    1990-01-01

    Ab initio calculations are reported of the spectroscopic constants for the low-lying states of the molecular ions ML2(+), where M = Li, Na, Mg, V, Fe, Co, Ni and Cu, and where L is usually Ar. Comparison with existing analogous calculations on the ML(+) ions shows how the bonding and binding energy change with the addition of a second noble gas atom. The second binding energy is predicted to be essentially the same as the first for the Li, Na, Mg, and V ions, but larger for the Fe, Co, Ni and Cu ions. The binding energies of the transition metal noble gas ions are not accurately predicted at the SCF level, because correlation is required to describe their M(0)Ln(+) character. All trends can be explained in terms of promotion and hybridization on the metal ion.

  19. Long-term stability of ketamine hydrochloride 50mg/ml injection in 3ml syringes.

    PubMed

    Huvelle, S; Godet, M; Hecq, J-D; Gillet, P; Bihin, B; Jamart, J; Galanti, L

    2016-07-01

    Ketamine hydrochloride (Ketalar(®)) injection is often used as a general anesthetic agent. It is particularly suited to short-term interventions. It can also be used as an inducer of anesthesia before the administration of other anesthetic agents. The aim of this study was to evaluate the stability of ketamine hydrochloride in 3ml polypropylene syringes after storage for up to 180days at room temperature. Syringes containing ketamine hydrochloride (50mg/ml) were prepared and stored at room temperature (25°C) for 180days. The concentrations were measured by validated ultra-performance liquid chromatography-diode array detection at 0, 7, 14, 28, 60, 84, 112, 140 and 180days. A degradation test was performed to evaluate the specificity of the analysis. At each time point, the pH, color and visible particles of each solution were also assessed. Degradation tests proved no interfering peaks with ketamine. All solutions were physically stable during the storage. The lower confidence limit of the concentration for these solutions remains superior to 90% of the initial concentration at this date as recommended by the Food and Drug Administration (FDA) until 180days (100%±2%). Solutions of ketamine (50mg/ml) were chemically stable for 180days in polypropylene syringes with storage at room temperature and could be prepared in advance by a centralized intravenous admixture service. Copyright © 2016 Académie Nationale de Pharmacie. Published by Elsevier Masson SAS. All rights reserved.

  20. Mini-fluid Challenge of 100 ml of Crystalloid Predicts Fluid Responsiveness in the Operating Room.

    PubMed

    Biais, Matthieu; de Courson, Hugues; Lanchon, Romain; Pereira, Bruno; Bardonneau, Guillaume; Griton, Marion; Sesay, Musa; Nouette-Gaulain, Karine

    2017-09-01

    Mini-fluid challenge of 100 ml colloids is thought to predict the effects of larger amounts of fluid (500 ml) in intensive care units. This study sought to determine whether a low quantity of crystalloid (50 and 100 ml) could predict the effects of 250 ml crystalloid in mechanically ventilated patients in the operating room. A total of 44 mechanically ventilated patients undergoing neurosurgery were included. Volume expansion (250 ml saline 0.9%) was given to maximize cardiac output during surgery. Stroke volume index (monitored using pulse contour analysis) and pulse pressure variations were recorded before and after 50 ml infusion (given for 1 min), after another 50 ml infusion (given for 1 min), and finally after 150 ml infusion (total = 250 ml). Changes in stroke volume index induced by 50, 100, and 250 ml were recorded. Positive fluid challenges were defined as an increase in stroke volume index of 10% or more from baseline after 250 ml. A total of 88 fluid challenges were performed (32% of positive fluid challenges). Changes in stroke volume index induced by 100 ml greater than 6% (gray zone between 4 and 7%, including 19% of patients) predicted fluid responsiveness with a sensitivity of 93% (95% CI, 77 to 99%) and a specificity of 85% (95% CI, 73 to 93%). The area under the receiver operating curve of changes in stroke volume index induced by 100 ml was 0.95 (95% CI, 0.90 to 0.99) and was higher than those of changes in stroke volume index induced by 50 ml (0.83 [95% CI, 0.75 to 0.92]; P = 0.01) and pulse pressure variations (0.65 [95% CI, 0.53 to 0.78]; P < 0.005). Changes in stroke volume index induced by rapid infusion of 100 ml crystalloid predicted the effects of 250 ml crystalloid in patients ventilated mechanically in the operating room.

  1. The CellML 1.1 Specification.

    PubMed

    Cuellar, Autumn; Hedley, Warren; Nelson, Melanie; Lloyd, Catherine; Halstead, Matt; Bullivant, David; Nickerson, David; Hunter, Peter; Nielsen, Poul

    2015-09-04

    This document specifies CellML 1.1, an XML-based language for describing and exchanging models of cellular and subcellular processes. MathML embedded in CellML documents is used to define the underlying mathematics of models. Models consist of a network of reusable components, each with variables and equations manipulating those variables. Models may import other models to create systems of increasing complexity. Metadata may be embedded in CellML documents using RDF.

  2. The XBabelPhish MAGE-ML and XML translator.

    PubMed

    Maier, Don; Wymore, Farrell; Sherlock, Gavin; Ball, Catherine A

    2008-01-18

    MAGE-ML has been promoted as a standard format for describing microarray experiments and the data they produce. Two characteristics of the MAGE-ML format compromise its use as a universal standard: First, MAGE-ML files are exceptionally large - too large to be easily read by most people, and often too large to be read by most software programs. Second, the MAGE-ML standard permits many ways of representing the same information. As a result, different producers of MAGE-ML create different documents describing the same experiment and its data. Recognizing all the variants is an unwieldy software engineering task, resulting in software packages that can read and process MAGE-ML from some, but not all producers. This Tower of MAGE-ML Babel bars the unencumbered exchange of microarray experiment descriptions couched in MAGE-ML. We have developed XBabelPhish - an XQuery-based technology for translating one MAGE-ML variant into another. XBabelPhish's use is not restricted to translating MAGE-ML documents. It can transform XML files independent of their DTD, XML schema, or semantic content. Moreover, it is designed to work on very large (> 200 Mb.) files, which are common in the world of MAGE-ML. XBabelPhish provides a way to inter-translate MAGE-ML variants for improved interchange of microarray experiment information. More generally, it can be used to transform most XML files, including very large ones that exceed the capacity of most XML tools.

  3. Model-based analysis and quantitative prediction of membrane chromatography: extreme scale-up from 0.08 ml to 1200 ml.

    PubMed

    Ghosh, Pranay; Vahedipour, Kaveh; Leuthold, Martin; von Lieres, Eric

    2014-03-07

    A model-based approach is presented for quantitatively decoupling the impacts of non-ideal flow and non-ideal binding in membrane chromatography (MC) capsules at different scales. The internal geometry of Sartobind capsules with 0.08 ml and 1200 ml membrane volume is reconstructed from MRI measurements and manufacturer data. Based on this information, computational fluid dynamics (CFD) simulations are used for computing internal flow patterns of both capsules. Measured breakthrough curves (BTC) under non-binding conditions are used for calibrating PFR and CSTR models of the holdup volumes in the Äkta systems. A suitable binding model is determined and the binding parameters are estimated from binding BTC data of the 0.08 ml capsule. Due to the decoupling of non-idealities, the binding parameters can be directly transferred between the CFD models of both capsules. This advantage is used for quantitatively predicting BTC data of the 1200 ml capsule under binding conditions. The model-based prediction excellently matches with independently measured BTC data, facilitating an extreme scale-up factor of 15,000. The presented approach has previously been shown to be universally applicable to capsules from other vendors with different flow configurations and membrane types.

  4. Programmed Intermittent Epidural Bolus for Labor Analgesia During First Stage of Labor: A Biased-Coin Up-and-Down Sequential Allocation Trial to Determine the Optimum Interval Time Between Boluses of a Fixed Volume of 10 mL of Bupivacaine 0.0625% With Fentanyl 2 μg/mL.

    PubMed

    Epsztein Kanczuk, Marcelo; Barrett, Nicholas Martin; Arzola, Cristian; Downey, Kristi; Ye, Xiang Y; Carvalho, Jose C A

    2017-02-01

    Most studies that have compared programmed intermittent epidural bolus (PIEB) with continuous epidural infusion regimens have included patient-controlled epidural analgesia and/or manual bolus as rescue analgesia for breakthrough pain. Consequently, the optimal time interval between PIEB is yet to be determined. We designed a study to establish the optimal time interval between PIEB of 10 mL of bupivacaine 0.0625% with fentanyl 2 μg/mL to produce effective analgesia in 90% of women during first stage of labor without breakthrough pain. We conducted a double-blind sequential allocation trial with a biased-coin up-down design to obtain the effective interval 90% for the PIEB regimen. We included American Society of Anesthesiologists physical status 2-3 nulliparous women at term undergoing spontaneous or induced labor requesting epidural analgesia. An ultrasound-assisted epidural catheter placement was performed at L2/3 or L3/4. A test dose of 3 mL of bupivacaine 0.125% plus fentanyl 3.3 μg/mL was followed by a loading dose of 12 mL of the same solution. PIEB was then started in women whose pain scores achieved Verbal Numerical Rating Score ≤1/10 within 20 minutes after the end of the loading dose. In all subjects, the programmed bolus dose was fixed at 10 mL of bupivacaine 0.0625% with fentanyl 2 μg/mL. The first bolus was delivered 1 hour after the loading dose. The PIEB interval was set at 60 minutes for the first patient and at varying time intervals (60, 50, 40, and 30 minutes; groups 60, 50, 40 and 30, respectively) for the subsequent patients, according to a biased-coin design. The primary outcome was effective analgesia, defined as no requirement for a patient-controlled epidural analgesia or a manual bolus for 6 hours after the initiation of the epidural analgesia or until the patient presented with full cervical dilatation, whichever event occurred first. Pain scores, sensory block levels to ice, degree of motor block, and blood pressure were assessed

  5. jmzML, an open-source Java API for mzML, the PSI standard for MS data.

    PubMed

    Côté, Richard G; Reisinger, Florian; Martens, Lennart

    2010-04-01

    We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com.

  6. jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions.

    PubMed

    Helsens, Kenny; Brusniak, Mi-Youn; Deutsch, Eric; Moritz, Robert L; Martens, Lennart

    2011-11-04

    We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions. The use of jTraML is demonstrated via a two-way conversion tool between TraML documents and vendor specific files, facilitating the adoption process of this new community standard. The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com . TraML files can also be converted online at http://iomics.ugent.be/jtraml .

  7. Engineering Study of 500 ML Sample Bottle Transportation Methods

    SciTech Connect

    BOGER, R.M.

    1999-08-25

    This engineering study reviews and evaluates all available methods for transportation of 500-mL grab sample bottles, reviews and evaluates transportation requirements and schedules and analyzes and recommends the most cost-effective method for transporting 500-mL grab sample bottles.

  8. Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO MOBILE LAUNCHER PLATFORM NO. 1. NASA, John F. Kennedy Space Center, Florida. Drawing 79K04401, Reynolds, Smith and Hills, March, 1975. ISOMETRIC: EXISTING ML NO. 3 LAUNCHER. Sheet A1 - Cape Canaveral Air Force Station, Launch Complex 39, Mobile Launcher Platforms, Launcher Road, East of Kennedy Parkway North, Cape Canaveral, Brevard County, FL

  9. Model-driven Service Engineering with SoaML

    NASA Astrophysics Data System (ADS)

    Elvesæter, Brian; Carrez, Cyril; Mohagheghi, Parastoo; Berre, Arne-Jørgen; Johnsen, Svein G.; Solberg, Arnor

    This chapter presents a model-driven service engineering (MDSE) methodology that uses OMG MDA specifications such as BMM, BPMN and SoaML to identify and specify services within a service-oriented architecture. The methodology takes advantage of business modelling practices and provides a guide to service modelling with SoaML. The presentation is case-driven and illuminated using the telecommunication example. The chapter focuses in particular on the use of the SoaML modelling language as a means for expressing service specifications that are aligned with business models and can be realized in different platform technologies.

  10. The Multi-Mission Maximum Likelihood Framework (3ML)

    NASA Astrophysics Data System (ADS)

    Burgess, J. M.; Vianello, G.

    2016-10-01

    We introduce a new tool for multi-messenger astronomy capable of fitting data from multiple instruments properly via the use of independent likelihood plugins. 3ML represents a step forward in spectral and spatial analysis across all wavelengths.

  11. AstroML: Machine learning and data mining in astronomy

    NASA Astrophysics Data System (ADS)

    VanderPlas, Jacob; Fouesneau, Morgan; Taylor, Julia

    2014-07-01

    Written in Python, AstroML is a library of statistical and machine learning routines for analyzing astronomical data in python, loaders for several open astronomical datasets, and a large suite of examples of analyzing and visualizing astronomical datasets. An optional companion library, astroML_addons, is available; it requires a C compiler and contains faster and more efficient implementations of certain algorithms in compiled code.

  12. The CellML Metadata Framework 2.0 Specification.

    PubMed

    Cooling, Michael T; Hunter, Peter

    2015-09-04

    The CellML Metadata Framework 2.0 is a modular framework that describes how semantic annotations should be made about mathematical models encoded in the CellML (www.cellml.org) format, and their elements. In addition to the Core specification, there are several satellite specifications, each designed to cater for model annotation in a different context. Basic Model Information, Citation, License and Biological Annotation specifications are presented.

  13. The jmzQuantML programming interface and validator for the mzQuantML data standard.

    PubMed

    Qi, Da; Krishna, Ritesh; Jones, Andrew R

    2014-03-01

    The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools (http://code.google.com/p/jmzquantml/). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool (http://code.google.com/p/mzquantml-validator/) for validating mzQuantML files, which is a formal part of the data standard. © 2014 The Authors. Proteomics published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. BindML/BindML+: Detecting Protein-Protein Interaction Interface Propensity from Amino Acid Substitution Patterns.

    PubMed

    Wei, Qing; La, David; Kihara, Daisuke

    2017-01-01

    Prediction of protein-protein interaction sites in a protein structure provides important information for elucidating the mechanism of protein function and can also be useful in guiding a modeling or design procedures of protein complex structures. Since prediction methods essentially assess the propensity of amino acids that are likely to be part of a protein docking interface, they can help in designing protein-protein interactions. Here, we introduce BindML and BindML+ protein-protein interaction sites prediction methods. BindML predicts protein-protein interaction sites by identifying mutation patterns found in known protein-protein complexes using phylogenetic substitution models. BindML+ is an extension of BindML for distinguishing permanent and transient types of protein-protein interaction sites. We developed an interactive web-server that provides a convenient interface to assist in structural visualization of protein-protein interactions site predictions. The input data for the web-server are a tertiary structure of interest. BindML and BindML+ are available at http://kiharalab.org/bindml/ and http://kiharalab.org/bindml/plus/ .

  15. Thogoto virus ML protein suppresses IRF3 function

    SciTech Connect

    Jennings, Stephanie . E-mail: stephanie.jennings@uniklinik-freiburg.de; Martinez-Sobrido, Luis . E-mail: Luis.Martinez@mssm.edu; Garcia-Sastre, Adolfo . E-mail: adolfo.garcia-sastre@mssm.edu; Weber, Friedemann . E-mail: friedemann.weber@uniklinik-freiburg.de; Kochs, Georg . E-mail: georg.kochs@uniklinik-freiburg.de

    2005-01-05

    The Thogoto virus (THOV) is a member of the family Orthomyxoviridae. It prevents induction of alpha/beta interferons (IFN) in cell culture and in vivo via the action of the viral ML protein. Phenotypically, the effect of THOV ML resembles that of the NS1 protein of influenza A virus (FLUAV) in that it blocks the expression of IFN genes. IFN expression depends on IFN regulatory factor 3 (IRF3). Upon activation, IRF3 forms homodimers and accumulates in the nucleus where it binds the transcriptional coactivator CREB-binding protein (CBP). Here, we show that expression of ML blocked the transcriptional activity of IRF3 after stimulation by virus infection. Further biochemical analysis revealed that ML acts by blocking IRF3 dimerization and association with CBP. Surprisingly, however, ML did not interfere with the nuclear transport of IRF3. Thus, the action of ML differs strikingly from that of FLUAV NS1 that prevents IFN induction by retaining IRF3 in the cytoplasm.

  16. From WaterML to TimeseriesML: Evolution and implications for cross-domain data interoperability

    NASA Astrophysics Data System (ADS)

    Arctur, D. K.; Taylor, P.; Lowe, D.; Tomkins, J.; Teng, W. L.; Ames, D. P.

    2015-12-01

    WaterML 2.0 part 1 was adopted by the Open Geospatial Consortium (OGC) in 2012 as an international standard profile of the Observations and Measurements conceptual model, for exchange of water observations time series data. It is implemented by national data producers such as the US Geological Survey for surface water time series, the NOAA/National Weather Service for forecast time series, the French Geological Survey for groundwater level monitoring, and the Australian Bureau of Meteorology for surface water observations. But WaterML 2.0 is not "just for water". The World Meteorological Organization (WMO) has recognized its potential role as a common time series description that could work for multiple application domains such as meteorology, climate, oceanography, and others. Accordingly, the WMO requested the OGC to migrate the non-hydrology parts of WaterML 2.0 to a new standard to be called TimeseriesML. This would then be considered by WMO for adoption as an operational standard globally. What does this mean for the geosciences? How far can this time series description be applied? What about time series of satellite retrievals? What will happen to WaterML 2.0 (and applications that work with it) when TimeseriesML is finished? These are among the questions we address in this presentation.

  17. QuakeML 2.0: Recent developments

    NASA Astrophysics Data System (ADS)

    Euchner, Fabian; Kästli, Philipp; Heiniger, Lukas; Saul, Joachim; Schorlemmer, Danijel; Clinton, John

    2016-04-01

    QuakeML is a community-backed data model for seismic event parameter description. Its current version 1.2, released in 2013, has become the gold standard for parametric data dissemination at seismological data centers, and has been adopted as an FDSN standard. It is supported by several popular software products and data services, such as FDSN event web services, QuakePy, and SeisComP3. Work on the successor version 2.0 is under way since 2015. The scope of QuakeML has been expanded beyond event parameter description. Thanks to a modular architecture, many thematic packages have been added, which cover peak ground motion, site and station characterization, hydraulic parameters of borehole injection processes, and macroseismics. The first three packages can be considered near final and implementations of program codes and SQL databases are in productive use at various institutions. A public community review process has been initiated in order to turn them into community-approved standards. The most recent addition is a package for single station quake location, which allows a detailed probabilistic description of event parameters recorded at a single station. This package adds some information elements such as angle of incidence, frequency-dependent phase picks, and dispersion relations. The package containing common data types has been extended with a generic type for probability density functions. While on Earth, single station methods are niche applications, they are of prominent interest in planetary seismology, e.g., the NASA InSight mission to Mars. So far, QuakeML is lacking a description of seismic instrumentation (inventory). There are two existing standards of younger age (FDSN StationXML and SeisComP3 Inventory XML). We discuss their respective strengths, differences, and how they could be combined into an inventory package for QuakeML, thus allowing full interoperability with other QuakeML data types. QuakeML is accompanied by QuakePy, a Python package

  18. ML 3.0 smoothed aggregation user's guide.

    SciTech Connect

    Sala, Marzio; Hu, Jonathan Joseph; Tuminaro, Raymond Stephen

    2004-05-01

    ML is a multigrid preconditioning package intended to solve linear systems of equations Az = b where A is a user supplied n x n sparse matrix, b is a user supplied vector of length n and x is a vector of length n to be computed. ML should be used on large sparse linear systems arising from partial differential equation (PDE) discretizations. While technically any linear system can be considered, ML should be used on linear systems that correspond to things that work well with multigrid methods (e.g. elliptic PDEs). ML can be used as a stand-alone package or to generate preconditioners for a traditional iterative solver package (e.g. Krylov methods). We have supplied support for working with the AZTEC 2.1 and AZTECOO iterative package [15]. However, other solvers can be used by supplying a few functions. This document describes one specific algebraic multigrid approach: smoothed aggregation. This approach is used within several specialized multigrid methods: one for the eddy current formulation for Maxwell's equations, and a multilevel and domain decomposition method for symmetric and non-symmetric systems of equations (like elliptic equations, or compressible and incompressible fluid dynamics problems). Other methods exist within ML but are not described in this document. Examples are given illustrating the problem definition and exercising multigrid options.

  19. ML314: A Biased Neurotensin Receptor Ligand for Methamphetamine Abuse.

    PubMed

    Barak, Larry S; Bai, Yushi; Peterson, Sean; Evron, Tama; Urs, Nikhil M; Peddibhotla, Satyamaheshwar; Hedrick, Michael P; Hershberger, Paul; Maloney, Patrick R; Chung, Thomas D Y; Rodriguiz, Ramona M; Wetsel, William C; Thomas, James B; Hanson, Glen R; Pinkerton, Anthony B; Caron, Marc G

    2016-07-15

    Pharmacological treatment for methamphetamine addiction will provide important societal benefits. Neurotensin receptor NTR1 and dopamine receptor distributions coincide in brain areas regulating methamphetamine-associated reward, and neurotensin peptides produce behaviors opposing psychostimulants. Therefore, undesirable methamphetamine-associated activities should be treatable with druggable NTR1 agonists, but no such FDA-approved therapeutics exist. We address this limitation with proof-of-concept data for ML314, a small-molecule, brain penetrant, β-arrestin biased, NTR1 agonist. ML314 attenuates amphetamine-like hyperlocomotion in dopamine transporter knockout mice, and in C57BL/6J mice it attenuates methamphetamine-induced hyperlocomotion, potentiates the psychostimulant inhibitory effects of a ghrelin antagonist, and reduces methamphetamine-associated conditioned place preference. In rats, ML314 blocks methamphetamine self-administration. ML314 acts as an allosteric enhancer of endogenous neurotensin, unmasking stoichiometric numbers of hidden NTR1 binding sites in transfected-cell membranes or mouse striatal membranes, while additionally supporting NTR1 endocytosis in cells in the absence of NT peptide. These results indicate ML314 is a viable, preclinical lead for methamphetamine abuse treatment and support an allosteric model of G protein-coupled receptor signaling.

  20. ML 3.1 smoothed aggregation user's guide.

    SciTech Connect

    Sala, Marzio; Hu, Jonathan Joseph; Tuminaro, Raymond Stephen

    2004-10-01

    ML is a multigrid preconditioning package intended to solve linear systems of equations Ax = b where A is a user supplied n x n sparse matrix, b is a user supplied vector of length n and x is a vector of length n to be computed. ML should be used on large sparse linear systems arising from partial differential equation (PDE) discretizations. While technically any linear system can be considered, ML should be used on linear systems that correspond to things that work well with multigrid methods (e.g. elliptic PDEs). ML can be used as a stand-alone package or to generate preconditioners for a traditional iterative solver package (e.g. Krylov methods). We have supplied support for working with the Aztec 2.1 and AztecOO iterative package [16]. However, other solvers can be used by supplying a few functions. This document describes one specific algebraic multigrid approach: smoothed aggregation. This approach is used within several specialized multigrid methods: one for the eddy current formulation for Maxwell's equations, and a multilevel and domain decomposition method for symmetric and nonsymmetric systems of equations (like elliptic equations, or compressible and incompressible fluid dynamics problems). Other methods exist within ML but are not described in this document. Examples are given illustrating the problem definition and exercising multigrid options.

  1. [Comparative evaluation of M.L. Cu. 250].

    PubMed

    van Os, W A; Haspels, A A; Rhemrev, P E; Loendersloot, E W; Lo Sin Sjoe, E; de Nooyer, C C

    1977-12-01

    The Multiload Cu 250 (ML Cu 250), a polyethylene IUD having flexible serrated tranverse arms and a copper-wound vertical axis, was tested in several Dutch clinics and compared with the Lippes Loop D, the copper T 200, and the copper T 220. There were 1700 insertions of the device for 12,142 woman-months of use. The pregnancy and expulsion rates were lower than those of the other IUDs tested, and it is now being used for postpartum insertions. Based on hysterectomies performed from 1 hour to 2 years after placement of the ML Cu 250, the device appears to conform well to uterine shape regardless of size, and no endometrial perforations have been noted. The ML Cu 250 is the 1st copper IUD simultaneously to satisfy the objectives of 1) easy insertion, 2) compatibility with varying uterine size, and 3) effective endometrial action without increase in the number of withdrawals for medical reasons.

  2. GeoSciML version 3: A GML application for geologic information

    NASA Astrophysics Data System (ADS)

    International Union of Geological Sciences., I. C.; Richard, S. M.

    2011-12-01

    orientation (e.g. 'miarolitic cavities'). The Earth material package allows for the description of both individual components, such as minerals, and compound materials, such as rocks or unconsolidated materials. Provision is made for alteration, weathering, metamorphism, particle geometry, fabric, and petrophysical descriptions. Mapped features describe the shape of the geological features using standard GML geometries, such as polygons, lines, points or 3D volumes. Geological events provide the age, process and environment of formation of geological features. The Earth Resource section includes features to represent mineral occurrences and mines and associated human activities independently. This addition allows description of resources and reserves that can comply with national and internationally accepted reporting codes. GeoSciML v3 is under consideration as the data model for INSPIRE annex 2 geologic reporting in Europe.

  3. CytometryML: a markup language for analytical cytology

    NASA Astrophysics Data System (ADS)

    Leif, Robert C.; Leif, Stephanie H.; Leif, Suzanne B.

    2003-06-01

    Cytometry Markup Language, CytometryML, is a proposed new analytical cytology data standard. CytometryML is a set of XML schemas for encoding both flow cytometry and digital microscopy text based data types. CytometryML schemas reference both DICOM (Digital Imaging and Communications in Medicine) codes and FCS keywords. These schemas provide representations for the keywords in FCS 3.0 and will soon include DICOM microscopic image data. Flow Cytometry Standard (FCS) list-mode has been mapped to the DICOM Waveform Information Object. A preliminary version of a list mode binary data type, which does not presently exist in DICOM, has been designed. This binary type is required to enhance the storage and transmission of flow cytometry and digital microscopy data. Index files based on Waveform indices will be used to rapidly locate the cells present in individual subsets. DICOM has the advantage of employing standard file types, TIF and JPEG, for Digital Microscopy. Using an XML schema based representation means that standard commercial software packages such as Excel and MathCad can be used to analyze, display, and store analytical cytometry data. Furthermore, by providing one standard for both DICOM data and analytical cytology data, it eliminates the need to create and maintain special purpose interfaces for analytical cytology data thereby integrating the data into the larger DICOM and other clinical communities. A draft version of CytometryML is available at www.newportinstruments.com.

  4. Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO MOBILE LAUNCHER PLATFORM NO. 1. NASA, John F. Kennedy Space Center, Florida. Drawing 79K04401, Reynolds, Smith and Hills, March, 1975. ISOMETRIC VIEW: MLP NO. 1. Sheet A10 - Cape Canaveral Air Force Station, Launch Complex 39, Mobile Launcher Platforms, Launcher Road, East of Kennedy Parkway North, Cape Canaveral, Brevard County, FL

  5. AstroML: Python-powered Machine Learning for Astronomy

    NASA Astrophysics Data System (ADS)

    Vander Plas, Jake; Connolly, A. J.; Ivezic, Z.

    2014-01-01

    As astronomical data sets grow in size and complexity, automated machine learning and data mining methods are becoming an increasingly fundamental component of research in the field. The astroML project (http://astroML.org) provides a common repository for practical examples of the data mining and machine learning tools used and developed by astronomical researchers, written in Python. The astroML module contains a host of general-purpose data analysis and machine learning routines, loaders for openly-available astronomical datasets, and fast implementations of specific computational methods often used in astronomy and astrophysics. The associated website features hundreds of examples of these routines being used for analysis of real astronomical datasets, while the associated textbook provides a curriculum resource for graduate-level courses focusing on practical statistics, machine learning, and data mining approaches within Astronomical research. This poster will highlight several of the more powerful and unique examples of analysis performed with astroML, all of which can be reproduced in their entirety on any computer with the proper packages installed.

  6. DocML: A Digital Library of University Data.

    ERIC Educational Resources Information Center

    Papadakis, Ioannis; Karakoidas, Vassileios; Chrissikopoulos, Vassileios

    2002-01-01

    Describes DocML, a Web-based digital library of university data that is used to build a system capable of preserving and managing student assignments. Topics include requirements for a digital library of university data; metadata and XML; three-tier architecture; user interface; searching; browsing; content delivery; and administrative issues.…

  7. DocML: A Digital Library of University Data.

    ERIC Educational Resources Information Center

    Papadakis, Ioannis; Karakoidas, Vassileios; Chrissikopoulos, Vassileios

    2002-01-01

    Describes DocML, a Web-based digital library of university data that is used to build a system capable of preserving and managing student assignments. Topics include requirements for a digital library of university data; metadata and XML; three-tier architecture; user interface; searching; browsing; content delivery; and administrative issues.…

  8. Range Condition and ML-EM Checkerboard Artifacts

    PubMed Central

    You, Jiangsheng; Wang, Jing; Liang, Zhengrong

    2007-01-01

    The expectation maximization (EM) algorithm for the maximum likelihood (ML) image reconstruction criterion generates severe checkerboard artifacts in the presence of noise. A classical remedy is to impose an a priori constraint for a penalized ML or maximum a posteriori probability solution. The penalty reduces the checkerboard artifacts and also introduces uncertainty because a priori information is usually unknown in clinic. Recent theoretical investigation reveals that the noise can be divided into two components: one is called null-space noise and the other is range-space noise. The null-space noise can be numerically estimated using filtered backprojection (FBP) algorithm. By the FBP algorithm, the null-space noise annihilates in the reconstruction while the range-space noise propagates into the reconstructed image. The aim of this work is to investigate the relation between the null-space noise and the checkerboard artifacts in the ML-EM reconstruction from noisy projection data. Our study suggests that removing the null-space noise from the projection data could improve the signal-to-noise ratio of the projection data and, therefore, reduce the checkerboard artifacts in the ML-EM reconstructed images. This study reveals an in-depth understanding of the different noise propagations in analytical and iterative image reconstructions, which may be useful to single photon emission computed tomography, where the noise has been a major factor for image degradation. The reduction of the ML-EM checkerboard artifacts by removing the null-space noise avoids the uncertainty of using a priori penalty. PMID:18449363

  9. Producing over 100 ml of highly concentrated hyperpolarized solution by means of dissolution DNP

    PubMed Central

    Comment, A.; Rentsch, J.; Kurdzesau, F.; Jannin, S.; Uffmann, K.; van Heeswijk, R. B.; Hautle, P.; Konter, J. A.; van den Brandt, B.; van der Klink, J. J.

    2008-01-01

    New low-temperature inserts compatible with an existing hyperpolarizer were developed to dynamically polarize nuclei in large samples. The performance of the system was tested on 8 ml glassy frozen solutions containing 13C-labeled molecules and doped with nitroxyl free radicals. The obtained 13C low-temperature polarization was comparable to the one measured on 20 times smaller sample volume with only 3–4 times higher microwave power. By using a dissolution insert that fits to the new design, it was possible to obtain about 120 ml of room-temperature hyperpolarized solution. The polarization as well as the molecule concentration was comparable to the values obtained in standard size hyperpolarized samples. Such large samples are interesting for future studies on larger animals and possibly for potential clinical applications. PMID:18595751

  10. Modeling Off-Nominal Behavior in SysML

    NASA Technical Reports Server (NTRS)

    Day, John C.; Donahue, Kenneth; Ingham, Michel; Kadesch, Alex; Kennedy, Andrew K.; Post, Ethan

    2012-01-01

    Specification and development of fault management functionality in systems is performed in an ad hoc way - more of an art than a science. Improvements to system reliability, availability, safety and resilience will be limited without infusion of additional formality into the practice of fault management. Key to the formalization of fault management is a precise representation of off-nominal behavior. Using the upcoming Soil Moisture Active-Passive (SMAP) mission for source material, we have modeled the off-nominal behavior of the SMAP system during its initial spin-up activity, using the System Modeling Language (SysML). In the course of developing these models, we have developed generic patterns for capturing off-nominal behavior in SysML. We show how these patterns provide useful ways of reasoning about the system (e.g., checking for completeness and effectiveness) and allow the automatic generation of typical artifacts (e.g., success trees and FMECAs) used in system analyses.

  11. Modeling Off-Nominal Behavior in SysML

    NASA Technical Reports Server (NTRS)

    Day, John C.; Donahue, Kenneth; Ingham, Michel; Kadesch, Alex; Kennedy, Andrew K.; Post, Ethan

    2012-01-01

    Specification and development of fault management functionality in systems is performed in an ad hoc way - more of an art than a science. Improvements to system reliability, availability, safety and resilience will be limited without infusion of additional formality into the practice of fault management. Key to the formalization of fault management is a precise representation of off-nominal behavior. Using the upcoming Soil Moisture Active-Passive (SMAP) mission for source material, we have modeled the off-nominal behavior of the SMAP system during its initial spin-up activity, using the System Modeling Language (SysML). In the course of developing these models, we have developed generic patterns for capturing off-nominal behavior in SysML. We show how these patterns provide useful ways of reasoning about the system (e.g., checking for completeness and effectiveness) and allow the automatic generation of typical artifacts (e.g., success trees and FMECAs) used in system analyses.

  12. Event reconstruction in NEXT using the ML-EM algorithm

    NASA Astrophysics Data System (ADS)

    Simón, A.; Ferrario, P.; Izmaylov, A.; NEXT Collaboration

    2016-04-01

    The NEXT collaboration aims to find the neutrinoless double beta decay in 136Xe. The rareness of this decay demands an exceptional background rejection. This can be obtained with an excellent energy resolution, which has been already demonstrated in the NEXT prototypes. In addition to this, the ββ 0 ν decay in gas produces a characteristic topological signal which could be an extremely useful extra handle to avoid background events. The need for a satisfactory topology reconstruction has led the NEXT Collaboration to implement the Maximum Likelihood Expectation Maximization method (ML-EM) in the data processing scheme. ML-EM is a generic iterative algorithm for many kinds of inverse problems. Although this method is well known in medical imaging and has been used widely in Positron Emission Tomography, it has never been applied to a time projection chamber. First results and studies of the performance of the method will be presented in this poster.

  13. IBM techexplorer and MathML: Interactive Multimodal Scientific Documents

    NASA Astrophysics Data System (ADS)

    Diaz, Angel

    2001-06-01

    The World Wide Web provides a standard publishing platform for disseminating scientific and technical articles, books, journals, courseware, or even homework on the internet; however, the transition from paper to web-based interactive content has brought new opportunities for creating interactive content. Students, scientists, and engineers are now faced with the task of rendering the 2D presentational structure of mathematics, harnessing the wealth of scientific and technical software, and creating truly accessible scientific portals across international boundaries and markets. The recent emergence of World Wide Web Consortium (W3C) standards such as the Mathematical Markup Language (MathML), Language (XSL), and Aural CSS (ACSS) provide a foundation whereby mathematics can be displayed, enlivened, computed, and audio formatted. With interoperability ensured by standards, software applications can be easily brought together to create extensible and interactive scientific content. In this presentation we will provide an overview of the IBM techexplorer Hypermedia Browser, a web browser plug-in and ActiveX control aimed at bringing interactive mathematics to the masses across platforms and applications. We will demonstrate "live" mathematics where documents that contain MathML expressions can be edited and computed right inside your favorite web browser. This demonstration will be generalized as we show how MathML can be used to enliven even PowerPoint presentations. Finally, we will close the loop by demonstrating a novel approach to spoken mathematics based on MathML, DOM, XSL, ACSS, techexplorer, and IBM ViaVoice. By making use of techexplorer as the glue that binds the rendered content to the web browser, the back-end computation software, the Java applets that augment the exposition, and voice-rendering systems such as ViaVoice, authors can indeed create truly extensible and interactive scientific content. For more information see: [http

  14. Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO MOBILE LAUNCHER PLATFORM NO. 1. NASA, John F. Kennedy Space Center, Florida. Drawing 79K04401, Reynolds, Smith and Hills, March, 1975. GENERAL ARRANGEMENT, MLP NO. 1, PLAN – DECK 0. Sheet A12 - Cape Canaveral Air Force Station, Launch Complex 39, Mobile Launcher Platforms, Launcher Road, East of Kennedy Parkway North, Cape Canaveral, Brevard County, FL

  15. Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO MOBILE LAUNCHER PLATFORM NO. 1. NASA, John F. Kennedy Space Center, Florida. Drawing 79K04401, Reynolds, Smith and Hills, March, 1975. GENERAL ARRANGEMENT, MLP NO. 1, SECTIONS II. Sheet A18 - Cape Canaveral Air Force Station, Launch Complex 39, Mobile Launcher Platforms, Launcher Road, East of Kennedy Parkway North, Cape Canaveral, Brevard County, FL

  16. Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO MOBILE LAUNCHER PLATFORM NO. 1. NASA, John F. Kennedy Space Center, Florida. Drawing 79K04401, Reynolds, Smith and Hills, March, 1975. GENERAL ARRANGEMENT, MLP NO. 1, ELEVATION – SIDE 1 & 2. Sheet A15 - Cape Canaveral Air Force Station, Launch Complex 39, Mobile Launcher Platforms, Launcher Road, East of Kennedy Parkway North, Cape Canaveral, Brevard County, FL

  17. Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO MOBILE LAUNCHER PLATFORM NO. 1. NASA, John F. Kennedy Space Center, Florida. Drawing 79K04401, Reynolds, Smith and Hills, March, 1975. GENERAL ARRANGEMENT, MLP NO. 1, PLAN – DECK B. Sheet A14 - Cape Canaveral Air Force Station, Launch Complex 39, Mobile Launcher Platforms, Launcher Road, East of Kennedy Parkway North, Cape Canaveral, Brevard County, FL

  18. Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO MOBILE LAUNCHER PLATFORM NO. 1. NASA, John F. Kennedy Space Center, Florida. Drawing 79K04401, Reynolds, Smith and Hills, March, 1975. GENERAL ARRANGEMENT, MLP NO. 1, ELEVATION – SIDE 3 & 4. Sheet A16 - Cape Canaveral Air Force Station, Launch Complex 39, Mobile Launcher Platforms, Launcher Road, East of Kennedy Parkway North, Cape Canaveral, Brevard County, FL

  19. Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO MOBILE LAUNCHER PLATFORM NO. 1. NASA, John F. Kennedy Space Center, Florida. Drawing 79K04401, Reynolds, Smith and Hills, March, 1975. GENERAL ARRANGEMENT, MLP NO. 1, PLAN – DECK A. Sheet A13 - Cape Canaveral Air Force Station, Launch Complex 39, Mobile Launcher Platforms, Launcher Road, East of Kennedy Parkway North, Cape Canaveral, Brevard County, FL

  20. Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO MOBILE LAUNCHER PLATFORM NO. 1. NASA, John F. Kennedy Space Center, Florida. Drawing 79K04401, Reynolds, Smith and Hills, March, 1975. GENERAL ARRANGEMENT, MLP NO. 1, SECTIONS IV. Sheet A20 - Cape Canaveral Air Force Station, Launch Complex 39, Mobile Launcher Platforms, Launcher Road, East of Kennedy Parkway North, Cape Canaveral, Brevard County, FL

  1. Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of drawing. MODIFICATIONS TO CONVERT ML NO. 3 TO MOBILE LAUNCHER PLATFORM NO. 1. NASA, John F. Kennedy Space Center, Florida. Drawing 79K04401, Reynolds, Smith and Hills, March, 1975. GENERAL ARRANGEMENT, MLP NO. 1, SECTIONS I. Sheet A17 - Cape Canaveral Air Force Station, Launch Complex 39, Mobile Launcher Platforms, Launcher Road, East of Kennedy Parkway North, Cape Canaveral, Brevard County, FL

  2. A Separate Compilation Extension to Standard ML (Revised and Expanded)

    DTIC Science & Technology

    2006-09-17

    Stone. A type -theoretic interpretation of Standard ML. In Gordon Plotkin, Colin Stirling , and Mads Tofte, editors, Proof, Language, and Interaction...specified by the programmer. A dependency may be mediated by an interface (the type of a unit); if so, the units can be compiled separately. Otherwise, they...a collection of information if it does not display a currently valid OMB control number. 1. REPORT DATE 17 SEP 2006 2. REPORT TYPE 3. DATES COVERED

  3. Certifying Compilation for Standard ML in a Type Analysis Framework

    DTIC Science & Technology

    2005-05-01

    speaking the certificate size seems to grow linearly with the program size. 9.8.5 Run time The LIL backend is not designed to be an optimizing backend. Code... designed to produce very efficient code. In order to do this, it compiles only complete programs . The Standard ML of NJ compiler is designed to be...Java. In Proceedings of the Conference on Programming Language Design and Implementation (PLDI’00), pages 95–107, Vancouver, Canada, June 2000. ACM

  4. ML shear wave velocity tomography for the Iranian Plateau

    NASA Astrophysics Data System (ADS)

    Maheri-Peyrov, Mehdi; Ghods, Abdolreza; Abbasi, Madjid; Bergman, Eric; Sobouti, Farhad

    2016-04-01

    Iranian Plateau reflects several different tectonic styles of collision, and large-scale strike-slip faults. We calculate a high-resolution 2-D ML shear velocity map for the Iranian Plateau to detect lateral crustal thickness changes associated with different tectonic boundaries. The ML velocity is very sensitive to strong lateral variations of crustal thickness and varies between the velocity of Lg and Sn phases. Our data set consists of 65 795 ML amplitude velocity measurements from 2531 precisely relocated events recorded by Iranian networks in the period 1996-2014. Using a constrained least-squares inversion scheme, we inverted the ML velocities for a 2-D shear velocity map of Iran. Our results show that the Zagros and South Caspian Basin (SCB) have shear wave velocities close to the Sn phase, and are thus Lg-blocking regions. High velocities in the High Zagros and the Simply Folded Belt imply significant crustal undulations within these zones. We note that in the central and south Zagros, the velocity border between the Zagros and central Iran is not coincident with the Zagros suture line that marks underthrusting of the Arabian plate beneath central Iran. The low plains of Gilan and Gorgan to the south of the Caspian Sea show high shear velocities similar to the SCB, implying that they are either underlain by an oceanic type crust or a transitional crust with a strong lateral crustal thickness gradient. The Lut block is an Lg-passing block implying that it is not surrounded by any sudden crustal thickness changes along its borders with central Iran. In the Alborz, NW Iran, Kopeh-Dagh, Binalud and most of the central Iran, low shear velocity near the Lg velocity is attributed to smooth or minor Moho undulations within these regions.

  5. Maintenance of sterility in 1-mL polypropylene syringes.

    PubMed

    Gonzalez, Serafin; Miller, Darlene; Murphy, Steven P

    2007-09-15

    The sterility of syringes filled with a growth-promoting broth when stored under various temperature conditions was studied. Samples of tryptic soy broth (TSB) were injected into 150 1-mL polypropylene syringes and incubated at 33-37 degrees C for 14 days, after which time they were visually inspected for microbial contamination. In addition to visual inspection, the sterility of all syringes was tested by inoculating samples into 10-mL tubes of thioglycollate broth, incubating at 35 degrees C, and observing for growth for 5 days. After the 14-day incubation period, 30 syringes were removed for sterility validation and microbial growth promotion. TSB from 15 syringes was transferred into sterile culture tubes and challenged with Staphylococcus aureus, Escherichia coli, Bacillus cereus, Candida albicans, and Aspergillus niger. The remaining 120 syringes were repackaged and stored at room temperature (22 degrees C), in a refrigerator (5 degrees C), or in a freezer (-20 degrees C). The sterility of the samples was evaluated at 30 days, 45 days, three months, and six months. No microbial growth was detected by visual inspection in any of the 15 syringes examined for turbidity during validation testing. All study syringes (n = 120) remained sterile throughout the respective evaluation periods, regardless of storage condition. Growth-promoting broth stored in 1-mL polypropylene syringes remained sterile when stored at room temperature, in a refrigerator, or in a freezer for six months.

  6. Nonlinear d10-ML2 Transition-Metal Complexes

    PubMed Central

    Wolters, Lando P; Bickelhaupt, F Matthias

    2013-01-01

    We have investigated the molecular geometries of a series of dicoordinated d10-transition-metal complexes ML2 (M=Co−, Rh−, Ir−, Ni, Pd, Pt, Cu+, Ag+, Au+; L=NH3, PH3, CO) using relativistic density functional theory (DFT) at ZORA-BLYP/TZ2P. Not all complexes have the expected linear ligand–metal–ligand (L–M–L) angle: this angle varies from 180° to 128.6° as a function of the metal as well as the ligands. Our main objective is to present a detailed explanation why ML2 complexes can become bent. To this end, we have analyzed the bonding mechanism in ML2 as a function of the L–M–L angle using quantitative Kohn–Sham molecular orbital (MO) theory in combination with an energy decomposition analysis (EDA) scheme. The origin of bent L–M–L structures is π backdonation. In situations of strong π backdonation, smaller angles increase the overlap of the ligand’s acceptor orbital with a higher-energy donor orbital on the metal-ligand fragment, and therefore favor π backdonation, resulting in additional stabilization. The angle of the complexes thus depends on the balance between this additional stabilization and increased steric repulsion that occurs as the complexes are bent. PMID:24551547

  7. CellML and associated tools and techniques.

    PubMed

    Garny, Alan; Nickerson, David P; Cooper, Jonathan; Weber dos Santos, Rodrigo; Miller, Andrew K; McKeever, Steve; Nielsen, Poul M F; Hunter, Peter J

    2008-09-13

    We have, in the last few years, witnessed the development and availability of an ever increasing number of computer models that describe complex biological structures and processes. The multi-scale and multi-physics nature of these models makes their development particularly challenging, not only from a biological or biophysical viewpoint but also from a mathematical and computational perspective. In addition, the issue of sharing and reusing such models has proved to be particularly problematic, with the published models often lacking information that is required to accurately reproduce the published results. The International Union of Physiological Sciences Physiome Project was launched in 1997 with the aim of tackling the aforementioned issues by providing a framework for the modelling of the human body. As part of this initiative, the specifications of the CellML mark-up language were released in 2001. Now, more than 7 years later, the time has come to assess the situation, in particular with regard to the tools and techniques that are now available to the modelling community. Thus, after introducing CellML, we review and discuss existing editors, validators, online repository, code generators and simulation environments, as well as the CellML Application Program Interface. We also address possible future directions including the need for additional mark-up languages.

  8. PCP-ML: protein characterization package for machine learning.

    PubMed

    Eickholt, Jesse; Wang, Zheng

    2014-11-18

    Machine Learning (ML) has a number of demonstrated applications in protein prediction tasks such as protein structure prediction. To speed further development of machine learning based tools and their release to the community, we have developed a package which characterizes several aspects of a protein commonly used for protein prediction tasks with machine learning. A number of software libraries and modules exist for handling protein related data. The package we present in this work, PCP-ML, is unique in its small footprint and emphasis on machine learning. Its primary focus is on characterizing various aspects of a protein through sets of numerical data. The generated data can then be used with machine learning tools and/or techniques. PCP-ML is very flexible in how the generated data is formatted and as a result is compatible with a variety of existing machine learning packages. Given its small size, it can be directly packaged and distributed with community developed tools for protein prediction tasks. Source code and example programs are available under a BSD license at http://mlid.cps.cmich.edu/eickh1jl/tools/PCPML/. The package is implemented in C++ and accessible as a Python module.

  9. Mass Spectrometer Output File Format mzML

    PubMed Central

    Deutsch, Eric W.

    2010-01-01

    Mass spectrometry is an important technique for analyzing proteins and other biomolecular compounds in biological samples. Each of the vendors of these mass spectrometers uses a different proprietary binary output file format, which has hindered data sharing and the development of open source software for downstream analysis. The solution has been to develop, with the full participation of academic researchers as well as software and hardware vendors, an open XML-based format for encoding mass spectrometer output files, and then to write software to use this format for archiving, sharing, and processing. This chapter presents the various components and information available for this format, mzML. In addition to the XML schema that defines the file structure, a controlled vocabulary provides clear terms and definitions for the spectral metadata, and a semantic validation rules mapping file allows the mzML semantic validator to insure that an mzML document complies with one of several levels of requirements. Complete documentation and example files insure that the format may be uniformly implemented. At the time of release there already existed several implementations of the format and vendors have committed to supporting the format in their products. PMID:20013381

  10. Mass spectrometer output file format mzML.

    PubMed

    Deutsch, Eric W

    2010-01-01

    Mass spectrometry is an important technique for analyzing proteins and other biomolecular compounds in biological samples. Each of the vendors of these mass spectrometers uses a different proprietary binary output file format, which has hindered data sharing and the development of open source software for downstream analysis. The solution has been to develop, with the full participation of academic researchers as well as software and hardware vendors, an open XML-based format for encoding mass spectrometer output files, and then to write software to use this format for archiving, sharing, and processing. This chapter presents the various components and information available for this format, mzML. In addition to the XML schema that defines the file structure, a controlled vocabulary provides clear terms and definitions for the spectral metadata, and a semantic validation rules mapping file allows the mzML semantic validator to insure that an mzML document complies with one of several levels of requirements. Complete documentation and example files insure that the format may be uniformly implemented. At the time of release, there already existed several implementations of the format and vendors have committed to supporting the format in their products.

  11. Testing and Evaluation of Archeological Sites 32ML404 and 32ML406 in McLean County, North Dakota.

    DTIC Science & Technology

    1978-09-01

    encountered in two separate locations, in the Sandstone Bluff II area, and in the Painted Woods area; both of these areas are on the left bank of the...pigeon, prairie chicken, raven , whistling swan, and whooping crane (Lehmer 1971: 55). Site Descriptions The Tick City site (32ML404) (U, 11 .) is in...Appendix A Project Scope of Work A-1 SCOPE OF WORK The scope of work of this project shall consist of comprehensive testing of the Sandstone Bluffs I

  12. QualityML: a dictionary for quality metadata encoding

    NASA Astrophysics Data System (ADS)

    Ninyerola, Miquel; Sevillano, Eva; Serral, Ivette; Pons, Xavier; Zabala, Alaitz; Bastin, Lucy; Masó, Joan

    2014-05-01

    The scenario of rapidly growing geodata catalogues requires tools focused on facilitate users the choice of products. Having quality fields populated in metadata allow the users to rank and then select the best fit-for-purpose products. In this direction, we have developed the QualityML (http://qualityml.geoviqua.org), a dictionary that contains hierarchically structured concepts to precisely define and relate quality levels: from quality classes to quality measurements. Generically, a quality element is the path that goes from the higher level (quality class) to the lowest levels (statistics or quality metrics). This path is used to encode quality of datasets in the corresponding metadata schemas. The benefits of having encoded quality, in the case of data producers, are related with improvements in their product discovery and better transmission of their characteristics. In the case of data users, particularly decision-makers, they would find quality and uncertainty measures to take the best decisions as well as perform dataset intercomparison. Also it allows other components (such as visualization, discovery, or comparison tools) to be quality-aware and interoperable. On one hand, the QualityML is a profile of the ISO geospatial metadata standards providing a set of rules for precisely documenting quality indicator parameters that is structured in 6 levels. On the other hand, QualityML includes semantics and vocabularies for the quality concepts. Whenever possible, if uses statistic expressions from the UncertML dictionary (http://www.uncertml.org) encoding. However it also extends UncertML to provide list of alternative metrics that are commonly used to quantify quality. A specific example, based on a temperature dataset, is shown below. The annual mean temperature map has been validated with independent in-situ measurements to obtain a global error of 0.5 ° C. Level 0: Quality class (e.g., Thematic accuracy) Level 1: Quality indicator (e.g., Quantitative

  13. Cellular cardiac electrophysiology modeling with Chaste and CellML

    PubMed Central

    Cooper, Jonathan; Spiteri, Raymond J.; Mirams, Gary R.

    2014-01-01

    Chaste is an open-source C++ library for computational biology that has well-developed cardiac electrophysiology tissue simulation support. In this paper, we introduce the features available for performing cardiac electrophysiology action potential simulations using a wide range of models from the Physiome repository. The mathematics of the models are described in CellML, with units for all quantities. The primary idea is that the model is defined in one place (the CellML file), and all model code is auto-generated at compile or run time; it never has to be manually edited. We use ontological annotation to identify model variables describing certain biological quantities (membrane voltage, capacitance, etc.) to allow us to import any relevant CellML models into the Chaste framework in consistent units and to interact with them via consistent interfaces. This approach provides a great deal of flexibility for analysing different models of the same system. Chaste provides a wide choice of numerical methods for solving the ordinary differential equations that describe the models. Fixed-timestep explicit and implicit solvers are provided, as discussed in previous work. Here we introduce the Rush–Larsen and Generalized Rush–Larsen integration techniques, made available via symbolic manipulation of the model equations, which are automatically rearranged into the forms required by these approaches. We have also integrated the CVODE solvers, a ‘gold standard’ for stiff systems, and we have developed support for symbolic computation of the Jacobian matrix, yielding further increases in the performance and accuracy of CVODE. We discuss some of the technical details of this work and compare the performance of the available numerical methods. Finally, we discuss how this is generalized in our functional curation framework, which uses a domain-specific language for defining complex experiments as a basis for comparison of model behavior. PMID:25610400

  14. Cellular cardiac electrophysiology modeling with Chaste and CellML.

    PubMed

    Cooper, Jonathan; Spiteri, Raymond J; Mirams, Gary R

    2014-01-01

    Chaste is an open-source C++ library for computational biology that has well-developed cardiac electrophysiology tissue simulation support. In this paper, we introduce the features available for performing cardiac electrophysiology action potential simulations using a wide range of models from the Physiome repository. The mathematics of the models are described in CellML, with units for all quantities. The primary idea is that the model is defined in one place (the CellML file), and all model code is auto-generated at compile or run time; it never has to be manually edited. We use ontological annotation to identify model variables describing certain biological quantities (membrane voltage, capacitance, etc.) to allow us to import any relevant CellML models into the Chaste framework in consistent units and to interact with them via consistent interfaces. This approach provides a great deal of flexibility for analysing different models of the same system. Chaste provides a wide choice of numerical methods for solving the ordinary differential equations that describe the models. Fixed-timestep explicit and implicit solvers are provided, as discussed in previous work. Here we introduce the Rush-Larsen and Generalized Rush-Larsen integration techniques, made available via symbolic manipulation of the model equations, which are automatically rearranged into the forms required by these approaches. We have also integrated the CVODE solvers, a 'gold standard' for stiff systems, and we have developed support for symbolic computation of the Jacobian matrix, yielding further increases in the performance and accuracy of CVODE. We discuss some of the technical details of this work and compare the performance of the available numerical methods. Finally, we discuss how this is generalized in our functional curation framework, which uses a domain-specific language for defining complex experiments as a basis for comparison of model behavior.

  15. SysML model of exoplanet archive functionality and activities

    NASA Astrophysics Data System (ADS)

    Ramirez, Solange

    2016-08-01

    The NASA Exoplanet Archive is an online service that serves data and information on exoplanets and their host stars to help astronomical research related to search for and characterization of extra-solar planetary systems. In order to provide the most up to date data sets to the users, the exoplanet archive performs weekly updates that include additions into the database and updates to the services as needed. These weekly updates are complex due to interfaces within the archive. I will be presenting a SysML model that helps us perform these update activities in a weekly basis.

  16. RAxML-Light: a tool for computing terabyte phylogenies

    PubMed Central

    Stamatakis, A.; Aberer, A.J.; Goll, C.; Smith, S.A.; Berger, S.A.; Izquierdo-Carrasco, F.

    2012-01-01

    Motivation: Due to advances in molecular sequencing and the increasingly rapid collection of molecular data, the field of phyloinformatics is transforming into a computational science. Therefore, new tools are required that can be deployed in supercomputing environments and that scale to hundreds or thousands of cores. Results: We describe RAxML-Light, a tool for large-scale phylogenetic inference on supercomputers under maximum likelihood. It implements a light-weight checkpointing mechanism, deploys 128-bit (SSE3) and 256-bit (AVX) vector intrinsics, offers two orthogonal memory saving techniques and provides a fine-grain production-level message passing interface parallelization of the likelihood function. To demonstrate scalability and robustness of the code, we inferred a phylogeny on a simulated DNA alignment (1481 taxa, 20 000 000 bp) using 672 cores. This dataset requires one terabyte of RAM to compute the likelihood score on a single tree. Code Availability: https://github.com/stamatak/RAxML-Light-1.0.5 Data Availability: http://www.exelixis-lab.org/onLineMaterial.tar.bz2 Contact: alexandros.stamatakis@h-its.org Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:22628519

  17. SMS: Smart Model Selection in PhyML.

    PubMed

    Lefort, Vincent; Longueville, Jean-Emmanuel; Gascuel, Olivier

    2017-09-01

    Model selection using likelihood-based criteria (e.g., AIC) is one of the first steps in phylogenetic analysis. One must select both a substitution matrix and a model for rates across sites. A simple method is to test all combinations and select the best one. We describe heuristics to avoid these extensive calculations. Runtime is divided by ∼2 with results remaining nearly the same, and the method performs well compared with ProtTest and jModelTest2. Our software, "Smart Model Selection" (SMS), is implemented in the PhyML environment and available using two interfaces: command-line (to be integrated in pipelines) and a web server (http://www.atgc-montpellier.fr/phyml-sms/). © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. ML and ML2 complex formation between Ca(ii) and d-glucose derivatives in aqueous solutions.

    PubMed

    Kutus, Bence; Ozsvár, Dániel; Varga, Norbert; Pálinkó, István; Sipos, Pál

    2017-01-24

    The complex formation equilibria between Ca(2+) ions and six carbohydrate derivatives related to d-glucose was quantitatively characterized by potentiometry, freezing point depression and polarimetry. Complexation could not be observed for d-glucose, while weak association was deduced for d-sorbitol and d-mannitol. Stronger complexes are formed with d-gluconate and d-heptagluconate due to the presence of the carboxylate group. In addition to the plausible 1 : 1 species, the 1 : 2 species can also be detected at higher ligand to metal ratios. The ML type complex is also formed with d-glucuronate and d-glucarate. The strong association for d-gluconate and d-heptagluconate was attested by freezing point depression measurements. Polarimetric results show that for these two ligands the specific rotation of the complexed and free anions is only slightly different. The stability of the 1 : 1 complexes follows the order: mannitol < sorbitol < glucuronate < heptagluconate ≈ gluconate < glucarate. The formation of the ML2 type species has been established for polyhydroxy ligands having at least one carboxylate group in addition to the conformational flexibility.

  19. Improving Interoperability by Incorporating UnitsML Into Markup Languages.

    PubMed

    Celebi, Ismet; Dragoset, Robert A; Olsen, Karen J; Schaefer, Reinhold; Kramer, Gary W

    2010-01-01

    Maintaining the integrity of analytical data over time is a challenge. Years ago, data were recorded on paper that was pasted directly into a laboratory notebook. The digital age has made maintaining the integrity of data harder. Nowadays, digitized analytical data are often separated from information about how the sample was collected and prepared for analysis and how the data were acquired. The data are stored on digital media, while the related information about the data may be written in a paper notebook or stored separately in other digital files. Sometimes the connection between this "scientific meta-data" and the analytical data is lost, rendering the spectrum or chromatogram useless. We have been working with ASTM Subcommittee E13.15 on Analytical Data to create the Analytical Information Markup Language or AnIML-a new way to interchange and store spectroscopy and chromatography data based on XML (Extensible Markup Language). XML is a language for describing what data are by enclosing them in computer-useable tags. Recording the units associated with the analytical data and metadata is an essential issue for any data representation scheme that must be addressed by all domain-specific markup languages. As scientific markup languages proliferate, it is very desirable to have a single scheme for handling units to facilitate moving information between different data domains. At NIST, we have been developing a general markup language just for units that we call UnitsML. This presentation will describe how UnitsML is used and how it is being incorporated into AnIML.

  20. Improving Interoperability by Incorporating UnitsML Into Markup Languages

    PubMed Central

    Celebi, Ismet; Dragoset, Robert A.; Olsen, Karen J.; Schaefer, Reinhold; Kramer, Gary W.

    2010-01-01

    Maintaining the integrity of analytical data over time is a challenge. Years ago, data were recorded on paper that was pasted directly into a laboratory notebook. The digital age has made maintaining the integrity of data harder. Nowadays, digitized analytical data are often separated from information about how the sample was collected and prepared for analysis and how the data were acquired. The data are stored on digital media, while the related information about the data may be written in a paper notebook or stored separately in other digital files. Sometimes the connection between this “scientific meta-data” and the analytical data is lost, rendering the spectrum or chromatogram useless. We have been working with ASTM Subcommittee E13.15 on Analytical Data to create the Analytical Information Markup Language or AnIML—a new way to interchange and store spectroscopy and chromatography data based on XML (Extensible Markup Language). XML is a language for describing what data are by enclosing them in computer-useable tags. Recording the units associated with the analytical data and metadata is an essential issue for any data representation scheme that must be addressed by all domain-specific markup languages. As scientific markup languages proliferate, it is very desirable to have a single scheme for handling units to facilitate moving information between different data domains. At NIST, we have been developing a general markup language just for units that we call UnitsML. This presentation will describe how UnitsML is used and how it is being incorporated into AnIML. PMID:27134778

  1. Activation of CS2 and CS by ML3 complexes.

    PubMed

    Ariafard, Alireza; Brookes, Nigel J; Stranger, Robert; Yates, Brian F

    2008-09-10

    The aim of this study was to determine the best neutral ML3 metal complexes for activating and cleaving the multiple bonds in CS2 and CS. Current experimental results show that, so far, only one bond in CS2 can be cleaved, and that CS can be activated but the bond is not broken. In the work described in this paper, density functional theory calculations have been used to evaluate the effectiveness of different ML3 complexes to activate the C-S bonds in CS2 and CS, with M = Mo, Re, W, and Ta and L = NH2. These calculations show that the combination of Re and Ta in the L3Re/CS2/TaL3 complex would be the most promising system for the cleavage of both C-S bonds of CS2. The reaction to cleave both C-S bonds is predicted to be exothermic by about 700 kJ mol(-1) and to proceed in an almost barrierless fashion. In addition, we are able to rationalize why the breaking of the C-S bond in CS has not been observed experimentally with M = Mo: this reaction is strongly endothermic. There is a subtle interplay between charge transfer and pi back-donation, and it appears that the Mo-C and Mo-S bonds are not strong enough to compensate for the breaking of the C-S bond. Our results suggest that, instead, CS could be cleaved with ReL3 or, even better, with a combination of ReL3 and TaL3. Molecular orbitals and Mulliken charges have been used to help explain these trends and to make predictions about the most promising systems for future experimental exploration.

  2. The Native Plasmid pML21 Plays a Role in Stress Tolerance in Enterococcus faecalis ML21, as Analyzed by Plasmid Curing Using Plasmid Incompatibility.

    PubMed

    Zuo, Fang-Lei; Chen, Li-Li; Zeng, Zhu; Feng, Xiu-Juan; Yu, Rui; Lu, Xiao-Ming; Ma, Hui-Qin; Chen, Shang-Wu

    2016-02-01

    To investigate the role of the native plasmid pML21 in Enterococcus faecalis ML21's response to abiotic stresses, the plasmid pML21 was cured based on the principle of plasmid incompatibility and segregational instability, generating E. faecalis mutant strain ML0. The mutant and the wild strains were exposed to abiotic stresses: bile salts, low pH, H2O2, ethanol, heat, and NaCl, and their survival rate was measured. We found that curing of pML21 lead to reduced tolerance to stress in E. faecalis ML0, especially oxidative and osmotic stress. Complementation analysis suggested that the genes from pML21 played different role in stress tolerance. The result indicated that pML21 plays a role in E. faecalis ML21's response to abiotic stresses.

  3. Investigational new insulin glargine 300 U/ml has the same metabolism as insulin glargine 100 U/ml.

    PubMed

    Steinstraesser, A; Schmidt, R; Bergmann, K; Dahmen, R; Becker, R H A

    2014-09-01

    Insulin glargine is processed in vivo into soluble 21(A) -Gly-human insulin (M1), the principal moiety responsible for metabolic effects, and subsequently into M2. This sub-study compared metabolism and metabolite pharmacokinetic (PK) profiles of investigational new insulin glargine U300 (Gla-300) with insulin glargine 100 U/ml (Gla-100, Lantus®, Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany) in people with type 1 diabetes. Participants received 0.4 (n = 18) or 0.6 U/kg Gla-300 (n = 12), and 0.4 U/kg Gla-100 (n = 30) once daily in randomized order for 8 days prior to a 36-h euglycaemic clamp. Metabolites were quantified using immunoaffinity enrichment and liquid chromatography tandem mass spectrometry (LC-MS/MS). Glargine metabolism was the same regardless of Gla-100 or Gla-300 administration; M1 was confirmed as the principal active moiety circulating in blood. Steady state concentrations of M1 were achieved after 2 days for Gla-100, and 4 days for Gla-300. Steady state M1 values defined prolonged and even flatter PK profiles after Gla-300 administration compared with M1 profiles after Gla-100.

  4. Application and performance of an ML-EM algorithm in NEXT

    NASA Astrophysics Data System (ADS)

    Simón, A.; Lerche, C.; Monrabal, F.; Gómez-Cadenas, J. J.; Álvarez, V.; Azevedo, C. D. R.; Benlloch-Rodríguez, J. M.; Borges, F. I. G. M.; Botas, A.; Cárcel, S.; Carrión, J. V.; Cebrián, S.; Conde, C. A. N.; Díaz, J.; Diesburg, M.; Escada, J.; Esteve, R.; Felkai, R.; Fernandes, L. M. P.; Ferrario, P.; Ferreira, A. L.; Freitas, E. D. C.; Goldschmidt, A.; González-Díaz, D.; Gutiérrez, R. M.; Hauptman, J.; Henriques, C. A. O.; Hernandez, A. I.; Hernando Morata, J. A.; Herrero, V.; Jones, B. J. P.; Labarga, L.; Laing, A.; Lebrun, P.; Liubarsky, I.; López-March, N.; Losada, M.; Martín-Albo, J.; Martínez-Lema, G.; Martínez, A.; McDonald, A. D.; Monteiro, C. M. B.; Mora, F. J.; Moutinho, L. M.; Muñoz Vidal, J.; Musti, M.; Nebot-Guinot, M.; Novella, P.; Nygren, D. R.; Palmeiro, B.; Para, A.; Pérez, J.; Querol, M.; Renner, J.; Ripoll, L.; Rodríguez, J.; Rogers, L.; Santos, F. P.; dos Santos, J. M. F.; Sofka, C.; Sorel, M.; Stiegler, T.; Toledo, J. F.; Torrent, J.; Tsamalaidze, Z.; Veloso, J. F. C. A.; Webb, R.; White, J. T.; Yahlali, N.

    2017-08-01

    The goal of the NEXT experiment is the observation of neutrinoless double beta decay in 136Xe using a gaseous xenon TPC with electroluminescent amplification and specialized photodetector arrays for calorimetry and tracking. The NEXT Collaboration is exploring a number of reconstruction algorithms to exploit the full potential of the detector. This paper describes one of them: the Maximum Likelihood Expectation Maximization (ML-EM) method, a generic iterative algorithm to find maximum-likelihood estimates of parameters that has been applied to solve many different types of complex inverse problems. In particular, we discuss a bi-dimensional version of the method in which the photosensor signals integrated over time are used to reconstruct a transverse projection of the event. First results show that, when applied to detector simulation data, the algorithm achieves nearly optimal energy resolution (better than 0.5% FWHM at the Q value of 136Xe) for events distributed over the full active volume of the TPC.

  5. Parallel and Scalable Big Data Analysis in the Earth Sciences with JuML

    NASA Astrophysics Data System (ADS)

    Goetz, M.

    2015-12-01

    Recent developments of using a significantly increasing number of sensors with better resolutions in the wide variety of different earth observation projects continously contribute to the availability of 'big data' in the earth sciences. Not only the volume, velocity, and variety of the datasets pose increasing challenges for its analysis, but also the complexity of datasets (e.g. high number of dimensions in hyper-spectral images) requires data algorithms that are able to scale. This contribution will provide insights about the Juelich Machine learning Library (JuML) and its contents that have been actively used in several scientific use cases in the earth sciences. We discuss and categorize challenges related to 'big data' analysis and outline parallel algorithmic solutions driven by those use cases.

  6. Early static (18)F-FET-PET scans have a higher accuracy for glioma grading than the standard 20-40 min scans.

    PubMed

    Albert, Nathalie L; Winkelmann, Isabel; Suchorska, Bogdana; Wenter, Vera; Schmid-Tannwald, Christine; Mille, Erik; Todica, Andrei; Brendel, Matthias; Tonn, Jörg-Christian; Bartenstein, Peter; la Fougère, Christian

    2016-06-01

    Current guidelines for glioma imaging by positron emission tomography (PET) using the amino acid analogue O-(2-[(18)F]fluoroethyl)-L-tyrosine ((18)F-FET) recommend image acquisition from 20-40 min post injection (p.i.). The maximal tumour-to-background evaluation (TBRmax) obtained in these summation images does not enable reliable differentiation between low and high grade glioma (LGG and HGG), which, however, can be achieved by dynamic (18)F-FET-PET. We investigated the accuracy of tumour grading using TBRmax values at different earlier time points after tracer injection. Three hundred and fourteen patients with histologically proven primary diagnosis of glioma (131 LGG, 183 HGG) who had undergone 40-min dynamic (18)F-FET-PET scans were retrospectively evaluated. TBRmax was assessed in the standard 20-40 min summation images, as well as in summation images from 0-10 min, 5-15 min, 5-20 min, and 15-30 min p.i., and kinetic analysis was performed. TBRmax values and kinetic analysis were correlated with histological classification. ROC analyses were performed for each time frame and sensitivity, specificity, and accuracy were assessed. TBRmax values in the earlier summation images were significantly better for tumour grading (P < 0.001) when compared to standard 20-40 min scans, with best results for the early 5-15 min scan. This was due to higher TBRmax in the HGG (3.9 vs. 3.3; p < 0.001), while TBRmax remained nearly stable in the LGG (2.2 vs. 2.1). Overall, accuracy increased from 70 % in the 20-40 min analysis to 77 % in the 5-15 min images, but did not reach the accuracy of dynamic analysis (80 %). Early TBRmax assessment (5-15 min p.i.) is more accurate for the differentiation between LGG and HGG than the standard static scan (20-40 min p.i.) mainly caused by the characteristic high (18)F-FET uptake of HGG in the initial phase. Therefore, when dynamic (18)F-FET-PET cannot be performed, early TBRmax assessment can be considered as an

  7. Reconstitution of lysosomal NAADP-TRP-ML1 signaling pathway and its function in TRP-ML1−/− cells

    PubMed Central

    Zhang, Fan; Xu, Ming; Han, Wei-Qing

    2011-01-01

    It is well known that the mutation of TRP-ML1 (transient receptor potential-mucolipin-1) causes mucolipidosis IV, a lysosomal storage disease. Given that lysosomal nicotinic acid adenine dinucleotide phosphate (NAADP)-Ca2+ release channel activity is associated with TRP-ML1, the present study was designed to test the hypothesis that NAADP regulates lysosome function via activation of TRP-ML1 channel activity. Using lysosomal preparations from wild-type (TRP-ML1+/+) human fibroblasts, channel reconstitution experiments demonstrated that NAADP (0.01–1.0 μM) produced a concentration-dependent increase in TRP-ML1 channel activity. This NAADP-induced activation of TRP-ML1 channels could not be observed in lysosomes from TRP-ML1−/− cells, but was restored by introducing a TRP-ML1 transgene into these cells. Microscopic Ca2+ fluorescence imaging showed that NAADP significantly increased intracellular Ca2+ concentration to 302.4 ± 74.28 nM (vs. 180 ± 44.13 nM of the basal) in TRP-ML1+/+ cells, but it had no effect in TRP-ML1−/− cells. If a TRP-ML1 gene was transfected into TRP-ML1−/− cells, the Ca2+ response to NAADP was restored to the level comparable to TRP-ML1+/+ cells. Functionally, confocal microscopy revealed that NAADP significantly enhanced the dynamic interaction of endosomes and lysosomes and the lipid delivery to lysosomes in TRP-ML1+/+ cells. This functional action of NAADP was abolished in TRP-ML1−/− cells, but restored after TRP-ML1 gene was rescued in these cells. Our results suggest that NAADP increases lysosomal TRP-ML1 channel activity to release Ca2+, which promotes the interaction of endosomes and lysosomes and thereby regulates lipid transport to lysosomes. Failure of NAADP-TRP-ML1 signaling may be one of the important mechanisms resulting in intracellular lipid trafficking disorder and consequent mucolipidosis. PMID:21613607

  8. SED-ML web tools: generate, modify and export standard-compliant simulation studies.

    PubMed

    Bergmann, Frank T; Nickerson, David; Waltemath, Dagmar; Scharm, Martin

    2017-04-15

    The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, an online application for creating, editing, simulating and validating SED-ML documents. The Web Tools implement all current SED-ML specifications and, thus, support complex modifications and co-simulation of models in SBML and CellML formats. Ultimately, the Web Tools lower the bar on working with SED-ML documents and help users create valid simulation descriptions. http://sysbioapps.dyndns.org/SED-ML_Web_Tools/ . fbergman@caltech.edu .

  9. Preclinical evaluation of 18F-ML-10 to determine timing of apoptotic response to chemotherapy in solid tumors

    DOE PAGES

    Demirci, Emre; Ahmed, Rafay; Ocak, Meltem; ...

    2017-01-10

    Here, we investigated 2-(5-fluoro-pentyl)-2-methyl-malonic acid (18F-ML-10) positron emission tomography (PET) imaging of apoptosis posttherapy to determine optimal timing for predicting chemotherapy response in a mouse head/neck xenograft cancer model. BALB/c nude mice (4-8 weeks old) were implanted with UM-SCC-22B tumors. The treatment group received 2 doses of doxorubicin (10 mg/kg, days 0, 2). Small animal 18F-ML-10 PET/computed tomography was performed before and on days 1, 3, and 7 postchemotherapy. Using regions of interest around tumors, 18F-ML-10 uptake change was measured as %ID/g and uptake relative to liver. Terminal Uridine Nick-End Labeling (TUNEL) immunohistochemistry assay was performed using tumor samples ofmore » baseline and on days 1, 3, and 7 posttreatment. As a result, treated mice demonstrated increased 18F-ML-10 uptake compared to baseline and controls, and 10 of 13 mice showed tumor volume decreases. All control mice showed tumor volume increases. Tumor-to-liver (T/L) ratios from the control group mice did not show significant change from baseline (P > .05); however, T/L ratios of the treatment group showed significant 18F-ML-10 uptake differences from baseline compared to days 3 and 7 posttreatment (P < .05), but no significant difference at 1 day posttreatment. In conclusion, 2-(5-Fluoro-pentyl)-2-methyl-malonic acid PET imaging has the potential for early assessment of treatment-induced apoptosis. Timing and image analysis strategies may require optimization, depending on the type of tumor and cancer treatment.« less

  10. RIF RuleML Rosetta Ring: Round-Tripping the Dlex Subset of Datalog RuleML and RIF-Core

    NASA Astrophysics Data System (ADS)

    Boley, Harold

    The RIF RuleML overlap area is of broad interest for Web rule interchange. Its kernel, Dlex, is defined syntactically and semantically as the common sublanguage of Datalog RuleML and RIF-Core restricted to positional arguments and non-conjunctive rule conclusions, and allowing equality plus externals in rule premises (only). Semantics-preserving mappings are then defined between the Dlex subset of the RIF Presentation Syntax and RIF/XML, RIF/XML and RuleML/XML, as well as RuleML/XML and the Prolog-like RuleML/POSL. These mappings are the basis for RIF RuleML feature comparison and translation. The slightly augmented mappings can be composed into a ('Rosetta') ring for round-tripping between all pairs of Dlex representations.

  11. jqcML: an open-source java API for mass spectrometry quality control data in the qcML format.

    PubMed

    Bittremieux, Wout; Kelchtermans, Pieter; Valkenborg, Dirk; Martens, Lennart; Laukens, Kris

    2014-07-03

    The awareness that systematic quality control is an essential factor to enable the growth of proteomics into a mature analytical discipline has increased over the past few years. To this aim, a controlled vocabulary and document structure have recently been proposed by Walzer et al. to store and disseminate quality-control metrics for mass-spectrometry-based proteomics experiments, called qcML. To facilitate the adoption of this standardized quality control routine, we introduce jqcML, a Java application programming interface (API) for the qcML data format. First, jqcML provides a complete object model to represent qcML data. Second, jqcML provides the ability to read, write, and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA). jqcML is released as open-source software under the permissive Apache 2.0 license and can be downloaded from https://bitbucket.org/proteinspector/jqcml .

  12. mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.

    PubMed

    Larralde, Martin; Lawson, Thomas N; Weber, Ralf J M; Moreno, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; Viant, Mark R; Steinbeck, Christoph; Salek, Reza M

    2017-08-15

    Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Overall, the use of mzML2ISA & nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets. mzML2ISA & nmrML2ISA are available under version 3 of the GNU General Public Licence at https://github.com/ISA-tools. Documentation is available from http://2isa.readthedocs.io/en/latest/. reza.salek@ebi.ac.uk or isatools@googlegroups.com. Supplementary data are available at Bioinformatics online.

  13. Graphical methods of psychometrical indicators in Georgian women (20-40 years old) of normal physical development according to forms of temperament and character.

    PubMed

    Nadashvili, L

    2009-04-01

    To establish temperament and forms of character and graphical image, we have studied 120 Georgian women of normal physical development, who were divided by 4 age groups with 5 years intervals. To establish temperament and forms of character we used Eysenck's questionnaire (57 questions) and Sheldon's scale of temperament. The material was worked out by the recognized methods of mathematical psychology. It was stated that Georgian women of young age (20-40 years old) are of sanguine temperament, by character extraverts, which means that they are strong, moving, balanced, stable.

  14. A comparison of 250 and 500 mL of terminal warm blood cardioplegia after global myocardial ischemia: a prospective randomized study.

    PubMed

    Akowuah, Enoch F; Riaz, Imran; Shrivastava, Vivek; Onyeaka, Patrick; Cooper, Graham

    2005-01-01

    Controlled reperfusion with terminal warm blood cardioplegia (TWBC) improves myocardial performance after global ischemia. However, the optimum volume required is unknown. Fifty patients undergoing elective coronary artery bypass graft surgery were prospectively randomized to receive either 250 or 500 mL of TWBC. During TWBC delivery, and for 10 minutes after cross-clamp removal, samples were taken from the aorta and coronary sinus to measure the hydrogen ion, lactate, and oxygen content. At the end of TWBC delivery, the 500 mL group had significantly less hydrogen ion washout (p = 0.006) compared with the 250 mL group. Also, more hydrogen ions (p = 0.02) and lactate (p = 0.02) had been washed out during the entire period of TWBC delivery in the 500 mL group compared with the 250 mL, indicating better metabolic recovery. By 4 minutes after aortic cross-clamp removal, hydrogen ion and lactate washout, as well as oxygen extraction was similar in the two groups. However, the time to return to regular mechanical activity was prolonged in the 500 mL group, 5.8 (3) versus 4.6 (3) minutes in the 250 mL group (p = 0.05). Though there was no difference in postoperative Troponin T levels, eight patients in the 500 mL group versus four in the 250 mL group required ionotropic support (p = 0.1). A total of 500 mL of hotshot achieves a better metabolic state after hotshot delivery. However, there is no clinical benefit or improvement in the postoperative Troponin T release suggesting that in a short ischemic time, 500 mL TWCB has a limited clinical benefit.

  15. Small-Volume Injections: Evaluation of Volume Administration Deviation From Intended Injection Volumes.

    PubMed

    Muffly, Matthew K; Chen, Michael I; Claure, Rebecca E; Drover, David R; Efron, Bradley; Fitch, William L; Hammer, Gregory B

    2017-10-01

    In the perioperative period, anesthesiologists and postanesthesia care unit (PACU) nurses routinely prepare and administer small-volume IV injections, yet the accuracy of delivered medication volumes in this setting has not been described. In this ex vivo study, we sought to characterize the degree to which small-volume injections (≤0.5 mL) deviated from the intended injection volumes among a group of pediatric anesthesiologists and pediatric postanesthesia care unit (PACU) nurses. We hypothesized that as the intended injection volumes decreased, the deviation from those intended injection volumes would increase. Ten attending pediatric anesthesiologists and 10 pediatric PACU nurses each performed a series of 10 injections into a simulated patient IV setup. Practitioners used separate 1-mL tuberculin syringes with removable 18-gauge needles (Becton-Dickinson & Company, Franklin Lakes, NJ) to aspirate 5 different volumes (0.025, 0.05, 0.1, 0.25, and 0.5 mL) of 0.25 mM Lucifer Yellow (LY) fluorescent dye constituted in saline (Sigma Aldrich, St. Louis, MO) from a rubber-stoppered vial. Each participant then injected the specified volume of LY fluorescent dye via a 3-way stopcock into IV tubing with free-flowing 0.9% sodium chloride (10 mL/min). The injected volume of LY fluorescent dye and 0.9% sodium chloride then drained into a collection vial for laboratory analysis. Microplate fluorescence wavelength detection (Infinite M1000; Tecan, Mannedorf, Switzerland) was used to measure the fluorescence of the collected fluid. Administered injection volumes were calculated based on the fluorescence of the collected fluid using a calibration curve of known LY volumes and associated fluorescence.To determine whether deviation of the administered volumes from the intended injection volumes increased at lower injection volumes, we compared the proportional injection volume error (loge [administered volume/intended volume]) for each of the 5 injection volumes using a linear

  16. Virtual Construction of Space Habitats: Connecting Building Information Models (BIM) and SysML

    NASA Technical Reports Server (NTRS)

    Polit-Casillas, Raul; Howe, A. Scott

    2013-01-01

    Current trends in design, construction and management of complex projects make use of Building Information Models (BIM) connecting different types of data to geometrical models. This information model allow different types of analysis beyond pure graphical representations. Space habitats, regardless their size, are also complex systems that require the synchronization of many types of information and disciplines beyond mass, volume, power or other basic volumetric parameters. For this, the state-of-the-art model based systems engineering languages and processes - for instance SysML - represent a solid way to tackle this problem from a programmatic point of view. Nevertheless integrating this with a powerful geometrical architectural design tool with BIM capabilities could represent a change in the workflow and paradigm of space habitats design applicable to other aerospace complex systems. This paper shows some general findings and overall conclusions based on the ongoing research to create a design protocol and method that practically connects a systems engineering approach with a BIM architectural and engineering design as a complete Model Based Engineering approach. Therefore, one hypothetical example is created and followed during the design process. In order to make it possible this research also tackles the application of IFC categories and parameters in the aerospace field starting with the application upon the space habitats design as way to understand the information flow between disciplines and tools. By building virtual space habitats we can potentially improve in the near future the way more complex designs are developed from very little detail from concept to manufacturing.

  17. Virtual Construction of Space Habitats: Connecting Building Information Models (BIM) and SysML

    NASA Technical Reports Server (NTRS)

    Polit-Casillas, Raul; Howe, A. Scott

    2013-01-01

    Current trends in design, construction and management of complex projects make use of Building Information Models (BIM) connecting different types of data to geometrical models. This information model allow different types of analysis beyond pure graphical representations. Space habitats, regardless their size, are also complex systems that require the synchronization of many types of information and disciplines beyond mass, volume, power or other basic volumetric parameters. For this, the state-of-the-art model based systems engineering languages and processes - for instance SysML - represent a solid way to tackle this problem from a programmatic point of view. Nevertheless integrating this with a powerful geometrical architectural design tool with BIM capabilities could represent a change in the workflow and paradigm of space habitats design applicable to other aerospace complex systems. This paper shows some general findings and overall conclusions based on the ongoing research to create a design protocol and method that practically connects a systems engineering approach with a BIM architectural and engineering design as a complete Model Based Engineering approach. Therefore, one hypothetical example is created and followed during the design process. In order to make it possible this research also tackles the application of IFC categories and parameters in the aerospace field starting with the application upon the space habitats design as way to understand the information flow between disciplines and tools. By building virtual space habitats we can potentially improve in the near future the way more complex designs are developed from very little detail from concept to manufacturing.

  18. Surface structure determination of Au(1 ML)/Fe(15 ML)/Au(100) using angle-resolved photoemission extended fine structure

    NASA Astrophysics Data System (ADS)

    Kellar, S. A.; Chen, Y.; Huff, W. R. A.; Moler, E. J.; Hussain, Z.; Shirley, D. A.

    1998-01-01

    We have determined the atomic surface structure of a thin film of Fe (15 ML) grown on the Au(100) surface, Au(1 ML)/Fe(15 ML)/Au(100), with angle-resolved photoemission extended fine structure (ARPEFS) using the Au 4f7/2 core level. We have confirmed that a bcc crystalline Fe film grows epitaxially on the Au(100) substrate with 1 ML of Au atoms remaining on the surface using angle-resolved photoemission spectroscopy. We analyzed the ARPEFS oscillations using an electron-scattering code based on the Rehr-Albers scattering matrix formalism. Our analysis finds that the surface Au atoms are positioned in the fourfold hollow sites 1.67+/-0.02 Å above the Fe surface. We also find that the grown Fe layers are very like bulk bcc Fe, with an interlayer spacing of 1.43+/-0.03 Å.

  19. Thulium laser resection versus plasmakinetic resection of prostates larger than 80 ml.

    PubMed

    Wei, Haibin; Shao, Yi; Sun, Feng; Sun, Xiaowen; Zhuo, Jian; Zhao, Fujun; Han, Bangmin; Jiang, Juntao; Chen, Huirong; Xia, Shujie

    2014-08-01

    To compare the safety and efficiency of thulium laser resection of the prostate-tangerine technique (TmLRP-TT) and plasmakinetic resection of the prostate (PKRP) for aged symptomatic benign prostatic hyperplasia (BPH) patients with large volume prostates (>80 ml) in a prospective randomized trial with an 18-month follow-up. From January 2010 to November 2011, 90 BPH patients with large volume prostates were randomized for surgical treatment with TmLRP-TT (n = 45, group 1) or PKRP (n = 45, group 2). The preoperative and postoperative parameters were recorded and compared. All patients were evaluated at 1, 6, 12 and 18 months postoperatively using the International Prostate Symptom Score (IPSS), quality of life score (QoL), maximum flow rate (Q max), postvoid residual urine volume (PVR) and the five-item version of the International Index of Erectile Function score. All perioperative complications were also documented and classified according to the modified Clavien classification system. Compared with the PKRP group, the TmLRP-TT group had a statistically lower hemoglobin drop (0.86 ± 0.42 vs. 1.34 ± 1.04 g/dl, P < 0.01), shorter catheterization time (1.91 ± 0.85 vs. 2.36 ± 0.74 days, P < 0.01) and hospital stay (3.80 ± 0.46 vs. 5.02 ± 0.54 days, P < 0.01). Within the observation period of 18 months, both groups had significant postoperative improvement in IPSS, QoL, Q max and PVR, although no difference was observed between the two groups. Only one patient receiving PKRP treatment required a blood transfusion perioperatively. During the 18-month follow-up, one patient in each group experienced urethral stricture and one patient in the PKRP group experienced bladder neck contracture. Minor complications that required no or noninterventional treatment occurred in 6 (13.33 %) of TmLRP-TT group (Clavien grade 1, 13.33 % and grade 2, 0 %) and 10 (22.22 %) of PKRP group (Clavien grade 1, 20.00 % and grade 2, 2.22 %). No severe complications required reinterventions

  20. Comparison of craniofacial linear measurements of 20-40 year-old males and females using digital lateral cephalometric radiography in Indonesia

    NASA Astrophysics Data System (ADS)

    Aurizanti, D.; Suryonegoro, H.; Priaminiarti, M.

    2017-08-01

    Craniofacial characteristics are one of the sex determination parameters of age after puberty. The aim of this study is to obtain linear measurements using lateral cephalometric radiography of adults aged 20-40 years based on sex in Indonesia. Ten linear craniofacial parameters on 100 digital lateral cephalometric radiographs were measured. Inter-intra observer reliability was tested using Technical Error Measurement. The independent t-test and the Mann-Whitney U test were used to evaluate the significance of the findings. There are significant differences between males and females on 10 of the linear measurements using lateral cephalometric radiography. Lateral cephalometric radiography showed that the linear measurements of 10 cephalometic parameters were higher in males than females, so it can be used to determine sex.

  1. Dual-frequency (20/40 kHz) ultrasonic assisted photocatalysis for degradation of methylene blue effluent: synergistic effect and kinetic study.

    PubMed

    Xiong, Shao Feng; Yin, Zhou Lan; Yuan, Zhang Fu; Yan, Wen Bin; Yang, Wen Yin; Liu, Jin Jian; Zhang, Fan

    2012-07-01

    Dual-frequency ultrasonic assisted photocatalysis (DUAP) was proposed to enhance the degradation efficiency of methylene blue (MB) solution. The influence of operational parameters, i.e., irradiation time, ultrasonic arrangement, TiO(2) concentration and power density, was studied. The results implied that the rapid degradation of MB solution was achieved in 18 min under DUAP with the dual frequencies of 20/40 kHz. Kinetic investigation of MB degradation for the DUAP process was conducted on the basis of first-order kinetic equation and the synergistic effect was assessed by examination of the apparent rate constant. The effect of ultrasonic arrangement was analyzed by comparison of the pressure amplitude of ultrasonic superposition field. The evolvement of intermediate products and the role of active species during DUAP were distinguished by UV-Vis spectra and the free radical scavenging experiment. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Body mass index gain between ages 20-40 years and lifestyle characteristics of men at ages 40-60 years: The Adventist Health Study-2

    PubMed Central

    Japas, Claudio; Knutsen, Synnøve; Dehom, Salem; Dos Santos, Hildemar; Tonstad, Serena

    2014-01-01

    Background Obesity increases risk of premature disease, and may be associated with unfavorable lifestyle changes that add to risk. This study analyzed the association of midlife BMI change with current lifestyle patterns among multiethnic men. Methods Men aged 40-60 years (n=9864) retrospectively reported body weight between ages 20-40 years and current dietary, TV, physical activity and sleep practices in the Adventist Health Study II, a study of church-goers in the US and Canada. In multivariate logistic regression analysis, odds ratios for BMI gain were calculated for each lifestyle practice controlling for sociodemographic and other lifestyle factors and current BMI. Results Men with median or higher BMI gain (2.79 kg/m2) between ages 20-40 years were more likely to consume a non-vegetarian diet, and engage in excessive TV watching and little physical activity and had a shorter sleep duration compared to men with BMI gain below the median (all p<0.001). In multivariate logistic analysis current BMI was significantly associated with all lifestyle factors in multivariate analyses (all p≤0.005). BMI gain was associated with lower odds of vegetarian diet (odds ratio [OR] 0.939; 95% confidence interval [CI] 0.921-0.957) and of physical activity ≥150 minutes/week (OR 0.979, 95% CI 0.960-0.999). Conclusions These findings imply that diet and less physical activity are associated with both gained and attained BMI, while inactivity (TV watching) and short sleep duration correlated only with attained BMI. Unhealthy lifestyle may add risk to that associated with BMI. Longitudinal and intervention studies are needed to infer causal relationships. PMID:25434910

  3. Freezing Baboon Red Blood Cells in the Original 800 ml Polyvinylchloride Plastic Bag With 40% W/V Glycerol and Storage at -80 C and Deglycerolization Using the IBM Code Blood Processor 2991

    DTIC Science & Technology

    1997-08-12

    primary bag with a volume of 800 ml. Each primary collection bag contains 63 ml of citrate-phosphate-dextrose-adenine (CPDA- 1) anticoagulant . After...22 C to prepare platelet-rich-plasma ( PRP ) and a red blood cell concentrate. Non-rejuvenated glycerolized red cells spun at 1248 X g for 10

  4. TRP-ML1 regulates lysosomal pH and acidic lysosomal lipid hydrolytic activity.

    PubMed

    Soyombo, Abigail A; Tjon-Kon-Sang, Sandra; Rbaibi, Youssef; Bashllari, Enkelejda; Bisceglia, Jill; Muallem, Shmuel; Kiselyov, Kirill

    2006-03-17

    Mucolipidosis type IV (MLIV) is caused by mutations in the ion channel mucolipin 1 (TRP-ML1). MLIV is typified by accumulation of lipids and membranous materials in intracellular organelles, which was hypothesized to be caused by the altered membrane fusion and fission events. How mutations in TRP-ML1 lead to aberrant lipolysis is not known. Here we present evidence that MLIV is a metabolic disorder that is not associated with aberrant membrane fusion/fission events. Thus, measurement of lysosomal pH revealed that the lysosomes in TRP-ML1(-/-) cells obtained from the patients with MLIV are over-acidified. TRP-ML1 can function as a H(+) channel, and the increased lysosomal acidification in TRP-ML1(-/-) cells is likely caused by the loss of TRP-ML1-mediated H(+) leak. Measurement of lipase activity using several substrates revealed a marked reduction in lipid hydrolysis in TRP-ML1(-/-) cells, which was rescued by the expression of TRP-ML1. Cell fractionation indicated specific loss of acidic lipase activity in TRP-ML1(-/-) cells. Furthermore, dissipation of the acidic lysosomal pH of TRP-ML1(-/-) cells by nigericin or chloroquine reversed the lysosomal storage disease phenotype. These findings provide a new mechanism to account for the pathogenesis of MLIV.

  5. NASA Engineering and Safety Center (NESC) Enhanced Melamine (ML) Foam Acoustic Test (NEMFAT)

    NASA Technical Reports Server (NTRS)

    McNelis, Anne M.; Hughes, William O.; McNelis, Mark E.

    2014-01-01

    The NASA Engineering and Safety Center (NESC) funded a proposal to achieve initial basic acoustic characterization of ML (melamine) foam, which could serve as a starting point for a future, more comprehensive acoustic test program for ML foam. A project plan was developed and implemented to obtain acoustic test data for both normal and enhanced ML foam. This project became known as the NESC Enhanced Melamine Foam Acoustic Test (NEMFAT). This document contains the outcome of the NEMFAT project.

  6. Towards a systematic convergence of Multi-Layer (ML) Multi-Configuration Time-Dependent Hartree nuclear wavefunctions: The ML-spawning algorithm

    NASA Astrophysics Data System (ADS)

    Mendive-Tapia, David; Firmino, Thiago; Meyer, Hans-Dieter; Gatti, Fabien

    2017-01-01

    The Multi-Layer (ML) variant of the Multi-Configuration Time-Dependent Hartree (MCTDH) method is a powerful tool for the efficient computation of nuclear quantum dynamics in high-dimensional systems. By providing an optimal choice of layered effective degrees of freedom in form of the so-called ML tree, one is able to reduce the computational cost to an amenable number of configurations. Nevertheless, the fact that one must also make a series of ad hoc decisions often based on intuition or experience at the outset - such as the number of configurations per node and the branching of the ML tree - directly affect the efficiency of the computation and make its use less straightforward than the standard MCTDH method. Therefore, herein we detail a new algorithm for adaptively expanding the size of every node on-the-fly (i.e. spawning) and a derived criterion for the selection of an efficient tree's branching.

  7. ML3: a novel regulator of herbivory-induced responses in Arabidopsis thaliana

    PubMed Central

    Bejai, Sarosh

    2013-01-01

    ML (MD2-related lipid recognition) proteins are known to enhance innate immune responses in mammals. This study reports the analysis of the putative ML gene family in Arabidopsis thaliana and suggests a role for the ML3 gene in herbivory-associated responses in plants. Feeding by larvae of the Lepidopteran generalist herbivore Spodoptera littoralis and larvae of the specialist herbivore Plutella xylostella activated ML3 transcription in leaf tissues. ML3 loss-of-function Arabidopsis plants were compromised in the upregulation of herbivory-induced genes and displayed a semi-dwarf phenotype. Herbivory bioassays showed that larvae of S. littoralis fed on ml3 mutant plants gained more weight compared to larvae fed on wild-type plants while larvae of P. xylostella did not show any significant difference. Virus-induced gene silencing of ML3 expression in plants compromised in jasmonic acid (JA) and salicylic acid (SA) signalling revealed a complex role of ML3 in JA/defence signalling affecting both JA- and SA-dependent responses. The data suggest that ML3 is involved in herbivory-mediated responses in Arabidopsis and that it has a potential role in herbivory-associated molecular pattern recognition. PMID:23314818

  8. ML3: a novel regulator of herbivory-induced responses in Arabidopsis thaliana.

    PubMed

    Fridborg, Ingela; Johansson, Anna; Lagensjö, Johanna; Leelarasamee, Natthanon; Floková, Kristyna; Tarkowská, Danuse; Meijer, Johan; Bejai, Sarosh

    2013-02-01

    ML (MD2-related lipid recognition) proteins are known to enhance innate immune responses in mammals. This study reports the analysis of the putative ML gene family in Arabidopsis thaliana and suggests a role for the ML3 gene in herbivory-associated responses in plants. Feeding by larvae of the Lepidopteran generalist herbivore Spodoptera littoralis and larvae of the specialist herbivore Plutella xylostella activated ML3 transcription in leaf tissues. ML3 loss-of-function Arabidopsis plants were compromised in the upregulation of herbivory-induced genes and displayed a semi-dwarf phenotype. Herbivory bioassays showed that larvae of S. littoralis fed on ml3 mutant plants gained more weight compared to larvae fed on wild-type plants while larvae of P. xylostella did not show any significant difference. Virus-induced gene silencing of ML3 expression in plants compromised in jasmonic acid (JA) and salicylic acid (SA) signalling revealed a complex role of ML3 in JA/defence signalling affecting both JA- and SA-dependent responses. The data suggest that ML3 is involved in herbivory-mediated responses in Arabidopsis and that it has a potential role in herbivory-associated molecular pattern recognition.

  9. Likelihood Estimation for Reduced-Complexity ML Detectors in a MIMO Spatial-Multiplexing System

    NASA Astrophysics Data System (ADS)

    Higashinaka, Masatsugu; Motoyoshi, Katsuyuki; Okazaki, Akihiro; Nagayasu, Takayuki; Kubo, Hiroshi; Shibuya, Akihiro

    This paper proposes a likelihood estimation method for reduced-complexity maximum-likelihood (ML) detectors in a multiple-input multiple-output (MIMO) spatial-multiplexing (SM) system. Reduced-complexity ML detectors, e. g., Sphere Decoder (SD) and QR decomposition (QRD)-M algorithm, are very promising as MIMO detectors because they can estimate the ML or a quasi-ML symbol with very low computational complexity. However, they may lose likelihood information about signal vectors having the opposite bit to the hard decision and bit error rate performance of the reduced-complexity ML detectors are inferior to that of the ML detector when soft-decision decoding is employed. This paper proposes a simple estimation method of the lost likelihood information suitable for the reduced-complexity ML detectors. The proposed likelihood estimation method is applicable to any reduced-complexity ML detectors and produces accurate soft-decision bits. Computer simulation confirms that the proposed method provides excellent decoding performance, keeping the advantage of low computational cost of the reduced-complexity ML detectors.

  10. FastML: a web server for probabilistic reconstruction of ancestral sequences

    PubMed Central

    Ashkenazy, Haim; Penn, Osnat; Doron-Faigenboim, Adi; Cohen, Ofir; Cannarozzi, Gina; Zomer, Oren; Pupko, Tal

    2012-01-01

    Ancestral sequence reconstruction is essential to a variety of evolutionary studies. Here, we present the FastML web server, a user-friendly tool for the reconstruction of ancestral sequences. FastML implements various novel features that differentiate it from existing tools: (i) FastML uses an indel-coding method, in which each gap, possibly spanning multiples sites, is coded as binary data. FastML then reconstructs ancestral indel states assuming a continuous time Markov process. FastML provides the most likely ancestral sequences, integrating both indels and characters; (ii) FastML accounts for uncertainty in ancestral states: it provides not only the posterior probabilities for each character and indel at each sequence position, but also a sample of ancestral sequences from this posterior distribution, and a list of the k-most likely ancestral sequences; (iii) FastML implements a large array of evolutionary models, which makes it generic and applicable for nucleotide, protein and codon sequences; and (iv) a graphical representation of the results is provided, including, for example, a graphical logo of the inferred ancestral sequences. The utility of FastML is demonstrated by reconstructing ancestral sequences of the Env protein from various HIV-1 subtypes. FastML is freely available for all academic users and is available online at http://fastml.tau.ac.il/. PMID:22661579

  11. The effectiveness of a pyriprole (125 mg/ml) and a metaflumizone (150 mg/ml) combined with amitraz (150 mg/ml) spot-on treatment in preventing Phlebotomus perniciosus from feeding on dogs.

    PubMed

    Thomas, C; Roques, M; Franc, M

    2008-03-01

    A controlled clinical trial was performed to assess the effectiveness of a pyriprole (125 mg/ml) and a metaflumizone (150 mg/ml) combined with amitraz (150 mg/ml) spot-on treatment (recommended dosage) in preventing adult female sandflies (Phlebotomus perniciosus) from feeding on dogs. Sandfly mortality was also assessed. Twelve beagle dogs were used in the study. Prior to treatment they were checked for their attractiveness to sandflies, ranked accordingly to generate partner triplets of equivalent sensitivity to sandflies: four control dogs, four treated with the pyriprole and four with the metaflumizone spot-on. The dogs were challenged with 50 unfed adult female sandflies (8-10 days old), in cages for one hour on Day 1 and Day 7. The sandflies were checked for blood feeding and mortality at one hour, 24 hours and 48 hours after exposure to the dogs. A very poor anti-feeding effect (near 7%) was seen on sandflies with the metaflumizone combined with amitraz and no antifeeding effect was seen with pyriprole. The sandfly mortality effect as a result of exposure to treated dogs was under 20% for the two spot-on. The two formulations could not be proposed in a leishmaniosis prevention program.

  12. The performance review of EEWS(Earthquake Early Warning System) about Gyeongju earthquakes with Ml 5.1 and Ml 5.8 in Korea

    NASA Astrophysics Data System (ADS)

    Park, Jung-Ho; Chi, Heon-Cheol; Lim, In-Seub; Seong, Yun-Jeong; Park, Jihwan

    2017-04-01

    EEW(Earthquake Early Warning) service to the public has been officially operated by KMA (Korea Meteorological Administration) from 2015 in Korea. For the KMA's official EEW service, KIGAM has adopted ElarmS from UC Berkeley BSL and modified local magnitude relation, 1-D travel time curves and association procedures with real time waveform from about 201 seismic stations of KMA, KIGAM, KINS and KEPRI. There were two moderate size earthquakes with magnitude Ml 5.1 and Ml 5.8 close to Gyeongju city located at the southeastern part of Korea on Sep. 12. 2016. We have checked the performance of EEWS(Earthquake Early Warning System) named as TrigDB by KIGAM reviewing of these two Gyeongju earthquakes. The nearest station to epicenters of two earthquakes Ml 5.1(35.7697 N, 129.1904 E) and Ml 5.8(35.7632 N, 129.1898 E) was MKL which detected P phases in about 2.1 and 3.6 seconds after the origin times respectively. The first events were issued in 6.3 and 7.0 seconds from each origin time. Because of the unstable results on the early steps due to very few stations and unexpected automated analysis, KMA has the policy to wait for more 20 seconds for confirming the reliability. For these events KMA published EEW alarms in about 26 seconds after origin times with M 5.3 and M 5.9 respectively.

  13. jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.

    PubMed

    Reisinger, Florian; Krishna, Ritesh; Ghali, Fawaz; Ríos, Daniel; Hermjakob, Henning; Vizcaíno, Juan Antonio; Jones, Andrew R

    2012-03-01

    We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Position systématique de Nupharanassa bohemica Mlíkovsky, 1999

    NASA Astrophysics Data System (ADS)

    Mourer-Chauviré, Cécile

    1999-07-01

    The species Nupharanassa bohemica Mlíkovsky, 1999, described as a Jacanidae (Aves: Charadriiformes) is very different from the recent and fossil Jacanidae and corresponds to a Coraciidae (Aves: Coraciiformes). It is here placed in the extinct genus Geranopterus and becomes Geranopterus bohemicus ( Mlíkovsky, 1999).

  15. Near-ML detection for MDL-impaired few-mode fiber transmission.

    PubMed

    Lobato, Adriana; Rabe, Johannes; Ferreira, Filipe; Kuschnerov, Maxim; Spinnler, Bernhard; Lankl, Berthold

    2015-04-20

    Few-mode fiber transmission systems are typically impaired by mode-dependent loss (MDL). In an MDL-impaired link, maximum-likelihood (ML) detection yields a significant advantage in system performance compared to linear equalizers, such as zero-forcing and minimum-mean square error equalizers. However, the computational effort of the ML detection increases exponentially with the number of modes and the cardinality of the constellation. We present two methods that allow for near-ML performance without being afflicted with the enormous computational complexity of ML detection: improved reduced-search ML detection and sphere decoding. Both algorithms are tested regarding their performance and computational complexity in simulations of three and six spatial modes with QPSK and 16QAM constellations.

  16. Polymorphic New World monkeys with more than three M/L cone types

    NASA Astrophysics Data System (ADS)

    Jacobs, Gerald H.; Deegan, Jess F.

    2005-10-01

    Most New World (platyrrhine) monkeys have M/L cone photopigment polymorphisms that map directly into individual variations in visual sensitivity and color vision. We used electroretinogram flicker photometry to examine M/L cone photopigments in the New World monkey Callicebus moloch (the dusky Titi). Like other New World monkeys, this species has an M/L cone photopigment polymorphism that reflects the presence of X-chromosome opsin gene alleles. However, unlike other platyrrhines in which three M/L photopigments are typical, Callicebus has a total of five M/L cone photopigments. The peak sensitivity values for these pigments extend across the range from 530 to 562 nm. The result is an enhanced array of potential color vision phenotypes in this species.

  17. More Effective Distributed ML via a Stale Synchronous Parallel Parameter Server

    PubMed Central

    Ho, Qirong; Cipar, James; Cui, Henggang; Kim, Jin Kyu; Lee, Seunghak; Gibbons, Phillip B.; Gibson, Garth A.; Ganger, Gregory R.; Xing, Eric P.

    2014-01-01

    We propose a parameter server system for distributed ML, which follows a Stale Synchronous Parallel (SSP) model of computation that maximizes the time computational workers spend doing useful work on ML algorithms, while still providing correctness guarantees. The parameter server provides an easy-to-use shared interface for read/write access to an ML model’s values (parameters and variables), and the SSP model allows distributed workers to read older, stale versions of these values from a local cache, instead of waiting to get them from a central storage. This significantly increases the proportion of time workers spend computing, as opposed to waiting. Furthermore, the SSP model ensures ML algorithm correctness by limiting the maximum age of the stale values. We provide a proof of correctness under SSP, as well as empirical results demonstrating that the SSP model achieves faster algorithm convergence on several different ML problems, compared to fully-synchronous and asynchronous schemes. PMID:25400488

  18. Are portable bladder scanning and real-time ultrasound accurate measures of bladder volume in postnatal women?

    PubMed

    Mathew, S; Horne, A W; Murray, L S; Tydeman, G; McKinley, C A

    2007-08-01

    Real-time ultrasound and portable bladder scanners are commonly used instead of catheterisation to determine bladder volumes in postnatal women but it is not known whether these are accurate. Change in bladder volumes measured by ultrasound and portable scanners were compared with actual voided volume (VV) in 100 postnatal women. The VV was on average 41 ml (CI 29 - 54 ml) higher than that measured by ultrasound, and 33 ml (CI 17 - 48 ml) higher than that measured by portable scanners. Portable scanner volumes were 9 ml (CI -8 - 26 ml) higher than those measured by ultrasound. Neither method is an accurate tool for detecting bladder volume in postnatal women.

  19. Image-Guided Ultrasound Characterization of Volatile Sub-Micron Phase-Shift Droplets in the 20-40 MHz Frequency Range.

    PubMed

    Sheeran, Paul S; Daghighi, Yasaman; Yoo, Kimoon; Williams, Ross; Cherin, Emmanuel; Foster, F Stuart; Burns, Peter N

    2016-03-01

    Phase-shift perfluorocarbon droplets are designed to convert from the liquid to the gas state by the external application of acoustic or optical energy. Although droplet vaporization has been investigated extensively at ultrasonic frequencies between 1 and 10 MHz, few studies have characterized performance at the higher frequencies commonly used in small animal imaging. In this study, we use standard B-mode imaging sequences on a pre-clinical ultrasound platform to both image and activate sub-micron decafluorobutane droplet populations in vitro and in vivo at center frequencies in the range of 20-40 MHz. Results show that droplets remain stable against vaporization at low imaging pressures but are vaporized at peak negative pressures near 3.5 MPa at the three frequencies tested. This study also found that a small number of size outliers present in the distribution can greatly influence droplet performance. Removal of these outliers results in a more accurate assessment of the vaporization threshold and produces free-flowing microbubbles upon vaporization in the mouse kidney.

  20. ML3 Is a NEDD8- and Ubiquitin-Modified Protein1[C][W][OPEN

    PubMed Central

    Hakenjos, Jana P.; Bejai, Sarosh; Ranftl, Quirin; Behringer, Carina; Vlot, A. Corina; Absmanner, Birgit; Hammes, Ulrich; Heinzlmeir, Stephanie; Kuster, Bernhard; Schwechheimer, Claus

    2013-01-01

    NEDD8 (NEURAL PRECURSOR CELL-EXPRESSED, DEVELOPMENTALLY DOWN-REGULATED PROTEIN8) is an evolutionarily conserved 8-kD protein that is closely related to ubiquitin and that can be conjugated like ubiquitin to specific lysine residues of target proteins in eukaryotes. In contrast to ubiquitin, for which a broad range of substrate proteins are known, only a very limited number of NEDD8 target proteins have been identified to date. Best understood, and also evolutionarily conserved, is the NEDD8 modification (neddylation) of cullins, core subunits of the cullin-RING-type E3 ubiquitin ligases that promote the polyubiquitylation of degradation targets in eukaryotes. Here, we show that Myeloid differentiation factor-2-related lipid-recognition domain protein ML3 is an NEDD8- as well as ubiquitin-modified protein in Arabidopsis (Arabidopsis thaliana) and examine the functional role of ML3 in the plant cell. Our analysis indicates that ML3 resides in the vacuole as well as in endoplasmic reticulum (ER) bodies. ER bodies are Brassicales-specific ER-derived organelles and, similar to other ER body proteins, ML3 orthologs can only be identified in this order of flowering plants. ML3 gene expression is promoted by wounding as well as by the phytohormone jasmonic acid and repressed by ethylene, signals that are known to induce and repress ER body formation, respectively. Furthermore, ML3 protein abundance is dependent on NAI1, a master regulator of ER body formation in Arabidopsis. The regulation of ML3 expression and the localization of ML3 in ER bodies and the vacuole is in agreement with a demonstrated importance of ML3 in the defense to herbivore attack. Here, we extend the spectrum of ML3 biological functions by demonstrating a role in the response to microbial pathogens. PMID:23903439

  1. RiverML: Standardizing the Communication of River Model Data (Invited)

    NASA Astrophysics Data System (ADS)

    Jackson, S.; Maidment, D. R.; Arctur, D. K.

    2013-12-01

    RiverML is a proposed language for conveying a description of river channel and floodplain geometry and flow characteristics through the internet in a standardized way. A key goal of the RiverML project is to allow interoperability between all hydraulic and hydrologic models, whether they are industry standard software packages or custom-built research tools. By providing a common transfer format for common model inputs and outputs, RiverML can shorten the development time and enhance the immediate utility of innovative river modeling tools. RiverML will provide descriptions of cross sections and multiple flow lines, allowing the construction of wireframe representations. In addition, RiverML will support descriptions of network connectivity, properties such as roughness coefficients, and time series observations such as water surface elevation and flow rate. The language is constructed in a modular fashion such that the geometry information, network information, and time series observations can be communicated independently of each other, allowing an arbitrary suite of software packages to contribute to a coherently modeled scenario. Funding for the development of RiverML is provided through an NSF grant to CUAHSI HydroShare project, a web-based collaborative environment for sharing data & models. While RiverML is geared toward the transfer of data, HydroShare will serve as a repository for storing water-related data and models of any format, while providing enhanced functionality for standardized formats such as RiverML, WaterML, and shapefiles. RiverML is a joint effort between the CUAHSI HydroShare development team, the Open Geospatial Consortium (OGC) Hydrology Domain Working Group, and an international community of data providers, data users, and software developers.

  2. ML3 is a NEDD8- and ubiquitin-modified protein.

    PubMed

    Hakenjos, Jana P; Bejai, Sarosh; Ranftl, Quirin; Behringer, Carina; Vlot, A Corina; Absmanner, Birgit; Hammes, Ulrich; Heinzlmeir, Stephanie; Kuster, Bernhard; Schwechheimer, Claus

    2013-09-01

    NEDD8 (NEURAL PRECURSOR CELL-EXPRESSED, DEVELOPMENTALLY DOWN-REGULATED PROTEIN8) is an evolutionarily conserved 8-kD protein that is closely related to ubiquitin and that can be conjugated like ubiquitin to specific lysine residues of target proteins in eukaryotes. In contrast to ubiquitin, for which a broad range of substrate proteins are known, only a very limited number of NEDD8 target proteins have been identified to date. Best understood, and also evolutionarily conserved, is the NEDD8 modification (neddylation) of cullins, core subunits of the cullin-RING-type E3 ubiquitin ligases that promote the polyubiquitylation of degradation targets in eukaryotes. Here, we show that Myeloid differentiation factor-2-related lipid-recognition domain protein ML3 is an NEDD8- as well as ubiquitin-modified protein in Arabidopsis (Arabidopsis thaliana) and examine the functional role of ML3 in the plant cell. Our analysis indicates that ML3 resides in the vacuole as well as in endoplasmic reticulum (ER) bodies. ER bodies are Brassicales-specific ER-derived organelles and, similar to other ER body proteins, ML3 orthologs can only be identified in this order of flowering plants. ML3 gene expression is promoted by wounding as well as by the phytohormone jasmonic acid and repressed by ethylene, signals that are known to induce and repress ER body formation, respectively. Furthermore, ML3 protein abundance is dependent on NAI1, a master regulator of ER body formation in Arabidopsis. The regulation of ML3 expression and the localization of ML3 in ER bodies and the vacuole is in agreement with a demonstrated importance of ML3 in the defense to herbivore attack. Here, we extend the spectrum of ML3 biological functions by demonstrating a role in the response to microbial pathogens.

  3. [Thulium vapoenucleation of prostates larger than 80 ml using a 1.9-µm and a 2-µm thulium laser. Early perioperative results from two centres].

    PubMed

    Netsch, C; Knoll, T; Gross, A J; Wendt-Nordahl, G

    2015-10-01

    Numerous studies have shown that thulium vapoenucleation of the prostate (ThuVEP) is a size-independent minimally invasive procedure for the treatment of benign prostatic enlargement. All ThuVEP series have been performed with a 2-µm thulium laser device so far. The aim of this study was to evaluate the complications and early postoperative results of two thulium-devices with different wavelengths for ThuVEP in prostates larger than 80 ml. A retrospective bi-centric matched-paired analysis with 296 patients was performed. Based on prostate size, 148 were matched at each centre and laser device, respectively. A 2-µm (RevoLix, LISA Laser products, Katlenburg, Germany n=148) and a 1.9-µm (vela XL, starmedtec, Starnberg, Germany, n=148) thulium laser with a power output of 90 and 80 W was used. Patients' data were assessed and compared. The median prostate volume (interquartile) was 100 ml (range 86.25-120 ml). At discharge, Qmax (preoperative 7.9 and 9 ml/s vs. postoperative 19.35 and 16.2 ml/s) and postvoiding-residual urine (preoperative 130 and 45 ml vs. postoperative 20 and 25 ml) were significantly improved after 2-µm and 1.9-µm ThuVEP (p<0.001). The median catheterization time and hospitalization times were 2 and 4 days in both groups. Perioperative complications occurred in 89 patients (30.1%): Clavien 1 (12.2%), Clavien 2 (9.1%), Clavien 3a (0.7%), Clavien 3b (7.1%), and Clavien 4a (1%). Regarding the occurrence of complications, there were no differences between the two thulium devices. ThuVEP represents a safe and effective treatment for prostates larger than 80 ml. Both thulium laser devices give satisfactory immediate micturition improvement with low perioperative morbidity.

  4. Lung volumes in giraffes, Giraffa camelopardalis.

    PubMed

    Mitchell, G; Skinner, J D

    2011-01-01

    We have measured lung mass and trachea dimensions in 46 giraffes of both genders ranging in body mass from 147 kg to 1441 kg, calculated static and dynamic lung volumes, and developed allometric equations that relate changes in them to growth. We found that relative lung mass is 0.6±0.2% of body mass which is significantly less than it is in other mammals (1.1±0.1%). Total lung volume is significantly smaller (46.2±5.9 mL kg⁻¹) than in similar sized mammals (75.0±2.1 mL kg⁻¹). The lung volume:body mass ratio decreases during growth rather than increase as it does in other mammals. Tracheal diameter is significantly narrower than in similar sized mammals but dead space volume (2.9±0.5 mL kg⁻¹) is larger than in similar sized mammals (2.4±0.1 mL kg⁻¹). Our calculations suggest that tidal volume (10.5±0.2 mL kg⁻¹) is increased compared to that in other mammals(10.0±0.2 mL kg⁻¹) so that the dead space:tidal volume ratio is the same as in other mammals. Calculated Functional Residual Capacity is smaller than predicted (53.4±3.5 vs 33.7±0.6 mL kg⁻¹) as is Expiratory Reserve Volume (47.4±2.6 vs 27.2±1.0 mL kg⁻¹, but Residual Volume (6.0±0.4 mL kg⁻¹) is the same as in other similar sized mammals (6.0±0.9 mL kg⁻¹. Our calculations suggest that Inspiratory Reserve Volume is significantly reduced in size (11.6±1.6 vs 3.8±2.4 mL kg⁻¹), and, if so, the capacity to increase tidal volume is limited. Calculated dynamic lung volumes were the same as in similar sized mammals. We have concluded that giraffe morphology has resulted in lung volumes that are significantly different to that of similar sized mammals, but these changes do not compromise ventilatory capacity.

  5. Evaluation of Lassa virus vaccine immunogenicity in a CBA/J-ML29 mouse model.

    PubMed

    Goicochea, Marco A; Zapata, Juan C; Bryant, Joseph; Davis, Harry; Salvato, Maria S; Lukashevich, Igor S

    2012-02-14

    Lassa fever (LF) is one of the most prevalent viral hemorrhagic fevers in West Africa responsible for thousands of deaths annually. The BSL-4 containment requirement and lack of small animal model to evaluate Lassa virus (LASV)-specific cell-mediated immunity (CMI) complicate development of effective LF vaccines. Here we have described a CBA/J-ML29 model allowing evaluation of LASV-specific CMI responses in mice. This model is based on Mopeia virus reassortant clone ML29, an attractive immunogenic surrogate for LASV. A single intraperitoneal (i.p.) immunization of CBA/J mice with ML29 protected animals against a lethal homologous intracerebral (i.c.) challenge with 588 LD(50). The ML29-immunized mice displayed negligible levels of LASV-specific antibody titers, but LASV-specific CMI responses were detectable early and peaked on day 8-10 after immunization. A T cell cytotoxicity assay in vivo showed a correlation between LASV-specific cytotoxicity and the timing of protection induced by the ML29 immunization. Notably, CBA/J mice that received CD8+ T cell-depleted splenocytes from ML29-immunized donors all succumbed to a lethal i.c. challenge, demonstrating that CD8+ T cells are critical in protection. The CBA/J-ML29 model can be useful immunological tool for the preliminary evaluation of immunogenicity and efficacy of vaccine candidates against LASV outside of BSL-4 containment facilities.

  6. The abstract geometry modeling language (AgML): experience and road map toward eRHIC

    NASA Astrophysics Data System (ADS)

    Webb, Jason; Lauret, Jerome; Perevoztchikov, Victor

    2014-06-01

    The STAR experiment has adopted an Abstract Geometry Modeling Language (AgML) as the primary description of our geometry model. AgML establishes a level of abstraction, decoupling the definition of the detector from the software libraries used to create the concrete geometry model. Thus, AgML allows us to support both our legacy GEANT 3 simulation application and our ROOT/TGeo based reconstruction software from a single source, which is demonstrably self- consistent. While AgML was developed primarily as a tool to migrate away from our legacy FORTRAN-era geometry codes, it also provides a rich syntax geared towards the rapid development of detector models. AgML has been successfully employed by users to quickly develop and integrate the descriptions of several new detectors in the RHIC/STAR experiment including the Forward GEM Tracker (FGT) and Heavy Flavor Tracker (HFT) upgrades installed in STAR for the 2012 and 2013 runs. AgML has furthermore been heavily utilized to study future upgrades to the STAR detector as it prepares for the eRHIC era. With its track record of practical use in a live experiment in mind, we present the status, lessons learned and future of the AgML language as well as our experience in bringing the code into our production and development environments. We will discuss the path toward eRHIC and pushing the current model to accommodate for detector miss-alignment and high precision physics.

  7. qcML: an exchange format for quality control metrics from mass spectrometry experiments.

    PubMed

    Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W P; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A; Kelstrup, Christian D; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S; Olsen, Jesper V; Heck, Albert J R; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

    2014-08-01

    Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml.

  8. qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments*

    PubMed Central

    Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W. P.; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A.; Kelstrup, Christian D.; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S.; Olsen, Jesper V.; Heck, Albert J. R.; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

    2014-01-01

    Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml. PMID:24760958

  9. Generation of Large Numbers of Antigen-Expressing Human Dendritic Cells Using CD14-ML Technology

    PubMed Central

    Imamura, Yuya; Haruta, Miwa; Tomita, Yusuke; Matsumura, Keiko; Ikeda, Tokunori; Yuno, Akira; Hirayama, Masatoshi; Nakayama, Hideki; Mizuta, Hiroshi; Nishimura, Yasuharu; Senju, Satoru

    2016-01-01

    We previously reported a method to expand human monocytes through lentivirus-mediated introduction of cMYC and BMI1, and we named the monocyte-derived proliferating cells, CD14-ML. CD14-ML differentiated into functional DC (CD14-ML-DC) upon addition of IL-4, resulting in the generation of a large number of DC. One drawback of this method was the extensive donor-dependent variation in proliferation efficiency. In the current study, we found that introduction of BCL2 or LYL1 along with cMYC and BMI1 was beneficial. Using the improved method, we obtained CD14-ML from all samples, regardless of whether the donors were healthy individuals or cancer patients. In vitro stimulation of peripheral blood T cells with CD14-ML-DC that were loaded with cancer antigen-derived peptides led to the establishment of CD4+ and CD8+ T cell lines that recognized the peptides. Since CD14-ML was propagated for more than 1 month, we could readily conduct genetic modification experiments. To generate CD14-ML-DC that expressed antigenic proteins, we introduced lentiviral antigen-expression vectors and subjected the cells to 2 weeks of culture for drug-selection and expansion. The resulting antigen-expressing CD14-ML-DC successfully induced CD8+ T cell lines that were reactive to CMVpp65 or MART1/MelanA, suggesting an application in vaccination therapy. Thus, this improved method enables the generation of a sufficient number of DC for vaccination therapy from a small amount of peripheral blood from cancer patients. Information on T cell epitopes is not necessary in vaccination with cancer antigen-expressing CD14-ML-DC; therefore, all patients, irrespective of HLA type, will benefit from anti-cancer therapy based on this technology. PMID:27050553

  10. Generation of Large Numbers of Antigen-Expressing Human Dendritic Cells Using CD14-ML Technology.

    PubMed

    Imamura, Yuya; Haruta, Miwa; Tomita, Yusuke; Matsumura, Keiko; Ikeda, Tokunori; Yuno, Akira; Hirayama, Masatoshi; Nakayama, Hideki; Mizuta, Hiroshi; Nishimura, Yasuharu; Senju, Satoru

    2016-01-01

    We previously reported a method to expand human monocytes through lentivirus-mediated introduction of cMYC and BMI1, and we named the monocyte-derived proliferating cells, CD14-ML. CD14-ML differentiated into functional DC (CD14-ML-DC) upon addition of IL-4, resulting in the generation of a large number of DC. One drawback of this method was the extensive donor-dependent variation in proliferation efficiency. In the current study, we found that introduction of BCL2 or LYL1 along with cMYC and BMI1 was beneficial. Using the improved method, we obtained CD14-ML from all samples, regardless of whether the donors were healthy individuals or cancer patients. In vitro stimulation of peripheral blood T cells with CD14-ML-DC that were loaded with cancer antigen-derived peptides led to the establishment of CD4+ and CD8+ T cell lines that recognized the peptides. Since CD14-ML was propagated for more than 1 month, we could readily conduct genetic modification experiments. To generate CD14-ML-DC that expressed antigenic proteins, we introduced lentiviral antigen-expression vectors and subjected the cells to 2 weeks of culture for drug-selection and expansion. The resulting antigen-expressing CD14-ML-DC successfully induced CD8+ T cell lines that were reactive to CMVpp65 or MART1/MelanA, suggesting an application in vaccination therapy. Thus, this improved method enables the generation of a sufficient number of DC for vaccination therapy from a small amount of peripheral blood from cancer patients. Information on T cell epitopes is not necessary in vaccination with cancer antigen-expressing CD14-ML-DC; therefore, all patients, irrespective of HLA type, will benefit from anti-cancer therapy based on this technology.

  11. cluML: A markup language for clustering and cluster validity assessment of microarray data.

    PubMed

    Bolshakova, Nadia; Cunningham, Pádraig

    2005-01-01

    cluML is a new markup language for microarray data clustering and cluster validity assessment. The XML-based format has been designed to address some of the limitations observed in traditional formats, such as inability to store multiple clustering (including biclustering) and validation results within a dataset. cluML is an effective tool to support biomedical knowledge representation in gene expression data analysis. Although cluML was developed for DNA microarray analysis applications, it can be effectively used for the representation of clustering and for the validation of other biomedical and physical data that has no limitations.

  12. SSA’s Journey to SW-CMM ML3 and Transition to CMMI

    DTIC Science & Technology

    2005-01-01

    Patent & Trademark Office. SSA’s Journey to SW-CMM® ML3 and Transition to CMMI® Rick Barbour, SEI Jon Gross, SEI Rod Waltersdorff, Social Security...SSA’s Journey to SW-CMM ML3 and Transition to CMMI 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER...interfaces provided focus in SSA Office of Systems Electronic Services (OSES) and SW- CMM ML3 2004- December Gap analysis demonstrated SSA Office of

  13. Rare A2ML1 variants confer susceptibility to otitis media

    PubMed Central

    Santos-Cortez, Regie Lyn P.; Chiong, Charlotte M.; Reyes-Quintos, Ma. Rina T.; Tantoco, Ma. Leah C.; Wang, Xin; Acharya, Anushree; Abbe, Izoduwa; Giese, Arnaud P.; Smith, Joshua D.; Allen, E. Kaitlynn; Li, Biao; Cutiongco-de la Paz, Eva Maria; Garcia, Marieflor Cristy; Llanes, Erasmo Gonzalo D.V.; Labra, Patrick John; Gloria-Cruz, Teresa Luisa I.; Chan, Abner L.; Wang, Gao T.; Daly, Kathleen A.; Shendure, Jay; Bamshad, Michael J.; Nickerson, Deborah A.; Patel, Janak A.; Riazuddin, Saima; Sale, Michele M.; Chonmaitree, Tasnee; Ahmed, Zubair M.; Abes, Generoso T.; Leal, Suzanne M.

    2015-01-01

    A duplication variant within middle-ear-specific gene A2ML1 co-segregates with otitis media in an indigenous Filipino pedigree (LOD score=7.5 at reduced penetrance) and lies within a founder haplotype that is also shared by three otitis-prone European- and Hispanic-American children, but is absent in non-otitis-prone children and >62,000 next-generation sequences. Seven additional A2ML1 variants were identified in six otitis-prone children. Collectively our studies support a role for A2ML1 in the pathophysiology of otitis media. PMID:26121085

  14. Rare A2ML1 variants confer susceptibility to otitis media.

    PubMed

    Santos-Cortez, Regie Lyn P; Chiong, Charlotte M; Reyes-Quintos, Ma Rina T; Tantoco, Ma Leah C; Wang, Xin; Acharya, Anushree; Abbe, Izoduwa; Giese, Arnaud P; Smith, Joshua D; Allen, E Kaitlynn; Li, Biao; Cutiongco-de la Paz, Eva Maria; Garcia, Marieflor Cristy; Llanes, Erasmo Gonzalo D V; Labra, Patrick John; Gloria-Cruz, Teresa Luisa I; Chan, Abner L; Wang, Gao T; Daly, Kathleen A; Shendure, Jay; Bamshad, Michael J; Nickerson, Deborah A; Patel, Janak A; Riazuddin, Saima; Sale, Michele M; Chonmaitree, Tasnee; Ahmed, Zubair M; Abes, Generoso T; Leal, Suzanne M

    2015-08-01

    A duplication variant within the middle ear-specific gene A2ML1 cosegregates with otitis media in an indigenous Filipino pedigree (LOD score = 7.5 at reduced penetrance) and lies within a founder haplotype that is also shared by 3 otitis-prone European-American and Hispanic-American children but is absent in non-otitis-prone children and >62,000 next-generation sequences. We identified seven additional A2ML1 variants in six otitis-prone children. Collectively, our studies support a role for A2ML1 in the pathophysiology of otitis media.

  15. Validation of a SysML based design for wireless sensor networks

    NASA Astrophysics Data System (ADS)

    Berrachedi, Amel; Rahim, Messaoud; Ioualalen, Malika; Hammad, Ahmed

    2017-07-01

    When developing complex systems, the requirement for the verification of the systems' design is one of the main challenges. Wireless Sensor Networks (WSNs) are examples of such systems. We address the problem of how WSNs must be designed to fulfil the system requirements. Using the SysML Language, we propose a Model Based System Engineering (MBSE) specification and verification methodology for designing WSNs. This methodology uses SysML to describe the WSNs requirements, structure and behaviour. Then, it translates the SysML elements to an analytic model, specifically, to a Deterministic Stochastic Petri Net. The proposed approach allows to design WSNs and study their behaviors and their energy performances.

  16. Comparison of actual tidal volume in neonatal lung model volume control ventilation using three ventilators.

    PubMed

    Toyama, H; Endo, Y; Ejima, Y; Matsubara, M; Kurosawa, S

    2011-07-01

    In neonates, small changes in tidal volumes (V(T)) may lead to complications. Previous studies have shown a significant difference between ventilator-measured tidal volume and tidal volume delivered (actual V(T)). We evaluated the accuracy of three different ventilators to deliver small V(T) during volume-controlled ventilation. We tested Servo 300, 840 ventilator and Evita 4 Neoflow ventilators with lung models simulating normal and injured neonatal lung compliance models. Gas volume delivered from the ventilator into the test circuit (V(TV)) and actual V(T) to the test lung were measured using Ventrak respiration monitors at set V(T) (30 ml). The gas volume increase of the breathing circuit was then calculated. Tidal volumes of the SV300 and PB840 in both lung models were similar to the set V(T) and the actual tidal volumes in the injured model (20.7 ml and 19.8 ml, respectively) were significantly less than that in the normal model (27.4 ml and 23.4 ml). PB840 with circuit compliance compensation could not improve the actual V(T). V(TV) of the EV4N in the normal and the injured models (37.8 ml and 46.6 ml) were markedly increased compared with set V(T), and actual V(T) were similar to set V(T) in the normal and injured model (30.2 ml and 31.9 ml, respectively). EV4N measuring V(T) close to the lung could match actual V(T) to almost the same value as the set V(T) however the gas volume of the breathing circuit was increased. If an accurate value for the patient's actual V(T) is needed, this V(T) must be measured by a sensor located between the Y-piece and the tracheal tube.

  17. The clinical application of the 100mL water swallow test in head and neck cancer.

    PubMed

    Patterson, Joanne M; Hildreth, Anthony; McColl, Elaine; Carding, Paul N; Hamilton, David; Wilson, Janet A

    2011-03-01

    Water swallow tests have been used as to screen patients with neurological dysphagia who are at risk of aspiration. This study examines the clinical utility of the 100mL water swallow test (WST) in head and neck cancer, by measuring its sensitivity and specificity for identifying aspiration and for monitoring swallow performance up to one year following (chemo)radiotherapy. Patients referred for (chemo)radiotherapy were assessed on the WST (n=173) pre-treatment and 3, 6 and 12months post-treatment. Patients failed the test if they coughed or had a wet voice quality post swallow or were unable to finish the task. A Flexible Endoscopic Evaluation of Swallowing was conducted at the same time points, to test for the presence of aspiration. The WST was timed and the number of swallows required was recorded. Sensitivity of the WST for predicting aspiration was >67%, specificity >46%. There was marked deterioration from pre- to 3months post-treatment for the time taken to drink 100mL (p=0.005), but this improved over the first year (p=0.001). Disease characteristics, patient demographics, radiotherapy dose, or treatment volume were not predictors of this improvement. The 100mL WST is a quick and simple assessment for identifying patients with aspiration, post (chemo)radiotherapy. This test is a useful adjunct to a clinical examination, helping to highlight patients who require an instrumental assessment such as videofluoroscopy. Furthermore, quantitative measures can be derived from this test, which can be used as a measure of swallow performance over time. Copyright © 2010 Elsevier Ltd. All rights reserved.

  18. [Levobupivacaine for Ultrasound-guided Interscalene Block: Block with 6 ml Leads to Less Occurrence of Respiratory Depression and Hemidiaphragmatic Paralysis].

    PubMed

    Nakamura, Taketo; Miyamoto, Shinnosuke; Aishin, Keikoh; Hashimoto, Megumi

    2015-07-01

    Interscalene brachial plexus block (ISBPB) complications depend usually on the dose administered. The object of this study was to determine whether ultrasound-guided ISBPB with 6 ml of 0.5% levobupivacaine would reduce occurrence of respiratory depression and hemidiaphragmatic paralysis. Patients undergoing arthroscopic shoulder surgery under nerve block with general anesthesia (n = 20) were recruited. There were no differences between pre and post operative respiratory function (forced expiratory volume 1.0 (sec) % and vital capacity). Hemidiaphragmatic paralysis on postoperative ultrasonography was found in two patients. The use of low-volume ultrasound-guided ISBPB is associated with less respiratory depression and hemidiaphragmatic paralysis.

  19. 116. CENTRAL CONTROL STATION ELEVATIONS & SECTIONS (ML870/1FS) October ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    116. CENTRAL CONTROL STATION - ELEVATIONS & SECTIONS (ML-8-70/1-FS) October 1933 - Upper Mississippi River 9-Foot Channel, Lock & Dam No. 8, On Mississippi River near Houston County, MN, Genoa, Vernon County, WI

  20. Executing medical logic modules expressed in ArdenML using Drools.

    PubMed

    Jung, Chai Young; Sward, Katherine A; Haug, Peter J

    2012-01-01

    The Arden Syntax is an HL7 standard language for representing medical knowledge as logic statements. Despite nearly 2 decades of availability, Arden Syntax has not been widely used. This has been attributed to the lack of a generally available compiler to implement the logic, to Arden's complex syntax, to the challenges of mapping local data to data references in the Medical Logic Modules (MLMs), or, more globally, to the general absence of decision support in healthcare computing. An XML representation (ArdenML) may partially address the technical challenges. MLMs created in ArdenML can be converted into executable files using standard transforms written in the Extensible Stylesheet Language Transformation (XSLT) language. As an example, we have demonstrated an approach to executing MLMs written in ArdenML using the Drools business rule management system. Extensions to ArdenML make it possible to generate a user interface through which an MLM developer can test for logical errors.

  1. 95. ARAIV. Aerial view of ML1. Shows test and control ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    95. ARA-IV. Aerial view of ML-1. Shows test and control buildings, berms, fencing. March 14, 1963. Ineel photo no. 63-1666. - Idaho National Engineering Laboratory, Army Reactors Experimental Area, Scoville, Butte County, ID

  2. SED-ED, a workflow editor for computational biology experiments written in SED-ML.

    PubMed

    Adams, Richard R

    2012-04-15

    The simulation experiment description markup language (SED-ML) is a new community data standard to encode computational biology experiments in a computer-readable XML format. Its widespread adoption will require the development of software support to work with SED-ML files. Here, we describe a software tool, SED-ED, to view, edit, validate and annotate SED-ML documents while shielding end-users from the underlying XML representation. SED-ED supports modellers who wish to create, understand and further develop a simulation description provided in SED-ML format. SED-ED is available as a standalone Java application, as an Eclipse plug-in and as an SBSI (www.sbsi.ed.ac.uk) plug-in, all under an MIT open-source license. Source code is at https://sed-ed-sedmleditor.googlecode.com/svn. The application itself is available from https://sourceforge.net/projects/jlibsedml/files/SED-ED/.

  3. 98. ARAIII. ML1 reactor pressure vessel is lowered into reactor ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    98. ARA-III. ML-1 reactor pressure vessel is lowered into reactor pit by hoist. July 13, 1963. Ineel photo no. 63-4049. Photographer: Lowin. - Idaho National Engineering Laboratory, Army Reactors Experimental Area, Scoville, Butte County, ID

  4. Using CellML with OpenCMISS to Simulate Multi-Scale Physiology

    PubMed Central

    Nickerson, David P.; Ladd, David; Hussan, Jagir R.; Safaei, Soroush; Suresh, Vinod; Hunter, Peter J.; Bradley, Christopher P.

    2014-01-01

    OpenCMISS is an open-source modeling environment aimed, in particular, at the solution of bioengineering problems. OpenCMISS consists of two main parts: a computational library (OpenCMISS-Iron) and a field manipulation and visualization library (OpenCMISS-Zinc). OpenCMISS is designed for the solution of coupled multi-scale, multi-physics problems in a general-purpose parallel environment. CellML is an XML format designed to encode biophysically based systems of ordinary differential equations and both linear and non-linear algebraic equations. A primary design goal of CellML is to allow mathematical models to be encoded in a modular and reusable format to aid reproducibility and interoperability of modeling studies. In OpenCMISS, we make use of CellML models to enable users to configure various aspects of their multi-scale physiological models. This avoids the need for users to be familiar with the OpenCMISS internal code in order to perform customized computational experiments. Examples of this are: cellular electrophysiology models embedded in tissue electrical propagation models; material constitutive relationships for mechanical growth and deformation simulations; time-varying boundary conditions for various problem domains; and fluid constitutive relationships and lumped-parameter models. In this paper, we provide implementation details describing how CellML models are integrated into multi-scale physiological models in OpenCMISS. The external interface OpenCMISS presents to users is also described, including specific examples exemplifying the extensibility and usability these tools provide the physiological modeling and simulation community. We conclude with some thoughts on future extension of OpenCMISS to make use of other community developed information standards, such as FieldML, SED-ML, and BioSignalML. Plans for the integration of accelerator code (graphical processing unit and field programmable gate array) generated from CellML models is also

  5. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

    PubMed

    Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

    2011-12-15

    The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research

  6. ML-o-Scope: A Diagnostic Visualization System for Deep Machine Learning Pipelines

    DTIC Science & Technology

    2014-05-16

    images scraped from the web . Despite its small size, CIFAR- 10’s origins make it a rich and challenging data set for object classification. ML-o-scope... Web Services, Google, SAP, The Thomas and Stacey Siebel Foundation, Apple, Inc., Cisco, Cloudera, EMC, Ericsson, Facebook, GameOnTalis, Guavus, HP...exploratory analysis ap- plied to convolutional neural network pipeline optimiza- tion. ML-o-scope is a light-weight web application that allows users

  7. GM-CPHD and ML-PDA Applied to the Metron Multi-Static Sonar Dataset

    DTIC Science & Technology

    2010-07-01

    7 GM-CPHD Results It should be mentioned that running the GM-CPHD without winnowing and without contact sifting resulted in unsatis- factory... run . Plots of the generated tracks are displayed in Figures 7-14. The ellipses reveal the location and covariance of the Gaussian modes, the magenta...datasets, such as Metron, in which there are sharp turns along the target trajectory. 8 ML-PDA Results TheML-PDA algorithm perfomed rather well on the

  8. The Miscanthus NAC transcription factor MlNAC9 enhances abiotic stress tolerance in transgenic Arabidopsis.

    PubMed

    Zhao, Xun; Yang, Xuanwen; Pei, Shengqiang; He, Guo; Wang, Xiaoyu; Tang, Qi; Jia, Chunlin; Lu, Ying; Hu, Ruibo; Zhou, Gongke

    2016-07-15

    NAC (NAM, ATAF1/2, and CUC2) transcription factors are known to play important roles in responses to abiotic stresses in plants. Currently, little information regarding the functional roles of NAC genes in stress tolerance is available in Miscanthus lutarioriparius, a promising bioenergy plant for cellulosic ethanol production. In this study, we carried out the functional characterization of MlNAC9 in abiotic stresses. MlNAC9 was shown to act as a nuclear localized transcription activator with the activation domain in its C-terminus. The overexpression of MlNAC9 in Arabidopsis conferred hypersensitivity to abscisic acid (ABA) at seed germination and root elongation stages. In addition, the overexpression of MlNAC9 led to increased seed germination rate and root growth under salt (NaCl) treatment. Meanwhile, the transgenic Arabidopsis overexpressing MlNAC9 showed enhanced tolerance to drought and cold stresses. The expression of stress-responsive marker genes was significantly increased in MlNAC9 overexpression lines compared to that of WT under ABA, drought, salt, and cold stresses. Correspondingly, the activities of antioxidant enzymes superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were significantly increased and the malondialdehyde (MDA) content was lower accumulated in MlNAC9 overexpression lines under drought and salt treatments. These results indicated that the overexpression of MlNAC9 improved the tolerance to abiotic stresses via an ABA-dependent pathway, and the enhanced tolerance of transgenic plants was mainly attributed to the increased expression of stress-responsive genes and the enhanced scavenging capability of reactive oxygen species (ROS).

  9. Using CellML with OpenCMISS to Simulate Multi-Scale Physiology.

    PubMed

    Nickerson, David P; Ladd, David; Hussan, Jagir R; Safaei, Soroush; Suresh, Vinod; Hunter, Peter J; Bradley, Christopher P

    2014-01-01

    OpenCMISS is an open-source modeling environment aimed, in particular, at the solution of bioengineering problems. OpenCMISS consists of two main parts: a computational library (OpenCMISS-Iron) and a field manipulation and visualization library (OpenCMISS-Zinc). OpenCMISS is designed for the solution of coupled multi-scale, multi-physics problems in a general-purpose parallel environment. CellML is an XML format designed to encode biophysically based systems of ordinary differential equations and both linear and non-linear algebraic equations. A primary design goal of CellML is to allow mathematical models to be encoded in a modular and reusable format to aid reproducibility and interoperability of modeling studies. In OpenCMISS, we make use of CellML models to enable users to configure various aspects of their multi-scale physiological models. This avoids the need for users to be familiar with the OpenCMISS internal code in order to perform customized computational experiments. Examples of this are: cellular electrophysiology models embedded in tissue electrical propagation models; material constitutive relationships for mechanical growth and deformation simulations; time-varying boundary conditions for various problem domains; and fluid constitutive relationships and lumped-parameter models. In this paper, we provide implementation details describing how CellML models are integrated into multi-scale physiological models in OpenCMISS. The external interface OpenCMISS presents to users is also described, including specific examples exemplifying the extensibility and usability these tools provide the physiological modeling and simulation community. We conclude with some thoughts on future extension of OpenCMISS to make use of other community developed information standards, such as FieldML, SED-ML, and BioSignalML. Plans for the integration of accelerator code (graphical processing unit and field programmable gate array) generated from CellML models is also

  10. CytometryML: a data standard which has been designed to interface with other standards

    NASA Astrophysics Data System (ADS)

    Leif, Robert C.

    2007-02-01

    Because of the differences in the requirements, needs, and past histories including existing standards of the creating organizations, a single encompassing cytology-pathology standard will not, in the near future, replace the multiple existing or under development standards. Except for DICOM and FCS, these standardization efforts are all based on XML. CytometryML is a collection of XML schemas, which are based on the Digital Imaging and Communications in Medicine (DICOM) and Flow Cytometry Standard (FCS) datatypes. The CytometryML schemas contain attributes that link them to the DICOM standard and FCS. Interoperability with DICOM has been facilitated by, wherever reasonable, limiting the difference between CytometryML and the previous standards to syntax. In order to permit the Resource Description Framework, RDF, to reference the CytometryML datatypes, id attributes have been added to many CytometryML elements. The Laboratory Digital Imaging Project (LDIP) Data Exchange Specification and the Flowcyt standards development effort employ RDF syntax. Documentation from DICOM has been reused in CytometryML. The unity of analytical cytology was demonstrated by deriving a microscope type and a flow cytometer type from a generic cytometry instrument type. The feasibility of incorporating the Flowcyt gating schemas into CytometryML has been demonstrated. CytometryML is being extended to include many of the new DICOM Working Group 26 datatypes, which describe patients, specimens, and analytes. In situations where multiple standards are being created, interoperability can be facilitated by employing datatypes based on a common set of semantics and building in links to standards that employ different syntax.

  11. Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

    PubMed Central

    2011-01-01

    Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from

  12. A Type-Theoretic Account of Standard ML 1996 (Version 1).

    DTIC Science & Technology

    1996-05-10

    for ML. In Proceedings of the ACM SIGPLAN 󈨤 Conference on Programming Language Design and Implementation, 1996. To appear. 85 [WF91] Andrew Wright...Abstract A type-theoretic de nition of a variant of the Standard ML (Revised 1996) programming language is given. The de nition consists of a syntax...directed translation of SML96 programs into a typed intermediate language. The intermediate language is an explicitly-typed -calculus with product

  13. QuakeML: XML for Seismological Data Exchange and Resource Metadata Description

    NASA Astrophysics Data System (ADS)

    Euchner, F.; Schorlemmer, D.; Becker, J.; Heinloo, A.; Kästli, P.; Saul, J.; Weber, B.; QuakeML Working Group

    2007-12-01

    QuakeML is an XML-based data exchange format for seismology that is under development. Current collaborators are from ETH, GFZ, USC, USGS, IRIS DMC, EMSC, ORFEUS, and ISTI. QuakeML development was motivated by the lack of a widely accepted and well-documented data format that is applicable to a broad range of fields in seismology. The development team brings together expertise from communities dealing with analysis and creation of earthquake catalogs, distribution of seismic bulletins, and real-time processing of seismic data. Efforts to merge QuakeML with existing XML dialects are under way. The first release of QuakeML will cover a basic description of seismic events including picks, arrivals, amplitudes, magnitudes, origins, focal mechanisms, and moment tensors. Further extensions are in progress or planned, e.g., for macroseismic information, location probability density functions, slip distributions, and ground motion information. The QuakeML language definition is supplemented by a concept to provide resource metadata and facilitate metadata exchange between distributed data providers. For that purpose, we introduce unique, location-independent identifiers of seismological resources. As an application of QuakeML, ETH Zurich currently develops a Python-based seismicity analysis toolkit as a contribution to CSEP (Collaboratory for the Study of Earthquake Predictability). We follow a collaborative and transparent development approach along the lines of the procedures of the World Wide Web Consortium (W3C). QuakeML currently is in working draft status. The standard description will be subjected to a public Request for Comments (RFC) process and eventually reach the status of a recommendation. QuakeML can be found at http://www.quakeml.org.

  14. High-efficiency DALI apheresis using 1,250 ml adsorbers in a hypercholesterolemic obese patient: a case report.

    PubMed

    Bosch, T; Lennertz, A; Samtleben, W

    2001-10-01

    Direct adsorption of lipoproteins (DALI) apheresis is the first method for direct adsorption of lipoproteins from whole blood and is therefore an easy and rapid procedure. The majority of patients reaches >60% acute low-density lipoprotein cholesterol (LDL-C) reduction using either the DALI 750 or 1000 configuration. However, in patients with extremely high LDL-C levels or very large blood volumes, these configurations may lead to suboptimal results. The current study was performed to test the safety and efficacy of DALI 1250. In a severely obese patient (185 cm, 133 kg, blood volume 7.2 L, LDL-C 239 mg/dl), 11 L of blood (1.53-fold patient blood volume) was processed at a flow rate of 80 ml/min in 2.5 h; a combined heparin-plus-citrate anticoagulation regimen was used. Commercially available DALI 1250 and DALI hardware and disposables were manufactured by Fresenius HemoCare Adsorber Technology, St. Wendel, Germany. Twenty weekly sessions were performed. Clinically and technically, the apheresis sessions were completely uneventful. As compared to DALI 1000 (n = 4 sessions), the reduction rates by DALI 1250 (n = 20) improved for LDL-C (from 52% to 66%), lipoprotein (a) (Lp[a]) (53% vs. 66%), and fibrinogen (11% vs. 16%). There was a slight increase in high-density lipoprotein cholesterol (HDL-C) loss (20% vs. 24%). Moreover, the absolute amount of LDL-C removed per session increased from 5.06 g to 5.94 g. Laboratory safety parameters remained within the normal range, the anticoagulation was well controlled, and the pressure gradients over the adsorber remained constant. In this case report, DALI 1250 was perfectly safe and significantly increased the efficacy of LDL-C and Lp(a) elimination compared to standard DALI. Thus, this high-efficiency version of DALI may be used in patients with extremely high LDL-C levels and/or large blood volumes.

  15. An Ontology for State Analysis: Formalizing the Mapping to SysML

    NASA Technical Reports Server (NTRS)

    Wagner, David A.; Bennett, Matthew B.; Karban, Robert; Rouquette, Nicolas; Jenkins, Steven; Ingham, Michel

    2012-01-01

    State Analysis is a methodology developed over the last decade for architecting, designing and documenting complex control systems. Although it was originally conceived for designing robotic spacecraft, recent applications include the design of control systems for large ground-based telescopes. The European Southern Observatory (ESO) began a project to design the European Extremely Large Telescope (E-ELT), which will require coordinated control of over a thousand articulated mirror segments. The designers are using State Analysis as a methodology and the Systems Modeling Language (SysML) as a modeling and documentation language in this task. To effectively apply the State Analysis methodology in this context it became necessary to provide ontological definitions of the concepts and relations in State Analysis and greater flexibility through a mapping of State Analysis into a practical extension of SysML. The ontology provides the formal basis for verifying compliance with State Analysis semantics including architectural constraints. The SysML extension provides the practical basis for applying the State Analysis methodology with SysML tools. This paper will discuss the method used to develop these formalisms (the ontology), the formalisms themselves, the mapping to SysML and approach to using these formalisms to specify a control system and enforce architectural constraints in a SysML model.

  16. VarioML framework for comprehensive variation data representation and exchange.

    PubMed

    Byrne, Myles; Fokkema, Ivo Fac; Lancaster, Owen; Adamusiak, Tomasz; Ahonen-Bishopp, Anni; Atlan, David; Béroud, Christophe; Cornell, Michael; Dalgleish, Raymond; Devereau, Andrew; Patrinos, George P; Swertz, Morris A; Taschner, Peter Em; Thorisson, Gudmundur A; Vihinen, Mauno; Brookes, Anthony J; Muilu, Juha

    2012-10-03

    Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.

  17. IMF-based chaotic characterization of AP and ML visually-driven postural responses

    NASA Astrophysics Data System (ADS)

    Azhar, Hanif; Giraudet, Guillaume; Faubert, Jocelyn

    2013-03-01

    The objective was to analyze visually driven postural responses and characterize any non-linear behaviour. We recorded physiological responses for two adults, 260 trials each. The subjects maintained quite stance while fixating for four seconds within an immersive room, EON Icube, where the reference to the visual stimuli, i.e., the virtual platform, randomly oscillated in Gaussian orientation 90° and 270° for antero-posterior (AP), and, 0° and 180° for medio-lateral (ML) at three different frequencies (0.125, 0.25, and 0.5 Hz). We accomplished stationary derivatives of posture time series by taking the intrinsic mode functions (IMFs). The phase space plot of IMF shows evidence of the existence of non-linear attractors in both ML and AP. Correlation integral slope with increasing embedding dimension is similar to random white noise for ML, and similar to non-linear chaotic series for AP. Next, recurrence plots indicate the existence of more non-linearity for AP than that for ML. The patterns of the dots after 200th time stamp (near onset) appears to be aperodic in AP. At higher temporal windows, AP entropy tends more toward chaotic series, than that of ML. There are stronger non-linear components in AP than that in ML regardless of the speed conditions.

  18. An Ontology for State Analysis: Formalizing the Mapping to SysML

    NASA Technical Reports Server (NTRS)

    Wagner, David A.; Bennett, Matthew B.; Karban, Robert; Rouquette, Nicolas; Jenkins, Steven; Ingham, Michel

    2012-01-01

    State Analysis is a methodology developed over the last decade for architecting, designing and documenting complex control systems. Although it was originally conceived for designing robotic spacecraft, recent applications include the design of control systems for large ground-based telescopes. The European Southern Observatory (ESO) began a project to design the European Extremely Large Telescope (E-ELT), which will require coordinated control of over a thousand articulated mirror segments. The designers are using State Analysis as a methodology and the Systems Modeling Language (SysML) as a modeling and documentation language in this task. To effectively apply the State Analysis methodology in this context it became necessary to provide ontological definitions of the concepts and relations in State Analysis and greater flexibility through a mapping of State Analysis into a practical extension of SysML. The ontology provides the formal basis for verifying compliance with State Analysis semantics including architectural constraints. The SysML extension provides the practical basis for applying the State Analysis methodology with SysML tools. This paper will discuss the method used to develop these formalisms (the ontology), the formalisms themselves, the mapping to SysML and approach to using these formalisms to specify a control system and enforce architectural constraints in a SysML model.

  19. WaterML: an XML Language for Communicating Water Observations Data

    NASA Astrophysics Data System (ADS)

    Maidment, D. R.; Zaslavsky, I.; Valentine, D.

    2007-12-01

    One of the great impediments to the synthesis of water information is the plethora of formats used to publish such data. Each water agency uses its own approach. XML (eXtended Markup Languages) are generalizations of Hypertext Markup Language to communicate specific kinds of information via the internet. WaterML is an XML language for water observations data - streamflow, water quality, groundwater levels, climate, precipitation and aquatic biology data, recorded at fixed, point locations as a function of time. The Hydrologic Information System project of the Consortium of Universities for the Advancement of Hydrologic Science, Inc (CUAHSI) has defined WaterML and prepared a set of web service functions called WaterOneFLow that use WaterML to provide information about observation sites, the variables measured there and the values of those measurments. WaterML has been submitted to the Open GIS Consortium for harmonization with its standards for XML languages. Academic investigators at a number of testbed locations in the WATERS network are providing data in WaterML format using WaterOneFlow web services. The USGS and other federal agencies are also working with CUAHSI to similarly provide access to their data in WaterML through WaterOneFlow services.

  20. Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output.

    PubMed

    Turewicz, Michael; Deutsch, Eric W

    2011-01-01

    This chapter describes Mass Spectrometry Markup Language (mzML), an XML-based and vendor-neutral standard data format for storage and exchange of mass spectrometer output like raw spectra and peak lists. It is intended to replace its two precursor data formats (mzData and mzXML), which had been developed independently a few years earlier. Hence, with the release of mzML, the problem of having two different formats for the same purposes is solved, and with it the duplicated effort of maintaining and supporting two data formats. The new format has been developed by a broad-based consortium of major instrument vendors, software vendors, and academic researchers under the aegis of the Human Proteome Organisation (HUPO), Proteomics Standards Initiative (PSI), with full participation of the main developers of the precursor formats. This comprehensive approach helped mzML to become a generally accepted standard. Furthermore, the collaborative development insured that mzML has adopted the best features of its precursor formats. In this chapter, we discuss mzML's development history, its design principles and use cases, as well as its main building components. We also present the available documentation, an example file, and validation software for mzML.

  1. Characteristic mutations found in the ML0411 gene of Mycobacterium leprae isolated in Northeast Asian countries.

    PubMed

    Kai, M; Nakata, N; Matsuoka, M; Sekizuka, T; Kuroda, M; Makino, M

    2013-10-01

    Genome analysis of Mycobacterium leprae strain Kyoto-2 in this study revealed characteristic nucleotide substitutions in gene ML0411, compared to the reference genome M. leprae strain TN. The ML0411 gene of Kyoto-2 had six SNPs compared to that of TN. All SNPs in ML0411 were non-synonymous mutations that result in amino acid replacements. In addition, a seventh SNP was found 41 bp upstream of the start codon in the regulatory region. The seven SNP sites in the ML0411 region were investigated by sequencing in 36 M. leprae isolates from the Leprosy Research Center in Japan. The SNP pattern in 14 of the 36 isolates showed similarity to that of Kyoto-2. Determination of the standard SNP types within the 36 stocked isolates revealed that almost all of the Japanese strains belonged to SNP type III, with nucleotide substitutions at position 14676, 164275, and 2935685 of the M. leprae TN genome. The geographical distribution pattern of east Asian M. leprae isolates by discrimination of ML0411 SNPs was investigated and interestingly turned out to be similar to that of tandem repeat numbers of GACATC in the rpoT gene (3 copies or 4 copies), which has been established as a tool for M. leprae genotyping. All seven Korean M. leprae isolates examined in this study, as well as those derived from Honshu Island of Japan, showed 4 copies of the 6-base tandem repeat plus the ML0411 SNPs observed in M. leprae Kyoto-2. They are termed Northeast Asian (NA) strain of M. leprae. On the other hand, many of isolates derived from the Okinawa Islands of Japan and from the Philippines showed 3 copies of the 6-base tandem repeat in addition to the M. leprae TN ML0411 type of SNPs. These results demonstrate the existence of M. leprae strains in Northeast Asian region having characteristic SNP patterns.

  2. A critical ('stress') evaluation of the combined ML Copper 250-short IUD in nulliparous women.

    PubMed

    Goldstuck, N D

    1981-10-01

    IUD tolerability is related to the size and shape of the carrier frame of the copper-containing IUD. This study evaluates a critically selected group of 30 nulliparous women (those with uterine cavity length of 3.5 cm or less) who underwent insertion of the combined Multiload Copper 250-short (ML Cu 250-short) IUD. The women were aged 18 to 36 years. They were followed up between 6 months and 1 year. 1 patient with a very small infantile uterus (3.5 cm) had 2 IUD insertions and expulsions and was deemed not fit for intrauterine contraception. Another patient requested removal because of persistent bleeding, probably due to a fragile endometrium or a local bleeding disorder. 6 patients (20%) reported pre- and inter-menstrual pain, while 12 (40%) patients, including the patient who requested device removal, complained of prolonged bleeding following insertion of the ML Cu 250-short. Bleeding continued in majority of the cases for about 14 days following insertion. The bleeding pattern returned to normal after 2 months. No infections or pregnancies were reported. 4 of the patients who continued to use the device experienced some pain and/or discomfort. None of the patients who had experienced pain with previous devices experienced pain with the ML Cu 250-short. The length and width of the ML Cu 250-short appears optimal for the endometrial cavity of nulliparous women. The horizontal width of the ML Cu 250-short (18 mm) most closely approximates the 20 mm nulliparous uterine cavity width while the ML Cu 250-mini with a fundal horizontal length of 12 mm appears destined for use only by women with very narrow uterus. Hassons' wing sound 11 allows clinical graphical representation of the uterine cavity, enabling the inserter to select anatomically optimal device immediately in the clinic. The ML Copper 250-short appears highly suitable for use by nulliparous women.

  3. The ML 3.5 earthquake sequence induced by the hydrothermal energy project in St. Gallen, Switzerland

    NASA Astrophysics Data System (ADS)

    Kraft, T.; Wiemer, S.; Deichmann, N.; Diehl, T.; Edwards, B.; Guilhem, A.; Haslinger, F.; Király, E.; Kissling, E. H.; Mignan, A.; Plenkers, K.; Roten, D.; Seif, S.; Woessner, J.

    2013-12-01

    within a few days but two weeks later was still far from reaching the background level. Here we report on the results of our analysis of the induced seismic sequence at Sankt Gallen: ML 3.5 event initiated near the borehole, had a comparatively low stress drop (3.5 bar) and a rupture length of ~1.1 km. Peak ground motions observed for the ML 3.5 eventare very similar to the ones observed in the ML 3.4 event induced in 2006 in Basel. Yet, macroseismic intensities in St. Gallen only reach IV (EMS) versus V (EMS) in Basel. Precise earthquake relative locations indicate that seismicity extends bi-laterally from the injection point, following the trend of the mapped fault segments. Fault plane solutions of the two largest events indicate a left lateral strike slip fault whose orientation agrees well with the aftershock locations and the imaged fault zone. The St. Gallen sequence shows the highest seismic productivity per injected fluid volume when compared to other injection-induced sequences, and challenges proposed relations between injected fluid volume and maximum observed magnitude or between hydraulic energy and released seismic energy.

  4. HepML, an XML-based format for describing simulated data in high energy physics

    NASA Astrophysics Data System (ADS)

    Belov, S.; Dudko, L.; Kekelidze, D.; Sherstnev, A.

    2010-10-01

    In this paper we describe a HepML format and a corresponding C++ library developed for keeping complete description of parton level events in a unified and flexible form. HepML tags contain enough information to understand what kind of physics the simulated events describe and how the events have been prepared. A HepML block can be included into event files in the LHEF format. The structure of the HepML block is described by means of several XML Schemas. The Schemas define necessary information for the HepML block and how this information should be located within the block. The library libhepml is a C++ library intended for parsing and serialization of HepML tags, and representing the HepML block in computer memory. The library is an API for external software. For example, Matrix Element Monte Carlo event generators can use the library for preparing and writing a header of an LHEF file in the form of HepML tags. In turn, Showering and Hadronization event generators can parse the HepML header and get the information in the form of C++ classes. libhepml can be used in C++, C, and Fortran programs. All necessary parts of HepML have been prepared and we present the project to the HEP community. Program summaryProgram title: libhepml Catalogue identifier: AEGL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 138 866 No. of bytes in distributed program, including test data, etc.: 613 122 Distribution format: tar.gz Programming language: C++, C Computer: PCs and workstations Operating system: Scientific Linux CERN 4/5, Ubuntu 9.10 RAM: 1 073 741 824 bytes (1 Gb) Classification: 6.2, 11.1, 11.2 External routines: Xerces XML library ( http://xerces.apache.org/xerces-c/), Expat XML Parser ( http://expat.sourceforge.net/) Nature of problem: Monte Carlo simulation in high

  5. Improvements in localized proton NMR spectroscopy of human brain. Water suppression, short echo times, and 1 ml resolution

    NASA Astrophysics Data System (ADS)

    Frahm, J.; Michaelis, T.; Merboldt, K. D.; Bruhn, H.; Gyngell, M. L.; Hänicke, W.

    Considerable technical improvements are reported for localized proton NMR spectroscopy using stimulated echoes. When compared to previous results, proton NMR spectra of the human brain are now obtainable (i) with in vivo water suppression factors of ⩾1000, (ii) with only minor T2 losses and negligible distortions due to J modulation at short echo times of 10-20 ms, and (iii) from volumes of interest as small as 1-8 ml within measuring times of 1-10 min. As a consequence, the detection of cerebral metabolites is greatly facilitated. This particularly applies to the assignment of those resonances (e.g., glutamate, taurine, inositols) that suffer from strong spin-spin coupling at the field strengths commonly in use for NMR in man. Studies of regional metabolite differences, tissue heterogeneity, and focal lesions in patients benefit from the increased spatial resolution and a concomitant reduction of partial volume effects. Localized proton NMR spectroscopy was performed on young healthy volunteers. Experiments were carried out on a 2.0 T whole-body MRI/MRS system using the standard headcoil for both imaging and spectroscopy.

  6. Physical Properties of Asteroid (10302) 1989 ML, a Potential Spacecraft Target, from Spitzer Observations

    NASA Astrophysics Data System (ADS)

    Mueller, Michael; Harris, A. W.

    2006-09-01

    We report on results from recent Spitzer observations of near-Earth asteroid (10302) 1989 ML, which is among the lowest-ranking objects in terms of the specific momentum Δv required to reach it from Earth. It was originally considered as a target for Hayabusa and is now under consideration as a target of the planned ESA mission Don Quijote. Unfortunately, little is known about the physical properties of 1989 ML, in particular its size and albedo are unknown. Its exhibits an X type reflection spectrum, so depending on its albedo, 1989 ML may be an E, M, or P type asteroid. Provisional results from thermal-infrared observations carried out with Spitzer indicate that the albedo of 1989 ML is compatible with an M- or E-type classification. We will discuss our results and their implications for the physical properties and the rotation period of 1989 ML, and its importance as a potential spacecraft target. This work is based on observations made with the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory, California Institute of Technology under a contract with NASA.

  7. The evolution of the CUAHSI Water Markup Language (WaterML)

    NASA Astrophysics Data System (ADS)

    Zaslavsky, I.; Valentine, D.; Maidment, D.; Tarboton, D. G.; Whiteaker, T.; Hooper, R.; Kirschtel, D.; Rodriguez, M.

    2009-04-01

    The CUAHSI Hydrologic Information System (HIS, his.cuahsi.org) uses web services as the core data exchange mechanism which provides programmatic connection between many heterogeneous sources of hydrologic data and a variety of online and desktop client applications. The service message schema follows the CUAHSI Water Markup Language (WaterML) 1.x specification (see OGC Discussion Paper 07-041r1). Data sources that can be queried via WaterML-compliant water data services include national and international repositories such as USGS NWIS (National Water Information System), USEPA STORET (Storage & Retrieval), USDA SNOTEL (Snowpack Telemetry), NCDC ISH and ISD(Integrated Surface Hourly and Daily Data), MODIS (Moderate Resolution Imaging Spectroradiometer), and DAYMET (Daily Surface Weather Data and Climatological Summaries). Besides government data sources, CUAHSI HIS provides access to a growing number of academic hydrologic observation networks. These networks are registered by researchers associated with 11 hydrologic observatory testbeds around the US, and other research, government and commercial groups wishing to join the emerging CUAHSI Water Data Federation. The Hydrologic Information Server (HIS Server) software stack deployed at NSF-supported hydrologic observatory sites and other universities around the country, supports a hydrologic data publication workflow which includes the following steps: (1) observational data are loaded from static files or streamed from sensors into a local instance of an Observations Data Model (ODM) database; (2) a generic web service template is configured for the new ODM instance to expose the data as a WaterML-compliant water data service, and (3) the new water data service is registered at the HISCentral registry (hiscentral.cuahsi.org), its metadata are harvested and semantically tagged using concepts from a hydrologic ontology. As a result, the new service is indexed in the CUAHSI central metadata catalog, and becomes

  8. Eradication of Staphylococcus aureus Catheter-Related Biofilm Infections Using ML:8 and Citrox

    PubMed Central

    Hogan, S.; Zapotoczna, M.; Stevens, N. T.; Humphreys, H.; O'Gara, J. P.

    2016-01-01

    Staphylococci are a leading cause of catheter-related infections (CRIs) due to biofilm formation. CRIs are typically managed by either device removal or systemic antibiotics, often in combination with catheter lock solutions (CLSs). CLSs provide high concentrations of the antimicrobial agent at the site of infection. However, the most effective CLSs against staphylococcal biofilm-associated infections have yet to be determined. The purpose of this study was to evaluate the efficacy and suitability of two newly described antimicrobial agents, ML:8 and Citrox, as CLSs against Staphylococcus aureus biofilms. ML:8 (1% [vol/vol]) and Citrox (1% [vol/vol]), containing caprylic acid and flavonoids, respectively, were used to treat S. aureus biofilms grown in vitro using newly described static and flow biofilm assays. Both agents reduced biofilm viability >97% after 24 h of treatment. Using a rat model of CRI, ML:8 was shown to inactivate early-stage S. aureus biofilms in vivo, while Citrox inactivated established, mature in vivo biofilms. Cytotoxicity and hemolytic activity of ML:8 and Citrox were equivalent to those of other commercially available CLSs. Neither ML:8 nor Citrox induced a cytokine response in human whole blood, and exposure of S. aureus to either agent for 90 days was not associated with any increase in resistance. Taken together, these data reveal the therapeutic potential of these agents for the treatment of S. aureus catheter-related biofilm infections. PMID:27458213

  9. ExaML version 3: a tool for phylogenomic analyses on supercomputers

    PubMed Central

    Kozlov, Alexey M.; Aberer, Andre J.; Stamatakis, Alexandros

    2015-01-01

    Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers. Results: We introduce several improvements and extensions to ExaML: Extensions of substitution models and supported data types, the integration of a novel load balance algorithm as well as a parallel I/O optimization that significantly improve parallel efficiency, and a production-level implementation for Intel MIC-based hardware platforms. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/ExaML. Contact: Alexandros.Stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25819675

  10. The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.

    PubMed

    Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W; Jones, Andrew R

    2010-09-01

    The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.

  11. ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

    PubMed Central

    Didelot, Xavier; Wilson, Daniel J.

    2015-01-01

    Recombination is an important evolutionary force in bacteria, but it remains challenging to reconstruct the imports that occurred in the ancestry of a genomic sample. Here we present ClonalFrameML, which uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. ClonalFrameML can analyse hundreds of genomes in a matter of hours, and we demonstrate its usefulness on simulated and real datasets. We find evidence for recombination hotspots associated with mobile elements in Clostridium difficile ST6 and a previously undescribed 310kb chromosomal replacement in Staphylococcus aureus ST582. ClonalFrameML is freely available at http://clonalframeml.googlecode.com/. PMID:25675341

  12. An overview of the CellML API and its implementation

    PubMed Central

    2010-01-01

    Background CellML is an XML based language for representing mathematical models, in a machine-independent form which is suitable for their exchange between different authors, and for archival in a model repository. Allowing for the exchange and archival of models in a computer readable form is a key strategic goal in bioinformatics, because of the associated improvements in scientific record accuracy, the faster iterative process of scientific development, and the ability to combine models into large integrative models. However, for CellML models to be useful, tools which can process them correctly are needed. Due to some of the more complex features present in CellML models, such as imports, developing code ab initio to correctly process models can be an onerous task. For this reason, there is a clear and pressing need for an application programming interface (API), and a good implementation of that API, upon which tools can base their support for CellML. Results We developed an API which allows the information in CellML models to be retrieved and/or modified. We also developed a series of optional extension APIs, for tasks such as simplifying the handling of connections between variables, dealing with physical units, validating models, and translating models into different procedural languages. We have also provided a Free/Open Source implementation of this application programming interface, optimised to achieve good performance. Conclusions Tools have been developed using the API which are mature enough for widespread use. The API has the potential to accelerate the development of additional tools capable of processing CellML, and ultimately lead to an increased level of sharing of mathematical model descriptions. PMID:20377909

  13. imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging.

    PubMed

    Römpp, Andreas; Schramm, Thorsten; Hester, Alfons; Klinkert, Ivo; Both, Jean-Pierre; Heeren, Ron M A; Stöckli, Markus; Spengler, Bernhard

    2011-01-01

    Imaging mass spectrometry is the method of scanning a sample of interest and generating an "image" of the intensity distribution of a specific analyte. The data sets consist of a large number of mass spectra which are usually acquired with identical settings. Existing data formats are not sufficient to describe an MS imaging experiment completely. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software.For this purpose, the MS imaging data is divided in two separate files. The mass spectral data is stored in a binary file to ensure efficient storage. All metadata (e.g., instrumental parameters, sample details) are stored in an XML file which is based on the standard data format mzML developed by HUPO-PSI. The original mzML controlled vocabulary was extended to include specific parameters of imaging mass spectrometry (such as x/y position and spatial resolution). The two files (XML and binary) are connected by offset values in the XML file and are unambiguously linked by a universally unique identifier. The resulting datasets are comparable in size to the raw data and the separate metadata file allows flexible handling of large datasets.Several imaging MS software tools already support imzML. This allows choosing from a (growing) number of processing tools. One is no longer limited to proprietary software, but is able to use the processing software which is best suited for a specific question or application. On the other hand, measurements from different instruments can be compared within one software application using identical settings for data processing. All necessary information for evaluating and implementing imzML can be found at http://www.imzML.org .

  14. VarioML framework for comprehensive variation data representation and exchange

    PubMed Central

    2012-01-01

    Background Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. Results The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. Conclusions VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity. PMID:23031277

  15. RED-ML: a novel, effective RNA editing detection method based on machine learning.

    PubMed

    Xiong, Heng; Liu, Dongbing; Li, Qiye; Lei, Mengyue; Xu, Liqin; Wu, Liang; Wang, Zongji; Ren, Shancheng; Li, Wangsheng; Xia, Min; Lu, Lihua; Lu, Haorong; Hou, Yong; Zhu, Shida; Liu, Xin; Sun, Yinghao; Wang, Jian; Yang, Huanming; Wu, Kui; Xu, Xun; Lee, Leo J

    2017-05-01

    With the advancement of second generation sequencing techniques, our ability to detect and quantify RNA editing on a global scale has been vastly improved. As a result, RNA editing is now being studied under a growing number of biological conditions so that its biochemical mechanisms and functional roles can be further understood. However, a major barrier that prevents RNA editing from being a routine RNA-seq analysis, similar to gene expression and splicing analysis, for example, is the lack of user-friendly and effective computational tools. Based on years of experience of analyzing RNA editing using diverse RNA-seq datasets, we have developed a software tool, RED-ML: RNA Editing Detection based on Machine learning (pronounced as "red ML"). The input to RED-ML can be as simple as a single BAM file, while it can also take advantage of matched genomic variant information when available. The output not only contains detected RNA editing sites, but also a confidence score to facilitate downstream filtering. We have carefully designed validation experiments and performed extensive comparison and analysis to show the efficiency and effectiveness of RED-ML under different conditions, and it can accurately detect novel RNA editing sites without relying on curated RNA editing databases. We have also made this tool freely available via GitHub ML>. We have developed a highly accurate, speedy and general-purpose tool for RNA editing detection using RNA-seq data. With the availability of RED-ML, it is now possible to conveniently make RNA editing a routine analysis of RNA-seq. We believe this can greatly benefit the RNA editing research community and has profound impact to accelerate our understanding of this intriguing posttranscriptional modification process. © The Author 2017. Published by Oxford University Press.

  16. The analysis results of EEWS(Earthquake Early Warning System) about Iksan(Ml4.3) and Ulsan(Ml5.0) earthquakes in Korea

    NASA Astrophysics Data System (ADS)

    Park, J. H.; Chi, H. C.; Lim, I. S.; Seong, Y. J.; Pak, J.

    2016-12-01

    EEW(Earthquake Early Warning) service to the public has been officially operated by KMA (Korea Meteorological Administration) from 2015 in Korea. For the KMA's official EEW service, KIGAM has adopted ElarmS from UC Berkeley BSL and modified local magnitude relation, 1-D travel time curves and association procedures with real time waveforms from about 160 seismic stations of KMA and KIGAM. We have checked the performance of EEWS(Earthquake Early Warning System) reviewing two moderate size earthquakes: one is Iksan Eq.(Ml4.3) inside of networks and the other is Ulsan Eq.(Ml5.0) happened at the southern east sea of Korea outside of networks. The first trigger time at NPR station of the Iksan Eq. took 2.3 sec and BUY and JEO2 stations were associated to produce the first event version in 10.07 sec from the origin time respectively. Because the epicentral distance of JEO2 station is about 30 km and the estimated travel time is 6.2 sec, the delay time including transmission and processing is estimated as 3.87 sec with assumption that P wave velocity is 5 km/sec and the focal depth is 8 km. The first magnitude was M4.9 which was a little bigger than Ml4.3 by KIGAM. After adding 3 more triggers of stations (CHO, KMSA, PORA), the estimated magnitude became to M4.6 and the final was settled down to M4.3 with 10 stations. In the case of Ulsan the first trigger time took 11.04 sec and the first alert time with 3 stations in 14.8 sec from the origin time (OT) respectively. The first magnitude was M5.2, however, the difference between the first EEW epicenter and the manual final result was about 63 km due to the poor azimuth coverage outside of seismic network. After 16.2 sec from OT the fourth station YSB was used to update the location near to the manual results within 6 km with magnitude 5.0 and location and magnitude were stable with more stations. Ulsan Eq. was the first case announced to the public by EEWS and the process and result were successful, however, we have to

  17. TumorML: Concept and requirements of an in silico cancer modelling markup language.

    PubMed

    Johnson, David; Cooper, Jonathan; McKeever, Steve

    2011-01-01

    This paper describes the initial groundwork carried out as part of the European Commission funded Transatlantic Tumor Model Repositories project, to develop a new markup language for computational cancer modelling, TumorML. In this paper we describe the motivations for such a language, arguing that current state-of-the-art biomodelling languages are not suited to the cancer modelling domain. We go on to describe the work that needs to be done to develop TumorML, the conceptual design, and a description of what existing markup languages will be used to compose the language specification.

  18. ProML--the protein markup language for specification of protein sequences, structures and families.

    PubMed

    Hanisch, Daniel; Zimmer, Ralf; Lengauer, Thomas

    2002-01-01

    We propose a specification language ProML for protein sequences, structures, and families based on the open XML standard. The language allows for portable, system-independent, machine-parsable and human-readable representation of essential features of proteins. The language is of immediate use for several bioinformatics applications: we discuss clustering of proteins into families and the representation of the specific shared features of the respective clusters. Moreover, we use ProML for specification of data used in fold recognition bench-marks exploiting experimentally derived distance constraints.

  19. Correlation of ultrasound estimated placental volume and umbilical cord blood volume in term pregnancy

    PubMed Central

    Pannopnut, Papinwit; Kitporntheranunt, Maethaphan; Paritakul, Panwara; Kongsomboon, Kittipong

    2015-01-01

    Objective To investigate the correlation between ultrasound measured placental volume and collected umbilical cord blood (UCB) volume in term pregnancy. Material and Methods An observational cross-sectional study of term singleton pregnant women in the labor ward at Maha Chakri Sirindhorn Medical Center was conducted. Placental thickness, height, and width were measured using two-dimensional (2D) ultrasound and calculated for placental volume using the volumetric mathematic model. After the delivery of the baby, UCB was collected and measured for its volume immediately. Then, birth weight, placental weight, and the actual placental volume were analyzed. The Pearson’s correlation was used to determine the correlation between each two variables. Results A total of 35 pregnant women were eligible for the study. The mean and standard deviation of estimated placental volume and actual placental volume were 534±180 mL and 575±118 mL, respectively. The median UCB volume was 140 mL (range 98–220 mL). The UCB volume did not have a statistically significant correlation with the estimated placental volume (correlation coefficient 0.15; p=0.37). However, the UCB volume was significantly correlated with the actual placental volume (correlation coefficient 0.62; p<0.001) and birth weight (correlation coefficient 0.38; p=0.02). Conclusion The estimated placental volume by 2D ultrasound was not significantly correlated with the UCB volume. Further studies to establish the correlation between the UCB volume and the estimated placental volume using other types of placental imaging may be needed. PMID:26097385

  20. Measurement and Structural Model Class Separation in Mixture CFA: ML/EM versus MCMC

    ERIC Educational Resources Information Center

    Depaoli, Sarah

    2012-01-01

    Parameter recovery was assessed within mixture confirmatory factor analysis across multiple estimator conditions under different simulated levels of mixture class separation. Mixture class separation was defined in the measurement model (through factor loadings) and the structural model (through factor variances). Maximum likelihood (ML) via the…

  1. Is the ML Chi-Square Ever Robust to Nonnormality? A Cautionary Note with Missing Data

    ERIC Educational Resources Information Center

    Savalei, Victoria

    2008-01-01

    Normal theory maximum likelihood (ML) is by far the most popular estimation and testing method used in structural equation modeling (SEM), and it is the default in most SEM programs. Even though this approach assumes multivariate normality of the data, its use can be justified on the grounds that it is fairly robust to the violations of the…

  2. ML Estimation of Mean and Covariance Structures with Missing Data Using Complete Data Routines.

    ERIC Educational Resources Information Center

    Jamshidian, Mortaza; Bentler, Peter M.

    1999-01-01

    Describes the maximum likelihood (ML) estimation of mean and covariance structure models when data are missing. Describes expectation maximization (EM), generalized expectation maximization, Fletcher-Powell, and Fisher-scoring algorithms for parameter estimation and shows how software can be used to implement each algorithm. (Author/SLD)

  3. 97. ARAIII. ML1 reactor has been moved into GCRE reactor ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    97. ARA-III. ML-1 reactor has been moved into GCRE reactor building (ARA-608) for examination of corrosion on its underside and repair. May 24, 1963. Ineel photo no. 63-3485. - Idaho National Engineering Laboratory, Army Reactors Experimental Area, Scoville, Butte County, ID

  4. Is the ML Chi-Square Ever Robust to Nonnormality? A Cautionary Note with Missing Data

    ERIC Educational Resources Information Center

    Savalei, Victoria

    2008-01-01

    Normal theory maximum likelihood (ML) is by far the most popular estimation and testing method used in structural equation modeling (SEM), and it is the default in most SEM programs. Even though this approach assumes multivariate normality of the data, its use can be justified on the grounds that it is fairly robust to the violations of the…

  5. Measurement and Structural Model Class Separation in Mixture CFA: ML/EM versus MCMC

    ERIC Educational Resources Information Center

    Depaoli, Sarah

    2012-01-01

    Parameter recovery was assessed within mixture confirmatory factor analysis across multiple estimator conditions under different simulated levels of mixture class separation. Mixture class separation was defined in the measurement model (through factor loadings) and the structural model (through factor variances). Maximum likelihood (ML) via the…

  6. Process for selecting engineering tools : applied to selecting a SysML tool.

    SciTech Connect

    De Spain, Mark J.; Post, Debra S.; Taylor, Jeffrey L.; De Jong, Kent

    2011-02-01

    Process for Selecting Engineering Tools outlines the process and tools used to select a SysML (Systems Modeling Language) tool. The process is general in nature and users could use the process to select most engineering tools and software applications.

  7. The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.

    PubMed

    Walzer, Mathias; Qi, Da; Mayer, Gerhard; Uszkoreit, Julian; Eisenacher, Martin; Sachsenberg, Timo; Gonzalez-Galarza, Faviel F; Fan, Jun; Bessant, Conrad; Deutsch, Eric W; Reisinger, Florian; Vizcaíno, Juan Antonio; Medina-Aunon, J Alberto; Albar, Juan Pablo; Kohlbacher, Oliver; Jones, Andrew R

    2013-08-01

    The range of heterogeneous approaches available for quantifying protein abundance via mass spectrometry (MS)(1) leads to considerable challenges in modeling, archiving, exchanging, or submitting experimental data sets as supplemental material to journals. To date, there has been no widely accepted format for capturing the evidence trail of how quantitative analysis has been performed by software, for transferring data between software packages, or for submitting to public databases. In the context of the Proteomics Standards Initiative, we have developed the mzQuantML data standard. The standard can represent quantitative data about regions in two-dimensional retention time versus mass/charge space (called features), peptides, and proteins and protein groups (where there is ambiguity regarding peptide-to-protein inference), and it offers limited support for small molecule (metabolomic) data. The format has structures for representing replicate MS runs, grouping of replicates (for example, as study variables), and capturing the parameters used by software packages to arrive at these values. The format has the capability to reference other standards such as mzML and mzIdentML, and thus the evidence trail for the MS workflow as a whole can now be described. Several software implementations are available, and we encourage other bioinformatics groups to use mzQuantML as an input, internal, or output format for quantitative software and for structuring local repositories. All project resources are available in the public domain from the HUPO Proteomics Standards Initiative http://www.psidev.info/mzquantml.

  8. Isolation of a recombination-deficient mutant of Streptococcus lactis ML3.

    PubMed

    Anderson, D G; McKay, L L

    1983-08-01

    A recombination-deficient mutant of Streptococcus lactis ML3 designated MMS36 was isolated on the basis of its sensitivity to methyl methanesulfonate. This mutant also displayed sensitivity to UV irradiation. The inability of MMS36 to mediate homologous recombination was demonstrated by transduction of plasmid-linked lactose fermenting ability but not chromosomally mediated streptomycin resistance.

  9. Cdc42 inhibitor ML141 enhances G-CSF-induced hematopoietic stem and progenitor cell mobilization.

    PubMed

    Chen, Chong; Song, Xuguang; Ma, Sha; Wang, Xue; Xu, Jie; Zhang, Huanxin; Wu, Qingyun; Zhao, Kai; Cao, Jiang; Qiao, Jianlin; Sun, Xiaoshen; Li, Depeng; Zeng, Lingyu; Li, Zhengyu; Xu, Kailin

    2015-01-01

    G-CSF is the most often used agent in clinical hematopoietic stem and progenitor cell (HSPC) mobilization. However, in about 10 % of patients, G-CSF does not efficiently mobilize HSPC in clinically sufficient amounts. Cdc42 activity is involved in HSPC mobilization. In the present study, we explore the impact of Cdc42 inhibitor ML141 on G-CSF-mediated HSPC mobilization in mice. We found that the use of ML141 alone only triggered modest HSPC mobilization effect in mice. However, combination of G-CSF and ML141 significantly promoted HPSC counts and colony forming units in peripheral blood, as compared to mice treated with G-CSF alone. ML141 did not significantly alter the levels of SDF-1 and MMP-9 in the bone marrow, when used alone or in combination with G-CSF. We also found that G-CSF administration significantly increases the level of GTP-bound Cdc42, but does not alter the expression of Cdc42 in the bone marrow. Our data indicate that the Cdc42 signal is a negative regulator in G-CSF-mediated HSPC mobilization, and that inhibition of the Cdc42 signal efficiently improves mobilization efficiency. These findings may provide a new strategy for efficient HSPC mobilization, especially in patients with poor G-CSF response.

  10. INTERIOR VIEW WITH MIXER TO LADLE TRANSFER. CRANE OPERATOR, M.L. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    INTERIOR VIEW WITH MIXER TO LADLE TRANSFER. CRANE OPERATOR, M.L. BROWN; SWITCHER, BILL CLARK; DESULPHUR OPERATORS, CHARLIE WILLIAMS AND TIM BUSH. - U.S. Steel, Fairfield Works, Q-Bop Furnace, North of Valley Road & West of Ensley, Pleasant Grove Road, Fairfield, Jefferson County, AL

  11. INTERIOR VIEW WITH MIXER TO LADLE TRANSFER. CRANE OPERATOR, M.L. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    INTERIOR VIEW WITH MIXER TO LADLE TRANSFER. CRANE OPERATOR, M.L. BROWN; SWITCHER, BILL CLARK; DESULPHUR OPERATORS, CHARLIE WILLIAMS AND TIM BUSH - U.S. Steel, Fairfield Works, Q-Bop Furnace, North of Valley Road & West of Ensley, Pleasant Grove Road, Fairfield, Jefferson County, AL

  12. 170. ARAIV Blast bunker installed after ML1 buildings were removed. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    170. ARA-IV Blast bunker installed after ML-1 buildings were removed. Isometric detail and section. EG&G Company. Date: June 1985. Ineel index code no. 066-0600-60-220-166261. - Idaho National Engineering Laboratory, Army Reactors Experimental Area, Scoville, Butte County, ID

  13. Identification and Characterization of ML352: A Novel, Noncompetitive Inhibitor of the Presynaptic Choline Transporter

    PubMed Central

    2015-01-01

    The high-affinity choline transporter (CHT) is the rate-limiting determinant of acetylcholine (ACh) synthesis, yet the transporter remains a largely undeveloped target for the detection and manipulation of synaptic cholinergic signaling. To expand CHT pharmacology, we pursued a high-throughput screen for novel CHT-targeted small molecules based on the electrogenic properties of transporter-mediated choline transport. In this effort, we identified five novel, structural classes of CHT-specific inhibitors. Chemical diversification and functional analysis of one of these classes identified ML352 as a high-affinity (Ki = 92 nM) and selective CHT inhibitor. At concentrations that fully antagonized CHT in transfected cells and nerve terminal preparations, ML352 exhibited no inhibition of acetylcholinesterase (AChE) or cholineacetyltransferase (ChAT) and also lacked activity at dopamine, serotonin, and norepinephrine transporters, as well as many receptors and ion channels. ML352 exhibited noncompetitive choline uptake inhibition in intact cells and synaptosomes and reduced the apparent density of hemicholinium-3 (HC-3) binding sites in membrane assays, suggesting allosteric transporter interactions. Pharmacokinetic studies revealed limited in vitro metabolism and significant CNS penetration, with features predicting rapid clearance. ML352 represents a novel, potent, and specific tool for the manipulation of CHT, providing a possible platform for the development of cholinergic imaging and therapeutic agents. PMID:25560927

  14. 94. ARAIV. Aerial view of ML1 area. Camera facing north. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    94. ARA-IV. Aerial view of ML-1 area. Camera facing north. Reactor test building is in center of view. Walking path and utility lines connect test building. Berm lies between. Road curves to left and continues to GCRE complex. Ineel photo no. 79-4707. - Idaho National Engineering Laboratory, Army Reactors Experimental Area, Scoville, Butte County, ID

  15. Executing medical logic modules expressed in ArdenML using Drools

    PubMed Central

    Jung, Chai Young; Sward, Katherine A

    2011-01-01

    The Arden Syntax is an HL7 standard language for representing medical knowledge as logic statements. Despite nearly 2 decades of availability, Arden Syntax has not been widely used. This has been attributed to the lack of a generally available compiler to implement the logic, to Arden's complex syntax, to the challenges of mapping local data to data references in the Medical Logic Modules (MLMs), or, more globally, to the general absence of decision support in healthcare computing. An XML representation (ArdenML) may partially address the technical challenges. MLMs created in ArdenML can be converted into executable files using standard transforms written in the Extensible Stylesheet Language Transformation (XSLT) language. As an example, we have demonstrated an approach to executing MLMs written in ArdenML using the Drools business rule management system. Extensions to ArdenML make it possible to generate a user interface through which an MLM developer can test for logical errors. PMID:22180871

  16. Complete genome sequence of channel catfish epidemic isolate Aeromonas hydrophila ML09-119

    USDA-ARS?s Scientific Manuscript database

    Aeromonas hydrophila is a Gram-negative, rod-shaped, mesophilic bacteria that infects both aquatic poikilothermic animals and mammals, including humans. Here, we present the complete genome sequence of Aeromonas hydrophila ML-09-119, which represents a clonal group of A. hydrophila isolates causing ...

  17. Complete Genome Sequence of a Channel Catfish Epidemic Isolate, Aeromonas hydrophila Strain ML09-119

    PubMed Central

    Tekedar, Hasan C.; Waldbieser, Geoffrey C.; Karsi, Attila; Liles, Mark R.; Griffin, Matt J.; Vamenta, Stefanie; Sonstegard, Tad; Hossain, Mohammad; Schroeder, Steven G.; Khoo, Lester

    2013-01-01

    Aeromonas hydrophila is a Gram-negative, rod-shaped, mesophilic bacterium that infects both aquatic poikilothermic animals and mammals, including humans. Here, we present the complete genome sequence of Aeromonas hydrophila strain ML09-119, which represents a clonal group of A. hydrophila isolates causing outbreaks of bacterial septicemia in channel catfish since 2009. PMID:24051325

  18. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

    PubMed

    Bergmann, Frank T; Cooper, Jonathan; Le Novère, Nicolas; Nickerson, David; Waltemath, Dagmar

    2015-09-04

    The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines. This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.

  19. The october 31 (Ml 5.4) and november 1 (Ml 5.3) Molise earthquakes (southern italy):first results from geochemistry

    NASA Astrophysics Data System (ADS)

    Pizzino, L.; Cinti, D.; Barbieri, M.; Galli, G.; Voltattorni, N.; Quattrocchi, F.

    2003-04-01

    Two geochemical surveys have been performed in November and December 2002 in the Molise region (southern Italy) and surrounding areas struck by two moderate size earthquakes on October 31 (M_l 5.4) and on November 1 (M_l 5.3). The main goals of this study were: i) to highlight eventual variations either in the physico-chemical features or in the chemistry of thermo-mineral and cold springs (already sampled in 1997) discharging in an area located 50 km far from the epicentral one (Sannio-Matese, Campania region),; ii) to determine the chemical features of the groundwater discharging in the epicentral area, identifying the location and the extension of the various existing aquifers; iii) to collect information about eventual changes occurred in springs and wells (variations in flows, groundwater level in wells, etc.). Moreover, twice a week samplings have been carried out for two months at two important sulphurous springs (Larino spring, in the epicentral area and Telese thermo-mineral spring, in the Sannio area) in order to gather temporal chemical trend during the ongoing seismicity. We sampled a total of 35 sites (8 springs and wells in the Sannio-Matese area and 27 in the epicentral one) measuring in the field: temperature, pH, Eh, electrical conductivity, as well as radon, bicarbonate and H_2S contents. In laboratory, analyses of major, minor and trace elements have been performed, together with dissolved gas compositions. On 10 selected samples δ13C and 87/86Sr analyses are in progress. Data collected in the second survey show, for springs and wells located in the epicentral area, an evident pH and Eh increase (probably they returned to normal pre-earthquake values) together with some chemical variations; on the contrary, springs located in the Sannio-Matese area showed no variations. Local people observed sin-earthquake flow increases and variations in turbidity in two springs discharging in the epicentral area. All detected groundwater changes are discussed

  20. The october 31 (Ml 5.4) and november 1 (Ml 5.0) 2002 Molise earthquakes: first results from fluid geochemistry

    NASA Astrophysics Data System (ADS)

    Pizzino, L.; Cinti, D.; Barbieri, M.; Galli, G.; Voltattorni, N.; Quattrocchi, F.

    2003-04-01

    Two geochemical surveys have been performed in November and December 2002 in the Molise region (southern Italy) and surrounding areas struck by two moderate size earthquakes on October 31 (M_l 5.4) and on November 1 (M_l 5.3). The main goals of this study were: i) to highlight eventual variations either in the physico-chemical features or in the chemistry of thermo-mineral and cold springs (already sampled in 1997) discharging in an area located 50 km far from the epicentral one (Sannio-Matese, Campania region),; ii) to determine the chemical features of the groundwater discharging in the epicentral area, identifying the location and the extension of the various existing aquifers; iii) to collect information about eventual changes occurred in springs and wells (variations in flows, groundwater level in wells, etc.). Moreover, twice a week samplings have been carried out for two months at two important sulphurous springs (Larino spring, in the epicentral area and Telese thermo-mineral spring, in the Sannio area) in order to gather temporal chemical trend during the ongoing seismicity. We sampled a total of 35 sites (8 springs and wells in the Sannio-Matese area and 27 in the epicentral one) measuring in the field: temperature, pH, Eh, electrical conductivity, as well as radon, bicarbonate and H_2S contents. In laboratory, analyses of major, minor and trace elements have been performed, together with dissolved gas compositions. On 10 selected samples δ13C and 87/86Sr analyses are in progress. Data collected in the second survey show, for springs and wells located in the epicentral area, an evident pH and Eh increase (probably they returned to normal pre-earthquake values) together with some chemical variations; on the contrary, springs located in the Sannio-Matese area showed no variations. Local people observed sin-earthquake flow increases and variations in turbidity in two springs discharging in the epicentral area. All detected groundwater changes are discussed

  1. WaterML, an Information Standard for the Exchange of in-situ hydrological observations

    NASA Astrophysics Data System (ADS)

    Valentine, D.; Taylor, P.; Zaslavsky, I.

    2012-04-01

    The WaterML 2.0 Standards Working Group (SWG), working within the Open Geospatial Consortium (OGC) and in cooperation with the joint OGC-World Meteorological Organization (WMO) Hydrology Domain Working Group (HDWG), has developed an open standard for the exchange of water observation data; WaterML 2.0. The focus of the standard is time-series data, commonly generated from in-situ style monitoring. This is high value data for hydrological applications such as flood forecasting, environmental reporting and supporting hydrological infrastructure (e.g. dams, supply systems), which is commonly exchanged, but a lack of standards inhibits efficient reuse and automation. The process of developing WaterML required doing a harmonization analysis of existing standards to identify overlapping concepts and come to agreement on a harmonized definition. Generally the formats captured similar requirements, all with subtle differences, such as how time-series point metadata was handled. The in-progress standard WaterML 2.0 incorporates the semantics of the hydrologic information: location, procedure, and observations, and is implemented as an application schema of the Geography Markup Language version 3.2.1, making use of the OGC Observations & Measurements standards. WaterML2.0 is designed as an extensible schema to allow encoding of data to be used in a variety of exchange scenarios. Example areas of usage are: exchange of data for operational hydrological monitoring programs; supporting operation of infrastructure (e.g. dams, supply systems); cross-border exchange of observational data; release of data for public dissemination; enhancing disaster management through data exchange; and exchange in support of national reporting The first phase of WaterML2.0 focused on structural definitions allowing for the transfer of time-series, with less work on harmonization of vocabulary items such as quality codes. Vocabularies from various organizations tend to be specific and take time to

  2. Long-term Treatment with Finasteride Resulted in a Significant Improvement Relative to Placebo in Clinical Progression of Benign Prostatic Hyperplasia (BPH) in Men with Enlarged Prostates (≥30 mL), But Not in Those with Smaller Prostates (<30 mL): Data from the Medical Therapy of Prostatic Symptoms (MTOPS) Trial

    PubMed Central

    Kaplan, Steven A.; Lee, Jeannette Y.; Meehan, Alan G.; Kusek, John W.

    2013-01-01

    Purpose This post hoc analysis of the Medical Therapy of Prostatic Symptoms (MTOPS) trial examined the effect of finasteride alone compared to placebo on clinical progression of benign prostatic hyperplasia (BPH) in men with baseline prostate volume (PV) <30 mL and ≥30 mL. Materials and Methods Men were randomized to placebo (n=737), doxazosin alone (4 to 8 mg) (n=756), finasteride alone (5 mg) (n=768), or doxazosin plus finasteride (n=786) (average duration of follow-up was 4.5 yrs); ~50% of patients had a baseline PV ≥30 mL. The present analysis was based on the finasteride alone and placebo arms only and included patients for whom baseline and end of study data were available. We examined the effect of treatment on the cumulative percentage of men who did not experience clinical progression of BPH by study end. Results In men with baseline PV ≥30 mL, treatment with finasteride produced a significant (p<0.001) increase relative to placebo in the cumulative percentage of patients who did not experience clinical progression of BPH (finasteride, 88.1%, versus placebo, 77.8%). There was no significant (p=0.441) between-group difference in men with baseline PV <30 mL (91.4% versus 89.1%, respectively). Conclusions Long-term treatment with finasteride led to a significant beneficial effect compared to placebo on clinical progression of BPH in LUTS patients with enlarged prostates (baseline PV ≥30 mL). Finasteride had no significant effect, compared to placebo on clinical progression of BPH in LUTS patients with smaller prostates (baseline PV <30 mL). PMID:21334655

  3. ExaML version 3: a tool for phylogenomic analyses on supercomputers.

    PubMed

    Kozlov, Alexey M; Aberer, Andre J; Stamatakis, Alexandros

    2015-08-01

    Phylogenies are increasingly used in all fields of medical and biological research. Because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. We present ExaML version 3, a dedicated production-level code for inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers. We introduce several improvements and extensions to ExaML: Extensions of substitution models and supported data types, the integration of a novel load balance algorithm as well as a parallel I/O optimization that significantly improve parallel efficiency, and a production-level implementation for Intel MIC-based hardware platforms. © The Author 2015. Published by Oxford University Press.

  4. Mission options for rendezvous with the most accessible Near-Earth Asteroid - 1989 ML

    NASA Technical Reports Server (NTRS)

    Mcadams, Jim V.

    1992-01-01

    The recent discovery of the Amor-class 1989 ML, the most accessible known asteroid for minimum-energy rendezvous missions, has expedited the search for frequent, low-cost Near-Earth Asteroid rendezvous and round-trip missions. This paper identifies trajectory characteristics and assesses mass performance for low Delta V ballistic rendezvous opportunities to 1989 ML during the period 1996-2010. This asteroid also offers occasional unique extended mission opportunities, such as the lowest known Delta V requirement for any asteroid sample return mission as well as pre-rendezvous asteroid flyby and post-rendezvous comet flyby opportunities requiring less than 5.25 km/sec total Delta V. This paper also briefly comments concerning mission opportunities for asteroid 1991 JW, which recently replaced other known asteroids as the most accessible Near-Earth Asteroid for fast rendezvous and round-trip missions.

  5. Mission options for rendezvous with the most accessible Near-Earth Asteroid - 1989 ML

    NASA Technical Reports Server (NTRS)

    Mcadams, Jim V.

    1992-01-01

    The recent discovery of the Amor-class 1989 ML, the most accessible known asteroid for minimum-energy rendezvous missions, has expedited the search for frequent, low-cost Near-Earth Asteroid rendezvous and round-trip missions. This paper identifies trajectory characteristics and assesses mass performance for low Delta V ballistic rendezvous opportunities to 1989 ML during the period 1996-2010. This asteroid also offers occasional unique extended mission opportunities, such as the lowest known Delta V requirement for any asteroid sample return mission as well as pre-rendezvous asteroid flyby and post-rendezvous comet flyby opportunities requiring less than 5.25 km/sec total Delta V. This paper also briefly comments concerning mission opportunities for asteroid 1991 JW, which recently replaced other known asteroids as the most accessible Near-Earth Asteroid for fast rendezvous and round-trip missions.

  6. Galaxy luminosity functions, M/L ratios, and closure of the Universe - Numbers and problems

    NASA Technical Reports Server (NTRS)

    Felten, J. E.

    1985-01-01

    Data on the luminosity function (LF) of galaxies are reviewed and compared, and the result of Kirshner et al. (1983) giving a 'standard LF' is chosen as a best guess. Departures from the 'standard LF' for specific galaxy types and environments (clusters, groups, field) are discussed briefly. A luminosity density of about 1.4 x 10 to the -2nd h 'galaxies' per cubic megaparsec is obtained. The mean M/L ratio needed to give critical cosmological density (Omega sub 0 = 1) is then 920 h in solar units on the face-on magnitude system. Comparison with measured M/L ratios for galaxies and clusters, and with constraints imposed by inflation and nucleosynthesis, poses two problems of 'invisible mass'.

  7. Determination of Stress-Corrosion Cracking in Aluminum-Lithium Alloy ML377

    NASA Technical Reports Server (NTRS)

    Valek, Bryan C.

    1995-01-01

    The use of aluminum-lithium alloys for aerospace applications is currently being studied at NASA Langley Research Center's Metallic Materials Branch. The alloys in question will operate under stress in a corrosive environment. These conditions are ideal for the phenomena of Stress-Corrosion Cracking (SCC) to occur. The test procedure for SCC calls for alternate immersion and breaking load tests. These tests were optimized for the lab equipment and materials available in the Light Alloy lab. Al-Li alloy ML377 specimens were then subjected to alternate immersion and breaking load tests to determine residual strength and resistance to SCC. Corrosion morphology and microstructure were examined under magnification. Data shows that ML377 is highly resistant to stress-corrosion cracking.

  8. First-derivative solid-phase spectrophotometric determination of molybdenum at the ng ml(-1) level.

    PubMed

    Molína-Diaz, A; Pascual-Reguera, M I; Liñán-Veganzones, E; Fernández de Córdova, M L; Capitán-Vallvey, L F

    1996-02-01

    Derivative spectrophotometry was applied to solid-phase spectrophotometry in order to enhance its sensitivity and remove the large background noise caused by the absorption of the resin layer itself, and avoid the necessity of preparing a blank. The determination of micro-amounts of molybdenum (at the ng ml(-1) level) with pyrocatechol violet to form a 11 blue complex in acid medium, which is fixed on a dextran-type anion-exchange resin (Sephadex QAE-A-25), is described as an example of the application of this technique. The absorbance of the resin, packed in a 1 mm spectrophotometric cell, was measured directly. The characteristic peak amplitude of the signal at 716 nm in the first-derivative spectra is useful for quantitative determination of molybdenum (2-8 ng ml(-1); RSD = 4, 30%) in natural and industrial water samples, plant tissues and soil extracts.

  9. ML Frame Synchronization for OFDM Systems Using a Known Pilot and Cyclic Prefixes

    NASA Astrophysics Data System (ADS)

    Huh, Heon

    Orthogonal frequency-division multiplexing (OFDM) is a popular air interface technology that is adopted as a standard modulation scheme for 4G communication systems owing to its excellent spectral efficiency. For OFDM systems, synchronization problems have received much attention along with peak-to-average power ratio (PAPR) reduction. In addition to frequency offset estimation, frame synchronization is a challenging problem that must be solved to achieve optimal system performance. In this paper, we present a maximum likelihood (ML) frame synchronizer for OFDM systems. The synchronizer exploits a synchronization word and cyclic prefixes together to improve the synchronization performance. Numerical results show that the performance of the proposed frame synchronizer is better than that of conventional schemes. The proposed synchronizer can be used as a reference for evaluating the performance of other suboptimal frame synchronizers. We also modify the proposed frame synchronizer to reduce the implementation complexity and propose a near-ML synchronizer for time-varying fading channels.

  10. ML-IKE: a multi-layer IKE protocol for TCP performance enhancement in wireless networks

    NASA Astrophysics Data System (ADS)

    Zhang, Ya-Hang; Cheng, Bo-Wen; Qing, Si-Han; Zou, Guang-Nan; Wen, Wei-Ping

    2009-12-01

    To solve the conflict between TCP accelerating technology based on PEP middle node and IPSec protocol used in the Satellite Network, NASA and the Hughes Research Laboratory (HRL) each independently proposed a solution named Multilayer IPsec protocol which can integrate IPSec with TCP PEPs. The problem is: Traditional IKE protocol can't work with Multilayer IPSec protocol. In this study, the traditional IKE main mode and quick mode are enhanced for layered IPSec protocol, and an improved layered key distribution protocol: ML-IKE is proposed. This key distribution protocol is used for key exchange between peers and middle node, so that different nodes have different security associations (SA), and different security associations correspond to different IP packet fields, so different SA nodes have different authorization to different IP packet fields. ML-IKE protocol is suitable for layered IPSec, thus layered IPSec can be used for automatic key distribution and update.

  11. Discovery of novel selective inhibitors for EGFR-T790M/L858R.

    PubMed

    Bai, Fang; Liu, Hongyan; Tong, Linjiang; Zhou, Wei; Liu, Li; Zhao, Zhenjiang; Liu, Xiaofeng; Jiang, Hualiang; Wang, Xicheng; Xie, Hua; Li, Honglin

    2012-02-01

    Through a receptor-based and ligand-based combined virtual screening protocol, 21 novel compounds covering 15 scaffolds were identified as novel inhibitors for EGFR-T790M/L858R, among which, 12 of them were identified as selective inhibitors for EGFR-T790M/L858R to wild-type EGFR, and 5 of them exhibited 'dual-effective' to wild-type and mutant EGFR. Meanwhile, their antiproliferative effects toward EGFR high-expressing human lung cancer cell (A549), epidermoid carcinoma cell (A431), and the mutant EGFR-dependent cell (NCI-H1975) were also evaluated. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Mission options for rendezvous with the most accessible Near-Earth Asteroid - 1989 ML

    NASA Astrophysics Data System (ADS)

    McAdams, Jim V.

    1992-08-01

    The recent discovery of the Amor-class 1989 ML, the most accessible known asteroid for minimum-energy rendezvous missions, has expedited the search for frequent, low-cost Near-Earth Asteroid rendezvous and round-trip missions. This paper identifies trajectory characteristics and assesses mass performance for low Delta V ballistic rendezvous opportunities to 1989 ML during the period 1996-2010. This asteroid also offers occasional unique extended mission opportunities, such as the lowest known Delta V requirement for any asteroid sample return mission as well as pre-rendezvous asteroid flyby and post-rendezvous comet flyby opportunities requiring less than 5.25 km/sec total Delta V. This paper also briefly comments concerning mission opportunities for asteroid 1991 JW, which recently replaced other known asteroids as the most accessible Near-Earth Asteroid for fast rendezvous and round-trip missions.

  13. A 500-ml plastic bottle: an effective spacer for children with asthma.

    PubMed

    Zar, Heather J; Asmus, Michael J; Weinberg, Eugene G

    2002-06-01

    Inhaled therapy using a metered-dose inhaler (MDI) with attached spacer has been increasingly recognized as the optimal method for delivering asthma medication for acute attacks and chronic prophylaxis. However, in developing countries the cost and availability of commercially produced spacers limit the use of MDI-spacer delivery systems. A 500-ml plastic bottle has been recently adapted to function as a spacer. This article reviews the current data on the efficacy of this bottle-spacer and discusses its advantages and limitations. It is concluded that a modified 500-ml plastic bottle is an effective spacer; modification and use of this device should be incorporated into international guidelines for the management of children with asthma.

  14. Leak Detection and Location of Water Pipes Using Vibration Sensors and Modified ML Prefilter.

    PubMed

    Choi, Jihoon; Shin, Joonho; Song, Choonggeun; Han, Suyong; Park, Doo Il

    2017-09-13

    This paper proposes a new leak detection and location method based on vibration sensors and generalised cross-correlation techniques. Considering the estimation errors of the power spectral densities (PSDs) and the cross-spectral density (CSD), the proposed method employs a modified maximum-likelihood (ML) prefilter with a regularisation factor. We derive a theoretical variance of the time difference estimation error through summation in the discrete-frequency domain, and find the optimal regularisation factor that minimises the theoretical variance in practical water pipe channels. The proposed method is compared with conventional correlation-based techniques via numerical simulations using a water pipe channel model, and it is shown through field measurement that the proposed modified ML prefilter outperforms conventional prefilters for the generalised cross-correlation. In addition, we provide a formula to calculate the leak location using the time difference estimate when different types of pipes are connected.

  15. Identification of ML251, a Potent Inhibitor of T. brucei and T. cruzi Phosphofructokinase

    PubMed Central

    2013-01-01

    Human African Trypanosomiasis (HAT) is a severe, often fatal disease caused by the parasitic protist Trypanosoma brucei. The glycolytic pathway has been identified as the sole mechanism for ATP generation in the infective stage of these organisms, and several glycolytic enzymes, phosphofructokinase (PFK) in particular, have shown promise as potential drug targets. Herein, we describe the discovery of ML251, a novel nanomolar inhibitor of T. brucei PFK, and the structure–activity relationships within the series. PMID:24900769

  16. Method for Growth and Purification of Bacteriophage 643 on Streptococcus lactis ML3.

    PubMed

    Lyttle, D J; Petersen, G B

    1984-07-01

    The yield of bacteriophage 643 was increased by infecting cultures of Streptococcus lactis ML3 in late-log phase growth, harvesting the infected cells, and suspending them in fresh, phosphate-buffered minimal medium. The cells lysed after this treatment and produced high titers of bacteriophage. The phage particles were dissociated from debris by 2 M NaCl and purified by differential and CsCl band centrifugation.

  17. Design and implementation of CUAHSI WaterML and WaterOneFlow Web Services

    NASA Astrophysics Data System (ADS)

    Valentine, D. W.; Zaslavsky, I.; Whitenack, T.; Maidment, D.

    2007-12-01

    WaterOneFlow is a term for a group of web services created by and for the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) community. CUAHSI web services facilitate the retrieval of hydrologic observations information from online data sources using the SOAP protocol. CUAHSI Water Markup Language (below referred to as WaterML) is an XML schema defining the format of messages returned by the WaterOneFlow web services. \

  18. Impact of deep freezing on the stability of 25 mg/ml vancomycin ophthalmic solutions.

    PubMed

    Sautou-Miranda, V; Libert, F; Grand-Boyer, A; Gellis, C; Chopineau, J

    2002-03-02

    For the treatment of certain eye infections, ophthalmic solutions 'laced' with 25 mg/ml vancomycin are sometimes prepared. Their physical and chemical stability and the maintenance of their sterility were studied after deep freezing at -20 +/- 2 degrees C and thawing, followed or not by refrigeration for 48 h at 4 +/- 2 degrees C. Physical and chemical analysis comprised visual inspection turbidity, determination of pH and osmolality, and assay of vancomycin by high performance liquid chromatography with ultraviolet detection. For microbiological analysis a 25 mg/ml vancomycin ophthalmic solution was filtered through two membranes and cultured on trypticase-soy and Sabouraud-glucose solid media. Any colonies were then counted. These physical, chemical and microbiological analyses demonstrated the stability of 25 mg/ml vancomycin ophthalmic solutions in 5% glucose deep frozen at -20 +/- 2 degrees C for 3 months. The vancomycin concentration varied by no more than 5% of the initial concentration, and no breakdown product was evidenced. Neither pH (mean=3.8 +/- 0.1) nor osmolality (mean=318.3 +/- 5.6 mOsm/kg) varied significantly, and remained compatible with intraocular administration. No particle or bacterial combination was found in the course of the study. The thawing procedure (at ambient temperature or under warm running water from a tap) did not modify the stability of the eye drops. Likewise, storage in a refrigerator for 48 h after thawing did not modify stability. The advantage of storing vancomycin 25 mg/ml ophthalmic solutions for 3 months in deep freeze is that a stock of chemically and microbiologically controlled preparations can be held ready for administration to patients, thereby allowing prompter dispensing, as the eye drops are not made up extemporaneously, while the improved control over production ensures that patients receive solutions of constant quality, as every batch prepared is systematically inspected.

  19. Comparison: Mediation Solutions of WSMOLX and WebML/WebRatio

    NASA Astrophysics Data System (ADS)

    Zaremba, Maciej; Zaharia, Raluca; Turati, Andrea; Brambilla, Marco; Vitvar, Tomas; Ceri, Stefano

    In this chapter we compare the WSMO/WSML/WSMX andWebML/WebRatio approaches to the SWS-Challenge workshop mediation scenario in terms of the utilized underlying technologies and delivered solutions. In the mediation scenario one partner uses Roset-taNet to define its B2B protocol while the other one operates on a proprietary solution. Both teams shown how these partners could be semantically integrated.

  20. TrExML: a maximum-likelihood approach for extensive tree-space exploration.

    PubMed

    Wolf, M J; Easteal, S; Kahn, M; McKay, B D; Jermiin, L S

    2000-04-01

    Maximum-likelihood analysis of nucleotide and amino acid sequences is a powerful approach for inferring phylogenetic relationships and for comparing evolutionary hypotheses. Because it is a computationally demanding and time-consuming process, most algorithms explore only a minute portion of tree-space, with the emphasis on finding the most likely tree while ignoring the less likely, but not significantly worse, trees. However, when such trees exist, it is equally important to identify them to give due consideration to the phylogenetic uncertainty. Consequently, it is necessary to change the focus of these algorithms such that near optimal trees are also identified. This paper presents the Advanced Stepwise Addition Algorithm for exploring tree-space and two algorithms for generating all binary trees on a set of sequences. The Advanced Stepwise Addition Algorithm has been implemented in TrExML, a phylogenetic program for maximum-likelihood analysis of nucleotide sequences. TrExML is shown to be more effective at finding near optimal trees than a similar program, fastDNAml, implying that TrExML offers a better approach to account for phylogenetic uncertainty than has previously been possible. A program, TreeGen, is also described; it generates binary trees on a set of sequences allowing for extensive exploration of tree-space using other programs. TreeGen, TrExML, and the sequence data used to test the programs are available from the following two WWW sites: http://whitetail.bemidji.msus. edu/trexml/and http://jcsmr.anu.edu.au/dmm/humgen.+ ++html.

  1. The DaveMLTranslator: An Interface for DAVE-ML Aerodynamic Models

    NASA Technical Reports Server (NTRS)

    Hill, Melissa A.; Jackson, E. Bruce

    2007-01-01

    It can take weeks or months to incorporate a new aerodynamic model into a vehicle simulation and validate the performance of the model. The Dynamic Aerospace Vehicle Exchange Markup Language (DAVE-ML) has been proposed as a means to reduce the time required to accomplish this task by defining a standard format for typical components of a flight dynamic model. The purpose of this paper is to describe an object-oriented C++ implementation of a class that interfaces a vehicle subsystem model specified in DAVE-ML and a vehicle simulation. Using the DaveMLTranslator class, aerodynamic or other subsystem models can be automatically imported and verified at run-time, significantly reducing the elapsed time between receipt of a DAVE-ML model and its integration into a simulation environment. The translator performs variable initializations, data table lookups, and mathematical calculations for the aerodynamic build-up, and executes any embedded static check-cases for verification. The implementation is efficient, enabling real-time execution. Simple interface code for the model inputs and outputs is the only requirement to integrate the DaveMLTranslator as a vehicle aerodynamic model. The translator makes use of existing table-lookup utilities from the Langley Standard Real-Time Simulation in C++ (LaSRS++). The design and operation of the translator class is described and comparisons with existing, conventional, C++ aerodynamic models of the same vehicle are given.

  2. Serology with ML Flow test in health professionals from three different states of Brazil*

    PubMed Central

    Calado, Karla Lucena Sampaio; Magnanini, Mônica Maria Ferreira; de Moura, Rodrigo Scaliante; Gallo, Maria Eugenia Noviski; Bührer-Sékula, Samira; de Oliveira, Maria Leide Wand-Del-Rey

    2013-01-01

    BACKGROUND In highly endemic countries, transmission and sub-clinical infection of leprosy are likely and the disease manifests itself in individuals without any known close contact with a leprosy patient. Health workers are social contacts belonging to the same network (the Health System) and some of them share the same social environment (nursing assistants) as patients with known patients and / or carriers. OBJECTIVE To identify ML Flow seropositivity among health professionals. METHODS We conducted a cross-sectional study using a serological survey with the ML Flow test in 450 health professionals (doctors, nurses and nursing assistants), in order to detect seropositivity in areas of high and low endemicity in municipalities from three Brazilian states (RJ, MS and RS). RESULTS The results showed general 16% seropositivity, higher in low endemic areas, regardless of whether there was direct care for leprosy patients. Paradoxically, a statistical association was observed between the area studied and seropositivity, as the place with the lowest endemicity (CA) had the highest seropositivity rate (p = 0.033). CONCLUSION The authors suggest these results are associated with a presence of an unspecified link to bovine serum albumin (BSA), carrier of PGL-1 in the ML Flow test, and recommend expanded seroepidemiological research utilizing tests with human and bovine albumin. PMID:24474100

  3. A standardized framing for reporting protein identifications in mzIdentML 1.2

    PubMed Central

    Seymour, Sean L.; Farrah, Terry; Binz, Pierre-Alain; Chalkley, Robert J.; Cottrell, John S.; Searle, Brian C.; Tabb, David L.; Vizcaíno, Juan Antonio; Prieto, Gorka; Uszkoreit, Julian; Eisenacher, Martin; Martínez-Bartolomé, Salvador; Ghali, Fawaz; Jones, Andrew R.

    2015-01-01

    Inferring which protein species have been detected in bottom-up proteomics experiments has been a challenging problem for which solutions have been maturing over the past decade. While many inference approaches now function well in isolation, comparing and reconciling the results generated across different tools remains difficult. It presently stands as one of the greatest barriers in collaborative efforts such as the Human Proteome Project and public repositories like the PRoteomics IDEntifications (PRIDE) database. Here we present a framework for reporting protein identifications that seeks to improve capabilities for comparing results generated by different inference tools. This framework standardizes the terminology for describing protein identification results, associated with the HUPO-Proteomics Standards Initiative (PSI) mzIdentML standard, while still allowing for differing methodologies to reach that final state. It is proposed that developers of software for reporting identification results will adopt this terminology in their outputs. While the new terminology does not require any changes to the core mzIdentML model, it represents a significant change in practice, and, as such, the rules will be released via a new version of the mzIdentML specification (version 1.2) so that consumers of files are able to determine whether the new guidelines have been adopted by export software. PMID:25092112

  4. The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative

    PubMed Central

    Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J. Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W; Jones, Andrew R

    2011-01-01

    The Human Proteome Organisation’s Proteomics Standards Initiative (HUPO-PSI) has developed the GelML data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for mass spectrometry data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications. PMID:20677327

  5. PredicT-ML: a tool for automating machine learning model building with big clinical data.

    PubMed

    Luo, Gang

    2016-01-01

    Predictive modeling is fundamental to transforming large clinical data sets, or "big clinical data," into actionable knowledge for various healthcare applications. Machine learning is a major predictive modeling approach, but two barriers make its use in healthcare challenging. First, a machine learning tool user must choose an algorithm and assign one or more model parameters called hyper-parameters before model training. The algorithm and hyper-parameter values used typically impact model accuracy by over 40 %, but their selection requires many labor-intensive manual iterations that can be difficult even for computer scientists. Second, many clinical attributes are repeatedly recorded over time, requiring temporal aggregation before predictive modeling can be performed. Many labor-intensive manual iterations are required to identify a good pair of aggregation period and operator for each clinical attribute. Both barriers result in time and human resource bottlenecks, and preclude healthcare administrators and researchers from asking a series of what-if questions when probing opportunities to use predictive models to improve outcomes and reduce costs. This paper describes our design of and vision for PredicT-ML (prediction tool using machine learning), a software system that aims to overcome these barriers and automate machine learning model building with big clinical data. The paper presents the detailed design of PredicT-ML. PredicT-ML will open the use of big clinical data to thousands of healthcare administrators and researchers and increase the ability to advance clinical research and improve healthcare.

  6. Recombinant plasmid associated cell aggregation and high-frequency conjugation of Streptococcus lactis ML3.

    PubMed

    Walsh, P M; McKay, L L

    1981-06-01

    Lactose-positive (Lac+) transconjugants resulting from matings between Streptococcus lactic ML3 and S. lactis LM2301 possess a single plasmid of approximately 60 megadaltons (Mdal) which is nearly twice the size of the lactose plasmid of the donor. The majority of these Lac+ transconjugants aggregated in broth and were able to transfer lactose-fermenting ability at a frequency higher than 10(-1) per donor on milk agar plates or in broth. Lac+ transconjugants which did not clump conjugated at a much lower frequency. Lactose-negative derivatives of Lac+ clumping transconjugants did not aggregate in broth and were missing the 60-Mdal plasmid. The ability to aggregates in broth was very unstable. Strains could lose the ability to clump but retain lactose-fermenting ability. The majority of these Lac+ nonclumping derivatives of clumping transconjugants contained a plasmid of approximately 33 Mdal, the size of the lactose plasmid of the original donor ML3. These strains transferred lactose-fermenting ability at a frequency of approximately 10(-6) per donor, resulting in both Lac+ clumping transconjugants which contained a 60-Mdal plasmid and Lac+ nonclumping transconjugants which possessed a 33-Mdal plasmid. Our results suggest that the genes responsible for cell aggregation and high-frequency conjugation are on the segment of deoxyribonucleic acid which recombined with the 33-Mdal lactose plasmid in S. lactis ML3.

  7. ML372 blocks SMN ubiquitination and improves spinal muscular atrophy pathology in mice

    PubMed Central

    Abera, Mahlet B.; Xiao, Jingbo; Nofziger, Jonathan; Titus, Steve; Moritz, Kasey E.; Ferrer, Marc; Cherry, Jonathan J.; Androphy, Elliot J.; Wang, Amy; Xu, Xin; Austin, Christopher; Fischbeck, Kenneth H.; Marugan, Juan J.; Burnett, Barrington G.

    2016-01-01

    Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disease and one of the leading inherited causes of infant mortality. SMA results from insufficient levels of the survival motor neuron (SMN) protein, and studies in animal models of the disease have shown that increasing SMN protein levels ameliorates the disease phenotype. Our group previously identified and optimized a new series of small molecules, with good potency and toxicity profiles and reasonable pharmacokinetics, that were able to increase SMN protein levels in SMA patient–derived cells. We show here that ML372, a representative of this series, almost doubles the half-life of residual SMN protein expressed from the SMN2 locus by blocking its ubiquitination and subsequent degradation by the proteasome. ML372 increased SMN protein levels in muscle, spinal cord, and brain tissue of SMA mice. Importantly, ML372 treatment improved the righting reflex and extended survival of a severe mouse model of SMA. These results demonstrate that slowing SMN degradation by selectively inhibiting its ubiquitination can improve the motor phenotype and lifespan of SMA model mice. PMID:27882347

  8. Different Approaches for Teaching Volume and Students' Visualization Ability.

    ERIC Educational Resources Information Center

    Gabel, Dorothy L.; Enochs, Larry G.

    1987-01-01

    Discusses a study which was designed to examine if spatial-visual skills are related to learning the volume concept and if a particular mode of presentation for teaching volume is preferable for students of differing spatial ability. Results indicate that students of low visual orientation benefit if volume is taught before area and length. (ML)

  9. A CellML simulation compiler and code generator using ODE solving schemes.

    PubMed

    Punzalan, Florencio Rusty; Yamashita, Yoshiharu; Soejima, Naoki; Kawabata, Masanari; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi; Amano, Akira

    2012-10-19

    : Models written in description languages such as CellML are becoming a popular solution to the handling of complex cellular physiological models in biological function simulations. However, in order to fully simulate a model, boundary conditions and ordinary differential equation (ODE) solving schemes have to be combined with it. Though boundary conditions can be described in CellML, it is difficult to explicitly specify ODE solving schemes using existing tools. In this study, we define an ODE solving scheme description language-based on XML and propose a code generation system for biological function simulations. In the proposed system, biological simulation programs using various ODE solving schemes can be easily generated. We designed a two-stage approach where the system generates the equation set associating the physiological model variable values at a certain time t with values at t + Δt in the first stage. The second stage generates the simulation code for the model. This approach enables the flexible construction of code generation modules that can support complex sets of formulas. We evaluate the relationship between models and their calculation accuracies by simulating complex biological models using various ODE solving schemes. Using the FHN model simulation, results showed good qualitative and quantitative correspondence with the theoretical predictions. Results for the Luo-Rudy 1991 model showed that only first order precision was achieved. In addition, running the generated code in parallel on a GPU made it possible to speed up the calculation time by a factor of 50. The CellML Compiler source code is available for download at http://sourceforge.net/projects/cellmlcompiler.

  10. EnzML: multi-label prediction of enzyme classes using InterPro signatures

    PubMed Central

    2012-01-01

    Background Manual annotation of enzymatic functions cannot keep up with automatic genome sequencing. In this work we explore the capacity of InterPro sequence signatures to automatically predict enzymatic function. Results We present EnzML, a multi-label classification method that can efficiently account also for proteins with multiple enzymatic functions: 50,000 in UniProt. EnzML was evaluated using a standard set of 300,747 proteins for which the manually curated Swiss-Prot and KEGG databases have agreeing Enzyme Commission (EC) annotations. EnzML achieved more than 98% subset accuracy (exact match of all correct Enzyme Commission classes of a protein) for the entire dataset and between 87 and 97% subset accuracy in reannotating eight entire proteomes: human, mouse, rat, mouse-ear cress, fruit fly, the S. pombe yeast, the E. coli bacterium and the M. jannaschii archaebacterium. To understand the role played by the dataset size, we compared the cross-evaluation results of smaller datasets, either constructed at random or from specific taxonomic domains such as archaea, bacteria, fungi, invertebrates, plants and vertebrates. The results were confirmed even when the redundancy in the dataset was reduced using UniRef100, UniRef90 or UniRef50 clusters. Conclusions InterPro signatures are a compact and powerful attribute space for the prediction of enzymatic function. This representation makes multi-label machine learning feasible in reasonable time (30 minutes to train on 300,747 instances with 10,852 attributes and 2,201 class values) using the Mulan Binary Relevance Nearest Neighbours algorithm implementation (BR-kNN). PMID:22533924

  11. A CellML simulation compiler and code generator using ODE solving schemes

    PubMed Central

    2012-01-01

    Models written in description languages such as CellML are becoming a popular solution to the handling of complex cellular physiological models in biological function simulations. However, in order to fully simulate a model, boundary conditions and ordinary differential equation (ODE) solving schemes have to be combined with it. Though boundary conditions can be described in CellML, it is difficult to explicitly specify ODE solving schemes using existing tools. In this study, we define an ODE solving scheme description language-based on XML and propose a code generation system for biological function simulations. In the proposed system, biological simulation programs using various ODE solving schemes can be easily generated. We designed a two-stage approach where the system generates the equation set associating the physiological model variable values at a certain time t with values at t + Δt in the first stage. The second stage generates the simulation code for the model. This approach enables the flexible construction of code generation modules that can support complex sets of formulas. We evaluate the relationship between models and their calculation accuracies by simulating complex biological models using various ODE solving schemes. Using the FHN model simulation, results showed good qualitative and quantitative correspondence with the theoretical predictions. Results for the Luo-Rudy 1991 model showed that only first order precision was achieved. In addition, running the generated code in parallel on a GPU made it possible to speed up the calculation time by a factor of 50. The CellML Compiler source code is available for download at http://sourceforge.net/projects/cellmlcompiler. PMID:23083065

  12. The ML1/alpha =2 Instability Strip of ZZ Ceti Stars

    NASA Astrophysics Data System (ADS)

    Kepler, S. O.; da Costa, A. F. M.; Giovannini, O.; Koester, D.

    We are obtaining high signal-to-noise optical spectra and time-series photometry of all known DA white dwarfs around the ZZ Ceti instability strip to derive their atmospheric parameters and masses. In this work we report the fundamental parameters for 13 DA stars using ML1/alpha =2 model atmospheres and analyze the ZZ Ceti instability strip with a sample of 92 DA white dwarfs. This sample has an average mass of 0.59 +/- 0.02 Msun with a dispersion of 0.15 Msun. Our study shows that the limits of the ZZ Ceti instability strip depend on the effective temperature and mass of the star.

  13. Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.

    PubMed

    Swat, M J; Moodie, S; Wimalaratne, S M; Kristensen, N R; Lavielle, M; Mari, A; Magni, P; Smith, M K; Bizzotto, R; Pasotti, L; Mezzalana, E; Comets, E; Sarr, C; Terranova, N; Blaudez, E; Chan, P; Chard, J; Chatel, K; Chenel, M; Edwards, D; Franklin, C; Giorgino, T; Glont, M; Girard, P; Grenon, P; Harling, K; Hooker, A C; Kaye, R; Keizer, R; Kloft, C; Kok, J N; Kokash, N; Laibe, C; Laveille, C; Lestini, G; Mentré, F; Munafo, A; Nordgren, R; Nyberg, H B; Parra-Guillen, Z P; Plan, E; Ribba, B; Smith, G; Trocóniz, I F; Yvon, F; Milligan, P A; Harnisch, L; Karlsson, M; Hermjakob, H; Le Novère, N

    2015-06-01

    The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps.

  14. Spin-Ml and El responses of nuclei probed by proton inelastic scattering

    NASA Astrophysics Data System (ADS)

    Tamii, Atsushi; Matsubara, Hiroaki

    2014-12-01

    We pick up two studies on the nuclear responses from the recent experiments of high-resolution proton inelastic scattering at the Research Center for Nuclear Physics, Osaka University; 1) study of the nuclear symmetry and the neutron skin thickness by the measurement of energy electric dipole (El) response of 208Pb, and 2) study of the tensor correlation in the ground state by the measurement of the spin-Ml responses of even-even self-conjugate nuclei in the sd-shell nuclei.

  15. The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.

    PubMed

    Kikuchi, Norihiro; Kameyama, Akihiko; Nakaya, Shuuichi; Ito, Hiromi; Sato, Takashi; Shikanai, Toshihide; Takahashi, Yoriko; Narimatsu, Hisashi

    2005-04-15

    Bioinformatics resources for glycomics are very poor as compared with those for genomics and proteomics. The complexity of carbohydrate sequences makes it difficult to define a common language to represent them, and the development of bioinformatics tools for glycomics has not progressed. In this study, we developed a carbohydrate sequence markup language (CabosML), an XML description of carbohydrate structures. The language definition (XML Schema) and an experimental database of carbohydrate structures using an XML database management system are available at http://www.phoenix.hydra.mki.co.jp/CabosDemo.html kikuchi@hydra.mki.co.jp.

  16. Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development

    PubMed Central

    Swat, MJ; Moodie, S; Wimalaratne, SM; Kristensen, NR; Lavielle, M; Mari, A; Magni, P; Smith, MK; Bizzotto, R; Pasotti, L; Mezzalana, E; Comets, E; Sarr, C; Terranova, N; Blaudez, E; Chan, P; Chard, J; Chatel, K; Chenel, M; Edwards, D; Franklin, C; Giorgino, T; Glont, M; Girard, P; Grenon, P; Harling, K; Hooker, AC; Kaye, R; Keizer, R; Kloft, C; Kok, JN; Kokash, N; Laibe, C; Laveille, C; Lestini, G; Mentré, F; Munafo, A; Nordgren, R; Nyberg, HB; Parra-Guillen, ZP; Plan, E; Ribba, B; Smith, G; Trocóniz, IF; Yvon, F; Milligan, PA; Harnisch, L; Karlsson, M; Hermjakob, H; Le Novère, N

    2015-01-01

    The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps. PMID:26225259

  17. Effects of temperature and glucose limitation on coal solubilization by Candida ML13

    SciTech Connect

    Evans, B. )

    1991-04-01

    Biological processing has received considerable attention in recent years as a technology for the utilization of low-ranked coals. Several fungi and actinomycetes have been shown to liquefy highly oxidized coal in pure culture under aerobic conditions. This report describes the optimization of cultural conditions for coal solubilization by Candida sp. ML13, an organism originally isolated from a naturally weathered coal seam. Coal solubilization by surface cultures of Candida sp. has previously been demonstrated. The author describes here the elicitation of the activity in submerged cultures as well as the effect of carbohydrate concentration, carbon source, temperature, and agitation rate on coal solubilization by this organism.

  18. Glass dissolution at 20, 40, 70 and 90 C: Short-term effects of solution chemistry and long-term Na release

    SciTech Connect

    Bakel, A.J.; Ebert, W.L.; Strachan, D.M.; Brown, N.R.

    1996-08-01

    The corrosion behavior of a borosilicate glass containing 20 mass 5 Na{sub 2}O was assessed using static dissolution tests. This glass (LD6-5412) is representative of high Na glasses that may be used to stabilize Hanford low-level radioactive waste. The normalized mass loss (NL) decreases as NL(Na) {approximately} NL(B) > NL(Si) in 20 and 40 C for tests conducted at glass surface area to leachant volume (S/V) ratio of 10 m{sup {minus}1}, and decreases as NL(Na) > NL(B) {approximately} NL(Si) in 90 C tests conducted at 10 m{sup {minus}1} and in all tests conducted at higher S/V. The difference in the corrosion behavior is probably caused by the influence of dissolved glass components in the leachates. The NL(Na) is greater than the NL(B) or NL(Si) in all the tests conducted. Results from long-term tests at 2,000 m{sup {minus}1} show that the preferential release of Na persists for longer than one year at all temperatures and indicate that Na is released from this glass by an ion exchange process.

  19. PepArML: A Meta-Search Peptide Identification Platform

    PubMed Central

    Edwards, Nathan J.

    2014-01-01

    The PepArML meta-search peptide identification platform provides a unified search interface to seven search engines; a robust cluster, grid, and cloud computing scheduler for large-scale searches; and an unsupervised, model-free, machine-learning-based result combiner, which selects the best peptide identification for each spectrum, estimates false-discovery rates, and outputs pepXML format identifications. The meta-search platform supports Mascot; Tandem with native, k-score, and s-score scoring; OMSSA; MyriMatch; and InsPecT with MS-GF spectral probability scores — reformatting spectral data and constructing search configurations for each search engine on the fly. The combiner selects the best peptide identification for each spectrum based on search engine results and features that model enzymatic digestion, retention time, precursor isotope clusters, mass accuracy, and proteotypic peptide properties, requiring no prior knowledge of feature utility or weighting. The PepArML meta-search peptide identification platform often identifies 2–3 times more spectra than individual search engines at 10% FDR. PMID:25663956

  20. Specifications of insilicoML 1.0: a multilevel biophysical model description language.

    PubMed

    Asai, Yoshiyuki; Suzuki, Yasuyuki; Kido, Yoshiyuki; Oka, Hideki; Heien, Eric; Nakanishi, Masao; Urai, Takahito; Hagihara, Kenichi; Kurachi, Yoshihisa; Nomura, Taishin

    2008-12-01

    An extensible markup language format, insilicoML (ISML), version 0.1, describing multi-level biophysical models has been developed and available in the public domain. ISML is fully compatible with CellML 1.0, a model description standard developed by the IUPS Physiome Project, for enhancing knowledge integration and model sharing. This article illustrates the new specifications of ISML 1.0 that largely extend the capability of ISML 0.1. ISML 1.0 can describe various types of mathematical models, including ordinary/partial differential/difference equations representing the dynamics of physiological functions and the geometry of living organisms underlying the functions. ISML 1.0 describes a model using a set of functional elements (modules) each of which can specify mathematical expressions of the functions. Structural and logical relationships between any two modules are specified by edges, which allow modular, hierarchical, and/or network representations of the model. The role of edge-relationships is enriched by key words in order for use in constructing a physiological ontology. The ontology is further improved by the traceability of history of the model's development and by linking between different ISML models stored in the model's database using meta-information. ISML 1.0 is designed to operate with a model database and integrated environments for model development and simulations for knowledge integration and discovery.

  1. Passive microrheology of normal and cancer cells after ML7 treatment by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Lyapunova, Elena; Nikituk, Alexander; Bayandin, Yuriy; Naimark, Oleg; Rianna, Carmela; Radmacher, Manfred

    2016-08-01

    Mechanical properties of living cancer and normal thyroidal cells were investigated by atomic force microscopy (AFM). Cell mechanics was compared before and after treatment with ML7, which is known to reduce myosin activity and induce softening of cell structures. We recorded force curves with extended dwell time of 6 seconds in contact at maximum forces from 500 pN to 1 nN. Data were analyzed within different frameworks: Hertz fit was applied in order to evaluate differences in Young's moduli among cell types and conditions, while the fluctuations of the cantilever in contact with cells were analyzed with both conventional algorithms (probability density function and power spectral density) and multifractal detrended fluctuation analysis (MF-DFA). We found that cancer cells were softer than normal cells and ML7 had a substantial softening effect on normal cells, but only a marginal one on cancer cells. Moreover, we observed that all recorded signals for normal and cancer cells were monofractal with small differences between their scaling parameters. Finally, the applicability of wavelet-based methods of data analysis for the discrimination of different cell types is discussed.

  2. Isolation of a novel LPS-induced component of the ML superfamily in Ciona intestinalis.

    PubMed

    Vizzini, Aiti; Bonura, Angela; Longo, Valeria; Sanfratello, Maria Antonietta; Parrinello, Daniela; Cammarata, Matteo; Colombo, Paolo

    2015-11-01

    ML superfamily represents a group of proteins playing important roles in lipid metabolism and innate immune response. In this study, we report the identification of the first component of the ML superfamily in the invertebrate Ciona intestinalis by means of a subtractive hybridization strategy. Sequence homology and phylogenetic analysis showed that this protein forms a specific clade with vertebrate components of the Niemann-Pick type C2 protein and, for this reason, it has been named Ci-NPC2. The putative Ci-NPC2 is a 150 amino acids long protein with a short signal peptide, seven cysteine residues, three putative lipid binding site and a three-dimensional model showing a characteristic β-strand structure. Gene expression analysis demonstrated that the Ci-NPC2 protein is positively upregulated after LPS inoculum with a peak of expression 1 h after challenge. Finally, in-situ hybridization demonstrated that the Ci-NPC2 protein is preferentially expressed in hemocytes inside the vessel lumen.

  3. In Vivo Cloning of lac Genes in Streptococcus lactis ML3.

    PubMed

    Anderson, D G; McKay, L L

    1984-02-01

    The isolation and characterization of a Streptococcus lactis ML3 strain which possessed a recombinant lactose plasmid is described. The recombination events generating this plasmid occurred in vivo in a recombination-deficient strain and appeared to be mediated by transposition events. Restriction mapping revealed that the recombinant plasmid, pDA0307, contained a region of the lactose plasmid, pSK08, linked to another resident plasmid, pSK07. Copy number determinations indicated that the lac genes were present at approximately 20 copies per cell in pDA0307, whereas the lac genes are normally present at approximately 10 copies per cell in pSK08. The strain containing pDA0307 displayed a 21 to 54% increase in the expression of the Lac enzyme phospho-beta-d-galactosidase. However, the strain containing pDA0307 both grew and produced lactic acid in milk at rates identical to that of a strain containing pSK08. This result suggests that lac gene dosage of plasmid-linked lac genes was not limiting the rate at which these derivatives of S. lactis ML3 fermented milk.

  4. The ML1Nx2 Phosphatidylinositol 3,5-Bisphosphate Probe Shows Poor Selectivity in Cells.

    PubMed

    Hammond, Gerald R V; Takasuga, Shunsuke; Sasaki, Takehiko; Balla, Tamas

    2015-01-01

    Phosphatidylinositol (3,5)-bisphosphate (PtdIns(3,5)P2) is a quantitatively minor phospholipid in eukaryotic cells that plays a fundamental role in regulating endocytic membrane traffic. Despite its clear importance for cellular function and organism physiology, mechanistic details of its biology have so far not been fully elucidated. In part, this is due to a lack of experimental tools that specifically probe for PtdIns(3,5)P2 in cells to unambiguously identify its dynamics and site(s) of action. In this study, we have evaluated a recently reported PtdIns(3,5)P2 biosensor, GFP-ML1Nx2, for its veracity as such a probe. We report that, in live cells, the localization of this biosensor to sub-cellular compartments is largely independent of PtdIns(3,5)P2, as assessed after pharmacological, chemical genetic or genomic interventions that block the lipid's synthesis. We therefore conclude that it is unwise to interpret the localization of ML1Nx2 as a true and unbiased biosensor for PtdIns(3,5)P2.

  5. Passive microrheology of normal and cancer cells after ML7 treatment by atomic force microscopy

    SciTech Connect

    Lyapunova, Elena; Nikituk, Alexander Bayandin, Yuriy; Naimark, Oleg; Rianna, Carmela Radmacher, Manfred

    2016-08-02

    Mechanical properties of living cancer and normal thyroidal cells were investigated by atomic force microscopy (AFM). Cell mechanics was compared before and after treatment with ML7, which is known to reduce myosin activity and induce softening of cell structures. We recorded force curves with extended dwell time of 6 seconds in contact at maximum forces from 500 pN to 1 nN. Data were analyzed within different frameworks: Hertz fit was applied in order to evaluate differences in Young’s moduli among cell types and conditions, while the fluctuations of the cantilever in contact with cells were analyzed with both conventional algorithms (probability density function and power spectral density) and multifractal detrended fluctuation analysis (MF-DFA). We found that cancer cells were softer than normal cells and ML7 had a substantial softening effect on normal cells, but only a marginal one on cancer cells. Moreover, we observed that all recorded signals for normal and cancer cells were monofractal with small differences between their scaling parameters. Finally, the applicability of wavelet-based methods of data analysis for the discrimination of different cell types is discussed.

  6. Using SysML for MBSE analysis of the LSST system

    NASA Astrophysics Data System (ADS)

    Claver, Charles F.; Dubois-Felsmann, Gregory; Delgado, Francisco; Hascall, Pat; Marshall, Stuart; Nordby, Martin; Schalk, Terry; Schumacher, German; Sebag, Jacques

    2010-07-01

    The Large Synoptic Survey Telescope is a complex hardware - software system of systems, making up a highly automated observatory in the form of an 8.4m wide-field telescope, a 3.2 billion pixel camera, and a peta-scale data processing and archiving system. As a project, the LSST is using model based systems engineering (MBSE) methodology for developing the overall system architecture coded with the Systems Modeling Language (SysML). With SysML we use a recursive process to establish three-fold relationships between requirements, logical & physical structural component definitions, and overall behavior (activities and sequences) at successively deeper levels of abstraction and detail. Using this process we have analyzed and refined the LSST system design, ensuring the consistency and completeness of the full set of requirements and their match to associated system structure and behavior. As the recursion process proceeds to deeper levels we derive more detailed requirements and specifications, and ensure their traceability. We also expose, define, and specify critical system interfaces, physical and information flows, and clarify the logic and control flows governing system behavior. The resulting integrated model database is used to generate documentation and specifications and will evolve to support activities from construction through final integration, test, and commissioning, serving as a living representation of the LSST as designed and built. We discuss the methodology and present several examples of its application to specific systems engineering challenges in the LSST design.

  7. Critical oxygen delivery in conscious humans is less than 7.3 ml O2 x kg(-1) x min(-1).

    PubMed

    Lieberman, J A; Weiskopf, R B; Kelley, S D; Feiner, J; Noorani, M; Leung, J; Toy, P; Viele, M

    2000-02-01

    The "critical" level of oxygen delivery (DO2) is the value below which DO2 fails to satisfy the metabolic need for oxygen. No prospective data in healthy, conscious humans define this value. The authors reduced DO2 in healthy volunteers in an attempt to determine the critical DO2. With Institutional Review Board approval and informed consent, the authors studied eight healthy, conscious volunteers, aged 19-25 yr. Hemodynamic measurements were obtained at steady state before and after profound acute isovolemic hemodilution with 5% albumin and autologous plasma, and again at the reduced hemoglobin concentration after additional reduction of DO2 by an infusion of a beta-adrenergic antagonist, esmolol. Reduction of hemoglobin from 12.5+/-0.8 g/dl to 4.8+/-0.2 g/dl (mean +/- SD) increased heart rate, stroke volume index, and cardiac index, and reduced DO2 (14.0+/-2.9 to 9.9+/-20 ml O2 x kg(-1) x min(-1); all P<0.001). Oxygen consumption (VO2; 3.0+/-0.5 to 3.4+/-0.6 ml O2 x kg(-1) x min(-1); P<0.05) and plasma lactate concentration (0.50+/-0.10 to 0.62+/-0.16 mM; P<0.05; n = 7) increased slightly. Esmolol decreased heart rate, stroke volume index, and cardiac index, and further decreased DO2 (to 7.3+/-1.4 ml O2 x kg(-1) x min(-1); all P<0.01 vs. before esmolol). VO2 (3.2+/-0.6 ml O2 x kg(-1) x min(-1); P>0.05) and plasma lactate (0.66+/-0.14 mM; P>0.05) did not change further. No value of plasma lactate exceeded the normal range. A decrease in DO2 to 7.3+/-1.4 ml O2 x kg(-1) min(-1) in resting, healthy, conscious humans does not produce evidence of inadequate systemic oxygenation. The critical DO2 in healthy, resting, conscious humans appears to be less than this value.

  8. Safety, immunogenicity, and efficacy of the ML29 reassortant vaccine for Lassa fever in small non-human primates✩

    PubMed Central

    Lukashevich, Igor S.; Carrion, Ricardo; Salvato, Maria S.; Mansfield, Keith; Brasky, Kathleen; Zapata, Juan; Cairo, Cristiana; Goicochea, Marco; Hoosien, Gia E.; Ticer, Anysha; Bryant, Joseph; Davis, Harry; Hammamieh, Rasha; Mayda, Maria; Jett, Marti; Patterson, Jean

    2008-01-01

    A single injection of ML29 reassortant vaccine for Lassa fever induces low, transient viremia, and low or moderate levels of ML29 replication in tissues of common marmosets depending on the dose of the vaccination. The vaccination elicits specific immune responses and completely protects marmosets against fatal disease by induction of sterilizing cell-mediated immunity. DNA array analysis of human peripheral blood mononuclear cells from healthy donors exposed to ML29 revealed that gene expression patterns in ML29-exposed PBMC and control, media-exposed PBMC, clustered together confirming safety profile of the ML29 in non-human primates. The ML29 reassortant is a promising vaccine candidate for Lassa fever. PMID:18692539

  9. Safety, immunogenicity, and efficacy of the ML29 reassortant vaccine for Lassa fever in small non-human primates.

    PubMed

    Lukashevich, Igor S; Carrion, Ricardo; Salvato, Maria S; Mansfield, Keith; Brasky, Kathleen; Zapata, Juan; Cairo, Cristiana; Goicochea, Marco; Hoosien, Gia E; Ticer, Anysha; Bryant, Joseph; Davis, Harry; Hammamieh, Rasha; Mayda, Maria; Jett, Marti; Patterson, Jean

    2008-09-26

    A single injection of ML29 reassortant vaccine for Lassa fever induces low, transient viremia, and low or moderate levels of ML29 replication in tissues of common marmosets depending on the dose of the vaccination. The vaccination elicits specific immune responses and completely protects marmosets against fatal disease by induction of sterilizing cell-mediated immunity. DNA array analysis of human peripheral blood mononuclear cells from healthy donors exposed to ML29 revealed that gene expression patterns in ML29-exposed PBMC and control, media-exposed PBMC, clustered together confirming safety profile of the ML29 in non-human primates. The ML29 reassortant is a promising vaccine candidate for Lassa fever.

  10. Increasing prostate biopsy cores based on volume vs the sextant biopsy: a prospective randomized controlled clinical study on cancer detection rates and morbidity.

    PubMed

    Mariappan, Paramananthan; Chong, Wooi Loong; Sundram, Murali; Mohamed, Sahabudin R

    2004-08-01

    To determine if a volume-adjusted increase in the number of biopsy cores could detect more prostate cancers than the standard sextant biopsy alone, without increasing morbidity, and to determine its applicability in Malaysian patients, as a standard sextant biopsy misses 20-25% of prostate malignancies. In a prospective randomized study of patients undergoing transrectal ultrasonography (TRUS)-guided biopsy for a prostate-specific antigen (PSA) level of 4-20 ng/mL without abnormal digital rectal examination (DRE), the men were divided into five main groups (A-E) with prostate volumes of <20, 20-40, 40-60, 60-80 and >80 mL, respectively. Patients in groups B-E were randomized into sextant (B1 to E1) and increased biopsy-core subgroups, i.e. B2 (eight cores), C2 (10 cores), D2 (12 cores) and E2 (14 cores). The morbidity profile was also evaluated during and after TRUS biopsy, assessing a pain score, rectal bleeding, haematuria, haemospermia and development of fever. In all, 132 patients were recruited (mean age 67.8 years; mean PSA 9.41 ng/mL). The overall cancer detection rate was 24% (32 men). Taking more cores detected 65.5% of cancers, and the sextant biopsy 34.5% (P = 0.0025), but did not increase the overall morbidity. The volume-adjusted, increased-core regimen significantly increased the positive biopsy rate of TRUS-guided prostate biopsies with no added morbidity.

  11. Five Methods of Breast Volume Measurement: A Comparative Study of Measurements of Specimen Volume in 30 Mastectomy Cases

    PubMed Central

    Kayar, Ragip; Civelek, Serdar; Cobanoglu, Murat; Gungor, Osman; Catal, Hidayet; Emiroglu, Mustafa

    2011-01-01

    Background: To compare breast volume measurement techniques in terms of accuracy, convenience, and cost. Methods: Breast volumes of 30 patients who were scheduled to undergo total mastectomy surgery were measured preoperatively by using five different methods (mammography, anatomic [anthropometric], thermoplastic casting, the Archimedes procedure, and the Grossman-Roudner device). Specimen volume after total mastectomy was measured in each patient with the water displacement method (Archimedes). The results were compared statistically with the values obtained by the five different methods. Results: The mean mastectomy specimen volume was 623.5 (range 150–1490) mL. The breast volume values were established to be 615.7 mL (r = 0.997) with the mammographic method, 645.4 mL (r = 0.975) with the anthropometric method, 565.8 mL (r = 0.934) with the Grossman-Roudner device, 583.2 mL (r = 0.989) with the Archimedes procedure, and 544.7 mL (r = 0.94) with the casting technique. Examination of r values revealed that the most accurate method was mammography for all volume ranges, followed by the Archimedes method. Conclusion: The present study demonstrated that the most accurate method of breast volume measurement is mammography, followed by the Archimedes method. However, when patient comfort, ease of application, and cost were taken into consideration, the Grossman-Roudner device and anatomic measurement were relatively less expensive, and easier methods with an acceptable degree of accuracy. PMID:21494401

  12. Five methods of breast volume measurement: a comparative study of measurements of specimen volume in 30 mastectomy cases.

    PubMed

    Kayar, Ragip; Civelek, Serdar; Cobanoglu, Murat; Gungor, Osman; Catal, Hidayet; Emiroglu, Mustafa

    2011-03-27

    To compare breast volume measurement techniques in terms of accuracy, convenience, and cost. Breast volumes of 30 patients who were scheduled to undergo total mastectomy surgery were measured preoperatively by using five different methods (mammography, anatomic [anthropometric], thermoplastic casting, the Archimedes procedure, and the Grossman-Roudner device). Specimen volume after total mastectomy was measured in each patient with the water displacement method (Archimedes). The results were compared statistically with the values obtained by the five different methods. The mean mastectomy specimen volume was 623.5 (range 150-1490) mL. The breast volume values were established to be 615.7 mL (r = 0.997) with the mammographic method, 645.4 mL (r = 0.975) with the anthropometric method, 565.8 mL (r = 0.934) with the Grossman-Roudner device, 583.2 mL (r = 0.989) with the Archimedes procedure, and 544.7 mL (r = 0.94) with the casting technique. Examination of r values revealed that the most accurate method was mammography for all volume ranges, followed by the Archimedes method. The present study demonstrated that the most accurate method of breast volume measurement is mammography, followed by the Archimedes method. However, when patient comfort, ease of application, and cost were taken into consideration, the Grossman-Roudner device and anatomic measurement were relatively less expensive, and easier methods with an acceptable degree of accuracy.

  13. A novel ML protein from Manduca sexta may function as a key accessory protein for lipopolysaccharide signaling.

    PubMed

    Ao, Jing-qun; Ling, Erjun; Rao, Xiang-jun; Yu, Xiao-Qiang

    2008-05-01

    Lipopolysaccharide (LPS) present on the outer membrane of Gram-negative bacteria is one of the most important pathogen-associated molecular patterns and a potent elicitor in innate immunity. In human, TLR4 (Toll-like receptor 4) and MD-2 (myeloid differiation-2) form a receptor complex to transduce the LPS signal into cells. However, in invertebrates, receptors that recognize LPS have not been determined. Here we report the purification, characterization and cDNA cloning of an ML (MD-2-related lipid-recognition) protein from the tobacco hornworm Manduca sexta. The full-length cDNA of this M. sexta ML protein, named MsML-1, is 532bp with an open reading frame of 456bp that encodes a polypeptide of 151 amino acids containing an ML domain. MsML-1 is a secreted glycoprotein and its mRNA is expressed in fat body and hemocytes. The expression level of MsML-1 mRNA in fat body and hemocytes as well as MsML-1 protein in hemolymph are not induced by immune challenge. Recombinant MsML-1 protein specifically binds to LPS from several Gram-negative bacteria and LPS Re mutant, as well as to lipid A, but not to KDO (2-keto-3-deoxyoctonate). Our results suggest that MsML-1 may function as a key accessory protein for LPS signaling in M. sexta against Gram-negative bacterial infection.

  14. A novel ML protein from Manduca sexta may function as a key accessory protein for lipopolysaccharide signaling

    PubMed Central

    Ao, Jing-qun; Ling, Erjun; Rao, Xiang-jun; Yu, Xiao-Qiang

    2015-01-01

    Lipopolysaccharide (LPS) present on the outer membrane of Gram-negative bacteria is one of the most important pathogen-associated molecular patterns and a potent elicitor in innate immunity. In human, TLR4 (Toll-like receptor 4) and MD-2 (myeloid differiation-2) form a receptor complex to transduce the LPS signal into cells. However, in invertebrates, receptors that recognize LPS have not been determined. Here we report the purification, characterization and cDNA cloning of an ML (MD-2-related lipid-recognition) protein from the tobacco hornworm Manduca sexta. The full-length cDNA of this M. sexta ML protein, named MsML-1, is 532 bp with an open reading frame of 456 bp that encodes a polypeptide of 151 amino acids containing an ML domain. MsML-1 is a secreted glycoprotein and its mRNA is expressed in fat body and hemocytes. The expression level of MsML-1 mRNA in fat body and hemocytes as well as MsML-1 protein in hemolymph are not induced by immune challenge. Recombinant MsML-1 protein specifically binds to LPS from several Gram-negative bacteria and LPS Re mutant, as well as to lipid A, but not to KDO (2-keto-3-deoxyoctonate). Our results suggest that MsML-1 may function as a key accessory protein for LPS signaling in M. sexta against Gram-negative bacterial infection. PMID:18343500

  15. The validity and reliability of computed tomography orbital volume measurements.

    PubMed

    Diaconu, Silviu C; Dreizin, David; Uluer, Mehmet; Mossop, Corey; Grant, Michael P; Nam, Arthur J

    2017-09-01

    Orbital volume calculations allow surgeons to design patient-specific implants to correct volume deficits. It is estimated that changes as small as 1 ml in orbital volume can lead to enophthalmos. Awareness of the limitations of orbital volume computed tomography (CT) measurements is critical to differentiate between true volume differences and measurement error. The aim of this study is to analyze the validity and reliability of CT orbital volume measurements. A total of 12 cadaver orbits were scanned using a standard CT maxillofacial protocol. Each orbit was dissected to isolate the extraocular muscles, fatty tissue, and globe. The empty bony orbital cavity was then filled with sculpting clay. The volumes of the muscle, fat, globe, and clay (i.e., bony orbital cavity) were then individually measured via water displacement. The CT-derived volumes, measured by manual segmentation, were compared to the direct measurements to determine validity. The difference between CT orbital volume measurements and physically measured volumes is not negligible. Globe volumes have the highest agreement with 95% of differences between -0.5 and 0.5 ml, bony volumes are more likely to be overestimated with 95% of differences between -1.8 and 2.6 ml, whereas extraocular muscle volumes have poor validity and should be interpreted with caution. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

  16. Magnetic Nickel iron Electroformed Trap (MagNET): a master/replica fabrication strategy for ultra-high throughput (>100 mL h(-1)) immunomagnetic sorting.

    PubMed

    Ko, Jina; Yelleswarapu, Venkata; Singh, Anup; Shah, Nishal; Issadore, David

    2016-08-02

    Microfluidic devices can sort immunomagnetically labeled cells with sensitivity and specificity much greater than that of conventional methods, primarily because the size of microfluidic channels and micro-scale magnets can be matched to that of individual cells. However, these small feature sizes come at the expense of limited throughput (ϕ < 5 mL h(-1)) and susceptibility to clogging, which have hindered current microfluidic technology from processing relevant volumes of clinical samples, e.g. V > 10 mL whole blood. Here, we report a new approach to micromagnetic sorting that can achieve highly specific cell separation in unprocessed complex samples at a throughput (ϕ > 100 mL h(-1)) 100× greater than that of conventional microfluidics. To achieve this goal, we have devised a new approach to micromagnetic sorting, the magnetic nickel iron electroformed trap (MagNET), which enables high flow rates by having millions of micromagnetic traps operate in parallel. Our design rotates the conventional microfluidic approach by 90° to form magnetic traps at the edges of pores instead of in channels, enabling millions of the magnetic traps to be incorporated into a centimeter sized device. Unlike previous work, where magnetic structures were defined using conventional microfabrication, we take inspiration from soft lithography and create a master from which many replica electroformed magnetic micropore devices can be economically manufactured. These free-standing 12 μm thick permalloy (Ni80Fe20) films contain micropores of arbitrary shape and position, allowing the device to be tailored for maximal capture efficiency and throughput. We demonstrate MagNET's capabilities by fabricating devices with both circular and rectangular pores and use these devices to rapidly (ϕ = 180 mL h(-1)) and specifically sort rare tumor cells from white blood cells.

  17. Magnetic Nickel iron Electroformed Trap (MagNET): a master/replica fabrication strategy for ultra-high throughput (>100 mL h−1) immunomagnetic sorting†

    PubMed Central

    Ko, Jina; Yelleswarapu, Venkata; Singh, Anup; Shah, Nishal

    2016-01-01

    Microfluidic devices can sort immunomagnetically labeled cells with sensitivity and specificity much greater than that of conventional methods, primarily because the size of microfluidic channels and micro-scale magnets can be matched to that of individual cells. However, these small feature sizes come at the expense of limited throughput (ϕ < 5 mL h−1) and susceptibility to clogging, which have hindered current microfluidic technology from processing relevant volumes of clinical samples, e.g. V > 10 mL whole blood. Here, we report a new approach to micromagnetic sorting that can achieve highly specific cell separation in unprocessed complex samples at a throughput (ϕ > 100 mL h−1) 100× greater than that of conventional microfluidics. To achieve this goal, we have devised a new approach to micromagnetic sorting, the magnetic nickel iron electroformed trap (MagNET), which enables high flow rates by having millions of micromagnetic traps operate in parallel. Our design rotates the conventional microfluidic approach by 90° to form magnetic traps at the edges of pores instead of in channels, enabling millions of the magnetic traps to be incorporated into a centimeter sized device. Unlike previous work, where magnetic structures were defined using conventional microfabrication, we take inspiration from soft lithography and create a master from which many replica electroformed magnetic micropore devices can be economically manufactured. These free-standing 12 µm thick permalloy (Ni80Fe20) films contain micropores of arbitrary shape and position, allowing the device to be tailored for maximal capture efficiency and throughput. We demonstrate MagNET's capabilities by fabricating devices with both circular and rectangular pores and use these devices to rapidly (ϕ = 180 mL h−1) and specifically sort rare tumor cells from white blood cells. PMID:27170379

  18. CO adsorption on Pd(111) at 0.5ML: A first principles study

    NASA Astrophysics Data System (ADS)

    Hooshmand, Zahra; Le, Duy; Rahman, Talat S.

    2017-01-01

    It is well-known experimentally that at ½ monolayer (ML) coverage CO forms a c(4 × 2) phase on Pd(111). There is, however, a debate about whether this adsorption is at the bridge or at the hollow (FCC and HCP) sites, or at a combination of these two types of sites. Using density functional theory based calculations to evaluate the structural and vibrational properties of the c(4×2) overlayer of CO on Pd(111), with all possible highly symmetric adsorption sites, we conclude that the CO molecules prefer to adsorb either only on the hollow (FCC or HCP) sites or only at sites which are located in-between the bridge and the FCC sites and that there is no stable overlayer structure in which the molecule binds only at the bridge sites or combination of bridge and hollow sites.

  19. A theoretical model for EM-ML reconstruction algorithms applied to rotating PET scanners

    PubMed Central

    Iriarte, A; Sorzano, C O S; Carazo, J M; Rubio, J L; Marabini, R

    2009-01-01

    In this paper we show how to compute the normalizing and the system matrix terms of the EM-ML reconstruction algorithm for rotating planar detector PET scanners. The method introduced is valid for either pixelated or continuous scintillators. We base our computations in geometrical considerations, but other effects of the PET process can be easily included. In this regard, the intrinsic resolution of the detection system, the depth of interaction (DOI) of the incident gamma rays and the efficiency of the scintillators have been modeled in our development. The computation of the normalizing term and the system matrix is valid for any basis function used for the discrete approximation of the radionuclide concentration. We show that our computations are comparable to those of a Monte Carlo method at a small fraction of the computational cost. PMID:19265206

  20. Software support for SBGN maps: SBGN-ML and LibSBGN

    PubMed Central

    van Iersel, Martijn P.; Villéger, Alice C.; Czauderna, Tobias; Boyd, Sarah E.; Bergmann, Frank T.; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Dogrusoz, Ugur; Matsuoka, Yukiko; Funahashi, Akira; Aladjem, Mirit I.; Mi, Huaiyu; Moodie, Stuart L.; Kitano, Hiroaki; Le Novère, Nicolas; Schreiber, Falk

    2012-01-01

    Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Availability and implementation: Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. Contact: sbgn-libsbgn@lists.sourceforge.net PMID:22581176

  1. A general CellML simulation code generator using ODE solving scheme description.

    PubMed

    Amano, Akira; Soejima, Naoki; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi

    2011-01-01

    To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify target computation resources or numerical calculation methods or simulation conditions. Typical biological function simulation software consists of 1) model equation, 2) boundary conditions and 3) ODE solving scheme. Introducing the description model file such as CellML is useful for generalizing the first point and partly second point, however, third point is difficult to handle. We introduce a simulation software generation system which use markup language based description of ODE solving scheme together with cell model description file. By using this software, we can easily generate biological simulation program code with different ODE solving schemes. To show the efficiency of our system, experimental results of several simulation models with different ODE scheme and different computation resources are shown.

  2. Modeling Complex Cross-Systems Software Interfaces Using SysML

    NASA Technical Reports Server (NTRS)

    Mandutianu, Sanda; Morillo, Ron; Simpson, Kim; Liepack, Otfrid; Bonanne, Kevin

    2013-01-01

    The complex flight and ground systems for NASA human space exploration are designed, built, operated and managed as separate programs and projects. However, each system relies on one or more of the other systems in order to accomplish specific mission objectives, creating a complex, tightly coupled architecture. Thus, there is a fundamental need to understand how each system interacts with the other. To determine if a model-based system engineering approach could be utilized to assist with understanding the complex system interactions, the NASA Engineering and Safety Center (NESC) sponsored a task to develop an approach for performing cross-system behavior modeling. This paper presents the results of applying Model Based Systems Engineering (MBSE) principles using the System Modeling Language (SysML) to define cross-system behaviors and how they map to crosssystem software interfaces documented in system-level Interface Control Documents (ICDs).

  3. Real-time combining of residual carrier array signals using ML weight estimates

    NASA Technical Reports Server (NTRS)

    Vilnrotter, Victor A.; Rodemich, Eugene R.; Dolinar, Samuel J., Jr.

    1992-01-01

    A real-time digital signal combining system for use with array feeds is proposed. The combining system attempts to compensate for signal-to-noise ratio (SNR) loss resulting from antenna deformations induced by gravitational and atmospheric effects. The combining weights are obtained directly from the observed residual carrier samples in each channel using a 'sliding-window' implementation of a maximum-likelihood (ML) parameter estimator. It is shown that with averaging times of about 0.1 s, combining loss for a seven-element array can be limited to about 0.1 dB in a realistic operational environment. This result suggests that the real-time combining system proposed here is capable of recovering virtually all of the signal power captured by the array feed, even in the presence of severe wind gusts and similar disturbances.

  4. Modeling Complex Cross-Systems Software Interfaces Using SysML

    NASA Technical Reports Server (NTRS)

    Mandutianu, Sanda; Morillo, Ron; Simpson, Kim; Liepack, Otfrid; Bonanne, Kevin

    2013-01-01

    The complex flight and ground systems for NASA human space exploration are designed, built, operated and managed as separate programs and projects. However, each system relies on one or more of the other systems in order to accomplish specific mission objectives, creating a complex, tightly coupled architecture. Thus, there is a fundamental need to understand how each system interacts with the other. To determine if a model-based system engineering approach could be utilized to assist with understanding the complex system interactions, the NASA Engineering and Safety Center (NESC) sponsored a task to develop an approach for performing cross-system behavior modeling. This paper presents the results of applying Model Based Systems Engineering (MBSE) principles using the System Modeling Language (SysML) to define cross-system behaviors and how they map to crosssystem software interfaces documented in system-level Interface Control Documents (ICDs).

  5. WaterML2.0: Harmonising standards for water observations data

    NASA Astrophysics Data System (ADS)

    Taylor, Peter; Walker, Gavin; Valentine, David; Cox, Simon

    2010-05-01

    Our ability to share and understand water information from various sources is currently limited by the use of incompatible information management and publication technologies. Water resource managers, hydro-power generators, meteorologists and other interested stakeholders all monitor water resources and store their data using a wide array of technologies. Standards are multi-party agreements that provide a common ground on which people can share information by minimising ambiguity and sharing definitions for domain concepts. They are most effective when surrounded by an active community who, along with taking part in defining such concepts, develop supporting tools that allow for easy transmission and interpretation of data sets. Existing standards for water observations only exist within organisations or countries; there are no internationally agreed upon standards for encoding such data. Groups such as the Consortium of Universities for the Advancement of Hydrological Sciences, the Australian Bureau of Meteorology, and others, have developed standards for national exchange of water information, such as WaterML1.1 and the Water Data Transfer Format; other standards such as Xhydro have been developed at the sub national level. An initial analysis of existing standards (including WaterML1.1, WDTF, XHydro and the UK EA format) found sufficient commonality to suggest a role for an international standard. Such a standard would reduce the load on organisations developing their own standards. The commonalities exist in the way in which measurements and observations are made and described, such as time series data produced from automated sensors commonly used for hydrological monitoring. The Observations and Measurements (O&M) standard, developed by the Open Geospatial Consortium (OGC), is capable of describing measurements made by sensors and humans in a common way, involving both remote and in-situ sensing. O&M is generic, in that it does not define the concepts for a

  6. Sensor metadata blueprints and computer-aided editing for disciplined SensorML

    NASA Astrophysics Data System (ADS)

    Tagliolato, Paolo; Oggioni, Alessandro; Fugazza, Cristiano; Pepe, Monica; Carrara, Paola

    2016-04-01

    The need for continuous, accurate, and comprehensive environmental knowledge has led to an increase in sensor observation systems and networks. The Sensor Web Enablement (SWE) initiative has been promoted by the Open Geospatial Consortium (OGC) to foster interoperability among sensor systems. The provision of metadata according to the prescribed SensorML schema is a key component for achieving this and nevertheless availability of correct and exhaustive metadata cannot be taken for granted. On the one hand, it is awkward for users to provide sensor metadata because of the lack in user-oriented, dedicated tools. On the other, the specification of invariant information for a given sensor category or model (e.g., observed properties and units of measurement, manufacturer information, etc.), can be labor- and timeconsuming. Moreover, the provision of these details is error prone and subjective, i.e., may differ greatly across distinct descriptions for the same system. We provide a user-friendly, template-driven metadata authoring tool composed of a backend web service and an HTML5/javascript client. This results in a form-based user interface that conceals the high complexity of the underlying format. This tool also allows for plugging in external data sources providing authoritative definitions for the aforementioned invariant information. Leveraging these functionalities, we compiled a set of SensorML profiles, that is, sensor metadata blueprints allowing end users to focus only on the metadata items that are related to their specific deployment. The natural extension of this scenario is the involvement of end users and sensor manufacturers in the crowd-sourced evolution of this collection of prototypes. We describe the components and workflow of our framework for computer-aided management of sensor metadata.

  7. Using SysML for verification and validation planning on the Large Synoptic Survey Telescope (LSST)

    NASA Astrophysics Data System (ADS)

    Selvy, Brian M.; Claver, Charles; Angeli, George

    2014-08-01

    This paper provides an overview of the tool, language, and methodology used for Verification and Validation Planning on the Large Synoptic Survey Telescope (LSST) Project. LSST has implemented a Model Based Systems Engineering (MBSE) approach as a means of defining all systems engineering planning and definition activities that have historically been captured in paper documents. Specifically, LSST has adopted the Systems Modeling Language (SysML) standard and is utilizing a software tool called Enterprise Architect, developed by Sparx Systems. Much of the historical use of SysML has focused on the early phases of the project life cycle. Our approach is to extend the advantages of MBSE into later stages of the construction project. This paper details the methodology employed to use the tool to document the verification planning phases, including the extension of the language to accommodate the project's needs. The process includes defining the Verification Plan for each requirement, which in turn consists of a Verification Requirement, Success Criteria, Verification Method(s), Verification Level, and Verification Owner. Each Verification Method for each Requirement is defined as a Verification Activity and mapped into Verification Events, which are collections of activities that can be executed concurrently in an efficient and complementary way. Verification Event dependency and sequences are modeled using Activity Diagrams. The methodology employed also ties in to the Project Management Control System (PMCS), which utilizes Primavera P6 software, mapping each Verification Activity as a step in a planned activity. This approach leads to full traceability from initial Requirement to scheduled, costed, and resource loaded PMCS task-based activities, ensuring all requirements will be verified.

  8. Volume Measurement by Diffusion-Weighted Imaging in Cervical Cancer.

    PubMed

    Fujii, Shinya; Iwata, Naoki; Inoue, Chie; Mukuda, Naoko; Fukunaga, Takeru; Ogawa, Toshihide

    2017-06-01

    The aim of this paper was to evaluate the validity of tumor volume measurement using diffusion-weighted (DW) imaging in cervical cancer. In this retrospective study, 22 patients, who underwent preoperative 3.0 T MR examinations with DW imaging were evaluated. Tumor volume measurement by oblique axial (short axis to the uterine cervix) T2-weighted imaging was performed by manually outlining the tumor on the monitor. The area of tumor in each slice was multiplied by the slice profile (slice thickness plus intersection gap), and the total tumor volume was calculated by summation of these obtained volumes. Meanwhile, one experienced radiological technologist generated three-dimensional DW images of cervical cancer using a volume-rendering algorithm at a computer workstation, and tumor volume was automatically calculated in the workstation. Analysis via the intraclass correlation coefficient (ICC) and Bland-Altman plots were used to assess the validity and reliability of these methods. Between tumor volumes measured by T2-weighted imaging methods and DW imaging methods, the ICC was excellent (0.962). The 95% limits of agreement of volume measurement were -52.7 and 35.7 mL (mean difference, -8.5 mL). In regards to intra-observer variability, the ICC was excellent (0.963). The 95% limits of agreement of volume measurement were -42.2 and 47.4 mL (mean difference, 2.6 mL). DW imaging can be used to measure cervical cancer volume.

  9. Generating GraphML XML Files for Graph Visualization of Architectures and Event Traces for the Monterey Phoenix Program

    DTIC Science & Technology

    2012-09-01

    files that conform to the Graph Markup Language (GraphML). MPGrapher compiles well-formed XML files that conform to the yEd GraphML schema. These...PLANARIZATION ........................................................................22 E. THE GRAPH MARKUP LANGUAGE ...26 F. ALTERNATIVES TO THE GRAPH MARKUP LANGUAGE ...............27 1. Graph Modelling Language (GML

  10. Detection of Mycobacterium leprae infection in wild nine-banded armadillos (Dasypus novemcinctus) using the rapid ML Flow test.

    PubMed

    Deps, Patrícia Duarte; Antunes, João Marcelo Azevedo de Paula; Tomimori-Yamashita, Jane

    2007-01-01

    Mycobaterium leprae infection was investigated in armadillos from the State of Espírito Santo, Brazil. The ML Flow test was performed on 37 nine-banded armadillos and positive results were found in 11 (29.7%). The ML Flow test may be used to identify possible sources of Mycobaterium leprae among wild armadillos.

  11. Multi-level continuous active source seismic monitoring (ML-CASSM): Application to shallow hydrofracture monitoring

    NASA Astrophysics Data System (ADS)

    Ajo Franklin, J. B.; Daley, T. M.; Butler-Veytia, B.; Peterson, J.; Gasperikova, E.; Hubbard, S. S.

    2010-12-01

    . This technique, which we refer to as ML-CASSM, was deployed at a DNAPL contaminated site undergoing bioremediation through hydrofracture emplacement. ML-CASSM was used to image fracture propagation in two crosswell profiles located several meters from the initiation point. Since the entire fracturing process occurred over a 45 minute period, traditional timelapse acquisition methods would have been incapable of capturing the stages of fracture growth. With ML-CASSM, 12 complete datasets were acquired over the course of fracturing allowing estimates of fracture propagation through the two imaging planes. In addition to these datasets, hundreds of sequential surveys acquired before and after the fracturing procedure allowed estimation of system stability at baseline and the combination of fracture consolidation and pressure dissipation afterwards. The fracture zone was visible seismically as a localized area of reduced P-wave velocity and increased P-wave attenuation. In addition to changes in the primary arrival, diffracted events and scattering from the fracture were observed leaving open the possibility of fracture characterization using later components of the wavefield.

  12. Loss of entorhinal cortex and hippocampal volumes compared to whole brain volume in normal aging: the SMART-Medea study.

    PubMed

    Knoops, Arnoud J G; Gerritsen, Lotte; van der Graaf, Yolanda; Mali, Willem P T M; Geerlings, Mirjam I

    2012-07-30

    In non-demented elderly age-related decline in hippocampal volume has often been observed, but it is not clear if this loss is disproportionate relative to other brain tissue. Few studies examined age-related volume loss of the entorhinal cortex. We investigated the association of age with hippocampal and entorhinal cortex (ERC) volumes in a large sample of middle-aged and older persons without dementia. Within the SMART-Medea study, cross-sectional analyses were performed in 453 non-demented subjects (mean age 62±9 years, 81% male) with a history of arterial disease. Hippocampal and ERC volumes were assessed by manual segmentation on three-dimensional fast field-echo sequence T1-weighted magnetic resonance images. Automated segmentation was used to quantify volumes of BV and ICV. Hippocampal and ERC volumes were divided by intracranial volume (ICV) as well as total brain volume (BV) to determine whether age-related differences were disproportionate relative to other brain tissue. Total crude hippocampal volume was 5.96±0.7 ml and total crude ERC volume was 0.34±0.06 ml. Linear regression analyses adjusted for sex showed that with increasing age, hippocampal volume divided by ICV decreased (B per year older=-0.01 ml; 95% CI -0.02 to -0.004). However, no age-related decline in hippocampal volume relative to BV was observed (B per year older=0.005 ml; 95% CI -0.002 to 0.01). No age-related decline in ERC volume relative to ICV or BV was observed. In this population of nondemented patients with a history of vascular disease no age-related decline in entorhinal cortex volume was observed and although hippocampal volume decreased with age, it was not disproportionate relative to total brain volume. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  13. The optimal dose of local anaesthetic in the orthogonal two-needle technique. Extent of sensory block after the injection of 20, 30 and 40 mL of anaesthetic solution.

    PubMed

    Rucci, F S; Barbagli, R; Pippa, P; Boccaccini, A

    1997-05-01

    Ninety patients undergoing scheduled upper limb orthopaedic surgery were studied to determine the optimal anaesthetic dose using the 'orthogonal two-needle technique'. The patients were randomly assigned to one of three groups to receive one of three different volumes (20, 30 and 40 mL) (n = 30) of anaesthetic solution (a mixture of equal parts of 0.5% bupivacaine with adrenaline 1:200,000 and 2% lignocaine). A significant correlation was found between the volume injected and the anaesthetic spread for all tested areas. A better analgesic spread to all the major branches of the plexus was obtained when increased volumes of anaesthetic solution were injected. The comparisons between the 20 mL group and the other two groups are significant in all the tested areas, as well as the comparisons between 30 and 40 mL groups in the areas innervated by radial and musculocutaneous nerves. Only the area innervated by the axillary nerve showed a weaker volume-analgesia relation, confirming the elusiveness of this area to anaesthesia in the axillary approaches. The improved results observed using greater amounts of anaesthetic solution might result from a higher intrasheath pressure with disruption of sheath septa, or from a greater availability of drug for all the terminal branches of brachial plexus, or both.

  14. libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience

    PubMed Central

    Vella, Michael; Cannon, Robert C.; Crook, Sharon; Davison, Andrew P.; Ganapathy, Gautham; Robinson, Hugh P. C.; Silver, R. Angus; Gleeson, Padraig

    2014-01-01

    NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell, and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two Application Programming Interfaces (APIs) written in Python (http://www.python.org), which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment. PMID:24795618

  15. libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.

    PubMed

    Vella, Michael; Cannon, Robert C; Crook, Sharon; Davison, Andrew P; Ganapathy, Gautham; Robinson, Hugh P C; Silver, R Angus; Gleeson, Padraig

    2014-01-01

    NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell, and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two Application Programming Interfaces (APIs) written in Python (http://www.python.org), which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment.

  16. Small Volume Resuscitation of Hypovolemic Shock

    DTIC Science & Technology

    1989-03-01

    the nature of the natriuresis / diuresis ; and the extent of resuscitation induced hypokalemia. Plasma volume expansion was measured during and after a...of hemorrhage with hypertonic saline (7.5%) induces a diuresis / natriuresis equal to that of large volume isotonic resuscitation. Circulatory Shock 24...after HSD (18-22 ml/kg) was similar in both groups; AO and cardiac output (CO) were equally improved in both groups. Dehydration blunted the diuresis of

  17. Infrared spectroscopic studies of myeloid leukemia (ML-1) cells at different phases of the cell cycle

    NASA Astrophysics Data System (ADS)

    Boydston-White, Susie; Diem, Max

    1999-06-01

    Advances in infrared spectroscopic methodology permit excellent infrared spectra to be collected from objects as small as single human cells. These advances have lead to an increased interest of the use of infrared spectroscopy as a medical diagnostic tool. Infrared spectra of myeloid leukemia (ML-1) cells are reported for cells derived from an asynchronous, exponentially-growing culture, as well as for cells that were fractionated according to their stage within the cell division cycle. The observed results suggest that the cells' DNA is detectable by infrared spectroscopy mainly when the cell is in the S phase, during the replication of DNA. In the G1 and G2 phases, the DNA is so tightly packed in the nucleus that it appears opaque to infrared radiation. Consequently, the nucleic acid spectral contributions in the G1 and G2 phases would be mostly that of cytoplasmic RNA. These results suggest that infrared spectral changes observed earlier between normal and abnormal cells may have been due to different distributions of cells within the stages of the cell division cycle.

  18. Fast nearly ML estimation of Doppler frequency in GNSS signal acquisition process.

    PubMed

    Tang, Xinhua; Falletti, Emanuela; Lo Presti, Letizia

    2013-04-29

    It is known that signal acquisition in Global Navigation Satellite System (GNSS) field provides a rough maximum-likelihood (ML) estimate based on a peak search in a two-dimensional grid. In this paper, the theoretical mathematical expression of the cross-ambiguity function (CAF) is exploited to analyze the grid and improve the accuracy of the frequency estimate. Based on the simple equation derived from this mathematical expression of the CAF, a family of novel algorithms is proposed to refine the Doppler frequency estimate with respect to that provided by a conventional acquisition method. In an ideal scenario where there is no noise and other nuisances, the frequency estimation error can be theoretically reduced to zero. On the other hand, in the presence of noise, the new algorithm almost reaches the Cramer-Rao Lower Bound (CRLB) which is derived as benchmark. For comparison, a least-square (LS) method is proposed. It is shown that the proposed solution achieves the same performance of LS, but requires a dramatically reduced computational burden. An averaging method is proposed to mitigate the influence of noise, especially when signal-to-noise ratio (SNR) is low. Finally, the influence of the grid resolution in the search space is analyzed in both time and frequency domains.

  19. A New Synthetic Peptide Having Two Target of Antibacterial Action in E. coli ML35.

    PubMed

    Barreto-Santamaría, Adriana; Curtidor, Hernando; Arévalo-Pinzón, Gabriela; Herrera, Chonny; Suárez, Diana; Pérez, Walter H; Patarroyo, Manuel E

    2016-01-01

    The increased resistance of microorganisms to the different antimicrobials available to today has highlighted the need to find new therapeutic agents, including natural and/or synthetic antimicrobial peptides (AMPs). This study has evaluated the antimicrobial activity of synthetic peptide 35409 (RYRRKKKMKKALQYIKLLKE) against Staphylococcus aureus ATCC 29213, Pseudomonas aeruginosa ATCC 15442 and Escherichia coli ML 35 (ATCC 43827). The results have shown that peptide 35409 inhibited the growth of these three bacterial strains, having 16-fold greater activity against E. coli and P. aeruginosa, but requiring less concentration regarding E. coli (22 μM). When analyzing this activity against E. coli compared to time taken, it was found that this peptide inhibited bacterial growth during the first 60 min and reduced CFU/mL 1 log after 120 min had elapsed. This AMP permeabilized the E. coli membrane by interaction with membrane phospholipids, mainly phosphatidylethanolamine, inhibited cell division and induced filamentation, suggesting two different targets of action within a bacterial cell. Cytotoxicity studies revealed that peptide 35409 had low hemolytic activity and was not cytotoxic for two human cell lines. We would thus propose, in the light of these findings, that the peptide 35409 sequence should provide a promising template for designing broad-spectrum AMPs.

  20. Specification and Design of Electrical Flight System Architectures with SysML

    NASA Technical Reports Server (NTRS)

    McKelvin, Mark L., Jr.; Jimenez, Alejandro

    2012-01-01

    Modern space flight systems are required to perform more complex functions than previous generations to support space missions. This demand is driving the trend to deploy more electronics to realize system functionality. The traditional approach for the specification, design, and deployment of electrical system architectures in space flight systems includes the use of informal definitions and descriptions that are often embedded within loosely coupled but highly interdependent design documents. Traditional methods become inefficient to cope with increasing system complexity, evolving requirements, and the ability to meet project budget and time constraints. Thus, there is a need for more rigorous methods to capture the relevant information about the electrical system architecture as the design evolves. In this work, we propose a model-centric approach to support the specification and design of electrical flight system architectures using the System Modeling Language (SysML). In our approach, we develop a domain specific language for specifying electrical system architectures, and we propose a design flow for the specification and design of electrical interfaces. Our approach is applied to a practical flight system.

  1. Architecting the Human Space Flight Program with Systems Modeling Language (SysML)

    NASA Technical Reports Server (NTRS)

    Jackson, Maddalena M.; Fernandez, Michela Munoz; McVittie, Thomas I.; Sindiy, Oleg V.

    2012-01-01

    The next generation of missions in NASA's Human Space Flight program focuses on the development and deployment of highly complex systems (e.g., Orion Multi-Purpose Crew Vehicle, Space Launch System, 21st Century Ground System) that will enable astronauts to venture beyond low Earth orbit and explore the moon, near-Earth asteroids, and beyond. Architecting these highly complex system-of-systems requires formal systems engineering techniques for managing the evolution of the technical features in the information exchange domain (e.g., data exchanges, communication networks, ground software) and also, formal correlation of the technical architecture to stakeholders' programmatic concerns (e.g., budget, schedule, risk) and design development (e.g., assumptions, constraints, trades, tracking of unknowns). This paper will describe how the authors have applied System Modeling Language (SysML) to implement model-based systems engineering for managing the description of the End-to-End Information System (EEIS) architecture and associated development activities and ultimately enables stakeholders to understand, reason, and answer questions about the EEIS under design for proposed lunar Exploration Missions 1 and 2 (EM-1 and EM-2).

  2. Distribution, production, and ecophysiology of Picocystis strain ML in Mono Lake, California

    USGS Publications Warehouse

    Roesler, Collin S.; Culbertson, Charles W.; Etheridge, Stacey M.; Goericke, Ralf; Kiene, Ronald P.; Miller, Laurence G.; Oremland, Ronald S.

    2002-01-01

    A recently described unicellular chlorophytic alga isolated from meromictic Mono Lake, California, occupies a niche that spans two environments: the upper oxic mixolimnion and the deeper anoxic and highly reducing monimolimnion. This organism, Picocystis sp. strain ML, accounts for nearly 25% of the primary production during the winter bloom and more than 50% at other times of the year. In incubations, it is heavily grazed by the brine shrimp, Artemia monica. We assessed growth and photosynthetic parameters over broad ranges of irradiance, salinity, and pH and under oxic and anoxic conditions. Picocystis appears to be particularly adapted to low irradiance; we observed an order of magnitude increase in the cellular pigment concentrations, as well as marked increases in cellspecific photosynthetic parameters for cells acclimated to low-growth irradiance. Growth rates of 0.3–1.5 d21 were observed over a salinity range of 0–260‰ and a pH range of 4–12, with maximal growth at ;50 mmol photons m22 s21 , 40‰, and pH 6–10. Growth and oxygenic photosynthesis were observed under anoxic conditions at rates comparable to those measured under oxic conditions. The ability of the organism to acclimate and grow under such a broad range of environmental conditions makes it an important component of the Mono Lake ecosystem and likely contributes to its dominance of the monimolimnion/mixolimnion interface.

  3. A New Synthetic Peptide Having Two Target of Antibacterial Action in E. coli ML35

    PubMed Central

    Barreto-Santamaría, Adriana; Curtidor, Hernando; Arévalo-Pinzón, Gabriela; Herrera, Chonny; Suárez, Diana; Pérez, Walter H.; Patarroyo, Manuel E.

    2016-01-01

    The increased resistance of microorganisms to the different antimicrobials available to today has highlighted the need to find new therapeutic agents, including natural and/or synthetic antimicrobial peptides (AMPs). This study has evaluated the antimicrobial activity of synthetic peptide 35409 (RYRRKKKMKKALQYIKLLKE) against Staphylococcus aureus ATCC 29213, Pseudomonas aeruginosa ATCC 15442 and Escherichia coli ML 35 (ATCC 43827). The results have shown that peptide 35409 inhibited the growth of these three bacterial strains, having 16-fold greater activity against E. coli and P. aeruginosa, but requiring less concentration regarding E. coli (22 μM). When analyzing this activity against E. coli compared to time taken, it was found that this peptide inhibited bacterial growth during the first 60 min and reduced CFU/mL 1 log after 120 min had elapsed. This AMP permeabilized the E. coli membrane by interaction with membrane phospholipids, mainly phosphatidylethanolamine, inhibited cell division and induced filamentation, suggesting two different targets of action within a bacterial cell. Cytotoxicity studies revealed that peptide 35409 had low hemolytic activity and was not cytotoxic for two human cell lines. We would thus propose, in the light of these findings, that the peptide 35409 sequence should provide a promising template for designing broad-spectrum AMPs. PMID:28066341

  4. Validation of the 50 ml3 drinking test for evaluation of post-stroke dysphagia.

    PubMed

    Gottlieb, D; Kipnis, M; Sister, E; Vardi, Y; Brill, S

    1996-10-01

    Aspiration pneumonias are frequent complications of cerebrovascular accidents (CVA). They occur mainly in patients suffering from swallowing disorders following the CVA. These patients can be diagnosed using a bedside swallowing evaluation. This evaluation is based on observation of some components of the oral and pharyngeal stages of the swallowing process and on a drinking test of 50 ml3 of clear liquids. Changing the mode of swallowing and the consistency of the diet according to the swallowing evaluation following CVA can reduce significantly the frequency of aspiration pneumonias. In our patient cohort, consisting of 180 patients admitted for stroke rehabilitation, aspiration pneumonias occurred in 10% and swallowing disorders were found in 28%. The administration of a structured swallowing evaluation was associated with a gradual reduction of frequency of pneumonia from 16% in the first group of 60 patients to 3% in the last group of 60 patients or, if considering only patients suffering from dysphagia, from 27% in the first group of patients to none in the last group of patients.

  5. Architecting the Human Space Flight Program with Systems Modeling Language (SysML)

    NASA Technical Reports Server (NTRS)

    Jackson, Maddalena M.; Fernandez, Michela Munoz; McVittie, Thomas I.; Sindiy, Oleg V.

    2012-01-01

    The next generation of missions in NASA's Human Space Flight program focuses on the development and deployment of highly complex systems (e.g., Orion Multi-Purpose Crew Vehicle, Space Launch System, 21st Century Ground System) that will enable astronauts to venture beyond low Earth orbit and explore the moon, near-Earth asteroids, and beyond. Architecting these highly complex system-of-systems requires formal systems engineering techniques for managing the evolution of the technical features in the information exchange domain (e.g., data exchanges, communication networks, ground software) and also, formal correlation of the technical architecture to stakeholders' programmatic concerns (e.g., budget, schedule, risk) and design development (e.g., assumptions, constraints, trades, tracking of unknowns). This paper will describe how the authors have applied System Modeling Language (SysML) to implement model-based systems engineering for managing the description of the End-to-End Information System (EEIS) architecture and associated development activities and ultimately enables stakeholders to understand, reason, and answer questions about the EEIS under design for proposed lunar Exploration Missions 1 and 2 (EM-1 and EM-2).

  6. Reversible inactivation of the isocitrate dehydrogenase of Escherichia coli ML308 during growth on acetate.

    PubMed

    Bennett, P M; Holms, W H

    1975-03-01

    During aerobic growth of Escherichia coli ML308 on acetate as sole carbon source, the apparent synthesis of isocitrate dehydrogenase was repressed relative to cultures on other carbon sources, such as glucose, which do not employ the glyoxylate bypass as an anaplerotic sequence. When cells were removed from an acetate medium, or when compounds were added which made the operation of the glyoxylate bypass unnecessary, the activity of isocitrate dehydrogenase rapidly increased 3- to 4-fold but fell again on restoration to an acetate medium. Changes in activity were rapid and, furthermore, could be demonstrated in the absence of protein synthesis. It is thus improbable that the mechanism involved degradation or de novo synthesis of the enzyme protein. Oxaloacetate and glyoxylate showed concerted inhibition of isocitrate dehydrogenase which could be relieved by dialysis. Because extracts of low enzyme activity, derived from acetate-metabolizing cells, could not be stimulated by dialysis or by addition of a wide range of metabolites, it is unlikely that low molecular weight, freely dissociable effectors were responsible for stimulation or inhibition of activity. Control of isocitrate dehydrogenase permitted the efficient utilization of acetate as sole source of carbon and energy but perserved the capacity of the cell to respond rapidly to an improvement in nutritional conditions. A limited survey showed that the mechanism is common but not universal among strains of E. coli and occurs in at least one strain each of Klebsiella aerogenes, Salmonella typhimurium and Serratia marcescens.

  7. Specification and Design of Electrical Flight System Architectures with SysML

    NASA Technical Reports Server (NTRS)

    McKelvin, Mark L., Jr.; Jimenez, Alejandro

    2012-01-01

    Modern space flight systems are required to perform more complex functions than previous generations to support space missions. This demand is driving the trend to deploy more electronics to realize system functionality. The traditional approach for the specification, design, and deployment of electrical system architectures in space flight systems includes the use of informal definitions and descriptions that are often embedded within loosely coupled but highly interdependent design documents. Traditional methods become inefficient to cope with increasing system complexity, evolving requirements, and the ability to meet project budget and time constraints. Thus, there is a need for more rigorous methods to capture the relevant information about the electrical system architecture as the design evolves. In this work, we propose a model-centric approach to support the specification and design of electrical flight system architectures using the System Modeling Language (SysML). In our approach, we develop a domain specific language for specifying electrical system architectures, and we propose a design flow for the specification and design of electrical interfaces. Our approach is applied to a practical flight system.

  8. Temperature-dependent growth kinetics of Escherichia coli ML 30 in glucose-limited continuous culture.

    PubMed Central

    Kovárová, K; Zehnder, A J; Egli, T

    1996-01-01

    Detailed comparison of growth kinetics at temperatures below and above the optimal temperature was carried out with Escherichia coli ML 30 (DSM 1329) in continuous culture. The culture was grown with glucose as the sole limiting source of carbon and energy (100 mg liter(-1) in feed medium), and the resulting steady-state concentrations of glucose were measured as a function of the dilution rate at 17.4, 28.4, 37, and 40 degrees C. The experimental data could not be described by the conventional Monod equation over the entire temperature range, but an extended form of the Monod model [mu = mu(max) x (s - s(min))/(Ks + s - s(min))], which predicts a finite substrate concentration at 0 growth rate (s(min)), provided a good fit. The two parameters mu(max) and s(min) were temperature dependent, whereas, surprisingly, fitting the model to the experimental data yielded virtually identical Ks values (approximately 33 microg liter(-1)) at all temperatures. A model that describes steady-state glucose concentrations as a function of temperature at constant growth rates is presented. In similar experiments with mixtures of glucose and galactose (1:1 mixture), the two sugars were utilized simultaneously at all temperatures examined, and their steady-state concentrations were reduced compared with to growth with either glucose or galactose alone. The results of laboratory-scale kinetic experiments are discussed with respect to the concentrations observed in natural environments. PMID:8755881

  9. Accuracy of Prehospital Intravenous Fluid Volume Measurement by Emergency Medical Services.

    PubMed

    Coppler, Patrick J; Padmanabhan, Rajagopala; Martin-Gill, Christian; Callaway, Clifton W; Yealy, Donald M; Seymour, Christopher W

    2016-01-01

    Prehospital treatment protocols call for intravenous (IV) fluid for patients with shock, yet the measurement accuracy of administered fluid volume is unknown. The purpose of the current study was to assess the accuracy of documented and self-reported fluid volumes administered to medical patients by paramedics during prehospital care. We conducted a pilot, observational study nested within a parent cohort study of prehospital biomarkers in a single EMS agency transporting patients to a tertiary care hospital in Pittsburgh, Pennsylvania over 8 months. Among eligible nontrauma, noncardiac arrest patients, we studied the self-reported IV fluid volume on ED arrival by paramedics, documented fluid volume in the EMS record, and compared those to the mass-derived fluid volume. We quantified the absolute error between methods, and determined EMS transport times or initial prehospital systolic blood pressure had any effect on error. We enrolled 50 patients who received prehospital IV fluid and had mass-derived fluid volume measured at ED arrival. Of these, 21 (42%) patients had IV fluid volume subsequently documented in EMS records. The median mass-derived fluid volume was 393 mL [IQR: 264-618 mL]. Mass-derived volume was similar for subjects who did (386 mL, IQR: 271-642 mL) or did not (399 mL, IQR: 253-602) have documented fluid administration (p > 0.05). The median self-reported fluid volume was 250 mL [IQR: 150-500 mL] and did not differ by documentation (p > 0.05). The median absolute error comparing self-reported to mass-derived fluid volume was 109 mL [IQR: 41-205 mL], and less than 250 mL in more than 80% of subjects. The median absolute error comparing documented fluid to mass-derived fluid volume was 142 mL [IQR: 64-265 mL], and was less than 250 mL in 71% of subjects. No difference in absolute error for either self-reported or document fluid volumes were modified by transport time or prehospital systolic blood pressure. Prehospital IV fluid administration is

  10. GeoSciML v3.0 - a significant upgrade of the CGI-IUGS geoscience data model

    NASA Astrophysics Data System (ADS)

    Raymond, O.; Duclaux, G.; Boisvert, E.; Cipolloni, C.; Cox, S.; Laxton, J.; Letourneau, F.; Richard, S.; Ritchie, A.; Sen, M.; Serrano, J.-J.; Simons, B.; Vuollo, J.

    2012-04-01

    GeoSciML version 3.0 (http://www.geosciml.org), released in late 2011, is the latest version of the CGI-IUGS* Interoperability Working Group geoscience data interchange standard. The new version is a significant upgrade and refactoring of GeoSciML v2 which was released in 2008. GeoSciML v3 has already been adopted by several major international interoperability initiatives, including OneGeology, the EU INSPIRE program, and the US Geoscience Information Network, as their standard data exchange format for geoscience data. GeoSciML v3 makes use of recently upgraded versions of several Open Geospatial Consortium (OGC) and ISO data transfer standards, including GML v3.2, SWE Common v2.0, and Observations and Measurements v2 (ISO 19156). The GeoSciML v3 data model has been refactored from a single large application schema with many packages, into a number of smaller, but related, application schema modules with individual namespaces. This refactoring allows the use and future development of modules of GeoSciML (eg; GeologicUnit, GeologicStructure, GeologicAge, Borehole) in smaller, more manageable units. As a result of this refactoring and the integration with new OGC and ISO standards, GeoSciML v3 is not backwardly compatible with previous GeoSciML versions. The scope of GeoSciML has been extended in version 3.0 to include new models for geomorphological data (a Geomorphology application schema), and for geological specimens, geochronological interpretations, and metadata for geochemical and geochronological analyses (a LaboratoryAnalysis-Specimen application schema). In addition, there is better support for borehole data, and the PhysicalProperties model now supports a wider range of petrophysical measurements. The previously used CGI_Value data type has been superseded in favour of externally governed data types provided by OGC's SWE Common v2 and GML v3.2 data standards. The GeoSciML v3 release includes worked examples of best practice in delivering geochemical

  11. Implementation of a Goal-Based Systems Engineering Process Using the Systems Modeling Language (SysML)

    NASA Technical Reports Server (NTRS)

    Breckenridge, Jonathan T.; Johnson, Stephen B.

    2013-01-01

    Building upon the purpose, theoretical approach, and use of a Goal-Function Tree (GFT) being presented by Dr. Stephen B. Johnson, described in a related Infotech 2013 ISHM abstract titled "Goal-Function Tree Modeling for Systems Engineering and Fault Management", this paper will describe the core framework used to implement the GFTbased systems engineering process using the Systems Modeling Language (SysML). These two papers are ideally accepted and presented together in the same Infotech session. Statement of problem: SysML, as a tool, is currently not capable of implementing the theoretical approach described within the "Goal-Function Tree Modeling for Systems Engineering and Fault Management" paper cited above. More generally, SysML's current capabilities to model functional decompositions in the rigorous manner required in the GFT approach are limited. The GFT is a new Model-Based Systems Engineering (MBSE) approach to the development of goals and requirements, functions, and its linkage to design. As a growing standard for systems engineering, it is important to develop methods to implement GFT in SysML. Proposed Method of Solution: Many of the central concepts of the SysML language are needed to implement a GFT for large complex systems. In the implementation of those central concepts, the following will be described in detail: changes to the nominal SysML process, model view definitions and examples, diagram definitions and examples, and detailed SysML construct and stereotype definitions.

  12. Implementation of a Goal-Based Systems Engineering Process Using the Systems Modeling Language (SysML)

    NASA Technical Reports Server (NTRS)

    Patterson, Jonathan D.; Breckenridge, Jonathan T.; Johnson, Stephen B.

    2013-01-01

    Building upon the purpose, theoretical approach, and use of a Goal-Function Tree (GFT) being presented by Dr. Stephen B. Johnson, described in a related Infotech 2013 ISHM abstract titled "Goal-Function Tree Modeling for Systems Engineering and Fault Management", this paper will describe the core framework used to implement the GFTbased systems engineering process using the Systems Modeling Language (SysML). These two papers are ideally accepted and presented together in the same Infotech session. Statement of problem: SysML, as a tool, is currently not capable of implementing the theoretical approach described within the "Goal-Function Tree Modeling for Systems Engineering and Fault Management" paper cited above. More generally, SysML's current capabilities to model functional decompositions in the rigorous manner required in the GFT approach are limited. The GFT is a new Model-Based Systems Engineering (MBSE) approach to the development of goals and requirements, functions, and its linkage to design. As a growing standard for systems engineering, it is important to develop methods to implement GFT in SysML. Proposed Method of Solution: Many of the central concepts of the SysML language are needed to implement a GFT for large complex systems. In the implementation of those central concepts, the following will be described in detail: changes to the nominal SysML process, model view definitions and examples, diagram definitions and examples, and detailed SysML construct and stereotype definitions.

  13. The maltose ABC transporter in Lactococcus lactis facilitates high-level sensitivity to the circular bacteriocin garvicin ML.

    PubMed

    Gabrielsen, Christina; Brede, Dag A; Hernández, Pablo E; Nes, Ingolf F; Diep, Dzung B

    2012-06-01

    We generated and characterized a series of spontaneous mutants of Lactococcus lactis IL1403 with average 6- to 11-fold-lowered sensitivities to the circular bacteriocin garvicin ML (GarML). Carbohydrate fermentation assays highlighted changes in carbohydrate metabolism, specifically loss of the ability to metabolize starch and maltose, in these mutants. PCR and sequencing showed that a 13.5-kb chromosomal deletion encompassing 12 open reading frames, mainly involved in starch and maltose utilization, had spontaneously occurred in the GarML-resistant mutants. Growth experiments revealed a correlation between sensitivity to GarML and carbon catabolite repression (CCR); i.e., sensitivity to GarML increased significantly when wild-type cells were grown on maltose and galactose as sole carbohydrates, an effect which was alleviated by the presence of glucose. Among the genes deleted in the mutants were malEFG, which encode a CCR-regulated membrane-bound maltose ABC transporter. The complementation of mutants with these three genes recovered normal sensitivity to the bacteriocin, suggesting an essential role of the maltose ABC transporter in the antimicrobial activity of GarML. This notion was supported by the fact that the level of sensitivity to GarML was dose dependent, increasing with higher expression levels of malEFG over a 50-fold range. To our knowledge, this is the first time a specific protein complex has been demonstrated to be involved in sensitivity to a circular bacteriocin.

  14. A library of near-infrared integral field spectra of young M-L dwarfs

    NASA Astrophysics Data System (ADS)

    Bonnefoy, M.; Chauvin, G.; Lagrange, A.-M.; Rojo, P.; Allard, F.; Pinte, C.; Dumas, C.; Homeier, D.

    2014-02-01

    Context. At young ages, low surface gravity affects the atmospheric properties of ultracool dwarfs. The impact on medium-resolution near-infrared (NIR) spectra has only been slightly investigated at the M-L transition so far. Aims: We present a library of NIR (1.1-2.45 μm) medium-resolution (R ~ 1500-2000) integral field spectra of 15 young M6-L0 dwarfs. We aim at deriving updated NIR spectral type, luminosity, and physical parameters (Teff, log g, M, L/L⊙) for each source. This work also aims at testing the latest generation of BT-SETTL atmospheric models. Methods: We estimated spectral types using spectral indices and the spectra of young objects classified in the optical. We used the 2010 and 2012 releases of the BT-SETTL synthetic spectral grid and cross-checked the results with the DRIFT-PHOENIX models to derive the atmospheric properties of the sources. Results: We do not find significant differences between the spectra of young companions and those of young isolated brown dwarfs in the same spectral type range. We derive infrared spectral types L0 ± 1, L0 ± 1, M9.5 ± 0.5, M9.5 ± 0.5, M9.25 ± 0.25, M8+0.5-0.75, and M8.5 ± 0.5 for AB Pic b, Cha J110913-773444, USco CTIO 108B, GSC 08047-00232 B, DH Tau B, CT Cha b, and HR7329B, respectively. The BT-SETTL and DRIFT-PHOENIX models yield close Teff and log g estimates for each source. The models seem to show a 600+600-300 K drop in the effective temperature at the M-L transition. Assuming the former temperatures are correct, we then derive new mass estimates that confirm that DH Tau B, USco CTIO 108B, AB Pic b, KPNO Tau 4, OTS 44, and Cha1109 lie inside or at the boundary of the planetary mass range. We combine the empirical luminosities of the M9.5-L0 sources to the Teff to derive semi-empirical radii estimates that do not match "hot-start" evolutionary models predictions at 1-3 Myr. We use complementary data to demonstrate that atmospheric models are able to reproduce the combined optical and infrared

  15. Macroseismic survey of the ML5.5, 2014 Orkney earthquake

    NASA Astrophysics Data System (ADS)

    Midzi, V.; Zulu, B.; Manzunzu, B.; Mulabisana, T.; Pule, T.; Myendeki, S.; Gubela, W.

    2015-07-01

    On 5 August 2014 at 1222 hours (local time), an earthquake of local magnitude ML = 5.5 occurred in the Orkney area in the North West Province, South Africa. The earthquake shaking was felt widely in South Africa as far as Cape Town as well as in Maputo, Mozambique, and Gaborone in Botswana. One person was killed when a wall collapsed on him, and more than 600 houses were damaged. Following the earthquake, many people submitted reports to the Council for Geoscience (CGS) through an online questionnaire which recorded their experience, whilst others reported the event and its effects on social networks like Twitter and in newspapers. The CGS also sent out a team of scientists to further assess the effects of the event in the community by interviewing members of the public and completing additional questionnaires. A total of 866 observations were collected. Analysis of the collected macroseismic data produced 170 intensity data points which showed that a maximum intensity of VII was experienced in communities located in the epicentral area. The observed attenuation of intensity values was comparable to that observed on the French stable continental region especially in the area of 600-km radius from the epicentre. Airborne geophysical data were used to try and identify the fault along which the earthquake occurred. This was necessary as there was no surface expression of the earthquake and no previously identified fault near the epicentre. The interpretation of the data showed a fault located about 500 m from the epicentre appearing to form a boundary to the east of located aftershocks.

  16. MQUAKE multicast software early warning demonstrated for 31 October 2001 Anza Ml5.1 earthquake

    NASA Astrophysics Data System (ADS)

    Eakins, J. A.; Hansen, T.; Vernon, F. L.; Braun, H.

    2003-12-01

    MQUAKE distributes real-time multicast parametric information from individual sensors as well as a summarized location and magnitude based on the data recorded from sensors of the ANZA seismic network with the goal of providing event notification prior to arrival of the actual shock wave at the client's location. The program gathers detection and triggering information from an operational Antelope real-time data collection system and sends them to clients via multicast and unicast UDP packets. Multicast packets are preferred as they allow multiple people to receive event packets in the fastest time possible (however, a unicast mode is available since most IP networks do not support multicast). These packets are decrypted in a client software which then produces a list of triggers/events that will be used in future versions of the code to generate wavefront estimate plots and approximate maximum shock wave travel times based on the client's location and limited current information. This systems works in both a wired and wireless environment, such as HPWREN, the High Performance Wireless Research and Education Network. A real-time example of this system was obtained during the Ml5.1 31 October 2001 earthquake that occurred directly under the ANZA seismic network, approximately 70 km away from an MQUAKE client. The MQUAKE program was able to deliver a warning of a significant "event" 10 seconds after the initial ground motion was recorded and about 4 seconds prior to ground motion reaching the client. An actual event location and magnitude approximation was received 71 seconds after the local ground shaking at the client's location (85 seconds after the event). Had the client been located along the coast of San Diego, they would have had additional warning time prior to the shaking. Clients in San Diego, the closest major metropolitan area to this event, could have received up to 12 seconds of early warning.

  17. Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data.

    PubMed

    Waddell, Peter J; Kishino, Hirohisa; Ota, Rissa

    2002-01-01

    Evolutionary trees sit at the core of all realistic models describing a set of related sequences, including alignment, homology search, ancestral protein reconstruction and 2D/3D structural change. It is important to assess the stochastic error when estimating a tree, including models using the most realistic likelihood-based optimizations, yet computation times may be many days or weeks. If so, the bootstrap is computationally prohibitive. Here we show that the extremely fast "resampling of estimated log likelihoods" or RELL method behaves well under more general circumstances than previously examined. RELL approximates the bootstrap (BP) proportions of trees better that some bootstrap methods that rely on fast heuristics to search the tree space. The BIC approximation of the Bayesian posterior probability (BPP) of trees is made more accurate by including an additional term related to the determinant of the information matrix (which may also be obtained as a product of gradient or score vectors). Such estimates are shown to be very close to MCMC chain values. Our analysis of mammalian mitochondrial amino acid sequences suggest that when model breakdown occurs, as it typically does for sequences separated by more than a few million years, the BPP values are far too peaked and the real fluctuations in the likelihood of the data are many times larger than expected. Accordingly, several ways to incorporate the bootstrap and other types of direct resampling with MCMC procedures are outlined. Genes evolve by a process which involves some sites following a tree close to, but not identical with, the species tree. It is seen that under such a likelihood model BP (bootstrap proportions) and BPP estimates may still be reasonable estimates of the species tree. Since many of the methods studied are very fast computationally, there is no reason to ignore stochastic error even with the slowest ML or likelihood based methods.

  18. An Innovative Needle-free Injection System: Comparison to 1 ml Standard Subcutaneous Injection.

    PubMed

    Kojic, Nikola; Goyal, Pragun; Lou, Cheryl Hamer; Corwin, Michael J

    2017-05-01

    A needle-free delivery system may lead to improved satisfaction and compliance, as well as reduced anxiety among patients requiring frequent or ongoing injections. This report describes a first-in-man assessment comparing Portal Instruments' innovative needle-free injection system with subcutaneous injections using a 27G needle. Forty healthy volunteer participants each received a total of four injections of 1.0 mL sterile saline solution, two with a standard subcutaneous injection using a 27G needle, and two using the Portal injection system. Perception of pain was measured using a 100-mm visual analog scale (VAS). Injection site reactions were assessed at 2 min and at 20-30 min after each injection. Follow-up contact was made 24-48 h after the injections. Subject preference regarding injection type was also assessed. VAS pain scores at Portal injection sites met the criteria to be considered non-inferior to the pain reported at 27G needle injection sites (i.e., upper 95% confidence bound less than +5 mm). Based on a mixed effects model, at time 0, accounting for potential confounding variables, the adjusted difference in VAS scores indicated that Portal injections were 6.5 mm lower than the 27G needle injections (95% CI -10.5, -2.5). No clinically important adverse events were noted. Portal injections were preferred by 24 (60%) of the subjects (P = 0.0015). As an early step in the development of this new needle-free delivery system, the current study has shown that a 1.0-mL saline injection can be given with less pain reported than a standard subcutaneous injection using a 27G needle.

  19. Increased Bolus Volume Effect on Delayed Pharyngeal Swallowing Response in Post-stroke Oropharyngeal Dysphagia: A Pilot Study

    PubMed Central

    2016-01-01

    Objective To confirm a relationship between the pharyngeal response and bolus volume, and examine whether increasing the fluid bolus volume can improve penetration and aspiration for stroke dysphagic patients. Methods Ten stroke patients with a delayed pharyngeal response problem confirmed by a videofluoroscopic swallowing study (VFSS) were enrolled. Each subject completed two swallows each of 2 mL, 5 mL, and 10 mL of barium liquid thinned with water. The pharyngeal delay time (PDT) and penetration-aspiration scale (PAS) were measured and the changes among the different volumes were analyzed. Results PDTs were shortened significantly when 5 mL and 10 mL of thin barium were swallowed compared to 2 mL. However, there was no significant difference in PAS as the bolus volume increased. Conclusion The increased fluid bolus volume reduced the pharyngeal delay time, but did not affect the penetration and aspiration status. PMID:28119831

  20. AstroML: "better, faster, cheaper" towards state-of-the-art data mining and machine learning

    NASA Astrophysics Data System (ADS)

    Ivezic, Zeljko; Connolly, Andrew J.; Vanderplas, Jacob

    2015-01-01

    We present AstroML, a Python module for machine learning and data mining built on numpy, scipy, scikit-learn, matplotlib, and astropy, and distributed under an open license. AstroML contains a growing library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical datasets (such as SDSS and other recent major surveys), and a large suite of examples of analyzing and visualizing astronomical datasets. AstroML is especially suitable for introducing undergraduate students to numerical research projects and for graduate students to rapidly undertake cutting-edge research. The long-term goal of astroML is to provide a community repository for fast Python implementations of common tools and routines used for statistical data analysis in astronomy and astrophysics (see http://www.astroml.org).

  1. A review of the safety and efficacy data for insulin glargine 300 units/ml, a new formulation of insulin glargine.

    PubMed

    Dailey, G; Lavernia, F

    2015-12-01

    Insulin glargine 100 units/ml (Gla-100) has become a standard of care in diabetes treatment over the past decade, providing 24-h basal insulin coverage after once-daily subcutaneous injection for many people with diabetes, with a well-established efficacy and safety profile. New insulin glargine 300 units/ml (Gla-300) is a basal insulin that provides the same number of units as Gla-100 in a third of the volume. Compared with Gla-100, Gla-300 has shown more constant and prolonged pharmacokinetic (PK)/pharmacodynamic (PD) profiles. This review summarizes the findings from the EDITION series of clinical trials that investigated Gla-300 in individuals with type 1 and type 2 diabetes mellitus. Overall, Gla-300 has been shown to achieve similar glycaemic control with less, or similar, nocturnal hypoglycaemia compared with Gla-100, and a trend towards lower hypoglycaemia at any time of day. The EDITION series of clinical trials also provides some evidence for less weight gain with Gla-300 than with Gla-100. In addition, the PK/PD profiles of Gla-300 may allow more flexibility in the timing of doses, improving convenience; thus, Gla-300 could offer several positive features for individuals with diabetes requiring basal insulin therapy.

  2. Renormalized Volume

    NASA Astrophysics Data System (ADS)

    Gover, A. Rod; Waldron, Andrew

    2017-09-01

    We develop a universal distributional calculus for regulated volumes of metrics that are suitably singular along hypersurfaces. When the hypersurface is a conformal infinity we give simple integrated distribution expressions for the divergences and anomaly of the regulated volume functional valid for any choice of regulator. For closed hypersurfaces or conformally compact geometries, methods from a previously developed boundary calculus for conformally compact manifolds can be applied to give explicit holographic formulæ for the divergences and anomaly expressed as hypersurface integrals over local quantities (the method also extends to non-closed hypersurfaces). The resulting anomaly does not depend on any particular choice of regulator, while the regulator dependence of the divergences is precisely captured by these formulæ. Conformal hypersurface invariants can be studied by demanding that the singular metric obey, smoothly and formally to a suitable order, a Yamabe type problem with boundary data along the conformal infinity. We prove that the volume anomaly for these singular Yamabe solutions is a conformally invariant integral of a local Q-curvature that generalizes the Branson Q-curvature by including data of the embedding. In each dimension this canonically defines a higher dimensional generalization of the Willmore energy/rigid string action. Recently, Graham proved that the first variation of the volume anomaly recovers the density obstructing smooth solutions to this singular Yamabe problem; we give a new proof of this result employing our boundary calculus. Physical applications of our results include studies of quantum corrections to entanglement entropies.

  3. Automatic publishing ISO 19115 metadata with PanMetaDocs using SensorML information

    NASA Astrophysics Data System (ADS)

    Stender, Vivien; Ulbricht, Damian; Schroeder, Matthias; Klump, Jens

    2014-05-01

    Terrestrial Environmental Observatories (TERENO) is an interdisciplinary and long-term research project spanning an Earth observation network across Germany. It includes four test sites within Germany from the North German lowlands to the Bavarian Alps and is operated by six research centers of the Helmholtz Association. The contribution by the participating research centers is organized as regional observatories. A challenge for TERENO and its observatories is to integrate all aspects of data management, data workflows, data modeling and visualizations into the design of a monitoring infrastructure. TERENO Northeast is one of the sub-observatories of TERENO and is operated by the German Research Centre for Geosciences (GFZ) in Potsdam. This observatory investigates geoecological processes in the northeastern lowland of Germany by collecting large amounts of environmentally relevant data. The success of long-term projects like TERENO depends on well-organized data management, data exchange between the partners involved and on the availability of the captured data. Data discovery and dissemination are facilitated not only through data portals of the regional TERENO observatories but also through a common spatial data infrastructure TEODOOR (TEreno Online Data repOsitORry). TEODOOR bundles the data, provided by the different web services of the single observatories, and provides tools for data discovery, visualization and data access. The TERENO Northeast data infrastructure integrates data from more than 200 instruments and makes data available through standard web services. Geographic sensor information and services are described using the ISO 19115 metadata schema. TEODOOR accesses the OGC Sensor Web Enablement (SWE) interfaces offered by the regional observatories. In addition to the SWE interface, TERENO Northeast also published data through DataCite. The necessary metadata are created in an automated process by extracting information from the SWE SensorML to

  4. ART-ML: a new markup language for modelling and representation of biological processes in cardiovascular diseases.

    PubMed

    Karvounis, E C; Exarchos, T P; Fotiou, E; Sakellarios, A I; Iliopoulou, D; Koutsouris, D; Fotiadis, D I

    2013-01-01

    With an ever increasing number of biological models available on the internet, a standardized modelling framework is required to allow information to be accessed and visualized. In this paper we propose a novel Extensible Markup Language (XML) based format called ART-ML that aims at supporting the interoperability and the reuse of models of geometry, blood flow, plaque progression and stent modelling, exported by any cardiovascular disease modelling software. ART-ML has been developed and tested using ARTool. ARTool is a platform for the automatic processing of various image modalities of coronary and carotid arteries. The images and their content are fused to develop morphological models of the arteries in 3D representations. All the above described procedures integrate disparate data formats, protocols and tools. ART-ML proposes a representation way, expanding ARTool, for interpretability of the individual resources, creating a standard unified model for the description of data and, consequently, a format for their exchange and representation that is machine independent. More specifically, ARTool platform incorporates efficient algorithms which are able to perform blood flow simulations and atherosclerotic plaque evolution modelling. Integration of data layers between different modules within ARTool are based upon the interchange of information included in the ART-ML model repository. ART-ML provides a markup representation that enables the representation and management of embedded models within the cardiovascular disease modelling platform, the storage and interchange of well-defined information. The corresponding ART-ML model incorporates all relevant information regarding geometry, blood flow, plaque progression and stent modelling procedures. All created models are stored in a model repository database which is accessible to the research community using efficient web interfaces, enabling the interoperability of any cardiovascular disease modelling software

  5. ACM SIGPLAN Workshop on ML and Its Applications Held in San Francisco, California on June 20-21, 1992

    DTIC Science & Technology

    1992-06-01

    University of Copenhagen Aooession For NTIS GIZA&I • DTIC TAB [ D’ic tj •-’ :2-Cr= D 8 Unarnounced C1 Di tiicut Avall an4tor Dist Special Foreword The...Consistency-Preserving Programs in Distributed ML Clifford D . Krumvieda (Cornell University) .................................... 157 Implementing ML on...some implementations of SML [App90], the representation of the datatype defined by datatype d = A I B of t, depends on the representation of t. If the

  6. First Selective 12-LOX Inhibitor, ML355, Impairs Thrombus Formation and Vessel Occlusion In Vivo With Minimal Effects on Hemostasis.

    PubMed

    Adili, Reheman; Tourdot, Benjamin E; Mast, Katherine; Yeung, Jennifer; Freedman, John C; Green, Abigail; Luci, Diane K; Jadhav, Ajit; Simeonov, Anton; Maloney, David J; Holman, Theodore R; Holinstat, Michael

    2017-10-01

    Adequate platelet reactivity is required for maintaining hemostasis. However, excessive platelet reactivity can also lead to the formation of occlusive thrombi. Platelet 12(S)-lipoxygenase (12-LOX), an oxygenase highly expressed in the platelet, has been demonstrated to regulate platelet function and thrombosis ex vivo, supporting a key role for 12-LOX in the regulation of in vivo thrombosis. However, the ability to pharmacologically target 12-LOX in vivo has not been established to date. Here, we studied the effect of the first highly selective 12-LOX inhibitor, ML355, on in vivo thrombosis and hemostasis. ML355 dose-dependently inhibited human platelet aggregation and 12-LOX oxylipin production, as confirmed by mass spectrometry. Interestingly, the antiplatelet effects of ML355 were reversed after exposure to high concentrations of thrombin in vitro. Ex vivo flow chamber assays confirmed that human platelet adhesion and thrombus formation at arterial shear over collagen were attenuated in whole blood treated with ML355 comparable to aspirin. Oral administration of ML355 in mice showed reasonable plasma drug levels by pharmacokinetic assessment. ML355 treatment impaired thrombus growth and vessel occlusion in FeCl3-induced mesenteric and laser-induced cremaster arteriole thrombosis models in mice. Importantly, hemostatic plug formation and bleeding after treatment with ML355 was minimal in mice in response to laser ablation on the saphenous vein or in a cremaster microvasculature laser-induced rupture model. Our data strongly support 12-LOX as a key determinant of platelet reactivity in vivo, and inhibition of platelet 12-LOX with ML355 may represent a new class of antiplatelet therapy. © 2017 American Heart Association, Inc.

  7. Effects of volume and periodicity on blood cultures.

    PubMed Central

    Li, J; Plorde, J J; Carlson, L G

    1994-01-01

    Blood specimens collected for culture by using the high-volume resin-based BACTEC system over an 18-month period at the Seattle Veterans Administration Center were examined in this study. Of 7,783 cultures obtained, 624 were classified as true positives. Patients in this group had between 20 and 60 ml of blood drawn per culture and separated into 10-ml aliquots for incubation. Analysis of the results stratified by cultured volume and time interval between specimen collection accorded yield advantage to culture volume at the maximal amounts tested. No advantage was observed with any particular interval of collection. Increasing cultured volume from 20 to 40 ml increased yield by 19%. Increasing cultured volume from 40 to 60 ml increased yield by an additional 10%. The same effect was seen whether cultures were drawn simultaneously or serially within 24 h. These observations support other reports demonstrating increased yield with increased cultured blood volume. However, they demonstrate increases in yield at volumes much higher than previously considered. In conclusion, this study demonstrates that high-volume blood cultures drawn serially or simultaneously return the best yields. PMID:7852579

  8. The minimum volume of pleural fluid required to diagnose malignant pleural effusion: A retrospective study

    PubMed Central

    Wu, Huimin; Khosla, Rahul; Rohatgi, Prashant K; Chauhan, Suman S; Paal, Edina; Chen, Wen

    2017-01-01

    Background: Pleural fluid cytology is a quick and accurate method to diagnose malignant pleural effusions. The optimal volume of fluid for cytological analysis has not yet been identified, and clinical recommendation based on some published clinical experiences has been to send large volumes of fluid for cytological analysis. A quality improvement initiative at our institution was conducted to determine the volume of fluid sufficient for a diagnosis of malignant pleural effusion. Materials and Methods: The study was approved by the Institutional Review Board. All pleural fluid specimens that were divided into three volumes (25 mL, 50 mL, and 150 mL) and sent for cytological examination were reviewed. Results: A total of 74 samples from 60 individual patients were evaluable. Thirty-six patients (60%) had a previous diagnosis of malignancy. Of the 74 specimens, 26 (35.1%) were positive for malignancy. The detection rate for malignant pleural effusion by cytology for 25 mL, 50 mL, and 150 mL were 88.5%, 96.2%, and 100.0%, respectively (P = 0.16). Two specimens that were negative in the 25 mL samples turned out to be positive in the 50 mL and 150 mL samples. One specimen was negative in the 25 mL and 50 mL samples but positive in the 150 mL sample. Conclusions: Our study did not show any statistically significant difference in the detection of malignant effusion in the 25 mL, 50 mL, and 150 mL group. PMID:28144058

  9. Contrail Cirrus Forecasts for the ML-CIRRUS Experiment and Some Comparison Results

    NASA Astrophysics Data System (ADS)

    Schumann, Ulrich; Graf, Kaspar; Bugliaro, Luca; Dörnbrack, Andreas; Giez, Andreas; Jurkat, Tina; Kaufmann, Stefan; Krämer, Martina; Minikin, Andreas; Schäfler, Andreas; Voigt, Christiane; Wirth, Martin; Zahn, Andreas; Ziereis, Helmut

    2015-04-01

    Model simulations with the contrail cirrus prediction model CoCiP driven by numerical weather prediction (NWP) data provided from the European Centre for Medium Range Forecasts (ECMWF) and global aircraft waypoint data show a mean computed cover (for optical depth larger than 0.1) of 0.23% globally, and 5.4% over mid Europe (Schumann and Graf, JGR, 2013). The computed mean longwave radiative forcing (RF) reaches 3 W m-2 over mid Europe (10°W-20°E and 40°N-55°N), and 0.13 W m-2 globally. The global net RF is about 40-60% smaller because of compensating shortwave cooling induced by contrails during daytime. The results depend on several model details such as the number of ice particles forming from aircraft soot emissions, the contrail plume dispersion, ice particle sedimentation etc., all influencing contrail life time and their optical properties. The quantitative results depend also strongly on ambient relative humidity, vertical motion and on ice water content of other cirrus predicted by the NWP model. In order to test and possibly improve this and other contrail models, high-quality observations are needed to which multi-parameter model output can be compared. The Mid-Latitude Cirrus Experiment ML-CIRRUS was performed (see C. Voigt et al., this conference) with a suite of in-situ and Lidar instruments for airborne measurements on the research aircraft HALO. Before and during the mission, CoCiP was run daily to provide 3-days forecasts of contrail cover using operational ECMWF forecasts and historical traffic data. CoCiP forecast output was made available in an internet tool twice a day for experiment planning. The one-day and two-day contrail forecasts often showed only small differences. Still, most recent forecasts and detailed satellite observations results were transmitted via satellite link to the crew for onboard campaign optimization. After the campaign, a data base of realistic air traffic data has been setup from various sources, and CoCiP was

  10. Effect of face mask dead volume, respiratory rate, and tidal volume on inhaled albuterol delivery.

    PubMed

    Chavez, Alma; McCracken, Andy; Berlinski, Ariel

    2010-03-01

    Pediatric patients often require metered-dose inhaler (MDI) with holding chamber (HC) to overcome lack of coordination when receiving inhaled therapy. In infants and young children unable to use a mouthpiece, it is necessary to use a mask interface. We compared the effect of varying mask static dead volume (SDV), respiratory rate (RR), and tidal volume (VT) on albuterol captured at the mouth opening (ACMO) in an in vitro model. An Aerochamber Max(R) without and with three mask sizes (SDV of 10, 36, 85, and 200 ml, respectively) was connected in series to a filter holder and breathing simulator. ACMO was measured at VTs = 36, 72, 145, and 290 ml and RR of 12 and 24. Each experiment comprised 10 puffs run for six respiratory cycles each. Albuterol was quantified via spectrophotometry at 276 nm. A P-value of 0.05 was considered significant. Increasing VT increased ACMO (all SDVs and RRs). Adding SDV decreased ACMO, except for the small mask at VTs = 145 and 290 ml at RR = 12. Increasing SDV decreased ACMO, except at VT = 36 ml (all masks) and VT = 72 ml (small = medium) at RR = 12 and VT = 36 ml (small = other and medium > large) at RR = 24. Increasing RR increased ACMO for all SDVs at VTs = 36 and 72 ml, but not for VTs = 145 and 290 ml, except for no and large mask at VT = 145 ml. In general, decreasing SDV, increasing VT, and increasing RR increase ACMO. Early transition from face mask to mouthpiece should be considered in children receiving albuterol via MDI with HC.

  11. Fissure Integrity and Volume Reduction in Emphysema: A Retrospective Study.

    PubMed

    de Oliveira, Hugo Goulart; de Oliveira, Silvia Martins; Rambo, Rafael Ramos; de Macedo Neto, Amarilio Vieira

    2016-01-01

    One-way endobronchial valves (EBVs) relieve symptoms of emphysema, particularly in patients without collateral ventilation between the target and adjacent lobes. Pretreatment knowledge of fissure integrity could serve as an aid in indicating EBV interventions. This study aimed to investigate the relationship between software-measured lung fissure integrity and clinically relevant lung volume reduction (≥350 ml) in emphysema patients treated with one-way EBVs using a lobar exclusion strategy. Of 108 patients treated between March 2008 and July 2014, 38 had both baseline and follow-up computed tomography (CT) scans acquired following a specific protocol for quantitative CT analysis and were included in the study (total of 39 treatments, two lungs treated in 1 patient). Outcome measures were fissure integrity measured on baseline CT scans, difference between pre- and postoperative lung volume (considering the lowest measured postoperative volume), and correlation between fissure integrity and volume change. Fissure integrity ≥75% correlated with volume reduction ≥350 ml (Spearman coefficient: -0.65; p < 0.01). The mean and median volume reductions were 1,223.96 ± 907.5 ml and 663 ml, respectively, for lungs with fissure integrity ≥75% (n = 31). The accuracy of fissure integrity ≥75% in predicting a volume reduction was 87.2%. The positive predictive value of fissure integrity ≥75% to predict a volume reduction ≥350 ml was 83.9%, and it was 70% for fissure integrity 75-90% and 90.5% for fissure integrity >90%. A target lobe volume reduction using EBVs is possible with lung fissure integrity ≥75%. For patients with fissure integrity between 75 and 90%, a further evaluation of interlobar ventilation should be performed. A clinically relevant volume reduction following treatment with EBVs is likely with any level of fissure integrity >90%. © 2016 S. Karger AG, Basel.

  12. Probabilistic distributions of M/L values for ultrafaint dwarf spheroidal galaxies: stochastic samplings of the initial mass function

    NASA Astrophysics Data System (ADS)

    Hernandez, X.

    2012-02-01

    We explore the ranges and distributions which will result for the intrinsic stellar mass-to-light ratio (M/L) values of single stellar populations, at fixed initial mass function (IMF), age and metallicity, from the discrete stochastic sampling of a probabilistic IMF. As the total mass of a certain stellar population tends to infinity, the corresponding M/L values quickly converge to fixed numbers associated with the particulars of the IMF, age, metallicity and star formation histories in question. When going to small stellar populations, however, a natural inherent spread will appear for the M/L values, which will become probabilistic quantities. For the recently discovered ultrafaint local dwarf spheroidal galaxies, with total luminosities dropping below 103LV/L⊙, it is important to asses the amplitude of the probabilistic spread in inherent M/L values mentioned above. The total baryonic masses of these systems are usually estimated from their observed luminosities, and the assumption of a fixed, deterministic M/L value, suitable for the infinite population limit of the assumed ages and metallicities of the stellar populations in question. This total baryonic masses are crucial for testing and calibrating of structure formation scenarios, as the local ultrafaint dwarf spheroidals represent the most extreme galactic scales known. Also, subject to reliable M/L values is the use of these systems as possible discriminants between dark matter and modified gravity theories. By simulating large collections of stellar populations, each consisting of a particular collection of individual stars, we compute statistical distributions for the resulting M/L values. We find that for total numbers of stars in the range of what is observed for the local ultrafaint dwarf spheroidals, the inherent M/L values of stellar populations can be expected to vary by factors of upwards of 3, interestingly, systematically skewed towards higher values than what is obtained for the

  13. Activation of Relaxin Family Receptor 1 from Different Mammalian Species by Relaxin Peptide and Small-Molecule Agonist ML290

    PubMed Central

    Huang, Zaohua; Myhr, Courtney; Bathgate, Ross A. D.; Ho, Brian A.; Bueno, Amaya; Hu, Xin; Xiao, Jingbo; Southall, Noel; Barnaeva, Elena; Agoulnik, Irina U.; Marugan, Juan J.; Ferrer, Marc; Agoulnik, Alexander I.

    2015-01-01

    Relaxin peptide (RLN), which signals through the relaxin family peptide 1 (RXFP1) GPCR receptor, has shown therapeutic effects in an acute heart failure clinical trial. We have identified a small-molecule agonist of human RXFP1, ML290; however, it does not activate the mouse receptor. To find a suitable animal model for ML290 testing and to gain mechanistic insights into the interaction of various ligands with RXFP1, we have cloned rhesus macaque, pig, rabbit, and guinea pig RXFP1s and analyzed their activation by RLN and ML290. HEK293T cells expressing macaque or pig RXFP1 responded to relaxin and ML290 treatment as measured by an increase of cAMP production. Guinea pig RXFP1 responded to relaxin but had very low response to ML290 treatment only at highest concentrations used. The rabbit RXFP1 amino acid sequence was the most divergent, with a number of unique substitutions within the ectodomain and the seven-transmembrane domain (7TM). Two splice variants of rabbit RXFP1 derived through alternative splicing of the fourth exon were identified. In contrast to the other species, rabbit RXFP1s were activated by ML290, but not with human, pig, mouse, or rabbit RLNs. Using FLAG-tagged constructs, we have shown that both rabbit RXFP1 variants are expressed on the cell surface. No binding of human Eu-labeled RLN to rabbit RXFP1 was detected, suggesting that in this species, RXFP1 might be non-functional. We used chimeric rabbit–human and guinea pig–human constructs to identify regions important for RLN or ML290 receptor activation. Chimeras with the human ectodomain and rabbit 7TM domain were activated by RLN, whereas substitution of part of the guinea pig 7TM domain with the human sequence only partially restored ML290 activation, confirming the allosteric mode of action for the two ligands. Our data demonstrate that macaque and pig models can be used for ML290 testing. PMID:26347712

  14. A platform for in silico modeling of physiological systems II. CellML compatibility and other extended capabilities.

    PubMed

    Suzuki, Yasuyuki; Asai, Yoshiyuki; Kawazu, Toshihiro; Nakanishi, Masao; Taniguchi, Yoshiki; Heien, Eric; Hagihara, Kenichi; Kurachi, Yoshihisa; Nomura, Taishin

    2008-01-01

    The number of biological models published in peer reviewed journals and complexity of each of those models are rapidly increasing, making it difficult to reproduce simulation results of the published models and to reuse the models by third persons. This paper is a continuation of our previous report on a software platform development as a solution to such difficulties. We describe progresses of our development. Those include improvement in functional capabilities to import and simulate published models in the CellML model repository, to browse and edit CellML models and then to export them as new models either with the CellML format or with a XML format defined for our platform (ISML), and to newly construct large scale models by connecting CellML/ISML models. Several advantages to use ISML in parallel with CellML are; 1) ISML can deal with geometry (morphology) of a model, enabling the user to perform geometry dependent modeling and simulations. 2) ISML can deal with time series data, both simulated and experimentally acquired data, for visualization of dynamics.

  15. Heritability of brain volume change and its relation to intelligence.

    PubMed

    Brouwer, Rachel M; Hedman, Anna M; van Haren, Neeltje E M; Schnack, Hugo G; Brans, Rachel G H; Smit, Dirk J A; Kahn, Rene S; Boomsma, Dorret I; Hulshoff Pol, Hilleke E

    2014-10-15

    Human brain volumes change throughout life, are highly heritable, and have been associated with general cognitive functioning. Cross-sectionally, this association between volume and cognition can largely be attributed to the same genes influencing both traits. We address the question whether longitudinal changes in brain volume or in surface area in young adults are under genetic control and whether these changes are also related to general cognitive functioning. We measured change in brain volume and surface area over a 5-year interval in 176 monozygotic and dizygotic twins and their non-twin siblings aged 19 to 56, using magnetic resonance imaging. Results show that changes in volumes of total brain (mean = -6.4 ml; 0.5% loss), cerebellum (1.4 ml, 1.0% increase), cerebral white matter (4.4 ml, 0.9% increase), lateral ventricles (0.6 ml; 4.8% increase) and in surface area (-19.7 cm(2),1.1% contraction) are heritable (h(2) = 43%; 52%; 29%; 31%; and 33%, respectively). An association between IQ (available for 91 participants) and brain volume change was observed, which was attributed to genes involved in both the variation in change in brain volume and in intelligence. Thus, dynamic changes in brain structure are heritable and may have cognitive significance in adulthood. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Whole genome sequences of a free-living Pseudomonas sp. strain ML96 isolated from a freshwater Maar Lake.

    PubMed

    Li, Xiuling; Blom, Jochen; Zeng, Yonghui

    2015-12-01

    A free living freshwater Pseudomonas strain ML96 was isolated from the Huguangyan Maar Lake in southern China. Genome sequencing of strain ML96 revealed a 4.7 Mb long draft genome consisting of 47 contigs with a G+C content of 64.8%. Its 16S and 23S rRNA gene sequences were 99.8% and 99.3% identical to those of its closest relative, Pseudomonas alcaligenes NBRC 14159, respectively. ML96's genome shared 73% orthologous CDS (3256/4457) with the genome of NBRC 14159. Comparative genomics analysis provide further insight into the diversity and evolution of aquatic Pseudomonas species, which may help enhance our understanding of this both environmentally and medically important group of bacteria.

  17. A novel method for blood volume estimation using trivalent chromium in rabbit models

    PubMed Central

    Baby, Prathap Moothamadathil; Kumar, Pramod; Kumar, Rajesh; Jacob, Sanu S.; Rawat, Dinesh; Binu, V. S.; Karun, Kalesh M.

    2014-01-01

    Background: Blood volume measurement though important in management of critically ill-patients is not routinely estimated in clinical practice owing to labour intensive, intricate and time consuming nature of existing methods. Aims: The aim was to compare blood volume estimations using trivalent chromium [51Cr(III)] and standard Evans blue dye (EBD) method in New Zealand white rabbit models and establish correction-factor (CF). Materials and Methods: Blood volume estimation in 33 rabbits was carried out using EBD method and concentration determined using spectrophotometric assay followed by blood volume estimation using direct injection of 51Cr(III). Twenty out of 33 rabbits were used to find CF by dividing blood volume estimation using EBD with blood volume estimation using 51Cr(III). CF is validated in 13 rabbits by multiplying it with blood volume estimation values obtained using 51Cr(III). Results: The mean circulating blood volume of 33 rabbits using EBD was 142.02 ± 22.77 ml or 65.76 ± 9.31 ml/kg and using 51Cr(III) was estimated to be 195.66 ± 47.30 ml or 89.81 ± 17.88 ml/kg. The CF was found to be 0.77. The mean blood volume of 13 rabbits measured using EBD was 139.54 ± 27.19 ml or 66.33 ± 8.26 ml/kg and using 51Cr(III) with CF was 152.73 ± 46.25 ml or 71.87 ± 13.81 ml/kg (P = 0.11). Conclusions: The estimation of blood volume using 51Cr(III) was comparable to standard EBD method using CF. With further research in this direction, we envisage human blood volume estimation using 51Cr(III) to find its application in acute clinical settings. PMID:25190922

  18. Fine Physical and Genetic Mapping of Powdery Mildew Resistance Gene MlIW172 Originating from Wild Emmer (Triticum dicoccoides)

    PubMed Central

    Han, Jun; Zhao, Xiaojie; Cui, Yu; Song, Wei; Huo, Naxin; Liang, Yong; Xie, Jingzhong; Wang, Zhenzhong; Wu, Qiuhong; Chen, Yong-Xing; Lu, Ping; Zhang, De-Yun; Wang, Lili; Sun, Hua; Yang, Tsomin; Keeble-Gagnere, Gabriel; Appels, Rudi; Doležel, Jaroslav; Ling, Hong-Qing; Luo, Mingcheng; Gu, Yongqiang; Sun, Qixin; Liu, Zhiyong

    2014-01-01

    Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7AL-16-0.86-0.90) via molecular marker analysis. MlIW172 was closely linked with the RFLP probe Xpsr680-derived STS marker Xmag2185 and the EST markers BE405531 and BE637476. This suggested that MlIW172 might be allelic to the Pm1 locus or a new locus closely linked to Pm1. By screening genomic BAC library of durum wheat cv. Langdon and 7AL-specific BAC library of hexaploid wheat cv. Chinese Spring, and after analyzing genome scaffolds of Triticum urartu containing the marker sequences, additional markers were developed to construct a fine genetic linkage map on the MlIW172 locus region and to delineate the resistance gene within a 0.48 cM interval. Comparative genetics analyses using ESTs and RFLP probe sequences flanking the MlIW172 region against other grass species revealed a general co-linearity in this region with the orthologous genomic regions of rice chromosome 6, Brachypodium chromosome 1, and sorghum chromosome 10. However, orthologous resistance gene-like RGA sequences were only present in wheat and Brachypodium. The BAC contigs and sequence scaffolds that we have developed provide a framework for the physical mapping and map-based cloning of MlIW172. PMID:24955773

  19. Therapy reduction in patients with Down syndrome and myeloid leukemia: the international ML-DS 2006 trial.

    PubMed

    Uffmann, Madita; Rasche, Mareike; Zimmermann, Martin; von Neuhoff, Christine; Creutzig, Ursula; Dworzak, Michael; Scheffers, Lenie; Hasle, Henrik; Zwaan, C Michel; Reinhardt, Dirk; Klusmann, Jan-Henning

    2017-06-22

    Children with myeloid leukemia associated with Down syndrome (ML-DS) have superior outcome compared with non-DS patients, but suffer from higher constitutional cytotoxic drug susceptibility. We analyzed the outcome of 170 pediatric patients with ML-DS enrolled in the prospective, multicenter, open-label, nonrandomized ML-DS 2006 trial by Nordic Society for Pediatric Hematology and Oncology (NOPHO), Dutch Childhood Oncology Group (DCOG), and Acute Myeloid Leukemia-Berlin-Frankfurt-Münster (AML-BFM) study group. Compared with the historical control arm (reduced-intensity protocol for ML-DS patients from the AML-BFM 98 trial), treatment intensity was reduced by lowering the cumulative dose of etoposide (950 to 450 mg/m(2)) and intrathecal central nervous system prophylaxis while omitting maintenance therapy. Still, 5-year overall survival (89% ± 3% vs 90% ± 4%; Plog-rank = .64), event-free survival (EFS; 87% ± 3% vs 89% ± 4%; Plog-rank = .71), and cumulative incidence of relapse/nonresponse (CIR/NR; 6% ± 3% vs 6% ± 2%; PGray = .03) did not significantly differ between the ML-DS 2006 trial and the historical control arm. Poor early treatment response (5-year EFS, 58% ± 16% vs 88% ± 3%; Plog rank = .0008) and gain of chromosome 8 (CIR/NR, 16% ± 7% vs 3% ± 2%, PGray = .02; 5-year EFS, 73% ± 8% vs 91% ± 4%, Plog rank = .018) were identified as independent prognostic factors predicting a worse EFS. Five of 7 relapsed patients (71%) with cytogenetic data had trisomy 8. Our study reveals prognostic markers for children with ML-DS and illustrates that reducing therapy did not impair excellent outcome. The trial was registered at EudraCT as #2007-006219-2. © 2017 by The American Society of Hematology.

  20. QuakeML: Recent Development and First Applications of the Community-Created Seismological Data Exchange Standard

    NASA Astrophysics Data System (ADS)

    Euchner, F.; Schorlemmer, D.; Kästli, P.; Quakeml Group, T

    2008-12-01

    QuakeML is an XML-based exchange format for seismological data which is being developed using a community-driven approach. It covers basic event description, including picks, arrivals, amplitudes, magnitudes, origins, focal mechanisms, and moment tensors. Contributions have been made from ETH, GFZ, USC, SCEC, USGS, IRIS DMC, EMSC, ORFEUS, GNS, ZAMG, BRGM, and ISTI. The current release (Version 1.1, Proposed Recommendation) reflects the results of a public Request for Comments process which has been documented online at http://quakeml.org/RFC_BED_1.0. QuakeML has recently been adopted as a distribution format for earthquake catalogs by GNS Science, New Zealand, and the European-Mediterranean Seismological Centre (EMSC). These institutions provide prototype QuakeML web services. Furthermore, integration of the QuakeML data model in the CSEP (Collaboratory for the Study of Earthquake Predictability, http://www.cseptesting.org) testing center software developed by SCEC is under way. QuakePy is a Python- based seismicity analysis toolkit which is based on the QuakeML data model. Recently, QuakePy has been used to implement the PMC method for calculating network recording completeness (Schorlemmer and Woessner 2008, in press). Completeness results for seismic networks in Southern California and Japan can be retrieved through the CompletenessWeb (http://completenessweb.org). Future QuakeML development will include an extension for macroseismic information. Furthermore, development on seismic inventory information, resource identifiers, and resource metadata is under way. Online resources: http://www.quakeml.org, http://www.quakepy.org

  1. Implementation of a Goal-Based Systems Engineering Process Using the Systems Modeling Language (SysML)

    NASA Technical Reports Server (NTRS)

    Breckenridge, Jonathan T.; Johnson, Stephen B.

    2013-01-01

    This paper describes the core framework used to implement a Goal-Function Tree (GFT) based systems engineering process using the Systems Modeling Language. It defines a set of principles built upon by the theoretical approach described in the InfoTech 2013 ISHM paper titled "Goal-Function Tree Modeling for Systems Engineering and Fault Management" presented by Dr. Stephen B. Johnson. Using the SysML language, the principles in this paper describe the expansion of the SysML language as a baseline in order to: hierarchically describe a system, describe that system functionally within success space, and allocate detection mechanisms to success functions for system protection.

  2. Transformation of Arden Syntax's medical logic modules into ArdenML for a business rules management system.

    PubMed

    Jung, Chai Young; Choi, Jong-Ye; Jeong, Seong Jik; Cho, Kyunghee; Koo, Yong Duk; Bae, Jin Hee; Kim, Sukil

    2016-05-16

    Arden Syntax is a Health Level Seven International (HL7) standard language that is used for representing medical knowledge as logic statements. Arden Syntax Markup Language (ArdenML) is a new representation of Arden Syntax based on XML. Compilers are required to execute medical logic modules (MLMs) in the hospital environment. However, ArdenML may also replace the compiler. The purpose of this study is to demonstrate that MLMs, encoded in ArdenML, can be transformed into a commercial rule engine format through an XSLT stylesheet and made executable in a target system. The target rule engine selected was Blaze Advisor. We developed an XSLT stylesheet to transform MLMs in ArdenML into Structured Rules Language (SRL) in Blaze Advisor, through a comparison of syntax between the two languages. The stylesheet was then refined recursively, by building and applying rules collected from the billing and coding guidelines of the Korean health insurance service. Two nurse coders collected and verified the rules and two information technology (IT) specialists encoded the MLMs and built the XSLT stylesheet. Finally, the stylesheet was validated by importing the MLMs into Blaze Advisor and applying them to claims data. The language comparison revealed that Blaze Advisor requires the declaration of variables with explicit types. We used both integer and real numbers for numeric types in ArdenML. "IF∼THEN" statements and assignment statements in ArdenML become rules in Blaze Advisor. We designed an XSLT stylesheet to solve this issue. In addition, we maintained the order of rule execution in the transformed rules, and added two small programs to support variable declarations and action statements. A total of 1489 rules were reviewed during this study, of which 324 rules were collected. We removed duplicate rules and encoded 241 unique MLMs in ArdenML, which were successfully transformed into SRL and imported to Blaze Advisor via the XSLT stylesheet. When applied to 73

  3. ML-Space: Hybrid Spatial Gillespie and Particle Simulation of Multi-level Rule-based Models in Cell Biology.

    PubMed

    Bittig, Arne; Uhrmacher, Adelinde

    2016-08-03

    Spatio-temporal dynamics of cellular processes can be simulated at different levels of detail, from (deterministic) partial differential equations via the spatial Stochastic Simulation algorithm to tracking Brownian trajectories of individual particles. We present a spatial simulation approach for multi-level rule-based models, which includes dynamically hierarchically nested cellular compartments and entities. Our approach ML-Space combines discrete compartmental dynamics, stochastic spatial approaches in discrete space, and particles moving in continuous space. The rule-based specification language of ML-Space supports concise and compact descriptions of models and to adapt the spatial resolution of models easily.

  4. A simple and feasible method to determine absolute blood volume in hemodialysis patients in clinical practice.

    PubMed

    Kron, Joachim; Schneditz, Daniel; Leimbach, Til; Aign, Sabine; Kron, Susanne

    2014-01-01

    We developed a simple method to determine the absolute blood volume (V) during hemodialysis in everyday clinical practice and examined its relationship with volume overload, clinical relevance, and accuracy. The increase in relative blood volume (RBVpost - RBVpre) measured before and after infusion of 240 ml of ultra-pure dialysate using the bolus function of a commercial online hemodiafiltration machine incorporating a relative blood volume monitor was applied to determine absolute blood volume. The specific blood volume (Vs, blood volume per kg body mass at dry weight, in ml/kg) was compared to volume status as assessed by bioimpedance analysis and clinical criteria. The blood volume measured in 30 stable hemodialysis patients was 6.51 ± 1.70 l at the beginning, corresponding to a specific blood volume of 80.1 ± 12.8 ml/kg, and dropped to 5.84 ± 1.61 l or 72.0 ± 12.1 ml/kg at the end of the dialysis session, respectively. Specific blood volume correlated with volume status assessed both clinically and by bioimpedance analysis. Intradialytic morbid events occurred only in treatments where specific blood volume fell below 65 ml/kg. The reproducibility of the technique was better than 4% and the in vitro accuracy corresponds to a resolution in Vs of better than 1 ml/kg. Absolute blood volume can be easily measured at the beginning of the dialysis session using the current dialysis technology. Information about V and Vs could be a promising tool to avoid intradialytic morbid events. This technique could be completely automated without altering the hardware of currently available online dialysis devices. Therefore, it is recommended that this technique be integrated into all hemodiafiltration machines. © 2014 S. Karger AG, Basel.

  5. SEM with Missing Data and Unknown Population Distributions Using Two-Stage ML: Theory and Its Application

    ERIC Educational Resources Information Center

    Yuan, Ke-Hai; Lu, Laura

    2008-01-01

    This article provides the theory and application of the 2-stage maximum likelihood (ML) procedure for structural equation modeling (SEM) with missing data. The validity of this procedure does not require the assumption of a normally distributed population. When the population is normally distributed and all missing data are missing at random…

  6. Effect of Cymbopogon citratus L. essential oil on growth and morphogenesis of Saccharomyces cerevisiae ML2-strain.

    PubMed

    Helal, G A; Sarhan, M M; Abu Shahla, A N K; Abou El-Khair, E K

    2006-01-01

    The growth of Saccharomyces cerevisiae was completely inhibited using 2.0 microl/ml or 4.0 microl/ml of Cymbopogon citratus essential oil applied by fumigation or contact method in Sabouraud's broth medium, respectively. This oil was found also to be fungicidal at the same concentrations. The sublethal doses 1.0 and 3.0 microl/ml inhibited about 98% of yeast growth after 24 hr of incubation as compared with the control. Microscopic observations using Light Microscope (LM), Scanning Electron Microscope (SEM) and Transmission Electron Microscope (TEM) showed morphogenic and ultrastructure changes in the fumigated cells with 1.0 microl/ml of the oil. These changes including decrease in cell size, depressions on the surface of the cells, alteration in cell wall thickness and disruption of plasma membrane. Moreover, Ca(+2), K(+) and Mg(+2) leakages increased from the fumigated cells and its total lipid content decreased. Also, the fatty acid composition was altered with decrease in the amount of saturated fatty acids and increase in the amount of unsaturated fatty acids.

  7. VeriML: A Dependently-Typed, User-Extensible and Language-Centric Approach to Proof Assistants

    DTIC Science & Technology

    2013-01-01

    VeriML idea to him. I would also like to thank the rest of my professors at Yale, especially Bryan Ford, Richard Yang, Gaja Jarosz, Yiorgos Makris and...Boutin, C. Cornes, J. Courant , Y. Coscoy, D. Delahaye, D. de Rauglaudre, J.C. Filliâtre, E. Giménez, H. Herbelin, et al. The Coq proof assistant

  8. Plane-dependent ML scatter scaling: 3D extension of the 2D simulated single scatter (SSS) estimate

    NASA Astrophysics Data System (ADS)

    Rezaei, Ahmadreza; Salvo, Koen; Vahle, Thomas; Panin, Vladimir; Casey, Michael; Boada, Fernando; Defrise, Michel; Nuyts, Johan

    2017-08-01

    Scatter correction is typically done using a simulation of the single scatter, which is then scaled to account for multiple scatters and other possible model mismatches. This scaling factor is determined by fitting the simulated scatter sinogram to the measured sinogram, using only counts measured along LORs that do not intersect the patient body, i.e. ‘scatter-tails’. Extending previous work, we propose to scale the scatter with a plane dependent factor, which is determined as an additional unknown in the maximum likelihood (ML) reconstructions, using counts in the entire sinogram rather than only the ‘scatter-tails’. The ML-scaled scatter estimates are validated using a Monte-Carlo simulation of a NEMA-like phantom, a phantom scan with typical contrast ratios of a 68Ga-PSMA scan, and 23 whole-body 18F-FDG patient scans. On average, we observe a 12.2% change in the total amount of tracer activity of the MLEM reconstructions of our whole-body patient database when the proposed ML scatter scales are used. Furthermore, reconstructions using the ML-scaled scatter estimates are found to eliminate the typical ‘halo’ artifacts that are often observed in the vicinity of high focal uptake regions.

  9. Spectroscopic Classification of ASASSN-16ml and AT2016hmq/PS16esl as Type II SNe

    NASA Astrophysics Data System (ADS)

    Prieto, J. L.; Seibert, M.; Shappee, B. J.; Dong, S.; Stanek, K. Z.

    2016-11-01

    We obtained optical spectra (range 3600-9200 Angs) of ASASSN-16ml/AT2016hpt (ATel #9697) and AT2016hmq/PS16esl (ATel #9686) on UT Oct. 31.0 with WFCCD mounted on the du Pont 2.5m telescope at Las Campanas Observatory.

  10. SEM with Missing Data and Unknown Population Distributions Using Two-Stage ML: Theory and Its Application

    ERIC Educational Resources Information Center

    Yuan, Ke-Hai; Lu, Laura

    2008-01-01

    This article provides the theory and application of the 2-stage maximum likelihood (ML) procedure for structural equation modeling (SEM) with missing data. The validity of this procedure does not require the assumption of a normally distributed population. When the population is normally distributed and all missing data are missing at random…

  11. Serum lipid levels and M/L55 allele distribution of HDL paraoxonase gene in Saami and Finnish men.

    PubMed

    Malin, R; Lehtinen, S; Luoma, P; Näyhä, S; Hassi, J; Koivula, T; Lehtimäki, T

    2001-01-01

    Paraoxonase (PON) is an antioxidative enzyme, which eliminates lipid peroxides. The mutation in codon 55 of PON1 gene causes a change of methionine (M-allele) to leucine (L-allele) and influences PON activity. The Saami are a population living in the northern part of Fennoscandia. In previous studies their death rate from coronary artery disease (CAD) was found to be low. We compared PON M/L55 allele frequencies of 68 Saami and 68 Finnish men and related the PON genotypes to plasma lipid levels and to the levels of autoantibodies against oxidized LDL. The M/L55 genotypes were determined by PCR and restriction enzyme digestion. ELISA was used to measure antibodies against oxidized LDL. The L- and M-allele frequencies were 64% and 36% in Saami population and 64% and 36% in Finnish men, respectively (p = NS, Fisher's exact test). There were also no significant differences in plasma lipid levels or in antibody levels against oxidized LDL between PON genotypes or between Saami and Finnish men. Our results indicate that the PON M/L55 genotype is not associated with plasma lipid levels or the levels of autoantibodies against oxidized LDL in these populations. The Saami men have the same PON M/L55 allele distribution as the Finnish men and the PON genotype might thus not be one factor protecting Saami against CAD.

  12. Label-free electrochemical impedance biosensor to detect human interleukin-8 in serum with sub-pg/ml sensitivity.

    PubMed

    Sharma, R; Deacon, S E; Nowak, D; George, S E; Szymonik, M P; Tang, A A S; Tomlinson, D C; Davies, A G; McPherson, M J; Wälti, C

    2016-06-15

    Biosensors with high sensitivity and short time-to-result that are capable of detecting biomarkers in body fluids such as serum are an important prerequisite for early diagnostics in modern healthcare provision. Here, we report the development of an electrochemical impedance-based sensor for the detection in serum of human interleukin-8 (IL-8), a pro-angiogenic chemokine implicated in a wide range of inflammatory diseases. The sensor employs a small and robust synthetic non-antibody capture protein based on a cystatin scaffold that displays high affinity for human IL-8 with a KD of 35 ± 10 nM and excellent ligand specificity. The change in the phase of the electrochemical impedance from the serum baseline, ∆θ(ƒ), measured at 0.1 Hz, was used as the measure for quantifying IL-8 concentration in the fluid. Optimal sensor signal was observed after 15 min incubation, and the sensor exhibited a linear response versus logarithm of IL-8 concentration from 900 fg/ml to 900 ng/ml. A detection limit of around 90 fg/ml, which is significantly lower than the basal clinical levels of 5-10 pg/ml, was observed. Our results are significant for the development of point-of-care and early diagnostics where high sensitivity and short time-to-results are essential.

  13. Label-free electrochemical impedance biosensor to detect human interleukin-8 in serum with sub-pg/ml sensitivity

    PubMed Central

    Sharma, R.; Deacon, S.E.; Nowak, D.; George, S.E.; Szymonik, M.P.; Tang, A.A.S.; Tomlinson, D.C.; Davies, A.G.; McPherson, M.J.; Wälti, C.

    2016-01-01

    Biosensors with high sensitivity and short time-to-result that are capable of detecting biomarkers in body fluids such as serum are an important prerequisite for early diagnostics in modern healthcare provision. Here, we report the development of an electrochemical impedance-based sensor for the detection in serum of human interleukin-8 (IL-8), a pro-angiogenic chemokine implicated in a wide range of inflammatory diseases. The sensor employs a small and robust synthetic non-antibody capture protein based on a cystatin scaffold that displays high affinity for human IL-8 with a KD of 35±10 nM and excellent ligand specificity. The change in the phase of the electrochemical impedance from the serum baseline, ∆θ(ƒ), measured at 0.1 Hz, was used as the measure for quantifying IL-8 concentration in the fluid. Optimal sensor signal was observed after 15 min incubation, and the sensor exhibited a linear response versus logarithm of IL-8 concentration from 900 fg/ml to 900 ng/ml. A detection limit of around 90 fg/ml, which is significantly lower than the basal clinical levels of 5–10 pg/ml, was observed. Our results are significant for the development of point-of-care and early diagnostics where high sensitivity and short time-to-results are essential. PMID:26897263

  14. Prostate biopsy volume predicts final tumor volume.

    PubMed

    Zavaski, Michael E; Korus, Adam; Staff, Ilene; Champagne, Alison; Fish-Furhman, Jamie; Tortora, Joseph; Meraney, Anoop; Kesler, Stuart; Wagner, Joseph

    2014-03-01

    To assess the ability of prostate biopsy volume to effectively predict actual tumor volume, and whether increasing the number of prostate biopsy cores improves the ability to forecast actual tumor volume. 765 patients who underwent robotic radical prostatectomy (2009-2010) were identified. Of these, 663 had complete demographics, biopsy, and final pathology data available. The number ofbiopsy samples, biopsy tumor volume, and actual tumor volume were calculated from pathology reports. Data from 663 radical prostatectomy specimens indicated a positive linearrelationship between biopsy tumor volume and actual tumor volume (R=0.524, P< 0.0001). The number ofbiopsy samples collected (i.e., < or =6, 7-8, 9-10, 11-12, 13-14, or > or =15) did not affect the ability of biopsy tumor volume to predict final tumor volume. The routine collection of biopsy tumor volume may prove useful in predicting actual tumor volume and the construction of more effective preoperative nomograms.

  15. Human Relaxin Receptor Is Fully Functional in Humanized Mice and Is Activated by Small Molecule Agonist ML290

    PubMed Central

    Kaftanovskaya, Elena M.; Soula, Mariluz; Myhr, Courtney; Ho, Brian A.; Moore, Stefanie N.; Yoo, Changwon; Cervantes, Briana; How, Javier; Marugan, Juan; Agoulnik, Irina U.; Agoulnik, Alexander I.

    2017-01-01

    Relaxin, a small peptide hormone of the insulin/relaxin family, demonstrated antifibrotic, organ protective, vasodilatory, and proangiogenic properties in clinical trials and several animal models of human diseases. Relaxin family peptide receptor 1 (RXFP1) is the relaxin cognate G protein-coupled receptor. We have identified a series of small molecule agonists of human RXFP1. The lead compound ML290 demonstrated preferred absorption, distribution, metabolism, and excretion profiles, is easy to synthesize, and has high stability in vivo. However, ML290 does not activate rodent RXFP1s and therefore cannot be tested in common preclinical animal models. Here we describe the production and analysis of a mouse transgenic model, a knock-out/knock-in of the human RXFP1 (hRXFP1) complementary DNA into the mouse Rxfp1 (mRxfp1) gene. Insertion of the vector into the mRxfp1 locus caused disruption of mRxfp1 and expression of hRXFP1. The transcriptional expression pattern of the hRXFP1 allele was similar to mRxfp1. Female mice homozygous for hRXFP1 showed relaxation of the pubic symphysis at parturition and normal development of mammary nipples and vaginal epithelium, indicating full complementation of mRxfp1 gene ablation. Intravenous injection of relaxin led to an increase in heart rate in humanized and wild-type females but not in Rxfp1-deficient mice, whereas ML290 increased heart rate in humanized but not wild-type animals, suggesting specific target engagement by ML290. Moreover, intraperitoneal injection of ML290 caused a decrease in blood osmolality. Taken together, our data show humanized RXFP1 mice can be used for testing relaxin receptor modulators in various preclinical studies. PMID:28825052

  16. Human Relaxin Receptor Is Fully Functional in Humanized Mice and Is Activated by Small Molecule Agonist ML290.

    PubMed

    Kaftanovskaya, Elena M; Soula, Mariluz; Myhr, Courtney; Ho, Brian A; Moore, Stefanie N; Yoo, Changwon; Cervantes, Briana; How, Javier; Marugan, Juan; Agoulnik, Irina U; Agoulnik, Alexander I

    2017-06-01

    Relaxin, a small peptide hormone of the insulin/relaxin family, demonstrated antifibrotic, organ protective, vasodilatory, and proangiogenic properties in clinical trials and several animal models of human diseases. Relaxin family peptide receptor 1 (RXFP1) is the relaxin cognate G protein-coupled receptor. We have identified a series of small molecule agonists of human RXFP1. The lead compound ML290 demonstrated preferred absorption, distribution, metabolism, and excretion profiles, is easy to synthesize, and has high stability in vivo. However, ML290 does not activate rodent RXFP1s and therefore cannot be tested in common preclinical animal models. Here we describe the production and analysis of a mouse transgenic model, a knock-out/knock-in of the human RXFP1 (hRXFP1) complementary DNA into the mouse Rxfp1 (mRxfp1) gene. Insertion of the vector into the mRxfp1 locus caused disruption of mRxfp1 and expression of hRXFP1. The transcriptional expression pattern of the hRXFP1 allele was similar to mRxfp1. Female mice homozygous for hRXFP1 showed relaxation of the pubic symphysis at parturition and normal development of mammary nipples and vaginal epithelium, indicating full complementation of mRxfp1 gene ablation. Intravenous injection of relaxin led to an increase in heart rate in humanized and wild-type females but not in Rxfp1-deficient mice, whereas ML290 increased heart rate in humanized but not wild-type animals, suggesting specific target engagement by ML290. Moreover, intraperitoneal injection of ML290 caused a decrease in blood osmolality. Taken together, our data show humanized RXFP1 mice can be used for testing relaxin receptor modulators in various preclinical studies.

  17. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

    PubMed

    Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent; Anisimova, Maria; Hordijk, Wim; Gascuel, Olivier

    2010-05-01

    PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

  18. Measurement of Pancreatic Volume by Abdominal MRI: A Validation Study

    PubMed Central

    Szczepaniak, Edward W.; Malliaras, Konstantinos; Nelson, Michael D.; Szczepaniak, Lidia S.

    2013-01-01

    Objective To develop abdominal magnetic resonance imaging (MRI) protocol to measure pancreatic volume in humans and to validate it in large animals. Materials and Methods We performed abdominal MRI in eight mini-pigs using a clinical 3T MRI system. We used consecutive parallel abdominal slices, covering the entire pancreas to calculate pancreatic volume. Following MRI, animals were sacrificed, the pancreas was removed, and the volume of the pancreas was measured by water displacement. We used the same MRI protocol to measure pancreatic volume in 21 humans. To assess reproducibility of in vivo measurement we repeated MRI pancreas volume evaluation within 24 hours in additional five humans. Results In mini-pigs the measurements of pancreatic volume by MRI and by water displacement were almost identical (R2 = 0.9867; p<0.0001). In humans the average pancreas volume was 72.7+/−4.5 ml, range from 35.0 to 105.5 ml. This result is in strong agreement with results of previous large postmortem and computed tomography (CT) studies. Repeated measurements of pancreatic volume in humans were highly reproducible. Pancreatic volume measured in vivo was negatively correlated with age, body fat mass, pancreatic TG levels, and visceral fat mass. Conclusions These initial results are highly encouraging and our protocol for pancreatic volume estimation in vivo may prove useful in obesity research to follow in vivo changes of pancreatic volume and structure during time course of obesity and type 2 diabetes development. PMID:23418491

  19. Validation of pre-procedural aortic aneurysm volume calculations to estimate procedural fill volume of endobags in endovascular aortic sealing.

    PubMed

    Boersen, Johannes T; van den Ham, Leo H; Heyligers, Jan M; Vahl, Anco C; Vriens, Patrick W; Reijnen, Michel M; de Vries, Jean-Paul P

    2017-10-01

    Endovascular aortic sealing (EVAS) with a sac anchoring endoprosthesis excludes abdominal aortic aneurysms based on polymer filling of endobags. Primary objective was to assess the reliability of pre-procedural computed tomography (CT) scans based calculations of required endobag volume in relation to intraoperative volume of the endobags. Forty elective EVAS patients were included. Pre-procedural estimations of endobag volume were based on CT segmentations of aortic flow lumen volume, including both automated and manually-adjusted segmentations, performed by two experienced users. Additionally, changes in maximum AAA diameter, thrombus volume and total AAA volume were calculated from pre- and post-procedural CT scans. Automatically determined volumes were comparable to manually-adjusted calculations (75.3 vs. 75.7 mL) and inter-observer agreement regarding pre-EVAS calculations of prefill volume appeared almost perfect with an intra-class correlation coefficient of 0.98 (95% CI: 0.96-0.99). The mean pressure of the endobags was 185 mmHg. Manually-adjusted pre-procedural volume calculations underestimated procedural volume of the endobags (-11.3±9.9 mL). Differences between pre-EVAS and procedural volume measurements were independent from endobag pressure (r=-0.06, P=0.72), prepocedural thrombus volume (r=-0.303, P=0.057) and changes in total AAA volume (r=0.02, P=0.91). A significant association was determined between differences in pre-EVAS and endobag volume versus changes in thrombus volume pre- and post-procedural (r=0.39, P=0.01). In this validation study, pre-procedural volume measurements underestimate the actual fill volume of the endobags. It should be advised to perform a prefill of the endobags during the EVAS procedure.

  20. Subcutaneous Injection Volume of Biopharmaceuticals-Pushing the Boundaries.

    PubMed

    Mathaes, Roman; Koulov, Atanas; Joerg, Susanne; Mahler, Hanns-Christian

    2016-08-01

    Administration into the subcutaneous (SC) tissue is a typical route of delivery for therapeutic proteins, especially for frequent treatments, long-term regimens, or self-administration. It is currently believed that the maximum volume for SC injections is approximately 1.5 mL. Larger SC injection volumes are considered to be associated with injection pain and adverse events at the injection site. However, no controlled clinical studies and actual evidence exist to support this assumption. In this review, we discuss current and publically available data related to SC administration volumes. We conclude that injection volumes higher than 3.5 mL are worth exploring if required for the development of efficacious drug treatments. Studying tissue back pressure, injection site leakage, local tolerability, and injection-related adverse events, such as injection pain, should be considered for the development of higher SC injection volumes. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

  1. Recommended summer sunlight exposure levels can produce sufficient (> or =20 ng ml(-1)) but not the proposed optimal (> or =32 ng ml(-1)) 25(OH)D levels at UK latitudes.

    PubMed

    Rhodes, Lesley E; Webb, Ann R; Fraser, Heather I; Kift, Richard; Durkin, Marie T; Allan, Donald; O'Brien, Sarah J; Vail, Andy; Berry, Jacqueline L

    2010-05-01

    Recommendations on limitation of summer sunlight exposure to prevent skin cancer may conflict with requirements to protect bone health through adequate vitamin D levels, the principal source being UVB in summer sunlight. We determined whether sufficient (> or =20 ng ml(-1)) and proposed optimal (> or =32 ng ml(-1)) 25(OH)D levels are attained by following UK guidance advising casual short exposures to UVB in summer sunlight, and performed the study under known conditions to enhance the specificity of future recommendations. During wintertime, when ambient UVB is negligible, 120 white Caucasians, aged 20-60 years, from Greater Manchester, UK (53.5 degrees N) received a simulated summer's sunlight exposures, specifically 1.3 standard erythemal dose, three times weekly for 6 weeks, while wearing T-shirt and shorts. The baseline winter data predict that 5% (confidence interval (CI): 2.7-8.6) of Greater Manchester white Caucasians have deficient (<5 ng ml(-1)) 25(OH)D, 62.5% (CI: 55.2-69.4) have insufficient, and only 2.9% (CI: 1.4-5.6) have proposed optimal levels. After the simulated summer exposures, 90 (CI: 84.9-93.7) and 26.2% (CI: 20.1-33.2) reached 20 and 32 ng ml(-1) 25(OH)D, respectively. Assuming midday UVB levels, sufficient but suboptimal vitamin D status is attained after a summer's short (13 minutes) sunlight exposures to 35% skin surface area; these findings will assist future public health guidance on vitamin D acquisition.

  2. Fatigue and Fracture of Titanium Aluminides. Volume 2

    DTIC Science & Technology

    1990-02-01

    WRDC-TR-89-4145 Volume II FATIGUE AND FRACTURE OF TITANIUM ALUMINIDES M.L. Gambone V) Allison Gas Turbine Division fl General Motors Corporation RO...77 I1 TITLE (Include Securty Classficaton) Fat igue & Fracture of Titanium Aluminides 12. PERSONAL AUTHOR(S) M.L. Gambone 13& TYPE OF REPORT 13b. TIME...CODES 18. SUBJECT TERMS (Continue on reuerse it neceuar’y and identify by block numberi FIELD GROUP SUB GR. Metal matrix composites, titanium aluminide

  3. Skeletal muscle volume following dehydration induced by exercise in heat

    PubMed Central

    2012-01-01

    Background Intracellular skeletal muscle water is redistributed into the extracellular compartment during periods of dehydration, suggesting an associated decline in muscle volume. The purpose of this study was to evaluate skeletal muscle volume in active (knee extensors (KE)) and less active (biceps/triceps brachii, deltoid) musculature following dehydration induced by exercise in heat. Methods Twelve participants (seven men, five women) cycled in the heat under two conditions: (1) dehydration (DHYD) resulting in 3% and 5% losses of estimated total body water (ETBW), which was assessed by changes in body mass, and (2) fluid replacement (FR) where 3% and 5% losses of ETBW were counteracted by intermittent (20 to 30 min) fluid ingestion via a carbohydrate-electrolyte beverage. During both conditions, serum osmolality and skeletal muscle volume (assessed by magnetic resonance imaging) were measured at baseline and at the 3% and 5% ETBW loss measurement points. Results In DHYD, serum osmolality increased at 3% (p = 0.005) and 5% (p < 0.001) ETBW losses, while FR decreased serum osmolality at the 5% loss of ETBW time point (p = 0.009). In DHYD, KE muscle volume declined from 1,464 ± 446 ml to 1,406 ± 425 ml (3.9%, p < 0.001) at 3% ETBW loss and to 1,378 ± 421 ml (5.9%, p < 0.001) at 5% ETBW loss. The largest decline in KE volume in DYHD occurred in the mid-belly (31 ml, p = 0.001) and proximal (24 ml, p = 0.001) regions of the grouped vasti muscles. There were no changes in volume for the biceps/triceps (p = 0.35) or deltoid (p = 0.92) during DHYD. FR prevented the loss of KE muscle volume at 3% (1,430 ± 435 ml, p = 0.074) and 5% (1,431 ± 439 ml, p = 0.156) ETBW loss time points compared to baseline (1,445 ± 436 ml). Conclusions Following exercise in the heat, the actively contracting muscles lost volume, while replacing lost fluids intermittently during exercise in heat prevented this decline

  4. Incidence rate of type 2 diabetes is >50% lower in GrassrootsHealth cohort with median serum 25-hydroxyvitamin D of 41 ng/ml than in NHANES cohort with median of 22 ng/ml.

    PubMed

    McDonnell, S L; Baggerly, L L; French, C B; Heaney, R P; Gorham, E D; Holick, M F; Scragg, R; Garland, C F

    2016-01-01

    Higher serum 25-hydroxyvitamin D [25(OH)D] concentrations have been associated with lower risk of type 2 diabetes. This study compared incidence rates of type 2 diabetes among participants aged ≥20 years in two U.S. cohorts with markedly different median 25(OH)D concentrations. The median 25(OH)D concentration in the GrassrootsHealth (GRH) cohort was 41 ng/ml (N=4933) while in the 2005-6 National Health and Nutrition Examination Survey (NHANES) it was 22 ng/ml (N=4078) (P<0.0001). The adjusted annual incidence rate of type 2 diabetes was 3.7 per 1000 population (95% confidence interval=1.9, 6.6) in the GRH cohort, compared to 9.3 per 1000 population (95% confidence interval=6.7, 12.6) in NHANES. In the NHANES cohort, the lowest 25(OH)D tertiles (<17, 17-24 ng/ml) had higher odds of developing diabetes than the highest tertile (OR: 4.9, P=0.02 and 4.8, P=0.01 respectively), adjusting for covariates. Differences in demographics and methods may have limited comparability. Raising serum 25(OH)D may be a useful tool for reducing risk of diabetes in the population.

  5. Validation of an ultrasound scanner for determing urinary volumes in surgical patients and volunteers.

    PubMed

    Brouwer, T A; Eindhoven, B G; Epema, A H; Henning, R H

    1999-08-01

    As bladder distension related to anaesthesia puts patients at risk for permanent dysfunction, peri-operative determination of bladder volume is of great importance. The aim of this study is to validate an ultrasonic imaging device for determing bladder urine volume. To evaluate a broad volume range, ultrasonically scanned volumes were compared to true urinary volumes both in surgical patients and in volunteers. After institutional approval and informed consent 60 healthy volunteers were asked not to void for as long as possible. After ultrasound measurements (BladderScan BVI 2500, Diagnostic Ultrasound, Redmond WA, U.S.A.) they voided and true urinary volumes were measured. Fifty surgical patients scheduled for procedures requiring urinary catheterisation were studied. Pre- and post-induction of anaesthesia ultrasound measurements were recorded, followed by urinary catheterisation and measurement of true urinary volume. Urine volumes were compared using Student t-tests and Wilcoxon Rank Tests (p < 0.05). For validation linear regression was used together with Bland-Altman analyses. Ultrasonic scanning underestimated the true urine volume by about 7% over the whole volume range (17 ml to 970 ml). Underestimation was larger in females than in males (p < 0.02). R2 values for correlation of measured and scanned urinary volumes ranged between 0.92 and 0.95. Bland and Altman analyses showed a bias of 31 ml in volunteers and of 19 ml in patients and a precision of 110 ml and 80 ml, respectively. The ultrasonic imaging device can be used peri-operatively to establish bladder volume, taking into account the 7% underestimation of the bladder volume.

  6. Volume Measurement by Diffusion-Weighted Imaging in Cervical Cancer

    PubMed Central

    Fujii, Shinya; Iwata, Naoki; Inoue, Chie; Mukuda, Naoko; Fukunaga, Takeru; Ogawa, Toshihide

    2017-01-01

    Background The aim of this paper was to evaluate the validity of tumor volume measurement using diffusion-weighted (DW) imaging in cervical cancer. Methods In this retrospective study, 22 patients, who underwent preoperative 3.0 T MR examinations with DW imaging were evaluated. Tumor volume measurement by oblique axial (short axis to the uterine cervix) T2-weighted imaging was performed by manually outlining the tumor on the monitor. The area of tumor in each slice was multiplied by the slice profile (slice thickness plus intersection gap), and the total tumor volume was calculated by summation of these obtained volumes. Meanwhile, one experienced radiological technologist generated three-dimensional DW images of cervical cancer using a volume-rendering algorithm at a computer workstation, and tumor volume was automatically calculated in the workstation. Analysis via the intraclass correlation coefficient (ICC) and Bland-Altman plots were used to assess the validity and reliability of these methods. Results Between tumor volumes measured by T2-weighted imaging methods and DW imaging methods, the ICC was excellent (0.962). The 95% limits of agreement of volume measurement were –52.7 and 35.7 mL (mean difference, –8.5 mL). In regards to intra-observer variability, the ICC was excellent (0.963). The 95% limits of agreement of volume measurement were –42.2 and 47.4 mL (mean difference, 2.6 mL). Conclusion DW imaging can be used to measure cervical cancer volume. PMID:28701894

  7. Potentials and limitations of low-concentration contrast medium (150 mg iodine/ml) in CT pulmonary angiography.

    PubMed

    Radon, M R; Kaduthodil, M J; Jagdish, J; Matthews, S; Hill, C; Bull, M J; Morcos, S K

    2011-01-01

    To assess the feasibility of producing diagnostic multidetector computed tomography (MDCT) pulmonary angiography with low iodine concentration contrast media (150 mg iodine/ml) in patients with suspected acute pulmonary embolism. Ninety-five randomized patients underwent MDCT (64 row) pulmonary angiography with 100ml iopromide either at low concentration (LC) of 150 mg iodine/ml (n=45) or high concentration (HC) of 300 mg iodine/ml (n=50), delivered at the rate of 5 ml/s via a power injector. Two experienced radiologists, blinded to the concentration used, subjectively assessed the diagnostic quality and confidence using a four-point scale [1=poor (not diagnostic), 2=satisfactory, 3=good, 4=excellent]. Attenuation values (in HU) were measured in the main proximal branches of the pulmonary arteries. The median diagnostic quality score for both observers was 3.5 (interquartile range 3-4) in the HC group and 2.5 (interquartile range 1.5-3) in the LC group (p<0.01). The median diagnostic confidence score for both observers was 4 (interquartile range 3-4) in the HC group and 3 (interquartile range 1.5-4) in the LC group (p<0.01). Both observers rated examinations as diagnostic in 69% of cases in the LC group, compared with 96% of cases in the HC group. Good interobserver agreement was found in both groups (K value 0.72 in the LC group and 0.73 in the HC). Obesity, poor scan timing, and dilution by venous return of non-opacified blood were the main reasons for a reduction in diagnostic quality of examinations in the LC group. Despite a 50% reduction of contrast medium dose in comparison to the standard technique, 150 mg iodine/ml can produce diagnostic MDCT pulmonary angiogram studies in the absence of obesity or high cardiac output and hyper-dynamic pulmonary circulation. Reducing the dose of contrast media would minimize the risk of contrast nephropathy in patients at risk of this complication, particularly those suffering from congestive heart failure in whom

  8. Comparable efficacy and safety of 8 weeks treatment with agomelatine 25-50mg or fluoxetine 20-40mg in Asian out-patients with major depressive disorder.

    PubMed

    Shu, L; Sulaiman, A H; Huang, Y S; Fones Soon Leng, C; Crutel, V Strijckmans; Kim, Y S

    2014-04-01

    This randomized, double-blind study evaluates the efficacy and tolerability of agomelatine, using fluoxetine as an active comparator, in Asian patients suffering from moderate to severe major depressive disorder (MDD). Patients were randomly assigned to receive either agomelatine (25-50mg/day, n=314) or fluoxetine (20-40mg/day, n=314) during an 8-week treatment period. The main outcome measure was the change in Hamilton Depression Rating Scale 17 items (HAM-D17) scores. Secondary efficacy criteria included scores on Clinical Global Impression Severity of illness (CGI-S) and Improvement of illness (CGI-I), patient sleeping improvement using the self-rating Leeds Sleep Evaluation Questionnaire (LSEQ) and anxiety using the Hamilton Anxiety Rating Scale (HAM-A) scores. Tolerability and safety evaluations were based on emergent adverse events. Agomelatine and fluoxetine exert a comparable antidepressant efficacy in the Asian population. Mean changes over 8 weeks were clinically relevant and similar in both groups (-14.8±7.3 and -15.0±8.1 on HAM-D17 scale in agomelatine and fluoxetine groups, respectively). The between-group difference reached statistical significance on non-inferiority test (p=0.015). Clinically relevant decreases in CGI-S and CGI-I scores were observed over the treatment period in both groups. The two treatments were equally effective on the symptoms of both anxiety and sleep. The good tolerability profile and safety of both doses of agomelatine was confirmed in the Asian population. Agomelatine and fluoxetine are equally effective in the treatment of MDD-associated symptoms in Asian depressed patients. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. Hand volume estimates based on a geometric algorithm in comparison to water displacement.

    PubMed

    Mayrovitz, H N; Sims, N; Hill, C J; Hernandez, T; Greenshner, A; Diep, H

    2006-06-01

    Assessing changes in upper extremity limb volume during lymphedema therapy is important for determining treatment efficacy and documenting outcomes. Although arm volumes may be determined by tape measure, the suitability of circumference measurements to estimate hand volumes is questionable because of the deviation in circularity of hand shape. Our aim was to develop an alternative measurement procedure and algorithm for routine use to estimate hand volumes. A caliper was used to measure hand width and depth in 33 subjects (66 hands) and volumes (VE) were calculated using an elliptical frustum model. Using regression analysis and limits of agreement (LOA), VE was compared to volumes determined by water displacement (VW), to volumes calculated from tape-measure determined circumferences (VC), and to a trapezoidal model (VT). VW and VE (mean +/- SD) were similar (363 +/- 98 vs. 362 +/-100 ml) and highly correlated; VE = 1.01VW -3.1 ml, r=0.986, p<0.001, with LOA of +/- 33.5 ml and +/- 9.9 %. In contrast, VC (480 +/- 138 ml) and VT (432 +/- 122 ml) significantly overestimated volume (p<0.0001). These results indicate that the elliptical algorithm can be a useful alternative to water displacement when hand volumes are needed and the water displacement method is contra-indicated, impractical to implement, too time consuming or not available.

  10. The volume of the human knee joint.

    PubMed

    Matziolis, Georg; Roehner, Eric; Windisch, Christoph; Wagner, Andreas

    2015-10-01

    Despite its clinical relevance, particularly in septic knee surgery, the volume of the human knee joint has not been established to date. Therefore, the objective of this study was to determine knee joint volume and whether or not it is dependent on sex or body height. Sixty-one consecutive patients (joints) who were due to undergo endoprosthetic joint replacement were enrolled in this prospective study. During the operation, the joint volume was determined by injecting saline solution until a pressure of 200 mmHg was achieved in the joint. The average volume of all knee joints was 131 ± 53 (40-290) ml. The volume was not found to be dependent on sex, but it was dependent on the patients' height (R = 0.312, p = 0.014). This enabled an estimation of the joint volume according to V = 1.6 height - 135. The considerable inter-individual variance of the knee joint volume would suggest that it should be determined or at least estimated according to body height if the joint volume has consequences for the diagnostics or therapy of knee disorders.

  11. Holmium laser enucleation versus photoselective vaporization for prostatic adenoma greater than 60 ml: preliminary results of a prospective, randomized clinical trial.

    PubMed

    Elmansy, Hazem; Baazeem, Abdulaziz; Kotb, Ahmed; Badawy, Hesham; Riad, Essam; Emran, Ashraf; Elhilali, Mostafa

    2012-07-01

    To our knowledge we report the first single center, prospective, randomized study comparing holmium laser enucleation and high performance GreenLight™ prostate photoselective vaporization as surgical treatment of prostatic adenomas greater than 60 ml. A total of 80 patients with a large prostatic adenoma were randomly assigned to surgical treatment with holmium laser enucleation or photoselective vaporization. International Prostate Symptom Score, International Index of Erectile Function-15, maximum flow rate, post-void residual urine, serum prostate specific antigen and transrectal ultrasound volume were recorded. Patient baseline characteristics were similar for holmium laser enucleation and photoselective vaporization. Operative time and catheter removal time were almost equal in the 2 groups (p = 0.7 and 0.2, respectively). Eight vaporization cases were converted to transurethral prostate resection or holmium laser enucleation intraoperatively due to bleeding. A significantly higher maximum flow rate and lower post-void residual urine were noted in holmium laser cases during the entire followup (at 1 year each p = 0.02). However, no significant difference in International Prostate Symptom Score, quality of life or International Index of Erectile Function-15 was detected. Prostate volume and serum PSA decreased 78% and 88% in the holmium laser group, and 52% and 60% in the vaporization group, respectively. Holmium laser enucleation and photoselective vaporization are effective for lower urinary tract symptoms due to a large prostatic adenoma. Early subjective functional results (maximum flow rate and post-void residual urine) of holmium laser enucleation appear to be superior to those of photoselective vaporization. In our hands cases intended to be treated with photoselective vaporization were at 22% risk of conversion to another modality. This could reflect our determination to vaporize to the capsule in all vaporization cases. Copyright © 2012 American

  12. Can you deliver accurate tidal volume by manual resuscitator?

    PubMed

    Lee, H M; Cho, K H; Choi, Y H; Yoon, S Y; Choi, Y H

    2008-10-01

    One of the problems with manual resuscitators is the difficulty in achieving accurate volume delivery. The volume delivered to the patient varies by the physical characteristics of the person and method. This study was designed to compare tidal volumes delivered by the squeezing method, physical characteristics and education and practice levels. 114 individuals trained in basic life support and bag-valve-mask ventilation participated in this study. Individual characteristics were obtained by the observer and the education and practice level were described by the subjects. Ventilation was delivered with a manual resuscitator connected to a microspirometer and volumes were measured. Subjects completed three procedures: one-handed, two-handed and two-handed half-compression. The mean (standard deviation) volumes for the one-handed method were 592.84 ml (SD 117.39), two-handed 644.24 ml (SD 144.7) and two-handed half-compression 458.31 ml (SD 120.91) (p<0.01). Tidal volume delivered by two hands was significantly greater than that delivered by one hand (r = 0.398, p<0.01). The physical aspects including hand size, volume and grip power had no correlation with the volume delivered. There were slight increases in tidal volume with education and practice, but correlation was weak (r = 0.213, r = 0.281, r = 0.131, p<0.01). The tidal volume delivered by a manual resuscitator shows large variations. There were significant differences in the volume delivered by compression methods, but physical characteristics are not a predictor of tidal volume delivery. The manual resuscitator is not a suitable device for accurate ventilation.

  13. Volume estimation of the preepiglottic and paraglottic space using spiral computed tomography.

    PubMed

    Hermans, R; Van der Goten, A; Baert, A L

    1997-01-01

    The purpose of this study was to estimate the volume variability of the preepiglottic and paraglottic space in the normal larynx. In 23 adult patients (12 women, 11 men), a spiral CT acquisition through the larynx was obtained. No laryngeal pathology was observed. The area of the this submucosal fat space was estimated on each slice by semi-automatic segmentation; the volume was calculated by the summation-of-areas technique. The obtained volumes were correlated with body area, body mass index and gender. The mean estimated volume of the preepiglottic and paraglottic space was 2.8 ml (SD 1.7 ml, range 0.7-5.9). No correlation with body mass index (p = 0.6), but a significant correlation with body area (p < 0.001) was found. A significant volume difference was present between men (mean 4.5 ml, SD 1.0 ml, range 2.8-5.9) and women (mean 1.4 ml, SD 0.5 ml, range 0.7-2.4)(p < 0.0001). Multiple regression analysis showed gender (p < 0.0001) to be a more important variable than body area (p = 0.17) in predicting the volume of the preepiglottic and paraglottic space. In conclusion, the volume of the preepiglottic and paraglottic space appears to be very variable, and should only be analysed with consideration of the gender of the examined subjects.

  14. Development, testing, and certification of the Northrup, Inc., ML series concentrating solar collector model NSC-01-0732

    NASA Technical Reports Server (NTRS)

    Parker, J. C.

    1979-01-01

    A summary is presented of the additional development work on the existing ML Series concentrating solar collector for use with solar heating and cooling systems. The report discusses the intended use of the final report, describes the development hardware, lists deliverable end items, deals with problems encountered during fabrication and testing, and includes certification statements of performance. This report shows that the products developed are marketable and suitable for public use.

  15. BioCompoundML: A General Biofuel Property Screening Tool for Biological Molecules Using Random Forest Classifiers

    DOE PAGES

    Whitmore, Leanne S.; Davis, Ryan W.; McCormick, Robert L.; ...

    2016-09-15

    Screening a large number of biologically derived molecules for potential fuel compounds without recourse to experimental testing is important in identifying understudied yet valuable molecules. Experimental testing, although a valuable standard for measuring fuel properties, has several major limitations, including the requirement of testably high quantities, considerable expense, and a large amount of time. This paper discusses the development of a general-purpose fuel property tool, using machine learning, whose outcome is to screen molecules for desirable fuel properties. BioCompoundML adopts a general methodology, requiring as input only a list of training compounds (with identifiers and measured values) and a listmore » of testing compounds (with identifiers). For the training data, BioCompoundML collects open data from the National Center for Biotechnology Information, incorporates user-provided features, imputes missing values, performs feature reduction, builds a classifier, and clusters compounds. BioCompoundML then collects data for the testing compounds, predicts class membership, and determines whether compounds are found in the range of variability of the training data set. We demonstrate this tool using three different fuel properties: research octane number (RON), threshold soot index (TSI), and melting point (MP). Here we provide measures of its success with these properties using randomized train/test measurements: average accuracy is 88% in RON, 85% in TSI, and 94% in MP; average precision is 88% in RON, 88% in TSI, and 95% in MP; and average recall is 88% in RON, 82% in TSI, and 97% in MP. The receiver operator characteristics (area under the curve) were estimated at 0.88 in RON, 0.86 in TSI, and 0.87 in MP. We also measured the success of BioCompoundML by sending 16 compounds for direct RON determination. Finally, we provide a screen of 1977 hydrocarbons/oxygenates within the 8696 compounds in MetaCyc, identifying compounds with high

  16. ArdenML: The Arden Syntax Markup Language (or Arden Syntax: It's Not Just Text Any More!)

    PubMed Central

    Sailors, R. Matthew

    2001-01-01

    It is no longer necessary to think of Arden Syntax as simply a text-based knowledge base format. The development of ArdenML (Arden Syntax Markup Language), an XML-based markup language allows structured access to most of the maintenance and library categories without the need to write or buy a compiler may lead to the development of simple commercial and freeware tools for processing Arden Syntax Medical Logic Modules (MLMs)

  17. REMOVAL: ML_Abstract.

    PubMed

    2017-03-01

    This article has been removed: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). Due to an administrative error, an issue was accidentally published here. This has now been removed. The publisher apologises for any inconvenience this may cause. Copyright © 2017.

  18. Refinement Types ML

    DTIC Science & Technology

    1994-03-16

    compiler is only given desugared code, it does not need to be prepared for if statements. To formalize this, we first define the abstract syntax for...appropriate sense. But first we must prepare the way with some lemmas. First we will show that as the assumptions in the environment get stronger, the set...183, these constraints give def cons : Ti(bev& bod)) --+ bev delf because bev >- cons(Ti..a * bod) E D and (bev & bod) !5 bod. Reasoning about def

  19. Effects of Cymbopogon citratus L. essential oil on the growth, lipid content and morphogenesis of Aspergillus niger ML2-strain.

    PubMed

    Helal, G A; Sarhan, M M; Abu Shahla, A N K; Abou El-Khair, E K

    2006-01-01

    The mycelial growth of Aspergillus niger van Tieghem was completely inhibited using 1.5 (microl/ml or 2.0 (microl/ml of Cymbopogon citratus essential oil applied by fumigation or contact method in Czapek liquid medium, respectively. This oil was found also to be fungicidal at the same concentrations. The sublethal doses 1.0 and 1.5 (microl/ml inhibited about 70% of fungal growth after five days of incubation and delayed conidiation as compared with the control. Microscopic observations using Light Microscope (LM), Scanning Electron Microscope (SEM) and Transmission Electron Microscope (TEM) were carried out to determine the ultra structural modifications of A. niger hyphae after treatment with C. citratus essential oil. The hyphal diameter and hyphal wall appeared markedly thinner. This oil also caused plasma membrane disruption and mitochondrial structure disorganization. Moreover, Ca+2, K+ and Mg+2 leakages increased from the fumigated mycelium and its total lipid content decreased, while the saturated fatty acids decreased and unsaturated fatty acids increased. These findings increase the possibility of exploiting C. citratus essential oil as an effective inhibitor of biodegrading and storage contaminating fungi and in fruit juice preservation.

  20. Effects of Cymbopogon citratus L. essential oil on the growth, morphogenesis and aflatoxin production of Aspergillus flavus ML2-strain.

    PubMed

    Helal, G A; Sarhan, M M; Abu Shahla, A N K; Abou El-Khair, E K

    2007-02-01

    The mycelial growth of Aspergillus flavus Link was completely inhibited using 1.5 (microl/ml or 2.0 (microl/ml of Cymbopogon citratus essential oil applied by fumigation or contact method in Czapek's liquid medium, respectively. This oil was found also to be fungicidal at the same concentrations. The sublethal doses 1.0 and 1.5 (microl/ml inhibited about 65% of fungal growth after five days of incubation and delayed conidiation as compared with the control. Microscopic observations using Light Microscope (LM), Scanning Electron Microscope (SEM) and Transmission Electron Microscope (TEM) were carried out to determine the ultra structural modifications of A. flavus hyphae after treatment with C. citratus essential oil. The hyphal diameter decreased and hyphal wall appeared as precipitates and disappeared in some regions. This oil also caused plasma membrane disruption and mitochondrial structure disorganization. Moreover, Ca(+2), K(+) and Mg(+2) leakages increased from the fumigated mycelium and its total lipid content decreased, while the saturated and unsaturated fatty acids increased. One of the most important results obtained during this study was the ability of C. citratus essential oil at its sublethal dose to completely inhibit aflatoxin B(1) production from A. flavus. These findings increase the possibility of exploiting C. citratus essential oil as an effective inhibitor of biodegradation and storage contaminating fungi and also in fruit juice preservation.

  1. Restriction endonuclease analysis of the lactose plasmid in Streptococcus lactis ML3 and two recombinant lactose plasmids.

    PubMed

    Walsh, P M; McKay, L L

    1982-05-01

    We investigated the molecular relationship between the 60-megadalton (Mdal) recombinant lactose plasmids in ML 3 x LM2301 lactose-positive (Lac+) transconjugants and the genetic material of Streptococcus lactis ML3. Lactose metabolism is linked to the 33-Mdal plasmid pSK08 in ML3, and the recipient LM2301 is cured of plasmid DNA. The plasmids were analyzed with a series of restriction enzymes. We found that the 60-Mdal plasmids of Lac+ transconjugants contained pSK08 DNA, but were not simply dimers of pSK08. The 60-Mdal plasmids contained a segment of DNA not apparent in pSK08. The restriction patterns of the 60-Mdal plasmid in a Lac+ nonclumping transconjugant and that in a Lac+ clumping transconjugant were different. This suggested that there was a molecular differences between these two recombinant plasmids. We conclude that the segment of DNA in the 60-Mdal plasmids that was not present in pSK08 was the proposed transfer factor responsible for cell aggregation and high-frequency conjugation.

  2. MMP2 and MMP9 participate in S1P-induced invasion of follicular ML-1 thyroid cancer cells.

    PubMed

    Kalhori, Veronica; Törnquist, Kid

    2015-03-15

    The bioactive lipid sphingosine-1-phosphate (S1P) has emerged as a potent inducer of cancer cell migration and invasion. Previously, we have shown that S1P induces invasion of ML-1 follicular thyroid cancer cells via S1P receptors 1 and 3 (S1P1,3). Matrix metalloproteinases (MMPs) are zinc-dependent proteolytic enzymes used by cells for degradation of the extracellular matrix during invasion and migration. In the present study, we examined the role of MMP2 and MMP9 for S1P-induced invasion of ML-1 cells, and found that S1P regulates the secretion and activity of MMP2 and MMP9 via S1P1,3. Both pharmacological inhibitors and siRNA knockdown of MMP2 and MMP9 could attenuate S1P-induced invasion. Additionally, we show that calpains and Rac1 mediate S1P-induced secretion of MMP2 and MMP9. In conclusion, MMP2 and MMP9 participate in S1P-evoked follicular ML-1 thyroid cancer cell invasion.

  3. Is the Ellipsoid Formula the New Standard for 3-Tesla MRI Prostate Volume Calculation without Endorectal Coil?

    PubMed

    Haas, Matthias; Günzel, Karsten; Miller, Kurt; Hamm, Bernd; Cash, Hannes; Asbach, Patrick

    2017-01-01

    Prostate volume in multiparametric MRI (mpMRI) is of clinical importance. For 3-Tesla mpMRI without endorectal coil, there is no distinctive standard for volume calculation. We tested the accuracy of the ellipsoid formula with planimetric volume measurements as reference and investigated the correlation of gland volume and cancer detection rate on MRI/ultrasound (MRI/US) fusion-guided biopsy. One hundred forty-three patients with findings on 3-Tesla mpMRI suspicious of cancer and subsequent MRI/US fusion-guided targeted biopsy and additional systematic biopsy were analyzed. T2-weighted images were used for measuring the prostate diameters and for planimetric volume measurement by a segmentation software. Planimetric and calculated prostate volumes were compared with clinical data. The median prostate volume was 48.1 ml (interquartile range (IQR) 36.9-62.1 ml). Volume calculated by the ellipsoid formula showed a strong concordance with planimetric volume, with a tendency to underestimate prostate volume (median volume 43.1 ml (IQR 31.2-58.8 ml); r = 0.903, p < 0.001). There was a moderate, significant inverse correlation of prostate volume to a positive biopsy result (r = -0.24, p = 0.004). The ellipsoid formula gives sufficient approximation of prostate volume on 3-Tesla mpMRI without endorectal coil. It allows a fast, valid volume calculation in prostate MRI datasets.

  4. Stroke volume variation as a guide for fluid resuscitation in patients undergoing large-volume liposuction.

    PubMed

    Jain, Anil Kumar; Khan, Asma M

    2012-09-01

    : The potential for fluid overload in large-volume liposuction is a source of serious concern. Fluid management in these patients is controversial and governed by various formulas that have been advanced by many authors. Basically, it is the ratio of what goes into the patient and what comes out. Central venous pressure has been used to monitor fluid therapy. Dynamic parameters, such as stroke volume and pulse pressure variation, are better predictors of volume responsiveness and are superior to static indicators, such as central venous pressure and pulmonary capillary wedge pressure. Stroke volume variation was used in this study to guide fluid resuscitation and compared with one guided by an intraoperative fluid ratio of 1.2 (i.e., Rohrich formula). : Stroke volume variation was used as a guide for intraoperative fluid administration in 15 patients subjected to large-volume liposuction. In another 15 patients, fluid resuscitation was guided by an intraoperative fluid ratio of 1.2. The amounts of intravenous fluid administered in the groups were compared. : The mean amount of fluid infused was 561 ± 181 ml in the stroke volume variation group and 2383 ± 1208 ml in the intraoperative fluid ratio group. The intraoperative fluid ratio when calculated for the stroke volume variation group was 0.936 ± 0.084. All patients maintained hemodynamic parameters (heart rate and systolic, diastolic, and mean blood pressure). Renal and metabolic indices remained within normal limits. : Stroke volume variation-guided fluid application could result in an appropriate amount of intravenous fluid use in patients undergoing large-volume liposuction. : Therapeutic, II.

  5. Otilonium bromide enhances sensory thresholds of volume and pressure in patients with irritable bowel syndrome.

    PubMed

    Czimmer, J; Süto, G; Király, A; Mózsik, G

    2001-01-01

    Visceral hyperalgesia has been suggested to play a role in the development of symptoms presented by irritable bowel syndrome patients. Otilonium bromide was developed to block smooth muscle Ca release to control cramping pain of these patients. to determine whether otilonium bromide can influence sensory thresholds of patients suffering from irritable bowel syndrome. 15 patients with Rome-II positive IBS were tested by Synectics Visceral Stimulator Barostat using rapid phasic distension (870 ml/min). The sensory threshold for first sensation, stool, pain and maximum tolerable volume and pressure were measured. All of the parameters were tested before and 1 week after the initiation of otilonium bromide (Spasmomen, Berlin Chemie, 3x40 mg) therapy. The perceptual thresholds for first sensation, stool, pain and maximum tolerable distention were, 8.8+/-1.7 Hgmm, 19.2+/-2.1 Hgmm, 26.3+/-2.8 Hgmm, 28.7+/-2.8 Hgmm for pressure, 90+/-21 ml, 145+/-28 ml, 208+/-25 ml, 213+/-28 ml for volume, before treatment, respectively. Otilonium bromide treatment did not influence the thresholds for first sensation and stool, 7.4+/-1.4 Hgmm, 20.7+/-4.6 Hgmm and 83+/-21 ml, 178+/-35.8 ml, respectively. The pressure threshold of pain was significantly higher 1 week after treatment (26.3+/-2.8 Hgmm vs. 29.1+/-5.5 Hgmm, P<0.05), but the volume threshold of this sensation remained unchanged (208+/-25 ml vs. 234+/-39 ml, not significant). The pressure (28.7+/-2.8 Hgmm vs. 38.1+/-3.4 Hgmm, P<0.05) and volume (213+/-28 ml vs. 278+/-27 ml, P<0.05) thresholds for maximum tolerable volume were increased by 7 days otilonium bromide treatment. These data suggest that otilonium bromide enhances sensory thresholds to recto-sigmoideal distention.

  6. 3D-Assisted Quantitative Assessment of Orbital Volume Using an Open-Source Software Platform in a Taiwanese Population

    PubMed Central

    Shyu, Victor Bong-Hang; Hsu, Chung-En; Chen, Chih-hao; Chen, Chien-Tzung

    2015-01-01

    Orbital volume evaluation is an important part of pre-operative assessments in orbital trauma and congenital deformity patients. The availability of the affordable, open-source software, OsiriX, as a tool for preoperative planning increased the popularity of radiological assessments by the surgeon. A volume calculation method based on 3D volume rendering-assisted region-of-interest computation was used to determine the normal orbital volume in Taiwanese patients after reorientation to the Frankfurt plane. Method one utilized 3D points for intuitive orbital rim outlining. The mean normal orbital volume for left and right orbits was 24.3±1.51 ml and 24.7±1.17 ml in male and 21.0±1.21 ml and 21.1±1.30 ml in female subjects. Another method (method two) based on the bilateral orbital lateral rim was also used to calculate orbital volume and compared with method one. The mean normal orbital volume for left and right orbits was 19.0±1.68 ml and 19.1±1.45 ml in male and 16.0±1.01 ml and 16.1±0.92 ml in female subjects. The inter-rater reliability and intra-rater measurement accuracy between users for both methods was found to be acceptable for orbital volume calculations. 3D-assisted quantification of orbital volume is a feasible technique for orbital volume assessment. The normal orbital volume can be used as controls in cases of unilateral orbital reconstruction with a mean size discrepancy of less than 3.1±2.03% in females and 2.7±1.32% in males. The OsiriX software can be used reliably by the individual surgeon as a comprehensive preoperative planning and imaging tool for orbital volume measurement and computed tomography reorientation. PMID:25774683

  7. 3D-assisted quantitative assessment of orbital volume using an open-source software platform in a Taiwanese population.

    PubMed

    Shyu, Victor Bong-Hang; Hsu, Chung-En; Chen, Chih-Hao; Chen, Chien-Tzung

    2015-01-01

    Orbital volume evaluation is an important part of pre-operative assessments in orbital trauma and congenital deformity patients. The availability of the affordable, open-source software, OsiriX, as a tool for preoperative planning increased the popularity of radiological assessments by the surgeon. A volume calculation method based on 3D volume rendering-assisted region-of-interest computation was used to determine the normal orbital volume in Taiwanese patients after reorientation to the Frankfurt plane. Method one utilized 3D points for intuitive orbital rim outlining. The mean normal orbital volume for left and right orbits was 24.3±1.51 ml and 24.7±1.17 ml in male and 21.0±1.21 ml and 21.1±1.30 ml in female subjects. Another method (method two) based on the bilateral orbital lateral rim was also used to calculate orbital volume and compared with method one. The mean normal orbital volume for left and right orbits was 19.0±1.68 ml and 19.1±1.45 ml in male and 16.0±1.01 ml and 16.1±0.92 ml in female subjects. The inter-rater reliability and intra-rater measurement accuracy between users for both methods was found to be acceptable for orbital volume calculations. 3D-assisted quantification of orbital volume is a feasible technique for orbital volume assessment. The normal orbital volume can be used as controls in cases of unilateral orbital reconstruction with a mean size discrepancy of less than 3.1±2.03% in females and 2.7±1.32% in males. The OsiriX software can be used reliably by the individual surgeon as a comprehensive preoperative planning and imaging tool for orbital volume measurement and computed tomography reorientation.

  8. Application of Magnetic Resonance Imaging to Measure Fasting and Postprandial Volumes in Humans

    PubMed Central

    Fidler, Jeff; Bharucha, Adil E.; Camilleri, Michael; Camp, Jon; Burton, Duane; Grimm, Roger; Riederer, Stephen J.; Robb, Richard A.; Zinsmeister, Alan R.

    2008-01-01

    Our aims were to measure the gastric volume response in excess of ingested meal volume (i.e., gastric accommodation), contribution of swallowed air to this excess, day-to-day variability of gastric volumes measured by MRI and their relationship to volumes measured by single-photon-emission computed tomography (SPECT). In 20 healthy volunteers, fasting and postprandial gastric volumes were measured after technetium99m-pertechnetate labeling of the gastric mucosa by SPECT and separately by MRI, using 3D gradient echo and 2D half-Fourier acquisition single-shot turbo spin echo (HASTE) sequences. Ten of these subjects had a second MRI exam to assess intra-individual variation. Thereafter, another 10 subjects had 2 MRI studies during which they ingested the nutrient in 30 or 150 mL aliquots. During MRI, the postprandial gastric volume change exceeded the ingested meal volume by 106 ± 12 mL (Mean ± SEM). The HASTE and gradient echo sequences distinguished air from fluid under fasting and postprandial conditions respectively. This postprandial excess mainly comprised air (61 ± 5 mL), which was not significantly different when ingested as 30 mL or 150 mL aliquots. Fasting and postprandial gastric volumes measured by MRI were generally reproducible within subjects. During SPECT, postprandial volumes increased by 158 ± 18 mL; gastric volumes measured by SPECT were higher than MRI. MRI measures gastric volumes with acceptable performance characteristics; the postprandial excess primarily consists of air, which is not affected by the mode of ingestion. Gastric volumes are technique specific and differ between MRI and SPECT. PMID:19019018

  9. Postradiotherapy PSA nadirs fail to support dose escalation study in patients with pretreatment PSA values < 10 ng/ml.

    PubMed

    Herold, D; Hanks, G; Movsas, B; Hanlon, A

    1997-01-01

    With three-dimensional conformal therapy, doses > 75 Gy have been delivered to the prostate with acceptable levels of morbidity; however, higher doses do appear to increase late gastrointestinal (GI) and genitourinary (GU) morbidity. Because patients with pretreatment prostate-specific antigen (PSA) values < 10 ng/ml can achieve 3-year actuarial bNED control rates of 90% after treatment with external beam radiotherapy to doses < 71 Gy, one might question the need for further dose escalation in this population. In this report, we examined the relationship between dose and PSA nadir for 90 patients with pretreatment PSA values < 10 ng/ml entered into a dose escalation study from March 1987 to October 1992. We wanted to see if nadir response data would predict a different outcome from our 3-year bNED control reports. All patients were treated with external beam radiotherapy to ICRU reporting point doses of 6,598 cGy to 7,895 cGy (median of 7,068 cGy). Minimum follow-up was 36 months (median, 47 months). Seven hundred thirty-nine posttreatment PSA nadir values were analyzed, yielding an average of 8.2 values per patient. Estimates of rates of bNED control and time to reach a posttreatment PSA of 1.0 ng/ml were calculated using the Kaplan-Meier product limit method. The log-rank test was used to evaluate differences in rates according to dose levels. Linear regression and Cox proportional hazard modeling were used to relate dose to bNED control on a continuum. Escalating doses from 66 to 79 Gy failed to increase the percentage of patients achieving nadir values < 1 ng/ml and similarly failed to increase the 3-year actuarial bNED control. Linear regression (P = .81) and the chi-square test of association (P = .23) supported the lack of a dose effect on nadir continuously and categorically, respectively, and the Cox regression model supported the conclusion that dose on a continuum has no effect on bNED control (P = .34). Furthermore, time to reach a posttreatment PSA

  10. Task-based performance analysis of FBP, SART and ML for digital breast tomosynthesis using signal CNR and Channelised Hotelling Observers.

    PubMed

    Van de Sompel, Dominique; Brady, Sir Michael; Boone, John

    2011-02-01

    We assess the performance of filtered backprojection (FBP), the simultaneous algebraic reconstruction technique (SART) and the maximum likelihood (ML) algorithm for digital breast tomosynthesis (DBT) under variations in key imaging parameters, including the number of iterations, number of projections, angular range, initial guess, and radiation dose. This is the first study to compare these algorithms for the application of DBT. We present a methodology for the evaluation of DBT reconstructions, and use it to conduct preliminary experiments investigating trade-offs between the selected imaging parameters. This investigation includes trade-offs not previously considered in the DBT literature, such as the use of a stationary detector versus a C-arm imaging geometry. A real breast CT volume serves as a ground truth digital phantom from which to simulate X-ray projections under the various acquisition parameters. The reconstructed image quality is measured using task-based metrics, namely signal CNR and the AUC of a Channelised Hotelling Observer with Laguerre-Gauss basis functions. The task at hand is the detection of a simulated mass inserted into the breast CT volume. We find that the image quality in limited view tomography is highly dependent on the particular acquisition and reconstruction parameters used. In particular, we draw the following conclusions. First, we find that optimising the FBP filter design and SART relaxation parameter yields significant improvements in reconstruction quality from the same projection data. Second, we show that the convergence rate of the maximum likelihood algorithm, optimised with paraboloidal surrogates and conjugate gradient ascent (ML-PSCG), can be greatly accelerated using view-by-view updates. Third, we find that the optimal initial guess is algorithm dependent. In particular, we obtained best results with a zero initial guess for SART, and an FBP initial guess for ML-PSCG. Fourth, when the exposure per view is constant

  11. Nasogastric tube feedings and gastric residual volume: a regional survey.

    PubMed

    Ahmad, Shoaib; Le, Vu; Kaitha, Sindhu; Morton, Jordan; Ali, Tauseef

    2012-08-01

    To maintain adequate nutrition for patients who are in need, enteral feeding via nasogastric tube (NGT) is necessary. Although the literature suggests the safety of continued NGT feeding at a gastric residual volume of <400 mL, inconsistencies in withholding tube feeding based on residual volume have been observed in clinical practice. We performed a regional survey to determine the range of current practice among nursing staff regarding the decision to withhold NGT feeding based on residual volume and the factors that influence the decision-making process. A questionnaire was designed to evaluate nursing practice patterns regarding the decision of withholding NGT feeding based on a certain residual volume, which was distributed to the nursing staff at all major hospitals in the Oklahoma City metropolitan area. Statistical analysis was done with the Fisher exact test. All of the statistical tests were carried out at α = 0.05. A total of 582 nurses completed the survey. Residual volumes (milliliters) resulting in the termination of NGT feeding occurred in 89% of nurses at volumes <300 mL and only 3% of nurses at volumes >400 mL. Three main reasons for nurses to withhold NGT feeding were risk of aspiration (90%), potential feeding intolerance (81%), and risk of regurgitation (67%). Other less common concerns were abdominal distension and abdominal discomfort. The decision of withholding NGT feeding varied among the nursing staff that were surveyed. A consensus is necessary for the standardization of withholding NGT feeding in clinical practice among nursing staff.

  12. Influence of attenuation on radionuclide stroke volume determinations

    SciTech Connect

    Burow, R.D.; Wilson, M.F.; Heath, P.W.; Corn, C.R.; Amil, A.; Thadani, U.

    1982-09-01

    Using a method for determination of absolute volumes, including correcting for attenuation, we have explored the ability of the method to determine stroke volume in humans by radionuclide techniques. Thermodilution cardiac output determinations and multigated equilibrium blood-pool scintigraphy in the LAO view were performed simultaneously in twenty patients in which no evidence of intracardiac shunts or valvular disease was present. The correlation was good between the attenuated radionuclide and thermodilution stroke volume (r . 0.80, s.e.e. of estimate . 12 ml; SVtd . 2.31 x SVr + 18 ml). When correction for attenuation was made, the correlation improved (r . 0.96, s.e.e. . 6 ml) and approached the line of identity (SVtd . 0.99 x SVr + 1.2 ml). The correlation was also good between radionuclide cardiac output, corrected for attenuation, and the thermodilution cardiac output (r . 0.89, s.e.e. . 0.36 l/min; COtd . 0.86 x COr + 0.67 l/min). Thus our method of correction for attenuation in the determination of absolute left-ventricular volumes has been shown to provide a reliable, noninvasive means of calculating stroke volume and cardiac output in humans, without the use of geometric assumptions or regression equations.

  13. INTERLABORATORY COMPARISON OF A REDUCED VOLUME MARINE SEDIMENT TOXICITY TEST METHOD USING AMPHIPOD AMPELISCA ABDITA

    EPA Science Inventory

    The U.S. Environmental Protection Agency has standardized methods for performing acute marine amphipod sediment toxicity tests. A test design reducing sediment volume from 200 to 50 ml and overlying water from 600 to 150 ml was recently proposed. An interlaboratory comparison wa...

  14. A PILOT STUDY TO DETERMINE THE WATER VOLUME INJESTED BY RECREATIONAL SWIMMERS

    EPA Science Inventory

    The volume of water ingested by recreational swimmers is unknown. Previous estimates by a number of investigators range from 10mL to 100mL. These estimates, however, are unsupported by empirical data. Many outdoor swimming pools are disinfected using cyanuric acid stabilized c...

  15. A PILOT STUDY TO DETERMINE THE WATER VOLUME INJESTED BY RECREATIONAL SWIMMERS

    EPA Science Inventory

    The volume of water ingested by recreational swimmers is unknown. Previous estimates by a number of investigators range from 10mL to 100mL. These estimates, however, are unsupported by empirical data. Many outdoor swimming pools are disinfected using cyanuric acid stabilized c...

  16. Impact of fill volume on ultrafiltration with icodextrin in children on chronic peritoneal dialysis.

    PubMed

    Rousso, Sharon; Banh, Tonny M; Ackerman, Susan; Piva, Elizabeth; Licht, Christoph; Harvey, Elizabeth A

    2016-10-01

    Icodextrin is a solution of glucose polymers developed to provide sustained ultrafiltration over an extended dwell. Our aim was to determine whether or not fill volume with icodextrin contributes to the ability to achieve ultrafiltration in children. The charts of all children on chronic peritoneal dialysis between January 2000 and July 2014 were screened for the use of an icodextrin day dwell. Data were extracted from the electronic chart and the HomeChoice™ Pro card and corrected for body surface area (BSA). Fifty children had an icodextrin day dwell. A linear correlation was found between the daytime fill volume and net ultrafiltration (p < 0.001). More ultrafiltration was achieved with a fill volume above 550 ml/m(2) BSA (107 ± 75 ml/m(2) BSA) than with smaller fill volumes (-8 ± 99 ml; p = 0.004). Ultrafiltration was achieved in 88 % of children with a fill volume above 550 ml/m(2) BSA versus only 44 % of patients with a smaller fill volume (p = 0.001). Icodextrin was well tolerated. Our observations reveal that the larger the fill volume the higher the likelihood of achieving ultrafiltration with icodextrin and suggest that a minimum day dwell volume of 550 ml/m(2) BSA seems to facilitate ultrafiltration in children. To our knowledge this is the largest study addressing ultrafiltration with icodextrin in children.

  17. Removal of Radioactively Marked Calcium Hydroxide from the Root Canal: Influence of Volume of Irrigation and Activation.

    PubMed

    Zorzin, José; Wießner, Jessica; Wießner, Thomas; Lohbauer, Ulrich; Petschelt, Anselm; Ebert, Johannes

    2016-04-01

    The purpose of this study was to evaluate the amount of calcium hydroxide (Ca[OH]2) removed by irrigation with different volumes and activation methods. One hundred thirty extracted straight, single-rooted human teeth were instrumented to size 45/.04. One hundred twenty teeth were filled with radioactively marked Ca(OH)2 and a gutta-percha point; 10 teeth with only gutta-percha served as a negative control. All specimens were stored in saline solution (7 days at 35°C). After storage, teeth were randomly divided into 12 groups (n = 10). The gutta-percha was taken out, and Ca(OH)2 was removed either by irrigation with different volumes (0 mL, 0.5 mL, 1 mL, 2 mL, 4 mL, or 8 mL) or mechanical activation with a 2- or 4-mL volume using a file (Instr) (FlexMaster size 45/.04; VDW, Munich, Germany), a brush (CanalBrush [CB]; Coltène/Whaledent, Langenau, Germany), or passive ultrasonic irrigation (PUI, smooth wire). Irrigation was performed by alternating 40% citric acid and 3% sodium hypochlorite. Residual Ca(OH)2 was measured by scintillation and expressed as a percentage of the original Ca(OH)2. Increasing the irrigation volume led to a significant decrease (P < .05) of residual Ca(OH)2 (0 mL [98.5%], 0.5 mL [21.7%], 1 mL [16.5%], 2 mL [12.9%], 4 mL [8.7%], 8 mL [5.0%], and negative control [0.0%]). Activation led to less residual Ca(OH)2 (2 mL Instr [12.0%], 2 mL CB [11.7%], 2 mL PUI [9.1%], 4 mL Instr [8.5%], 4 mL CB [7.4%], and 4 mL PUI [6.2%]), with significant differences according to the PUI (P < .05). No irrigation procedure was able to remove Ca(OH)2 completely. PUI was the most effective activation method. However, irrigation with an 8-mL volume was the most effective. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  18. Calcium transport in protoplasts isolated from ml-o barley isolines resistant and susceptible to powdery mildew. [Hordeum vulgare L

    SciTech Connect

    Wrona, A.F.; Spanswick, R.M.; Aist, J.R. )

    1988-12-01

    Free cytoplasmic calcium has been postulated to play a role in preventing powdery mildew in a series of homozygous ml-o mutants of barley, Hordeum vulgare L. Protoplasts isolated from 7-day-old plants of the ml-o resistant-susceptible (R-S) barley isolines, Riso 5678/3* {times} Carlsberg II R and S, were used to test for differences in fluxes of Ca{sup 2+} across the plasmalemma. Greater influx or lesser efflux might account for a higher free cytosolic Ca{sup 2+} postulated to exist in ml-o R mutants. Uniform patterns of uptake were maintained for 3 hours from solutions of 0.2 and 2 millimolar Ca{sup 2+}. Washout curves of {sup 45}Ca{sup 2+} from R and S protoplasts revealed three compartments - presumed to represent release from the vacuole, organelles, and the cytoplasm (which included bound as well as free Ca{sup 2+}). Uptake and washout did not differ between isolines. On the basis of recent determinations of submicromolar levels of free cytoplasmic Ca{sup 2+} and their initial rates of {sup 45}ca-labeled Ca{sup 2+} uptake, they show that measurement of the unidirectional influx of Ca{sup 2+} across the plasmalemma is not feasible because the specific activity of the pool of free cytoplasmic calcium increases almost instantaneously to a level that would result in a significant, but unknown, efflux of label. Similarly, measurement of the efflux of Ca{sup 2+} across the plasmalemma is not possible since the activity of the pool of free cytoplasmic calcium is a factor of 350 smaller than the most rapid component of the washout experiment. This pool of cytoplasmic free Ca{sup 2+} will wash out too rapidly and be too small to detect under the conditions of these experiments.

  19. Chloroprocaine 10 mg/ml for low-dose spinal anaesthesia in perianal surgery - a randomised dose finding study.

    PubMed

    Gebhardt, V; Mueller-Hansen, L; Schwarz, A; Bussen, D; Weiss, C; Schmittner, M D

    2017-02-01

    Low-dose spinal anaesthesia is a safe and reliable anaesthesia technique in outpatient perianal surgery. Regarding its short duration of action and its trend to hyperbaric characteristics, plain chloroprocaine 10 mg/ml seems to be ideal to perform low-dose spinal anaesthesia. The aim of this trial was to determine the optimal dosage of chloroprocaine for this indication. Hundred and twenty patients undergoing perianal surgery were enrolled and randomly allocated to receive 10, 20 or 30 mg of chloroprocaine 10 mg/ml intrathecally. Patients had to sit upright for at least 10 min after injection. We measured the expansion of sensory and motor block and the times until voiding, walking without assistance and home discharge. The expansion of the sensory (P ≤ 0.0059) and the motor block (P ≤ 0.0086) gained with increasing doses. At a dose of 30 mg the incidence of a profound, clinically relevant motor block was significantly higher compared to 10 and 20 mg (P ≤ 0.0004). In the 10 mg group two patients suffered from nociceptive pain due to an incomplete block and five patients announced discomfort during procedure. Doses of 10 and 20 mg led to a significantly earlier discharge compared to 30 mg (P = 0.0003; P = 0.0406). Plain chloroprocaine 10 mg/ml can successfully be used for low-dose spinal anaesthesia in perianal outpatient surgery. Regarding the unfavourable motor block and later discharge-times in the 30 mg group on the one hand and the block-failures in the 10 mg group on the other, 20 mg can be recommended as the optimal dose. © 2016 The Acta Anaesthesiologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  20. Human transcription factor USF stimulates transcription through the initiator elements of the HIV-1 and the Ad-ML promoters.

    PubMed Central

    Du, H; Roy, A L; Roeder, R G

    1993-01-01

    Earlier in vitro studies identified USF as a cellular factor which activates the adenovirus major late (Ad-ML) promoter by binding to an E-box motif located at position -60 with respect to the cap site. Purified USF contains 44 and 43 kDa polypeptides, and the latter was found (by cDNA cloning) to be a helix-loop-helix protein. In this report, we demonstrate a 25-to 30-fold stimulation of transcription via an upstream binding site by ectopic expression of the 43 kDa form of USF (USF43) in transient transfection assays. More recent data have also revealed alternate interactions of USF43 at pyrimidine-rich (consensus YYAYTCYY) initiator (Inr) elements present in a variety of core promoters. In agreement with this observation, we show here that USF43 can recognize the initiator elements of the HIV-1 promoter, as well as those in the Ad-ML promoter, and that ectopic expression of USF43 can stimulate markedly the corresponding core promoters (TATA and initiator elements) when analyzed in transient co-transfection assays. Mutations in either Inr 1 or Inr 2 reduced the USF43-dependent transcription activity in vivo. In addition, in vitro transcription assays showed that mutations in either or both of the Inr 1 and Inr 2 sequences of the HIV-1 and Ad-ML promoters could affect transcription efficiency, but not the position of the transcriptional start site. These results indicate that USF43 can stimulate transcription through initiator elements in two viral promoters, although the exact mechanism and physiological significance of this effect remain unclear. Images PMID:8440240

  1. The 12 September 2016 ML5.8 midcrustal earthquake in the Korean Peninsula and its seismic implications

    NASA Astrophysics Data System (ADS)

    Hong, Tae-Kyung; Lee, Junhyung; Kim, Woohan; Hahm, In-Kyeong; Woo, Nam Chil; Park, Seongjun

    2017-04-01

    The seismicity in the Korean Peninsula has increased since the 2011 Mw9.0 Tohoku-Oki megathrust earthquake. Two strike-slip earthquakes with magnitudes of ML5.1 and 5.8 occurred in the southeastern Korean Peninsula on 12 September 2016. The two events occurred within 48 min. The ML5.8 earthquake was the largest event in the Korean Peninsula since 1978 when national seismic monitoring began. Both events produced strong high-frequency ground motions. More than 500 aftershocks with local magnitudes greater than or equal to 1.5 followed the events for 2 months. An unreported subsurface strike-slip fault with a dip of 65° to the east and a strike of N27°E was responsible for the earthquakes. The fault ruptured at depths of 11-16 km, resulting in a rupture plane of ˜26 km2. The aftershock distribution displayed horizontal streaks at a depth of ˜14 km, which was consistent with the focal mechanism solutions from long-period waveform inversion. The number of aftershocks decreased exponentially with time. The two ML5.1 and 5.8 earthquakes produced regional Coulomb stress changes of -4.9 to 2.5 bar. The spatial distribution of the aftershocks correlated with the Coulomb stress changes. The peak dynamic stress induced by strong ground motions reached 14.2 bar. The groundwater levels changed coseismically in some regions of decreased static stresses. The earthquakes on previously unidentified faults raised attention for the potential seismic hazards by earthquakes with long recurrence intervals.

  2. Intraarticular volume and clearance in human synovial effusions

    SciTech Connect

    Wallis, W.J.; Simkin, P.A.; Nelp, W.B.; Foster, D.M.

    1985-04-01

    Intraarticular volumes were measured by radiolabeled albumin (RISA) distribution in chronic knee effusions from 11 rheumatoid arthritis patients and 9 osteoarthritis patients. Volumes of synovial fluid obtained at joint aspiration were substantially less than those found by RISA dilution. Up to 24 hours was needed for full distribution of RISA throughout the intraarticular compartment. Measured 123I and RISA radioactivity over the knee described monoexponential rate constants, lambda (minute-1). The clearance of 123I and RISA from synovial effusions was derived by the formulation volume (ml) X lambda (minute-1) = clearance (ml/minute). RISA clearance in rheumatoid effusions was significantly greater than that found in osteoarthritis effusions. Intraarticular volume and isotope clearance were easily quantified and provide measures for further evaluating the microvascular physiology of synovial effusions.

  3. Thawed human sperm quality is influenced by the volume of the cryopreserved specimen.

    PubMed

    Abush, Ayelet; Hauser, Ron; Paz, Gedalia; Kleiman, Sandra E; Lehavi, Ofer; Yavetz, Haim; Yogev, Leah

    2014-03-01

    To test the effect of sperm specimen volume in the freezing-thawing process on specimen quality. Experimental prospective study. Tertiary academic medical center. Fifty high-quality sperm donors donated ∼3 times each. Sperm samples were split into two aliquots and frozen in volumes of 0.25 mL and 0.5 mL. Semen analyses. Eight sperm quality parameters of thawed specimens. Thawed 0.5-mL specimens had a higher percentage of motility and viability, progressive motility concentration, percentage of cells with high mitochondrial membrane potential, and intact chromatin compared with 0.25-mL specimens. Although there were fewer cells with intact acrosomes in the 0.5-mL thawed samples, they had a similar ability to respond to ionophore by acrosome reaction as the 0.25-mL specimens. Both groups had similar percentages of cells with oxidative stress and numbers of cells that bound to the zona pellucida. The remaining air volume in the straw and freezing medium composition had a minimal effect on tested parameters. Better quality thawed human sperm was achieved after cryopreservation of high volumes compared with low volumes of specimens. Air volume in the straw had no influence on specimen quality. Copyright © 2014 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  4. Impact of bolus volume on small intestinal intra-luminal impedance in healthy subjects

    PubMed Central

    Nguyen, Nam Q; Bryant, Laura K; Burgstad, Carly M; Fraser, Robert J; Sifrim, Daniel; Holloway, Richard H

    2010-01-01

    AIM: To assess the impact of bolus volume on the characteristics of small intestinal (SI) impedance signals. METHODS: Concurrent SI manometry-impedance measurements were performed on 12 healthy volunteers to assess the pattern of proximal jejunal fluid bolus movement over a 14 cm-segment. Each subject was given 34 boluses of normal saline (volume from 1 to 30 mL) via the feeding tube placed immediately above the proximal margin of the studied segment. A bolus-induced impedance event occurred if there was > 12% impedance drop from baseline, over ≥ 3 consecutive segments within 10 s of bolus injection. A minor or major impedance event was defined as a duration of impedance drop < 60 s or ≥ 60 s, respectively. RESULTS: The minimum volume required for a detectable SI impedance event was 2 mL. A direct linear relationship between the SI bolus volume and the occurrence of impedance events was noted until SI bolus volume reached 10 mL, a volume which always produced an impedance flow event. There was a moderate correlation between the bolus volume and the duration of impedance drop (r = 0.63, P < 0.0001) and the number of propagated channels (r = 0.50, P < 0.0001). High volume boluses were associated with more major impedance events (≥ 10 mL boluses = 63%, 3 mL boluses = 17%, and < 3 mL boluses = 0%, P = 0.02). CONCLUSION: Bolus volume had an impact on the type and length of propagation of SI impedance events and a threshold of 2 mL is required to produce an event. PMID:20440856

  5. Membrane traffic and turnover in TRP-ML1–deficient cells: a revised model for mucolipidosis type IV pathogenesis

    PubMed Central

    Miedel, Mark T.; Rbaibi, Youssef; Guerriero, Christopher J.; Colletti, Grace; Weixel, Kelly M.; Weisz, Ora A.; Kiselyov, Kirill

    2008-01-01

    The lysosomal storage disorder mucolipidosis type IV (MLIV) is caused by mutations in the transient receptor potential–mucolipin-1 (TRP-ML1) ion channel. The “biogenesis” model for MLIV pathogenesis suggests that TRP-ML1 modulates postendocytic delivery to lysosomes by regulating interactions between late endosomes and lysosomes. This model is based on observed lipid trafficking delays in MLIV patient fibroblasts. Because membrane traffic aberrations may be secondary to lipid buildup in chronically TRP-ML1–deficient cells, we depleted TRP-ML1 in HeLa cells using small interfering RNA and examined the effects on cell morphology and postendocytic traffic. TRP-ML1 knockdown induced gradual accumulation of membranous inclusions and, thus, represents a good model in which to examine the direct effects of acute TRP-ML1 deficiency on membrane traffic. Ratiometric imaging revealed decreased lysosomal pH in TRP-ML1–deficient cells, suggesting a disruption in lysosomal function. Nevertheless, we found no effect of TRP-ML1 knockdown on the kinetics of protein or lipid delivery to lysosomes. In contrast, by comparing degradation kinetics of low density lipoprotein constituents, we confirmed a selective defect in cholesterol but not apolipoprotein B hydrolysis in MLIV fibroblasts. We hypothesize that the effects of TRP-ML1 loss on hydrolytic activity have a cumulative effect on lysosome function, resulting in a lag between TRP-ML1 loss and full manifestation of MLIV. PMID:18504305

  6. ToxML, a data exchange standard with content controlled vocabulary used to build better (Q)SAR models.

    PubMed

    Ali, M; Patel, M; Wilkinson, D; Judson, P; Cross, K; Bower, D

    2013-01-01

    Development of accurate quantitative structure-activity relationship (QSAR) models requires the availability of high quality validated data. International regulations such as REACH in Europe will now accept (Q)SAR-based evaluations for risk assessment. The number of toxicity datasets available for those wishing to share knowledge, or to use for data mining and modelling, is continually expanding. The challenge is the current use of a multitude of different data formats. The issues of comparing or combining disparate data apply both to public and proprietary sources. The ToxML project addresses the need for a common data exchange standard that allows the representation and communication of these data in a well-structured electronic format. It is an open standard based on Extensible Markup Language (XML). Supporting information for overall toxicity endpoint data can be included within ToxML files. This makes it possible to assess the quality and detail of the data used in a model. The data file model allows the aggregation of experimental data to the compound level in the detail needed to support (Q)SAR work. The standard is published on a website together with tools to view, edit and download it.

  7. Natural Language Processing and Machine Learning (NLP/ML): Applying Advances in Biomedicine to the Earth Sciences

    NASA Astrophysics Data System (ADS)

    Duerr, R.; Myers, S.; Palmer, M.; Jenkins, C. J.; Thessen, A.; Martin, J.

    2015-12-01

    Semantics underlie many of the tools and services available from and on the web. From improving search results to enabling data mashups and other forms of interoperability, semantic technologies have proven themselves. But creating semantic resources, especially re-usable semantic resources, is extremely time consuming and labor intensive. Why? Because it is not just a matter of technology but also of obtaining rough consensus if not full agreement amongst community members on the meaning and order of things. One way to develop these resources in a more automated way would be to use NLP/ML techniques to extract the required resources from large corpora of subject-specific text such as peer-reviewed papers where presumably a rough consensus has been achieved at least about the basics of the particular discipline involved. While not generally applied to Earth Sciences, considerable resources have been spent in other fields such as medicine on these types of techniques with some success. The NSF-funded ClearEarth project is applying the techniques developed for biomedicine to the cryosphere, geology, and biology in order to spur faster development of the semantic resources needed in these fields. The first area being addressed by the project is the cryosphere, specifically sea ice nomenclature where an existing set of sea ice ontologies are being used as the "Gold Standard" against which to test and validate the NLP/ML techniques. The processes being used, lessons learned and early results will be described.

  8. Anisotropic surface melting in lyotropic cubic crystals. Part 1: Pn3m/L1 interface, poor faceting

    NASA Astrophysics Data System (ADS)

    Grenier, J.; Plötzing, T.; Rohe, D.; Pieranski, P.

    2006-02-01

    From experiments with ice or metal crystals, in the vicinity of their crystal/liquid/vapor triple points, it is known that melting of crystals starts on their surfaces and is anisotropic. It is shown here by direct observations under an optical microscope that this anisotropic surface melting phenomenon occurs also in lyotropic systems. In the case of C12EO2/water mixture, it takes place in the vicinity of the peritectic Pn3m/L3/L1 triple point. Above the peritectic triple point, where the Pn3m and L1 phases coexist in the bulk, the surface of a Pn3m-in-L1 crystal is composed of (111)-type facets surrounded by rough surfaces. The angular junction suggests that rough surfaces are wet by a L3-like layer while facets stay “dry”. This is analogous to the pre-melting at rough surfaces in solid crystals. Upon cooling below the peritectic triple point, where L3 and L1 phases coexist in the bulk, a thick layer of the L3 phase grows from the pre-melted, rough Pn3m/L1 interface. Simultaneously, facets stay dry and their radius decreases. In this tri-phasic configuration, stable in a narrow temperature range, the L3/L1 and L3/Pn3m interfaces have shapes of constant mean curvature surfaces having common borders: edges of facets.

  9. Benefits of small volume and small syringe for bone marrow aspirations of mesenchymal stem cells.

    PubMed

    Hernigou, Philippe; Homma, Yasuhiro; Flouzat Lachaniette, Charles Henri; Poignard, Alexandre; Allain, Jerome; Chevallier, Nathalie; Rouard, Helene

    2013-11-01

    Aspirating bone marrow from the iliac crest using small volumes of 1-4 ml with a 10-ml syringe has been historically proposed for harvesting adult mesenchymal stem cells and described as a standard technique to avoid blood dilution. The disadvantage of repeated small aspirations is that there is a significantly increased time to harvest the bone marrow. However, it is not known if a large volume syringe can improve the rate of bone marrow aspiration without increasing blood dilution, thus reducing the quality of the aspirate. We compared the concentrations of mesenchymal stem cells obtained under normal conditions with two different size syringes. Thirty adults (16 men and 14 women with a mean age of 49 ± 14 years) underwent surgery with aspiration of bone marrow from their iliac crest. Bilateral aspirates were obtained from the iliac crest of the same patients with a 10-ml syringe and a 50-ml syringe. Cell analysis determined the frequencies of mesenchymal stem cells (as determined by the number of colonies) from each size of syringe. The cell count, progenitor cell concentration (colonies/ml marrow) and progenitor cell frequency (per million nucleated cells) were calculated. All bone marrow aspirates were harvested by the same surgeon. Aspirates of bone marrow demonstrated greater concentrations of mesenchymal stem cells with a 10-ml syringe compared with matched controls using a 50-ml syringe. Progenitor cell concentrations were on average 300 % higher using a 10-ml syringe than matched controls using a 50-ml syringe (p < 0.01). In normal human donors, bone marrow aspiration from 30 patients demonstrated a reduced mesenchymal stem cell number in aspirates obtained using a larger volume syringe (50 ml) as compared with a smaller volume syringe (10 ml).

  10. [The reproducibility of stroke-volume measurements by impedance cardiography. A critical analysis (author's transl)].

    PubMed

    Stick, C

    1978-12-01

    40 determinations of the stroke volume were carried out by impedance cardiography in one and the same subject. The stroke volume varied between 136 and 209 ml (x, x = 169 ml, S.D. = 17.5 ml). The mean error was in the same range as obtained by the Fick principle or by dye-dilution technique as referred to the literature. However, analysing the factors affecting the variability of the determined stroke volumes we may infer, the Kubicek formula for stroke volume is neither theoretically nor empirically sufficiently proved. A quantitative determination of the stroke volume or of any other circulatory quantity by the impedance cardiography seems to be impossible by our present method of procedure.

  11. Does Glass Size and Shape Influence Judgements of the Volume of Wine?

    PubMed

    Pechey, Rachel; Attwood, Angela S; Couturier, Dominique-Laurent; Munafò, Marcus R; Scott-Samuel, Nicholas E; Woods, Andy; Marteau, Theresa M

    2015-01-01

    Judgements of volume may influence the rate of consumption of alcohol and, in turn, the amount consumed. The aim of the current study was to examine the impact of the size and shape of wine glasses on perceptions of wine volume. Online experiment: Participants (n = 360; recruited via Mechanical Turk) were asked to match the volume of wine in two wine glasses, specifically: 1. the Reference glass holding a fixed reference volume, and 2. the Comparison glass, for which the volume could be altered until participants perceived it matched the reference volume. One of three comparison glasses was shown in each trial: 'wider' (20% wider but same capacity); 'larger' (same width but 25% greater capacity); or 'wider-and-larger' (20% wider and 25% greater capacity). Reference volumes were 125 ml, 175 ml and 250 ml, in a fully factorial within-subjects design: 3 (comparison glass) x 3 (reference volume). Non-zero differences between the volumes with which participants filled comparison glasses and the corresponding reference volumes were identified using sign-rank tests. Participants under-filled the wider glass relative to the reference glass for larger reference volumes, and over-filled the larger glass relative to the reference glass for all reference volumes. Results for the wider-and-larger glass showed a mixed pattern across reference volume. For all comparison glasses, in trials with larger reference volumes participants tended to fill the comparison glass less, relative to trials with smaller reference volumes for the same comparison glass. These results are broadly consistent with people using the relative fullness of glasses to judge volume, and suggest both the shape and capacity of wine glasses may influence perceived volume. Perceptions that smaller glasses contain more than larger ones (despite containing the same volume), could slow drinking speed and overall consumption by serving standard portions in smaller glasses. This hypothesis awaits testing.

  12. Does Glass Size and Shape Influence Judgements of the Volume of Wine?

    PubMed Central

    Pechey, Rachel; Attwood, Angela S.; Couturier, Dominique-Laurent; Munafò, Marcus R.; Scott-Samuel, Nicholas E.; Woods, Andy; Marteau, Theresa M.

    2015-01-01

    Background Judgements of volume may influence the rate of consumption of alcohol and, in turn, the amount consumed. The aim of the current study was to examine the impact of the size and shape of wine glasses on perceptions of wine volume. Methods Online experiment: Participants (n = 360; recruited via Mechanical Turk) were asked to match the volume of wine in two wine glasses, specifically: 1. the Reference glass holding a fixed reference volume, and 2. the Comparison glass, for which the volume could be altered until participants perceived it matched the reference volume. One of three comparison glasses was shown in each trial: ‘wider’ (20% wider but same capacity); ‘larger’ (same width but 25% greater capacity); or ‘wider-and-larger’ (20% wider and 25% greater capacity). Reference volumes were 125ml, 175ml and 250ml, in a fully factorial within-subjects design: 3 (comparison glass) x 3 (reference volume). Non-zero differences between the volumes with which participants filled comparison glasses and the corresponding reference volumes were identified using sign-rank tests. Results Participants under-filled the wider glass relative to the reference glass for larger reference volumes, and over-filled the larger glass relative to the reference glass for all reference volumes. Results for the wider-and-larger glass showed a mixed pattern across reference volume. For all comparison glasses, in trials with larger reference volumes participants tended to fill the comparison glass less, relative to trials with smaller reference volumes for the same comparison glass. Conclusions These results are broadly consistent with people using the relative fullness of glasses to judge volume, and suggest both the shape and capacity of wine glasses may influence perceived volume. Perceptions that smaller glasses contain more than larger ones (despite containing the same volume), could slow drinking speed and overall consumption by serving standard portions in smaller

  13. Time and volume dependence of dead space in healthy and surfactant-depleted rat lungs during spontaneous breathing and mechanical ventilation.

    PubMed

    Dassow, Constanze; Schwenninger, David; Runck, Hanna; Guttmann, Josef

    2013-11-01

    Volumetric capnography is a standard method to determine pulmonary dead space. Hereby, measured carbon dioxide (CO2) in exhaled gas volume is analyzed using the single-breath diagram for CO2. Unfortunately, most existing CO2 sensors do not work with the low tidal volumes found in small animals. Therefore, in this study, we developed a new mainstream capnograph designed for the utilization in small animals like rats. The sensor was used for determination of dead space volume in healthy and surfactant-depleted rats (n = 62) during spontaneous breathing (SB) and mechanical ventilation (MV) at three different tidal volumes: 5, 8, and 11 ml/kg. Absolute dead space and wasted ventilation (dead space volume in relation to tidal volume) were determined over a period of 1 h. Dead space increase and reversibility of the increase was investigated during MV with different tidal volumes and during SB. During SB, the dead space volume was 0.21 ± 0.14 ml and increased significantly at MV to 0.39 ± 0.03 ml at a tidal volume of 5 ml/kg and to 0.6 ± 0.08 ml at a tidal volume of 8 and 11 ml/kg. Dead space and wasted ventilation during MV increased with tidal volume. This increase was mostly reversible by switching back to SB. Surfactant depletion had no further influence on the dead space increase during MV, but impaired the reversibility of the dead space increase.

  14. Investigating relationships between left atrial volume, symmetry, and sphericity

    NASA Astrophysics Data System (ADS)

    Menon, Prahlad G.; Nedios, Sotiris; Hindricks, Gerhard; Bollmann, Andreas

    2016-03-01

    Catheter ablation is a safe and effective therapy for drug-refractory patients symptomatic of atrial fibrillation (AF), with up to 80% of patients experiencing long-term arrhythmia-free survival. However, up to 20-40% of patients require more than one procedure in order to become arrhythmia-free. Therefore, appropriate patient selection is paramount to the effective implementation and long-term success of ablation therapy for patients with atrial fibrillation (AF). In this study, as a precursor to evaluating clinical significance of specific LA shape metrics as pre-procedural predictors of AF recurrence following ablative pulmonary vein isolation therapy, we report on a computational geometric analysis in a pilot cohort evaluating relationships between various patient-specific metrics of LA shape which might have such predictive value. This study specifically is focused on establishing the relationship between LA volume and sphericity, using a novel methodology for computing atrial sphericity based on regional shape.

  15. New insulin glargine 300 Units · mL-1 provides a more even activity profile and prolonged glycemic control at steady state compared with insulin glargine 100 Units · mL-1.

    PubMed

    Becker, Reinhard H A; Dahmen, Raphael; Bergmann, Karin; Lehmann, Anne; Jax, Thomas; Heise, Tim

    2015-04-01

    To characterize the pharmacokinetics (PK) and pharmacodynamics (PD) of a new insulin glargine comprising 300 units · mL(-1) (Gla-300), compared with insulin glargine 100 units · mL(-1) (Gla-100) at steady state in people with type 1 diabetes. A randomized, double-blind, crossover study (N = 30) was conducted, applying the euglycemic clamp technique over a period of 36 h. In this multiple-dose to steady-state study, participants received once-daily subcutaneous administrations of either 0.4 (cohort 1) or 0.6 units · kg(-1) (cohort 2) Gla-300 for 8 days in one treatment period and 0.4 units · kg(-1) Gla-100 for 8 days in the other. Here we focus on the results of a direct comparison between 0.4 units · kg(-1) of each treatment. PK and PD assessments performed on the last treatment day included serum insulin measurements using a radioimmunoassay and the automated euglycemic glucose clamp technique over 36 h. At steady state, insulin concentration (INS) and glucose infusion rate (GIR) profiles of Gla-300 were more constant and more evenly distributed over 24 h compared with those of Gla-100 and lasted longer, as supported by the later time (∼ 3 h) to 50% of the area under the serum INS and GIR time curves from time zero to 36 h post dosing. Tight blood glucose control (≤ 105 mg · dL(-1)) was maintained for approximately 5 h longer (median of 30 h) with Gla-300 compared with Gla-100. Gla-300 provides more even steady-state PK and PD profiles and a longer duration of action than Gla-100, extending blood glucose control well beyond 24 h. © 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  16. Peritoneal residual volume induces variability of ultrafiltration with icodextrin.

    PubMed

    Akonur, Alp; Holmes, Clifford J; Leypoldt, John K

    2014-01-01

    Icodextrin induces ultrafiltration (UF) during long-dwell exchanges by creating a difference in oncotic pressure between the peritoneal cavity and plasma; however, the mechanisms governing intra-patient and inter-patient variability in UF when icodextrin is used remain largely unexplained. In the present study, we show theoretically that differences in peritoneal residual volume (VR) have a more profound effect on UF with icodextrin use than with glucose use. This phenomenon is attributed to a differential effect of VR on oncotic, rather than osmotic, pressure between the peritoneal cavity and plasma. ♢ The three-pore model was used to calculate the effect on UF of VR between 150 mL and 1200 mL when 7.5% icodextrin (ICO) or 3.86% glucose solution is used at the end of a 12-hour dwell in the four patient transport groups (that is, fast to slow). Oncotic (with ICO) and osmotic (with glucose) pressure differences averaged over the entire dwell were also calculated. ♢ As expected, at a nominal VR of 300 mL, UF with glucose differed substantially between the four patient transport groups (2 - 804 mL), whereas UF with ICO did not (556 - 573 mL). When VR was increased to 1200 mL from 150 mL, the concentrations of the oncotic and osmotic agents at the start of the dwell with an infusion volume of 2 L decreased to 4.9% from 7.0% with ICO and to 2.5% from 3.6% with glucose. The decrease in UF on average was greater with ICO [to 252 mL from 624 mL: that is, a reduction of 372 mL (60%)] than with glucose [to 292 mL from 398 mL: that is, a reduction of 106 mL (27%)]. Those trends agreed with the calculated reductions in the oncotic pressure difference with ICO [reduction of 12 mmHg (49%)] and the osmotic pressure difference with glucose [reduction of 19 mmHg (33%)]. ♢ When ICO is used, VR modifies the oncotic pressure difference between the peritoneal cavity and plasma to substantially alter UF. This modification suggests that potential causes of increased VR should be

  17. Peritoneal Residual Volume Induces Variability of Ultrafiltration with Icodextrin

    PubMed Central

    Akonur, Alp; Holmes, Clifford J.; Leypoldt, John K.

    2014-01-01

    ♦ Background: Icodextrin induces ultrafiltration (UF) during long-dwell exchanges by creating a difference in oncotic pressure between the peritoneal cavity and plasma; however, the mechanisms governing intra-patient and inter-patient variability in UF when icodextrin is used remain largely unexplained. In the present study, we show theoretically that differences in peritoneal residual volume (VR) have a more profound effect on UF with icodextrin use than with glucose use. This phenomenon is attributed to a differential effect of VR on oncotic, rather than osmotic, pressure between the peritoneal cavity and plasma. ♦ Methods: The three-pore model was used to calculate the effect on UF of VR between 150 mL and 1200 mL when 7.5% icodextrin (ICO) or 3.86% glucose solution is used at the end of a 12-hour dwell in the four patient transport groups (that is, fast to slow). Oncotic (with ICO) and osmotic (with glucose) pressure differences averaged over the entire dwell were also calculated. ♦ Results: As expected, at a nominal VR of 300 mL, UF with glucose differed substantially between the four patient transport groups (2 - 804 mL), whereas UF with ICO did not (556 - 573 mL). When VR was increased to 1200 mL from 150 mL, the concentrations of the oncotic and osmotic agents at the start of the dwell with an infusion volume of 2 L decreased to 4.9% from 7.0% with ICO and to 2.5% from 3.6% with glucose. The decrease in UF on average was greater with ICO [to 252 mL from 624 mL: that is, a reduction of 372 mL (60%)] than with glucose [to 292 mL from 398 mL: that is, a reduction of 106 mL (27%)]. Those trends agreed with the calculated reductions in the oncotic pressure difference with ICO [reduction of 12 mmHg (49%)] and the osmotic pressure difference with glucose [reduction of 19 mmHg (33%)]. ♦ Conclusions: When ICO is used, VR modifies the oncotic pressure difference between the peritoneal cavity and plasma to substantially alter UF. This modification suggests

  18. Foot volume estimates based on a geometric algorithm in comparison to water displacement.

    PubMed

    Mayrovitz, H N; Sims, N; Litwin, B; Pfister, S

    2005-03-01

    Assessing lower extremity limb volume and its change during and after lymphedema therapy is important for determining treatment efficacy and documenting outcomes. Although leg volumes may be determined by tape measure and other methods, there is no metric method to routinely assess foot volumes. Exclusion of foot volumes can under- or overestimate therapeutic progress. Our aim was to develop and test a metric measurement procedure and algorithm for practicing therapists to use to estimate foot volumes. The method uses a caliper and ruler to measure foot dimensions at standardized locations and calculates foot volume (VM) by a mathematical algorithm. VM was compared to volumes measured by water displacement (Vw) in 30 subjects (60 feet) using regression analysis and limits of agreement (LOA). Vw and VM (mean +/- sd) were similar 857 +/- 150 ml vs. 859 +/- 154 ml, and were highly correlated VM = 1.00Vw + 1.67 ml, r = 0.965, p < 0.001. The LOA for absolute volume differences and percentages were respectively +/- 79.6 ml and +/- 9.28 %. These results indicate that this metric method can be a useful alternative to water displacement when foot volumes are needed, but the water displacement method is contraindicated, impractical to implement, too time consuming or is not available.

  19. Sample volume optimization for radon-in-water detection by liquid scintillation counting.

    PubMed

    Schubert, Michael; Kopitz, Juergen; Chałupnik, Stanisław

    2014-08-01

    Radon is used as environmental tracer in a wide range of applications particularly in aquatic environments. If liquid scintillation counting (LSC) is used as detection method the radon has to be transferred from the water sample into a scintillation cocktail. Whereas the volume of the cocktail is generally given by the size of standard LSC vials (20 ml) the water sample volume is not specified. Aim of the study was an optimization of the water sample volume, i.e. its minimization without risking a significant decrease in LSC count-rate and hence in counting statistics. An equation is introduced, which allows calculating the ²²²Rn concentration that was initially present in a water sample as function of the volumes of water sample, sample flask headspace and scintillation cocktail, the applicable radon partition coefficient, and the detected count-rate value. It was shown that water sample volumes exceeding about 900 ml do not result in a significant increase in count-rate and hence counting statistics. On the other hand, sample volumes that are considerably smaller than about 500 ml lead to noticeably lower count-rates (and poorer counting statistics). Thus water sample volumes of about 500-900 ml should be chosen for LSC radon-in-water detection, if 20 ml vials are applied.

  20. Measuring Stroke Volume: Impedance Cardiography vs Phase-Contrast Magnetic Resonance Imaging.

    PubMed

    Borzage, Matthew; Heidari, Kimia; Chavez, Thomas; Seri, Istvan; Wood, John C; Blüml, Stefan

    2017-09-01

    Determination of cardiac output requires measurement of both heart rate and stroke volume. Techniques for measuring heart rate are widespread, and 1 technique for bedside monitoring of stroke volume is electrical impedance cardiography. To determine the accuracy and precision of stroke volume measured via impedance cardiography and whether the technique can be used to detect trends. Eleven healthy research participants (22-52 years old) were examined with simultaneous impedance cardiography and phase-contrast magnetic resonance imaging at rest and during exercise. Bland-Altman analysis with repeated-measures correction was used to compare stroke volumes determined with the 2 methods. The suitability of impedance cardiography for detecting trends in stroke volume was analyzed by using the Critchley radial limits of agreement method. Phase-contrast magnetic resonance imaging indicated a mean stroke volume of 87 (SD, 16) mL at rest; in 9 volunteers, it changed during exercise (P = .04 to P < .001); in 2 volunteers, it did not (P = .32, P = .06). For the range of stroke-volume measurements (60-122 mL), impedance cardiography yielded underestimates of stroke volumes at the low end (bias, -17 mL) and overestimates at the high end (bias, +17 mL; P < .001). Corresponding 95% limits of agreement were 64 mL, a 73% overestimate or underestimate of stroke volume at rest. Critchley radial limits of agreement indicated poor concordance of stroke-volume trends. Impedance cardiography had low accuracy and precision in measuring absolute stroke volume and was a poor detector of stroke-volume trends. ©2017 American Association of Critical-Care Nurses.

  1. Do new anesthesia ventilators deliver small tidal volumes accurately during volume-controlled ventilation?

    PubMed

    Bachiller, Patricia R; McDonough, Joseph M; Feldman, Jeffrey M

    2008-05-01

    During mechanical ventilation of infants and neonates, small changes in tidal volume may lead to hypo- or hyperventilation, barotrauma, or volutrauma. Partly because breathing circuit compliance and fresh gas flow affect tidal volume delivery by traditional anesthesia ventilators in volume-controlled ventilation (VCV) mode, pressure-controlled ventilation (PCV) using a circle breathing system has become a common approach to minimizing the risk of mechanical ventilation for small patients, although delivered tidal volume is not assured during PCV. A new generation of anesthesia machine ventilators addresses the problems of VCV by adjusting for fresh gas flow and for the compliance of the breathing circuit. In this study, we evaluated the accuracy of new anesthesia ventilators to deliver small tidal volumes. Four anesthesia ventilator systems were evaluated to determine the accuracy of volume delivery to the airway during VCV at tidal volume settings of 100, 200, and 500 mL under different conditions of breathing circuit compliance (fully extended and fully contracted circuits) and lung compliance. A mechanical test lung (adult and infant) was used to simulate lung compliances ranging from 0.0025 to 0.03 L/cm H(2)O. Volumes and pressures were measured using a calibrated screen pneumotachograph and custom software. We tested the Smartvent 7900, Avance, and Aisys anesthesia ventilator systems (GE Healthcare, Madison, WI) and the Apollo anesthesia ventilator (Draeger Medical, Telford, PA). The Smartvent 7900 and Avance ventilators use inspiratory flow sensors to control the volume delivered, whereas the Aisys and Apollo ventilators compensate for the compliance of the circuit. We found that the anesthesia ventilators that use compliance compensation (Aisys and Apollo) accurately delivered both large and small tidal volumes to the airway of the test lung under conditions of normal and low lung compliance during VCV (ranging from 95.5% to 106.2% of the set tidal volume

  2. Assisted editing od SensorML with EDI. A bottom-up scenario towards the definition of sensor profiles.

    NASA Astrophysics Data System (ADS)

    Oggioni, Alessandro; Tagliolato, Paolo; Fugazza, Cristiano; Bastianini, Mauro; Pavesi, Fabio; Pepe, Monica; Menegon, Stefano; Basoni, Anna; Carrara, Paola

    2015-04-01

    Sensor observation systems for environmental data have become increasingly important in the last years. The EGU's Informatics in Oceanography and Ocean Science track stressed the importance of management tools and solutions for marine infrastructures. We think that full interoperability among sensor systems is still an open issue and that the solution to this involves providing appropriate metadata. Several open source applications implement the SWE specification and, particularly, the Sensor Observation Services (SOS) standard. These applications allow for the exchange of data and metadata in XML format between computer systems. However, there is a lack of metadata editing tools supporting end users in this activity. Generally speaking, it is hard for users to provide sensor metadata in the SensorML format without dedicated tools. In particular, such a tool should ease metadata editing by providing, for standard sensors, all the invariant information to be included in sensor metadata, thus allowing the user to concentrate on the metadata items that are related to the specific deployment. RITMARE, the Italian flagship project on marine research, envisages a subproject, SP7, for the set-up of the project's spatial data infrastructure. SP7 developed EDI, a general purpose, template-driven metadata editor that is composed of a backend web service and an HTML5/javascript client. EDI can be customized for managing the creation of generic metadata encoded as XML. Once tailored to a specific metadata format, EDI presents the users a web form with advanced auto completion and validation capabilities. In the case of sensor metadata (SensorML versions 1.0.1 and 2.0), the EDI client is instructed to send an "insert sensor" request to an SOS endpoint in order to save the metadata in an SOS server. In the first phase of project RITMARE, EDI has been used to simplify the creation from scratch of SensorML metadata by the involved researchers and data managers. An interesting by

  3. Medium-Range Predictability of Contrail-Cirrus Demonstrated during Experiments Ml-Cirrus and Access-Ii

    NASA Astrophysics Data System (ADS)

    Schumann, U.

    2015-12-01

    The Contrail Cirrus Prediction model CoCiP (doi:10.5194/gmd-5-543-2012) has been applied quasi operationally to predict contrails for flight planning of ML-CIRRUS (C. Voigt, DLR, et al.) in Europe and for ACCESS II in California (B. Anderson, NASA, et al.) in March-May 2014. The model uses NWP data from ECMWF and past airtraffic data (actual traffic data are used for analysis). The forecasts provided a sequence of hourly forecast maps of contrail cirrus optical depth for 3.5 days, every 12 h. CoCiP has been compared to observations before, e.g. within a global climate-aerosol-contrail model (Schumann, Penner et al., ACPD, 2015, doi:10.5194/acpd-15-19553-2015). Good predictions would allow for climate optimal routing (see, e.g., US patent by Mannstein and Schumann, US 2012/0173147 A1). The predictions are tested by: 1) Local eyewitness reports and photos, 2) satellite observed cloudiness, 3) autocorrelation analysis of predictions for various forecast periods, 4) comparisons of computed with observed optical depth from COCS (doi:10.5194/amt-7-3233-2014, 2014) by IR METEOSAT-SEVIRI observations over Europe. The results demonstrate medium-range predictability of contrail cirrus to a useful degree for given traffic, soot emissions, and high-quality NWP data. A growing set of satellite, Lidar, and in-situ data from ML-CIRRUS and ACCENT are becoming available and will be used to further test the forecast quality. The autocorrelation of optical depth predictions is near 70% for 3-d forecasts for Europe (outside times with high Sahara dust loads), and only slightly smaller for continental USA. Contrail cirrus is abundant over Europe and USA. More than 1/3 of all cirrus measured with the research aircraft HALO during ML-CIRRUS was impacted by contrails. The radiative forcing (RF) is strongly daytime and ambience dependent. The net annual mean RF, based on our global studies, may reach up to 0.08 W/m2 globally, and may well exceed 1 W/m2 regionally, with maximum over Europe

  4. Primary standards for measuring flow rates from 100 nl/min to 1 ml/min - gravimetric principle.

    PubMed

    Bissig, Hugo; Petter, Harm Tido; Lucas, Peter; Batista, Elsa; Filipe, Eduarda; Almeida, Nelson; Ribeiro, Luis Filipe; Gala, João; Martins, Rui; Savanier, Benoit; Ogheard, Florestan; Niemann, Anders Koustrup; Lötters, Joost; Sparreboom, Wouter

    2015-08-01

    Microflow and nanoflow rate calibrations are important in several applications such as liquid chromatography, (scaled-down) process technology, and special health-care applications. However, traceability in the microflow and nanoflow range does not go below 16 μl/min in Europe. Furthermore, the European metrology organization EURAMET did not yet validate this traceability by means of an intercomparison between different National Metrology Institutes (NMIs). The NMIs METAS, Centre Technique des Industries Aérauliques et Thermiques, IPQ, Danish Technological Institute, and VSL have therefore developed and validated primary standards to cover the flow rate range from 0.1 μl/min to at least 1 ml/min. In this article, we describe the different designs and methods of the primary standards of the gravimetric principle and the results obtained at the intercomparison for the upper flow rate range for the various NMIs and Bronkhorst High-Tech, the manufacturer of the transfer standards used.

  5. Geophysical setting of the 2000 ML 5.2 Yountville, California, earthquake: Implications for seismic Hazard in Napa Valley, California

    USGS Publications Warehouse

    Langenheim, V.E.; Graymer, R.W.; Jachens, R.C.

    2006-01-01

    The epicenter of the 2000 ML 5.2 Yountville earthquake was located 5 km west of the surface trace of the West Napa fault, as defined by Helley and Herd (1977). On the basis of the re-examination of geologic data and the analysis of potential field data, the earthquake occurred on a strand of the West Napa fault, the main basin-bounding fault along the west side of Napa Valley. Linear aeromagnetic anomalies and a prominent gravity gradient extend the length of the fault to the latitude of Calistoga, suggesting that this fault may be capable of larger-magnitude earthquakes. Gravity data indicate an ???2-km-deep basin centered on the town of Napa, where damage was concentrated during the Yountville earthquake. It most likely played a minor role in enhancing shaking during this event but may lead to enhanced shaking caused by wave trapping during a larger-magnitude earthquake.

  6. The hazard map of ML6.6 0206 Meinong earthquake near Guanmiao and its Neotectonic implication

    NASA Astrophysics Data System (ADS)

    Chung, L. H.; Shyu, J. B. H.; Huang, M. H.; Yang, K. M.; Le Beon, M.; Lee, Y. H.; Chuang, R.; Yi, D.

    2016-12-01

    The serious damage was occurred in SW Taiwan by ML 6.6 0206 Meinong earthquake. Based on InSAR result, 10 cm oval-raised surface deformation is 15 km away from its epicenter, and two obviously N-S trend sharp phase change nearby Guanmiao area. Our field investigation shows bulling damage and surface fracture are high related with the two sharp phase change. Here, we perform the detailed shallow underground geometry by using reflection seismic data, geologic data, and field hazard investigation. This N-S trend surface deformation may be induced by local shallow folding, while the huge uplift west of Guanmiao may be related with pure shear deformation of thick clayey Gutingkeng (GTK) Formation. Our results imply that not only a moderate lower crustal earthquake can trigger active structure at shallower depth, but also those minor shallow active structures are occurred serious damage and surface deformation.

  7. 2013 Apparition of Near-Earth Asteroid (52760) 1998 ML14: Radar and Optical Constraints on Shape and Spin State

    NASA Astrophysics Data System (ADS)

    Sharkey, Benjamin N. L.; Taylor, Patrick A.; Nolan, Michael C.; Howell, Ellen S.; Benner, Lance A. M.

    2016-10-01

    Radar images taken by the Arecibo and Goldstone planetary radar systems in 1998 were used by Ostro et al. (Meteoritics & Planetary Science, 36, 1225-1236, 2001) to produce a shape model of the approximately 1-km diameter near-Earth asteroid (52760) 1998 ML14; however, the spin state (pole orientation and rotation period) was not well determined in their modeling. The published shape model was produced using a 14.83 h sidereal rotation period, consistent with the synodic period of 14.98 ± 0.06 h found by optical observations in 1998 (Hicks & Weissman, IAU Circular 6987, 1, 1998). Optical observations in 2013 found a faster synodic period of 14.28 ± 0.01 h (Warner, The Minor Planet Bulletin, 41, 2, 113-124, 2014). Further radar observations at Arecibo in 2013 are inconsistent with the 14.83 h sidereal period. Use of Arecibo radar images from both apparitions, with resolution as fine as 15 m per pixel, are best fit by a sidereal period within 1% of 14.28 h and constrain the pole orientation to within approximately ten degrees. This period is consistent with all radar and lightcurve data. An updated shape model, combining all known observations, will be presented in light of the constraints on ML14's spin state. The model suggests the presence of several smaller topographic features not previously seen, but remains consistent with major features of the previously published model (notably a distinctive saddle-like region).This improved model illustrates the power of multiple radar apparitions for better determining the true shapes and spin states of near-Earth asteroids, as well as the benefits of multiple observers operating at different wavelength regimes.

  8. 3D position of radiation sources using an automated gamma camera and ML algorithm with energy-dependent response functions

    NASA Astrophysics Data System (ADS)

    Lee, Wonho; Wehe, David

    2004-09-01

    Portable γ-ray imaging systems operating from 100keV to 3MeV are used in nuclear medicine, astrophysics and industrial applications. 2D images of γ-rays are common in many fields using radiation-detection systems (Appl. Opt. 17 (3) (1978) 337; IEEE Trans. Nucl. Sci. Ns- 31 (1984) 771; IEEE Trans. Nucl. Sci. NS- 44 (3) (1997) 911). In this work, the 3D position of a radiation source is determined by a portable gamma-ray imaging system. 2D gamma-ray images were obtained from different positions of the gamma camera and the third dimension, the distance between the detector and the radiation source, was calculated using triangulation. The imaging system consists of a 4×4 array of CsI(Tl) detectors coupled to photodiode detectors that are mounted on an automated table which can precisely position the angular axis of the camera. Lead shields the detector array from the background radiation. Additionally, a CCD camera is attached to the top of the gamma camera and provides coincident 2D visual information. The inferred distances from the center of the two measurement points and a radiation source had less than a 3% error within a range of 3m. The radiation image from the gamma camera and the visual image from CCD camera are superimposed into one combined image using a maximum-likelihood (ML) algorithm to make the image more precise. The response functions for the ML algorithm depend on the energy of incident radiation, and are obtained from both experiments and simulations. The energy-dependent response functions are shown to yield better imaging performance compared with the fixed energy response function commonly used previously.

  9. Biological properties of a new volumizing hyaluronic acid filler: a systematic review.

    PubMed

    Ho, Derek; Jagdeo, Jared

    2015-01-01

    Hyaluronic acid (HA) dermal fillers are effective and safe for correction of facial rhytides. A new volumizing HA filler, 20 mg/ml HA dermal filler (Juvéderm® Voluma®, Allergan Inc., Irvine, CA), is the only HA filler with a FDA indication for facial volumization due to age-related facial volume loss. Evaluate the biological properties, including biochemical, biophysical and rheological, of this new 20 mg/ml HA dermal filler and discuss the importance of these properties in clinical applications. A systematic search of the computerized bibliographic databases Medline, Embase, Embal, Biosis, SciSearch, Pascal, HCAPlus, IPA, and Dissertation Abstracts with key term "Voluma." Four articles on the biological properties of this new 20 mg/ ml HA dermal filler were suitable for inclusion in this review. Biological analysis of elasticity and viscosity values of this new 20 mg/ml HA dermal filler demonstrated intermediate properties in three studies and high in one study compared to other HA dermal fillers. This 20 mg/ml HA dermal filler retained the highest elasticity and viscosity values at temperature of 37°C. Histology demonstrated that this 20 mg/ml HA dermal filler has an intermediate pattern of distribution within the superficial and deep reticular dermis. This 20 mg/ml HA dermal filler demonstrated volumizing ability, and maintaining viscosity and free-flowing characteristics for easy injection, tissue lifting, and molding. We hope future research incorporates biological properties analysis of this HA dermal filler in clinical trials.

  10. New insulin glargine 300 U/ml versus glargine 100 U/ml in Japanese adults with type 1 diabetes using basal and mealtime insulin: glucose control and hypoglycaemia in a randomized controlled trial (EDITION JP 1).

    PubMed

    Matsuhisa, M; Koyama, M; Cheng, X; Takahashi, Y; Riddle, M C; Bolli, G B; Hirose, T

    2016-04-01

    To compare efficacy and safety of new insulin glargine 300 U/ml (Gla-300) with that of insulin glargine 100 U/ml (Gla-100) in Japanese adults with type 1 diabetes. The EDITION JP 1 study (NCT01689129) was a 6-month, multicentre, open-label, phase III study. Participants (n = 243) were randomized to Gla-300 or Gla-100 while continuing mealtime insulin. Basal insulin was titrated with the aim of achieving a fasting self-monitored plasma glucose target of 4.4-7.2 mmol/l. The primary endpoint was change in glycated haemoglobin (HbA1c) over 6 months. Safety measures included hypoglycaemia and change in body weight. Gla-300 was non-inferior to Gla-100 for the primary endpoint of HbA1c change over the 6-month period {least squares [LS] mean difference 0.13 % [95 % confidence interval (CI) -0.03 to 0.29]}. The annualized rate of confirmed (≤3.9 mmol/l) or severe hypoglycaemic events was 34 % lower with Gla-300 than with Gla-100 at night [rate ratio 0.66 (95 % CI 0.48-0.92)] and 20 % lower at any time of day [24 h; rate ratio 0.80 (95 % CI 0.65-0.98)]; this difference was most pronounced during the first 8 weeks of treatment. Severe hypoglycaemia was infrequent. The basal insulin dose increased in both groups (month 6 dose: Gla-300 0.35 U/kg/day, Gla-100 0.29 U/kg/day). A between-treatment difference in body weight change over 6 months favouring Gla-300 was observed [LS mean difference -0.6 kg (95 % CI -1.1 to -0.0); p = 0.035]. Adverse event rates were comparable between the groups. In Japanese adults with type 1 diabetes using basal plus mealtime insulin, less hypoglycaemia was observed with Gla-300 than with Gla-100, particularly during the night, while glycaemic control did not differ. © 2015 The Authors. Diabetes, Obesity and Metabolism published by John Wiley & Sons Ltd.

  11. New insulin glargine 300 U/ml compared with glargine 100 U/ml in insulin-naïve people with type 2 diabetes on oral glucose-lowering drugs: a randomized controlled trial (EDITION 3).

    PubMed

    Bolli, G B; Riddle, M C; Bergenstal, R M; Ziemen, M; Sestakauskas, K; Goyeau, H; Home, P D

    2015-04-01

    To compare the efficacy and safety of new insulin glargine 300 U/ml (Gla-300) with that of glargine 100 U/ml (Gla-100) in insulin-naïve people with type 2 diabetes using oral glucose-lowering drugs. The EDITION 3 study was a multicentre, open-label, parallel-group study. Participants were randomized to Gla-300 or Gla-100 once daily for 6 months, discontinuing sulphonylureas and glinides, with a dose titration aimed at achieving pre-breakfast plasma glucose concentrations of 4.4-5.6 mmol/l (80-100 mg/dl). The primary endpoint was change in glycated haemoglobin (HbA1c) from baseline to month 6. The main secondary endpoint was percentage of participants with ≥1 nocturnal confirmed [≤3.9 mmol/l (≤70 mg/dl)] or severe hypoglycaemia from week 9 to month 6. Other measures of glycaemia and hypoglycaemia, weight change and insulin dose were assessed. Randomized participants (n = 878) had a mean (standard deviation) age of 57.7 (10.1) years, diabetes duration 9.8 (6.4) years, body mass index 33.0 (6.7) kg/m(2) and HbA1c 8.54 (1.06) % [69.8 (11.6) mmol/mol]. HbA1c levels decreased by equivalent amounts with the two treatments; the least squares mean difference in change from baseline was 0.04 [95% confidence interval (CI) -0.09 to 0.17] % or 0.4 (-1.0 to 1.9) mmol/mol. Numerically fewer participants reported ≥1 nocturnal confirmed (≤3.9 mmol/l) or severe hypoglycaemia from week 9 to month 6 [relative risk (RR) 0.89 (95% CI 0.66 to 1.20)] with Gla-300 versus Gla-100; a significantly lower risk of hypoglycaemia with this definition was found over the 6-month treatment period [RR 0.76 (95% CI 0.59 to 0.99)]. No between-treatment differences in adverse events were identified. Gla-300 is as effective as Gla-100 in reducing HbA1c in insulin-naïve people with type 2 diabetes, with lower hypoglycaemia risk. © 2015 The Authors. Diabetes, Obesity and Metabolism published by John Wiley & Sons Ltd.

  12. Effects of clear liquids on gastric volume and pH in healthy volunteers.

    PubMed

    Shevde, K; Trivedi, N; Gross, M

    1991-04-01

    The effects of clear liquids on gastric volume and pH were examined in 30 healthy ASA physical status I volunteers. After overnight fasting, a Salem-sump nasogastric tube was inserted and gastric contents were removed for measurement of volume and pH. Gastric contents were then reinserted through the nasogastric tube into the stomach. The volunteers were randomly divided into three groups: group 1 (n = 10) received 240 mL water, group 2 (n = 10) received 240 mL coffee, and group 3 (n = 10) received 240 mL pulp-free orange juice. All liquids were administered orally. Gastric contents were then again aspirated, measured for volume and pH, and reinserted through the nasogastric tube every half hour until gastric volume was less than 25 mL. All volunteers had gastric volumes less than 25 mL with a slight decrease in pH within 2 h of orally taking one of the three 240-mL liquids. These data suggest that if patients have ingested a moderate amount of clear liquids it is safe to conduct general anesthesia after a 2-h fast in healthy surgical patients.

  13. Use of urinary bladder measurements from a point-of-care cysto-colic ultrasonographic view to estimate urinary bladder volume in dogs and cats.

    PubMed

    Lisciandro, Gregory R; Fosgate, Geoffrey T

    2017-09-26

    To develop a point-of-care ultrasound-derived formula to estimate urinary bladder volume noninvasively in dogs and cats. Prospective case series. Private 24-hour veterinary emergency center. Client-owned dogs and cats requiring urethral catheterization. Ultrasound measurements of length, width, and height of balloons filled with known water volumes were used to develop a formula to estimate urinary bladder volume using linear regression. The formula was then applied to point-of-care ultrasound-derived cysto-colic view measurements, and calculations were compared to total aspirated urine volume. Fifteen balloons with known volumes (median, 126 mL [range, 27-689 mL]) were used to identify length × width × height (cm) × 0.2 × π as the best formula to estimate urinary bladder volume in milliliters. Fourteen cats and 14 dogs were used for comparison of formula-derived volume estimate to actual urinary bladder volume. Median aspirated urine volume, bias (formula-derived minus actual aspirated), and percentage difference were 80 mL, -4.1 mL, and -6.6% for cats, respectively. For dogs, the results were 78 mL, 3.4 mL, and 3.6%, respectively. The point-of-care ultrasound-derived formula may be useful to estimate urine volume noninvasively in dogs and cats. © Veterinary Emergency and Critical Care Society 2017.

  14. Long-term testicular volume after orchiopexy at diagnosis of acquired undescended testis.

    PubMed

    van der Plas, Evelyn M; Zijp, Gerda W; Froeling, Frank M J A; van der Voort-Doedens, Laszla M; Meij-de Vries, Annebeth; Goede, Joery; Hack, Wilfried W M

    2013-07-01

    We studied long-term outcomes of orchiopexy at diagnosis of acquired undescended testes using ultrasound to determine testicular volume. Patients who had undergone orchiopexy for acquired undescended testis at diagnosis were recruited to assess testicular volume. Testis volume was measured by ultrasound and compared with recently developed normative values for testicular size. For young adults (older than 18 years) volumes were grouped and compared to normative values reported in the literature. In all unilateral cases testicular volume was compared with its counterpart. A total of 155 patients 5.1 to 26.6 years old (181 acquired undescended testes) were included in the study. Mean ± SD followup was 6.6 ± 3.8 years (range 1.4 to 15.5). For all patients 18 years old or younger (125 patients, 143 testes) operated testis volume was 0.1 to 12.7 ml (mean ± SD 2.5 ± 2.9), which was significantly smaller than the normative values (50th percentile) for the same age (p <0.001). Mean ± SD testis volume in young adults (38 testes) was 8.1 ± 3.7 ml, compared to a mean volume of 13.4 ml reported in the literature (p <0.001). In unilateral cases the mean volume of the testes fixed by orchiopexy differed significantly from their counterparts (3.4 ± 3.3 ml vs 4.6 ± 4.6 ml, p <0.001). The long-term volumes at diagnosis of acquired undescended testes after orchiopexy were significantly less than the normative values at all ages. In unilateral cases the volumes were also significantly less compared to the contralateral testes. Copyright © 2013 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  15. Gastric residual volume (GRV) and gastric contents measurement by refractometry.

    PubMed

    Chang, Wei-Kuo; McClave, Stephen A; Hsieh, Chung-Bao; Chao, You-Chen

    2007-01-01

    Traditional use of gastric residual volumes (GRVs), obtained by aspiration from a nasogastric tube, is inaccurate and cannot differentiate components of the gastric contents (gastric secretion vs delivered formula). The use of refractometry and 3 mathematical equations has been proposed as a method to calculate the formula concentration, GRV, and formula volume. In this paper, we have validated these mathematical equations so that they can be implemented in clinical practice. Each of 16 patients receiving a nasogastric tube had 50 mL of water followed by 100 mL of dietary formula (Osmolite HN, Abbott Laboratories, Columbus, OH) infused into the stomach. After mixing, gastric content was aspirated for the first Brix value (BV) measurement by refractometry. Then, 50 mL of water was infused into the stomach and a second BV was measured. The procedure of infusion of dietary formula (100 mL) and then water (50 mL) was repeated and followed by subsequent BV measurement. The same procedure was performed in an in vitro experiment. Formula concentration, GRV, and formula volume were calculated from the derived mathematical equations. The formula concentrations, GRVs, and formula volumes calculated by using refractometry and the mathematical equations were close to the true values obtained from both in vivo and in vitro validation experiments. Using this method, measurement of the BV of gastric contents is simple, reproducible, and inexpensive. Refractometry and the derived mathematical equations may be used to measure formula concentration, GRV, and formula volume, and also to serve as a tool for monitoring the gastric contents of patients receiving nasogastric feeding.

  16. Synovial fluid replication in knee wear testing: an investigation of the fluid volume.

    PubMed

    Reinders, Jörn; Sonntag, Robert; Kretzer, Jan Philippe

    2015-01-01

    Wear testing cannot replicate the variations in wear rates and wear mechanisms seen in vivo, which may be related to differences between in vivo and in vitro conditions. A considerable difference exists between the in vivo synovial fluid volume (few milliliter) and the in vitro substituted bovine serum volume (several hundred milliliter). The aim of this study was to analyze the effects of a reduced fluid volume on the wear behavior in a knee wear simulator study. Four wear tests with decreasing fluid volumes (250, 150, 75, and 45 ml) were carried out. Using a large fluid volume of 250 ml for wear testing resulted in a wear rate of 9.7±1.2 mm3/10(6)  cycles. Decreasing the fluid volume consecutively reduced the wear rate to down to 8.8±1.4 mm3/10(6) for 150 ml (p=1.00), 5.6±1.2 mm3/10(6) for 75 ml (p=0.01), and 1.0±0.2 mm3/10(6) cycles for 45 ml fluid volume (p≤0.01). Additionally, higher serum degradation and larger wear particles were observed with smaller fluid volumes used for testing. This study demonstrates the high relevance of the protein-based lubricant on the wear behavior and the technical limitation to replicate the synovial fluid in simulator tests. Wear testing should be carried out using larger fluid volumes (e.g., 250 ml) to generate physiological relevant wear masses. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  17. 77 FR 25760 - Low-Level Radioactive Waste Management and Volume Reduction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-01

    ... COMMISSION Low-Level Radioactive Waste Management and Volume Reduction AGENCY: Nuclear Regulatory Commission... Commission) is revising its 1981 Policy Statement on Low-Level Radioactive Waste (LLRW) Volume Reduction..., ``Blending of Low-Level Radioactive Waste'' (ADAMS Accession No. ML090410531), and referenced the Policy...

  18. A technique for fast and accurate measurement of hand volumes using Archimedes' principle.

    PubMed

    Hughes, S; Lau, J

    2008-03-01

    A new technique for measuring hand volumes using Archimedes principle is described. The technique involves the immersion of a hand in a water container placed on an electronic balance. The volume is given by the change in weight divided by the density of water. This technique was compared with the more conventional technique of immersing an object in a container with an overflow spout and collecting and weighing the volume of overflow water. The hand volume of two subjects was measured. Hand volumes were 494 +/- 6 ml and 312 +/- 7 ml for the immersion method and 476 +/- 14 ml and 302 +/- 8 ml for the overflow method for the two subjects respectively. Using plastic test objects, the mean difference between the actual and measured volume was -0.3% and 2.0% for the immersion and overflow techniques respectively. This study shows that hand volumes can be obtained more quickly than the overflow method. The technique could find an application in clinics where frequent hand volumes are required.

  19. Complete Genome Sequence of Sphingobacterium sp. Strain ML3W, Isolated from Wings of Myotis lucifugus Infected with White Nose Syndrome.

    PubMed

    Smith, Stephen A; Krasucki, Stephen P; McDowell, John V; Balke, Virginia L

    2015-01-22

    Sphingobacterium sp. strain ML3W was isolated from the wing of a bat infected with white nose syndrome. We report the complete 5.33-Mb genome sequence of Sphingobacterium sp. strain ML3W, obtained using Pacific Biosciences technology. Being the second complete Sphingobacterium sequence, this will increase knowledge of the genus. Copyright © 2015 Smith et al.

  20. Developing a Valid Version of an Inventory to Measure Anger in Mexican Adolescents of Middle School Level: The ML-STAXI-MS

    ERIC Educational Resources Information Center

    Alcázar-Olán, Raúl J.; Deffenbacher, Jerry L.; Escamilla-Tecalco, Héctor

    2016-01-01

    The goals were to develop a valid version of the Multicultural Latin American Inventory of Anger Expression and Hostility (ML-STAXI) for middle school Mexican youth (ML-STAXI-MS) and to test a new Questionnaire about Anger Expression with Physical Aggression (QAEPA). Five hundred and four adolescents (258 males, 246 females); (M[subscript age] =…

  1. Developing a Valid Version of an Inventory to Measure Anger in Mexican Adolescents of Middle School Level: The ML-STAXI-MS

    ERIC Educational Resources Information Center

    Alcázar-Olán, Raúl J.; Deffenbacher, Jerry L.; Escamilla-Tecalco, Héctor

    2016-01-01

    The goals were to develop a valid version of the Multicultural Latin American Inventory of Anger Expression and Hostility (ML-STAXI) for middle school Mexican youth (ML-STAXI-MS) and to test a new Questionnaire about Anger Expression with Physical Aggression (QAEPA). Five hundred and four adolescents (258 males, 246 females); (M[subscript age] =…

  2. Ontological Encoding of GeoSciML and INSPIRE geological standard vocabularies and schemas: application to geological mapping

    NASA Astrophysics Data System (ADS)

    Lombardo, Vincenzo; Piana, Fabrizio; Mimmo, Dario; Fubelli, Giandomenico; Giardino, Marco

    2016-04-01

    Encoding of geologic knowledge in formal languages is an ambitious task, aiming at the interoperability and organic representation of geological data, and semantic characterization of geologic maps. Initiatives such as GeoScience Markup Language (last version is GeoSciML 4, 2015[1]) and INSPIRE "Data Specification on Geology" (an operative simplification of GeoSciML, last version is 3.0 rc3, 2013[2]), as well as the recent terminological shepherding of the Geoscience Terminology Working Group (GTWG[3]) have been promoting information exchange of the geologic knowledge. There have also been limited attempts to encode the knowledge in a machine-readable format, especially in the lithology domain (see e.g. the CGI_Lithology ontology[4]), but a comprehensive ontological model that connect the several knowledge sources is still lacking. This presentation concerns the "OntoGeonous" initiative, which aims at encoding the geologic knowledge, as expressed through the standard vocabularies, schemas and data models mentioned above, through a number of interlinked computational ontologies, based on the languages of the Semantic Web and the paradigm of Linked Open Data. The initiative proceeds in parallel with a concrete case study, concerning the setting up of a synthetic digital geological map of the Piemonte region (NW Italy), named "GEOPiemonteMap" (developed by the CNR Institute of Geosciences and Earth Resources, CNR IGG, Torino), where the description and classification of GeologicUnits has been supported by the modeling and implementation of the ontologies. We have devised a tripartite ontological model called OntoGeonous that consists of: 1) an ontology of the geologic features (in particular, GeologicUnit, GeomorphologicFeature, and GeologicStructure[5], modeled from the definitions and UML schemata of CGI vocabularies[6], GeoScienceML and INSPIRE, and aligned with the Planetary realm of NASA SWEET ontology[7]), 2) an ontology of the Earth materials (as defined by the

  3. Intracranial CSF volumes: natural variations and physiological changes measured by MRI.

    PubMed

    Teasdale, G M; Grant, R; Condon, B; Patterson, J; Lawrence, A; Hadley, D M; Wyper, D

    1988-01-01

    Cranial CSF volumes, for the first time including CSF in the subarachnoid space, can be measured by Magnetic Resonance Imaging (MRI). The MRI sequence causes signal from the grey matter and white matter to cancel producing a contrast of 200: 1 between a unit of CSF and a unit of brain. We have assessed the variations between normal individuals and investigated some of the physiological factors that might influence cranial CSF volumes. Total CSF volumes were measured in 64 normal subjects, aged from 18-64 years (mean 38 years). Ventricular, cortical sulcal and posterior fossa volumes were also calculated separately. In 20 females with a normal menstrual cycle, CSF volumes were measured mid cycle and premenstrually; 10 post menopausal females and 10 males were rescanned after an interval of 2 weeks. Total cranial CSF volume were calculated before and during inhalation of 7% CO2 and before and during hyperventilation while breathing 60% O2, in 12 normal subjects. Total intracranial CSF volume ranged from 57.1-286.5 ml. Total intracranial and cortical sulcal CSF volumes increased more steeply with age than ventricular or posterior fossa CSF volumes. Males had more cranial CSF than females. Total CSF volume increased premenstrually in 19 females. Males and post-menopausal females did not have a significant change in CSF volume, on repeat examination. CO2 inhalation produced a mean increase of paCO2 of 17.2 mmHg and CSF volume decreased in all subjects (mean 9.4 ml). Cranial CSF volume increased in 11 subjects during O2 inhalation (range -0.5 to +26.7 ml mean 10.9 ml).(ABSTRACT TRUNCATED AT 250 WORDS)

  4. Enhanced Geothermal Systems in Urban Areas - Lessons Learned from the 2006 Basel ML3.4 Earthquake

    NASA Astrophysics Data System (ADS)

    Kraft, T.; Mai, P. M.; Wiemer, S.; Deichmann, N.; Ripperger, J.; Kästli, P.; Bachmann, C. E.; Fäh, D.; Woessner, J.; Giardini, D.

    2009-12-01

    We report on a recent deep-heat mining experiment carried out in 2006/2007 in the city of Basel (Switzerland). This pilot project was designed to produce renewable geothermal energy using the Enhanced Geothermal System (EGS) methodology. For developing the geothermal reservoir, a deep borehole was brought down to 5 km depth. Then, in December 2006, the deep-heat-mining project entered the first critical phase when the water injections started for generating micro-fracturing of the rock. These fractures increase the permeability of the host rock, needed for efficient heat exchange between the rock and the cold water; however, these fracture are also source of micro-seismicity - small earthquakes that are continuously recorded and monitored by dedicated local seismic networks. In this stimulation phase, the seismic activity increased rapidly above the usual background seismicity, and culminated in a widely felt ML 3.4 earthquake, which caused some damage in the city of Basel. Due to the higher-than-expected seismic activity, and the reaction of the population, the media, and the politicians, the experiment was stalled only 6 days after the stimulations began. Although the injected water was allowed to escape immediately after the mainshock and pressure at the wellhead dropped rapidly, the seismic activity declined only slowly, with three ML > 3 events occurring one to two months later. Although the EGS technology has been applied and studied at various sites since the 1970s, the physical processes and parameters that control injection-induced seismicity - in terms of earthquake rate, size distribution and maximum magnitude - are still poorly understood. Consequently, the seismic hazard and risk associated with the creation and operation of EGS are difficult to estimate. The very well monitored Basel seismic sequence provides an excellent opportunity to advance the understanding of the physics of EGS. The Swiss Seismological Service (SED) is investigating the Basel

  5. Delivery of tidal volume from four anaesthesia ventilators during volume-controlled ventilation: a bench study.

    PubMed

    Wallon, G; Bonnet, A; Guérin, C

    2013-06-01

    Tidal volume (V(T)) must be accurately delivered by anaesthesia ventilators in the volume-controlled ventilation mode in order for lung protective ventilation to be effective. However, the impact of fresh gas flow (FGF) and lung mechanics on delivery of V(T) by the newest anaesthesia ventilators has not been reported. We measured delivered V(T) (V(TI)) from four anaesthesia ventilators (Aisys™, Flow-i™, Primus™, and Zeus™) on a pneumatic test lung set with three combinations of lung compliance (C, ml cm H2O(-1)) and resistance (R, cm H2O litre(-1) s(-2)): C60R5, C30R5, C60R20. For each CR, three FGF rates (0.5, 3, 10 litre min(-1)) were investigated at three set V(T)s (300, 500, 800 ml) and two values of PEEP (0 and 10 cm H2O). The volume error = [(V(TI) - V(Tset))/V(Tset)] ×100 was computed in body temperature and pressure-saturated conditions and compared using analysis of variance. For each CR and each set V(T), the absolute value of the volume error significantly declined from Aisys™ to Flow-i™, Zeus™, and Primus™. For C60R5, these values were 12.5% for Aisys™, 5% for Flow-i™ and Zeus™, and 0% for Primus™. With an increase in FGF, absolute values of the volume error increased only for Aisys™ and Zeus™. However, in C30R5, the volume error was minimal at mid-FGF for Aisys™. The results were similar at PEEP 10 cm H2O. Under experimental conditions, the volume error differed significantly between the four new anaesthesia ventilators tested and was influenced by FGF, although this effect may not be clinically relevant.

  6. Root restriction: A tool for improving volume utilization efficiency in bioregenerative life-support systems

    NASA Astrophysics Data System (ADS)

    Graham, Thomas; Wheeler, Raymond

    2016-06-01

    The objective of this study was to evaluate root restriction as a tool to increase volume utilization efficiency in spaceflight crop production systems. Bell pepper plants (Capsicum annuum cv. California Wonder) were grown under restricted rooting volume conditions in controlled environment chambers. The rooting volume was restricted to 500 ml and 60 ml in a preliminary trial, and 1500 ml (large), 500 ml (medium), and 250 ml (small) for a full fruiting trial. To reduce the possible confounding effects of water and nutrient restrictions, care was taken to ensure an even and consistent soil moisture throughout the study, with plants being watered/fertilized several times daily with a low concentration soluble fertilizer solution. Root restriction resulted in a general reduction in biomass production, height, leaf area, and transpiration rate; however, the fruit production was not significantly reduced in the root restricted plants under the employed environmental and horticultural conditions. There was a 21% reduction in total height and a 23% reduction in overall crown diameter between the large and small pot size in the fruiting study. Data from the fruiting trial were used to estimate potential volume utilization efficiency improvements for edible biomass in a fixed production volume. For fixed lighting and rooting hardware situations, the majority of improvement from root restriction was in the reduction of canopy area per plant, while height reductions could also improve volume utilization efficiency in high stacked or vertical agricultural systems.

  7. Root restriction: A tool for improving volume utilization efficiency in bioregenerative life-support systems.

    PubMed

    Graham, Thomas; Wheeler, Raymond

    2016-06-01

    The objective of this study was to evaluate root restriction as a tool to increase volume utilization efficiency in spaceflight crop production systems. Bell pepper plants (Capsicum annuum cv. California Wonder) were grown under restricted rooting volume conditions in controlled environment chambers. The rooting volume was restricted to 500ml and 60ml in a preliminary trial, and 1500ml (large), 500ml (medium), and 250ml (small) for a full fruiting trial. To reduce the possible confounding effects of water and nutrient restrictions, care was taken to ensure an even and consistent soil moisture throughout the study, with plants being watered/fertilized several times daily with a low concentration soluble fertilizer solution. Root restriction resulted in a general reduction in biomass production, height, leaf area, and transpiration rate; however, the fruit production was not significantly reduced in the root restricted plants under the employed environmental and horticultural conditions. There was a 21% reduction in total height and a 23% reduction in overall crown diameter between the large and small pot size in the fruiting study. Data from the fruiting trial were used to estimate potential volume utilization efficiency improvements for edible biomass in a fixed production volume. For fixed lighting and rooting hardware situations, the majority of improvement from root restriction was in the reduction of canopy area per plant, while height reductions could also improve volume utilization efficiency in high stacked or vertical agricultural systems.

  8. Pharyngeal swallow adaptations to bolus volume measured with high resolution manometry

    PubMed Central

    Hoffman, Matthew R.; Ciucci, Michelle R.; Mielens, Jason D.; Jiang, Jack J.; McCulloch, Timothy M.

    2012-01-01

    Objective To determine the effect of bolus volume on pharyngeal swallowing using high resolution manometry (HRM). Study design Repeated measures with subjects serving as own controls. Methods Twelve subjects swallowed four bolus volumes in the neutral head position: saliva; 5 ml water; 10 ml water; and 20 ml water. Pressure measurements were taken along the length of the pharynx using a high resolution manometer, with emphasis placed on the velopharynx, tongue base, and upper esophageal sphincter (UES). Variables were analyzed across bolus volumes using three-way repeated measures analysis of co-variance (ANCOVA) investigating the effect of sex, bolus volume, and pharynx length. Pearson’s product moment tests were performed to evaluate how pharyngeal pressure and timing events changed across bolus volume. Results Velopharyngeal duration, maximum tongue base pressure, tongue base pressure rise rate, UES opening duration, and total swallow duration varied significantly across bolus volume. Sex did not have an effect, while pharynx length appeared to affect tongue base pressure duration. Maximum velopharyngeal pressure and minimum UES pressure had a direct relationship with bolus volume, while maximum tongue base pressure had an inverse relationship. Velopharyngeal pressure duration, UES opening duration, and total swallow duration increased as bolus volume increased. Conclusions Differences in pharyngeal pressures and timing of key pressure events were detected across varying bolus volumes. Knowing the relationships between bolus volume and pharyngeal pressure activity can be valuable when diagnosing and treating dysphagic patients. Level of evidence N/A. PMID:21108425

  9. Prediction of final infarct volume on subacute MRI by quantifying cerebral edema in ischemic stroke.

    PubMed

    Tipirneni-Sajja, Aaryani; Christensen, Soren; Straka, Matus; Inoue, Manabu; Lansberg, Maarten G; Mlynash, Michael; Bammer, Roland; Parsons, Mark W; Donnan, Geoffrey A; Davis, Stephen M; Albers, Gregory W

    2016-01-01

    Final infarct volume in stroke trials is assessed on images obtained between 30 and 90 days after stroke onset. Imaging at such delayed timepoints is problematic because patients may be lost to follow-up or die before the scan. Obtaining an early assessment of infarct volume on subacute scans avoids these limitations; however, it overestimates true infarct volume because of edema. The aim of this study was to develop a novel approach to quantify edema so that final infarct volumes can be approximated on subacute scans. We analyzed data from 20 stroke patients (median age, 75 years) who had baseline, subacute (fu5d) and late (fu90d) MRI scans. Edema displaces CSF from sulci and ventricles; therefore, edema volume was estimated as change in CSF volume between baseline and spatially coregistered fu5d ADC maps. The median (interquartile range, IQR) estimated edema volume was 13.3 (7.5-37.7) mL. The fu5d lesion volumes correlated well with fu90d infarct volumes with slope: 1.24. With edema correction, fu5d infarct volumes are in close agreement, slope: 0.97 and strongly correlated with actual fu90d volumes. The median (IQR) difference between actual and predicted infarct volumes was 0.1 (-3.0-5.7) mL. In summary, this novel technique for estimation of edema allows final infarct volume to be predicted from subacute MRI.

  10. Multivariate volume rendering

    SciTech Connect

    Crawfis, R.A.

    1996-03-01

    This paper presents a new technique for representing multivalued data sets defined on an integer lattice. It extends the state-of-the-art in volume rendering to include nonhomogeneous volume representations. That is, volume rendering of materials with very fine detail (e.g. translucent granite) within a voxel. Multivariate volume rendering is achieved by introducing controlled amounts of noise within the volume representation. Varying the local amount of noise within the volume is used to represent a separate scalar variable. The technique can also be used in image synthesis to create more realistic clouds and fog.

  11. Pancreaticoduodenectomy: Volume is not Associated with Outcome within an Academic Health Care System

    PubMed Central

    Schell, Micheal T.; Barcia, Anthony; Spitzer, Austin L.; Harris, Hobart W.

    2008-01-01

    Hypothesis. Smaller and lower-volume hospitals can attain surgical outcomes similar to high-volume centers if they incorporate the expertise and health care pathways of high-volume centers. Setting. The academic tertiary care center, Moffit-Long Hospital (ML); the community-based Mount Zion Hospital (ZION); the San Francisco County General Hospital (SFGH); and the Veterans Affairs Medical Center of San Francisco (VAMC). Patients. 369 patients who underwent pancreaticoduodenectomy between October 1989 and June 2003 at the University of California, San Francisco (UCSF) affiliated hospitals. Interventions. Pancreaticoduodenectomy. Design. Retrospective chart review. To correct for the potentially confounding effect of small case volumes and event rates, data for SFGH, VAMC, and ZION was combined (Small Volume Hospital Group; SVHG) and compared against data for ML. Main Outcome Measures. Complication rates; three-year and five-year survival rates. Results. The average patient age and health, as determined by ASA score, were similar between ML and the SVHG. The postoperative complication rate did not differ significantly between ML and the SVGH (58.8% versus 63.1%). Patients that experienced a complication averaged 2.5 complications in both groups. The perioperative mortality rate was 4% for patients undergoing pancreaticoduodenectomy at either ML or the SVGH. Although the 3-year survival rate for patients with adenocarcinoma of the pancreas was nearly twice as high at ML (31.2% versus 18.3% at SVHG), there was no significant difference in the 5-year survival rates (19% at ML versus 18.3% at SVHG). Conclusions. Low-volume hospitals can achieve similar outcomes to high-volume tertiary care centers provided they import the expertise and care pathways necessary for improved results. PMID:18475317

  12. The volume and energy content of meals as determinants of gastric emptying.

    PubMed Central

    Hunt, J N; Stubbs, D F

    1975-01-01

    1. Results were collected from thirty-three published and unpublished studies of gastric emptying. The volumes of the meals ranged from 50 to 1250 ml., and composition varied from pure carbohydrates to ordinary food. 2. From the published composition of the meals, their nutritive density, as kcal/ml. (4-18 KJ/ml.) was computed: it ranged from zero to 2-3 kcal/ml. 3. The volume of each meal, or test meal, delivered to the duodenum in 30 min was determined, assuming that gastric emptying was exponential. 4. The greater the nutritive density of a meal, the less was the volume transferred to the duodenum in 30 min. The original volume of meal given was not a determinant of the rate of emptying (ml./min). 5. The slowing of gastric emptying with a meal of high nutritive density was not sufficient to prevent an increased rate of delivery of energy to the duodenum (nutritive density times volume delivered in unit time) with a meal of high nutritive density. 6. Assuming an appropriate relationship for the interaction of a stimulus (kcal/ml.) and duodenal receptors, it was possible to predict a rate of gastric emptying for each meal, given its nutritive density. Knowing the initial volume of the meal, it was possible to predict the mean half time for its emptying. 7. There were eight sets of anomalous results: in four the volumes of meal given were less than 200 ml.; explanations of the anomalies in the other four results could not be provided. 8. The results are consistent with equal slowing of gastric emptying by the duodenal action of the products of digestion of isocaloric amounts of fat, protein and carbohydrate, for example, 4 g fat or 9 g carbohydrate, both 36 kcal, taking carbohydrate and protein as 4 kcal/g and fat as 9 kcal/g. PMID:1127608

  13. Discovery of ML314, a Brain Penetrant Nonpeptidic β-Arrestin Biased Agonist of the Neurotensin NTR1 Receptor

    PubMed Central

    2013-01-01

    The neurotensin 1 receptor (NTR1) is an important therapeutic target for a range of disease states including addiction. A high-throughput screening campaign, followed by medicinal chemistry optimization, led to the discovery of a nonpeptidic β-arrestin biased agonist for NTR1. The lead compound, 2-cyclopropyl-6,7-dimethoxy-4-(4-(2-methoxyphenyl)-piperazin-1-yl)quinazoline, 32 (ML314), exhibits full agonist behavior against NTR1 (EC50 = 2.0 μM) in the primary assay and selectivity against NTR2. The effect of 32 is blocked by the NTR1 antagonist SR142948A in a dose-dependent manner. Unlike peptide-based NTR1 agonists, compound 32 has no significant response in a Ca2+ mobilization assay and is thus a biased agonist that activates the β-arrestin pathway rather than the traditional Gq coupled pathway. This bias has distinct biochemical and functional consequences that may lead to physiological advantages. Compound 32 displays good brain penetration in rodents, and studies examining its in vivo properties are underway. PMID:24611085

  14. Determination of optimal collimation parameters for a rotating slat collimator system: a system matrix method using ML-EM

    NASA Astrophysics Data System (ADS)

    Boisson, F.; Bekaert, V.; Brasse, D.

    2016-03-01

    Nowadays, Single Photon imaging has become an essential part of molecular imaging and nuclear medicine. Whether to establish a diagnosis or in the therapeutic monitoring, this modality presents performance that continues to improve. For over 50 years, several collimators have been proposed. Mainly governed by collimation parameters, the resolution-sensitivity trade-off is the factor determining the collimator the most suitable for an intended study. One alternative to the common approaches is the rotating slat collimator (RSC). In the present study, we are aiming at developing a preclinical system equipped with a RSC dedicated to mice and rats imaging, which requires both high sensitivity and spatial resolution. We investigated the resolution-sensitivity trade-offs obtained by varying different collimation parameters: (i) the slats height (H), and (ii) the gap between two consecutive slats (g), considering different intrinsic spatial resolutions. One system matrix was generated for each set of collimation parameters (H,g). Spatial resolutions, Signal-to-Noise Ratio (SNR) and sensitivity obtained for all the set of collimation parameters (H,g) were measured in the 2D projections reconstructed with ML-EM. According to our results, 20 mm high slats and a 1 mm gap were chosen as a good RSC candidate for a preclinical detection module. This collimator will ensure a sensitivity greater than 0.2% and a system spatial resolution below 1 mm, considering an intrinsic spatial resolution below 0.8 mm.

  15. Analysis of the possibility of SysML and BPMN application in formal data acquisition system description

    NASA Astrophysics Data System (ADS)

    Ćwikła, G.; Gwiazda, A.; Banaś, W.; Monica, Z.; Foit, K.

    2017-08-01

    The article presents the study of possible application of selected methods of complex description, that can be used as a support of the Manufacturing Information Acquisition System (MIAS) methodology, describing how to design a data acquisition system, allowing for collecting and processing real-time data on the functioning of a production system, necessary for management of a company. MIAS can allow conversion into Cyber-Physical Production System. MIAS is gathering and pre-processing data on the state of production system, including e.g. realisation of production orders, state of machines, materials and human resources. Systematised approach and model-based development is proposed for improving the quality of the design of MIAS methodology-based complex systems supporting data acquisition in various types of companies. Graphical specification can be the baseline for any model-based development in specified areas. The possibility of application of SysML and BPMN, both being UML-based languages, representing different approaches to modelling of requirements, architecture and implementation of the data acquisition system, as a tools supporting description of required features of MIAS, were considered.

  16. Slip heterogeneity and directivity of the ML 6.0, 2016, Amatrice earthquake estimated with rapid finite-fault inversion

    NASA Astrophysics Data System (ADS)

    Tinti, E.; Scognamiglio, L.; Michelini, A.; Cocco, M.

    2016-10-01

    On 24 August 2016 a magnitude ML 6.0 occurred in the Central Apennines (Italy) between Amatrice and Norcia causing nearly 300 fatalities. The main shock ruptured a NNW-SSE striking, WSW dipping normal fault. We invert waveforms from 26 three-component strong motion accelerometers, filtered between 0.02 and 0.5 Hz, within 45 km from the fault. The inferred slip distribution is heterogeneous and characterized by two shallow slip patches updip and NW from the hypocenter, respectively. The rupture history shows bilateral propagation and a relatively high rupture velocity (3.1 km/s). The imaged rupture history produced evident directivity effects both N-NW and SE of the hypocenter, explaining near-source peak ground motions. Fault dimensions and peak slip values are large for a moderate-magnitude earthquake. The retrieved rupture model fits the recorded ground velocities up to 1 Hz, corroborating the effects of rupture directivity and slip heterogeneity on ground shaking and damage pattern.

  17. Amplification-free point of care immunosensor for detecting type V collagen at a concentration level of ng/ml

    NASA Astrophysics Data System (ADS)

    Chung, Pei-Yu; Bracho-Sanchez, Evelyn R.; Jiang, Peng; Seagrave, JeanClare; Duncan, Matthew R.; Grotendorst, Gary R.; Schultz, Gregory; Batich, Christopher

    2011-06-01

    Point-of-care testing (POCT) is applicable in the immediate vicinity of the patient, where timely diagnosis or prognostic information could help doctors decide the following treatment. Among types of developed POCT, gold nanoparticle based lateral flow strip technology provides advantages such as simple operation, cost-effectiveness, and a user-friendly platform. Therefore, this type of POCT is most likely to be used in battlefields and developing countries. However, conventional lateral flow strips suffer from low detection limits. Although enzyme-linked amplification was demonstrated to improve the detection limit and sensitivity by stronger visible lines or by permitting electrochemical analytical instrumentation, the enzyme labels have potential to cause interference with other enzymes in our body fluids. To eliminate this limitation, we developed an amplification-free gold nanoparticle-based immunosensor applied for detecting collagen type V, which is produced or released abnormally during rejection of lung transplants and sulfur mustard exposure. By using suitable blocking protein to stabilize gold nanoparticles as the reporter probe, a low detection limit of ng/ml was achieved. This strategy is a promising platform for clinical POCT, with potential applications in military or disaster response.

  18. In plastico: laboratory material newness affects growth and reproduction of Daphnia magna reared in 50-ml polypropylene tubes.

    PubMed

    Cuhra, Marek; Bøhn, Thomas; Cuhra, Petr

    2017-04-20

    Plastic laboratory materials are found to affect vital parameters of the waterflea Daphnia magna. The main responsible factor is defined as "newness" of the materials. Juvenile D. magna were raised individually in; a) new laboratory-standard 50 ml polypropylene tubes, and; b) identical tubes which had been washed and aerated for several weeks. Newness had significant effects on growth and fecundity of D. magna. New tubes caused delayed maturation, reduced reproduction and reduced growth when compared to washed and re-used tubes of the same commercial brand. The findings indicate that newness of tubes has inhibiting or toxic effects on D. magna. Often laboratory plastics are intended for single-use due to sterility demands. Newness might be an important confounding factor in research results and should not be disregarded. Disposable plastic utensils may come with a seemingly ignored cost and induce adverse effects in biological test-organisms and systems. The presented findings accentuate continued need for general awareness concerning confounding factors stemming from material laboratory environment. Based on the present findings the authors suggest that plastics intended for use in sensitive research may need to be washed and aerated prior to use.

  19. Expression of benzene dioxygenase from Pseudomonas putida ML2 in cis-1,2-cyclohexanediol-degrading pseudomonads.

    PubMed

    Swift, R J; Carter, S F; Widdowson, D A; Mason, J R; Leak, D J

    2001-06-01

    Benzene dioxygenase (BDO; EC 1.14.12.3) from Pseudomonas putida ML2 dihydroxylates benzene to produce cis-1,2-dihydroxy-cyclohexa-3,5-diene. As well as oxidising benzene and toluene, cell-free extracts of Escherichia coli JM109 expressing recombinant BDO oxidised cyclohexene, 1-methylcyclohexene and 3-methylcyclohexene. In an attempt to construct a novel metabolic pathway for the degradation of cyclohexene (via an initial BDO-mediated dihydroxylation of cyclohexene), cis-1,2-cyclohexanediol-degrading bacteria were isolated by enrichment culture. The bedC1C2BA genes encoding BDO (under the control of the tac promoter) were sub-cloned into pLAFR5, successfully conjugated into seven of the Gram-negative cis-1,2-cyclo-hexanediol-degrading isolates and stably maintained and expressed in three of them. However, despite their ability to grow on cis-1,2-cyclohexanediol as sole carbon source, express an active BDO and oxidise cyclohexene, none of the three strains was able to grow on cyclohexene as sole carbon source. Analysis revealed that BDO oxidised cyclohexene to a mixture of two products, a monohydroxylated (2-cyclohexen-1-ol) product and a dihydroxylated (cis-1,2-cyclohexanediol) product; and failure to grow on cyclohexene was attributed to the toxicity of metabolic intermediates accumulating from the 2-cyclohexen-1-ol metabolism.

  20. A Comparison of ML, WLSMV, and Bayesian Methods for Multilevel Structural Equation Models in Small Samples: A Simulation Study.

    PubMed

    Holtmann, Jana; Koch, Tobias; Lochner, Katharina; Eid, Michael

    2016-01-01

    Multilevel structural equation models are increasingly applied in psychological research. With increasing model complexity, estimation becomes computationally demanding, and small sample sizes pose further challenges on estimation methods relying on asymptotic theory. Recent developments of Bayesian estimation techniques may help to overcome the shortcomings of classical estimation techniques. The use of potentially inaccurate prior information may, however, have detrimental effects, especially in small samples. The present Monte Carlo simulation study compares the statistical performance of classical estimation techniques with Bayesian estimation using different prior specifications for a two-level SEM with either continuous or ordinal indicators. Using two software programs (Mplus and Stan), differential effects of between- and within-level sample sizes on estimation accuracy were investigated. Moreover, it was tested to which extent inaccurate priors may have detrimental effects on parameter estimates in categorical indicator models. For continuous indicators, Bayesian estimation did not show performance advantages over ML. For categorical indicators, Bayesian estimation outperformed WLSMV solely in case of strongly informative accurate priors. Weakly informative inaccurate priors did not deteriorate performance of the Bayesian approach, while strong informative inaccurate priors led to severely biased estimates even with large sample sizes. With diffuse priors, Stan yielded better results than Mplus in terms of parameter estimates.