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Sample records for stairs db marquis

  1. The Marquis de Sade and induced abortion.

    OpenAIRE

    Farr, A D

    1980-01-01

    In 1795 the Marquis de Sade published his La Philosophic dans le boudoir, in which he proposed the use of induced abortion for social reasons and as a means of population control. It is from this time that medical and social acceptance of abortion can be dated, although previously the subject had not been discussed in public in modern times. It is suggested that it was largely due to de Sade's writing that induced abortion received the impetus which resulted in its subsequent spread in wester...

  2. Two puzzles for Marquis's conservative view on abortion.

    Science.gov (United States)

    Card, Robert F

    2006-09-01

    Don Marquis argues that abortion is morally wrong in most cases since it deprives the fetus of the value of its future. I criticize Marquis's argument for the modified conservative view by adopting an argumentative strategy in which I work within his basic account: if it is granted that his fundamental idea is sound, what follows about the morality of abortion? I conclude that Marquis is faced with a dilemma: either his position must shift towards the extreme conservative view on which abortion is never morally permissible, or he must abandon any recognizably conservative view. This dilemma suggests that Marquis's view is either deeply implausible or that he cannot use this argument to successfully support his preferred position.

  3. Elevators or stairs?

    Science.gov (United States)

    Shah, Sachin; O’Byrne, Michael; Wilson, Merne; Wilson, Thomas

    2011-01-01

    Background: Staff in hospitals frequently travel between floors and choose between taking the stairs or elevator. We compared the time savings with these two options. Methods: Four people aged 26–67 years completed 14 trips ranging from one to six floors, both ascending and descending. We compared the amount of time per floor travelled by stairs and by two banks of elevators. Participants reported their fatigue levels using a modified Borg scale. We performed two-way analysis of variance to compare the log-transformed data, with participant and time of day as independent variables. Results: The mean time taken to travel between each floor was 13.1 (standard deviation [SD] 1.7) seconds by stairs and 37.5 (SD 19.0) and 35.6 (SD 23.1) seconds by the two elevators (F = 8.61, p elevator equaled about 15 minutes a day. Self-reported fatigue was less than 13 (out of 20) on the Borg scale for all participants, and they all stated that they were able to continue their duties without resting. The extra time associated with elevator use was because of waiting for its arrival. There was a difference in the amount of time taken to travel by elevator depending on the time of day and day of the week. Interpretation: Taking the stairs rather than the elevator saved about 15 minutes each workday. This 3% savings per workday could translate into improved productivity as well as increased fitness. PMID:22159365

  4. The complete Bible of the Marquis of Santillana

    Directory of Open Access Journals (Sweden)

    Andrés Enrique-Arias

    2017-07-01

    Full Text Available The Bible of the Marquis of Santillana has been partially preserved in two fragments: manuscript BNE MSS/10288, with the Latter Prophets and some Writings, and BNE MSS/9556, with the Gospels and Pauline Epistles. It is assumed that a first volume, now lost, contained the rest of the Bible. By means of detailed textual comparisons and a computational analysis of authorship, we show that the missing parts had been preserved in the codex Escorial I.i.4. Likewise, we offer a reconstruction of the contents of the lost volume along with evidence that the entire Bible was translated from Hebrew and Latin by the Jewish convert to Christianity Martín de Lucena.

  5. Alexandre de Humboldt et le Marquis de Laplace

    Directory of Open Access Journals (Sweden)

    Eberhard Knobloch

    2014-12-01

    Full Text Available Pierre-Simon Marquis de Laplace joua un rôle éminent dans la vie scientifique d’Alexandre de Humboldt. Humboldt avait fait la connaissance du savant français qui avait vingt ans de plus que lui-même à Paris en 1798. L’article de Eberhard Knobloch examine la relation entre ces deux géants de la science en s’appuyant entre autre pour la première fois sur des documents inédits: les quatre lettres de Laplace à Humboldt, le journal d’Humboldt et sur le matériel d’archives conservé aux Archives de l’Académie des Sciences de Berlin-Brandebourg.

  6. Spontaneous abortion and unexpected death: a critical discussion of Marquis on abortion.

    Science.gov (United States)

    Coleman, Mary Clayton

    2013-02-01

    In his classic paper, 'Why abortion is immoral', Don Marquis argues that what makes killing an adult seriously immoral is that it deprives the victim of the valuable future he/she would have otherwise had. Moreover, Marquis contends, because abortion deprives a fetus of the very same thing, aborting a fetus is just as seriously wrong as killing an adult. Marquis' argument has received a great deal of critical attention in the two decades since its publication. Nonetheless, there is a potential challenge to it that seems to have gone unnoticed. A significant percentage of fetuses are lost to spontaneous abortion. Once we bring this fact to our attention, it becomes less clear whether Marquis can use his account of the wrongness of killing to show that abortion is the moral equivalent of murder. In this paper, I explore the relevance of the rate of spontaneous abortion to Marquis' classic anti-abortion argument. I introduce a case I call Unexpected Death in which someone is about to commit murder, but, just as the would-be murderer is about to strike, his would-be victim dies unexpectedly. I then ask: what does Marquis' account of killing imply about the moral status of what the would-be murderer was about to do? I consider four responses Marquis could give to this question, and I examine what implications these responses have for Marquis' strategy of using his account of the wrongness of killing an adult to show that abortion is in the same moral category.

  7. Does a video displaying a stair climbing model increase stair use in a worksite setting?

    Science.gov (United States)

    Van Calster, L; Van Hoecke, A-S; Octaef, A; Boen, F

    2017-08-01

    This study evaluated the effects of improving the visibility of the stairwell and of displaying a video with a stair climbing model on climbing and descending stair use in a worksite setting. Intervention study. Three consecutive one-week intervention phases were implemented: (1) the visibility of the stairs was improved by the attachment of pictograms that indicated the stairwell; (2) a video showing a stair climbing model was sent to the employees by email; and (3) the same video was displayed on a television screen at the point-of-choice (POC) between the stairs and the elevator. The interventions took place in two buildings. The implementation of the interventions varied between these buildings and the sequence was reversed. Improving the visibility of the stairs increased both stair climbing (+6%) and descending stair use (+7%) compared with baseline. Sending the video by email yielded no additional effect on stair use. By contrast, displaying the video at the POC increased stair climbing in both buildings by 12.5% on average. One week after the intervention, the positive effects on stair climbing remained in one of the buildings, but not in the other. These findings suggest that improving the visibility of the stairwell and displaying a stair climbing model on a screen at the POC can result in a short-term increase in both climbing and descending stair use. Copyright © 2017 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

  8. Avoiding the Personhood Issue: Abortion, Identity, and Marquis's 'Future-Like-Ours' Argument.

    Science.gov (United States)

    Reitan, Eric

    2016-05-01

    One reason for the persistent appeal of Don Marquis' 'future like ours' argument (FLO) is that it seems to offer a way to approach the debate about the morality of abortion while sidestepping the difficult task of establishing whether the fetus is a person. This essay argues that in order to satisfactorily address both of the chief objections to FLO - the 'identity objection' and the 'contraception objection' - Marquis must take a controversial stand on what is most essential to being the kind of entity that an adult human being is. Such a stand amounts to a controversial account of personhood. To the extent that FLO's success depends on accepting such a controversial metaphysical view, one apparent attraction of FLO proves illusory. © 2015 John Wiley & Sons Ltd.

  9. Learning from MARQuIS: future direction of quality and safety in hospital care in the European Union

    NARCIS (Netherlands)

    Groene, O.; Klazinga, N.; Walshe, K.; Cucic, C.; Shaw, C.D.; Suñol, R.

    2009-01-01

    This article summarises the significant lessons to be drawn from, and the policy implications of, the findings of the Methods of Assessing Response to Quality Improvement Strategies (MARQuIS) project-a part of the suite of research projects intended to support policy established by the European

  10. Use of stairs in a hospital increased by a sign near the stairs or the elevator

    NARCIS (Netherlands)

    Houweling, ST; Stoopendaal, J; Kleefstra, N; Meyboom-de Jong, B; Bilo, HJG

    2005-01-01

    Objective. To investigate whether signs encouraging taking the stairs or discouraging taking the elevator lead to an increasing number of patients taking the stairs instead of the elevator in a hospital. Design. Interventional study. Method. During a period of 6 weeks in the period October-December

  11. Estimating Stair Running Performance Using Inertial Sensors

    Directory of Open Access Journals (Sweden)

    Lauro V. Ojeda

    2017-11-01

    Full Text Available Stair running, both ascending and descending, is a challenging aerobic exercise that many athletes, recreational runners, and soldiers perform during training. Studying biomechanics of stair running over multiple steps has been limited by the practical challenges presented while using optical-based motion tracking systems. We propose using foot-mounted inertial measurement units (IMUs as a solution as they enable unrestricted motion capture in any environment and without need for external references. In particular, this paper presents methods for estimating foot velocity and trajectory during stair running using foot-mounted IMUs. Computational methods leverage the stationary periods occurring during the stance phase and known stair geometry to estimate foot orientation and trajectory, ultimately used to calculate stride metrics. These calculations, applied to human participant stair running data, reveal performance trends through timing, trajectory, energy, and force stride metrics. We present the results of our analysis of experimental data collected on eleven subjects. Overall, we determine that for either ascending or descending, the stance time is the strongest predictor of speed as shown by its high correlation with stride time.

  12. Application of quality improvement strategies in 389 European hospitals: results of the MARQuIS project.

    Science.gov (United States)

    Lombarts, M J M H; Rupp, I; Vallejo, P; Suñol, R; Klazinga, N S

    2009-02-01

    This study was part of the Methods of Assessing Response to Quality Improvement Strategies (MARQuIS) research project investigating the impact of quality improvement strategies on hospital care in various countries of the European Union (EU), in relation to specific needs of cross-border patients. This paper describes how EU hospitals have applied seven quality improvement strategies previously defined by the MARQuIS study: organisational quality management programmes; systems for obtaining patients' views; patient safety systems; audit and internal assessment of clinical standards; clinical and practice guidelines; performance indicators; and external assessment. A web-based questionnaire was used to survey acute care hospitals in eight EU countries. The reported findings were later validated via on-site survey and site visits in a sample of the participating hospitals. Data collection took place from April to August 2006. 389 hospitals participated in the survey; response rates varied per country. All seven quality improvement strategies were widely used in European countries. Activities related to external assessment were the most broadly applied across Europe, and activities related to patient involvement were the least widely implemented. No one country implemented all quality strategies at all hospitals. There were no differences between participating hospitals in western and eastern European countries regarding the application of quality improvement strategies. Implementation varied per country and per quality improvement strategy, leaving considerable scope for progress in quality improvements. The results may contribute to benchmarking activities in European countries, and point to further areas of research to explore the relationship between the application of quality improvement strategies and actual hospital performance.

  13. [Use of stairs in a hospital increased by a sign near the stairs or the elevator].

    Science.gov (United States)

    Houweling, S T; Stoopendaal, J; Kleefstra, N; Meyboom-de Jong, B; Bilo, H J G

    2005-12-24

    To investigate whether signs encouraging taking the stairs or discouraging taking the elevator lead to an increasing number of patients taking the stairs instead of the elevator in a hospital. Interventional study. During a period of 6 weeks in the period October-December 2004, an investigator recorded how many patients took the stairs and how many took the elevator on the first floor of a hospital close to a diabetes outpatient clinic. A baseline measurement was done over a period of 2 weeks and 4 weeks were used for evaluating the effect of 2 different interventions, each lasting 2 weeks. During the first intervention, a sign was hung up near the elevator, which read: 'Exercise is healthy, take the stairs'. During the second intervention the sign read: 'Use of this elevator is exclusively for personnel and persons with restricted mobility'. Staff members and disabled patients were excluded from the study. A total of 2674 movements were counted. Use of the stairs increased statistically significantly during both interventions: from 54.6% to 63.4% during the first intervention and to 70.4% during the second intervention. Signs in a diabetes outpatient clinic that either encouraged the use of the stairs or discouraged the use of the elevator increased the patients' use of the stairs.

  14. Factors affecting stair-ascent patterns in unilateral transfemoral amputees.

    Science.gov (United States)

    Hobara, Hiroaki; Kobayashi, Yoshiyuki; Tominaga, Shuichi; Nakamura, Takashi; Yamasaki, Nobuya; Ogata, Toru

    2013-06-01

    Patterns and ease of stair ambulation influence amputees' level of satisfaction with their rehabilitation, confidence level, and motivation for continued rehabilitation, demonstrating the importance of stair-ascent data for rehabilitation. However, little is known about the determinants of stair-ascent patterns in unilateral transfemoral amputees. To investigate the factors affecting stair-ascent patterns in transfemoral amputees. Cross-sectional survey. Stair-ascent patterns were evaluated using the Stair Assessment Index. We collected Stair Assessment Index data as well as demographic and clinical data (sex, age, height, mass, amputation side, reason for amputation, time since amputation, and residual limb length) from 25 transfemoral amputees. Statistical analyses revealed that age was negatively correlated and time since amputation was positively correlated with Stair Assessment Index. In contrast, height, body mass, and residual limb lengths were not correlated with Stair Assessment Index. The results of this study suggest that in unilateral transfemoral amputee, (1) both age and time since amputation could affect stair-climbing patterns and (2) residual limb length should not be a limiting factor for stair climbing if the transfemoral amputee has a certain minimum residual limb length. Rehabilitation teams should carefully consider nonmodifiable predisposing factors such as age and time since amputation. However, they may be able to carry on stair-ascent rehabilitation for transfemoral amputees disregarding residual limb length (depending on the length).

  15. Study of Movement Speeds Down Stairs

    CERN Document Server

    Hoskins, Bryan L

    2013-01-01

    The Study of Movement Speeds Down Stairs closely examines forty-three unique case studies on movement patterns down stairwells. These studies include observations made during evacuation drills, others made during normal usage, interviews with people after fire evacuations, recommendations made from compiled studies, and detailed results from laboratory studies. The methodology used in each study for calculating density and movement speed, when known, are also presented, and this book identifies an additional seventeen variables linked to altering movement speeds. The Study of Movement Speeds Down Stairs is intended for researchers as a reference guide for evaluating pedestrian evacuation dynamics down stairwells. Practitioners working in a related field may also find this book invaluable.

  16. Control of a stair climbing wheelchair

    Directory of Open Access Journals (Sweden)

    Nor Maniha Abdul Ghani

    2012-08-01

    Full Text Available This paper presents investigations into the control of a stair climbing wheelchair particularly for indoor usage. A virtual wheelchair model is developed using Visual Nastran software and linked with Matlab/Simulink for control purposes. The goals are to have a simple, compact and stable stairs climbing wheelchair in order to complete the ascending and descending tasks. The challenges are to ensure the wheelchair seat always stay at the upright position and to control both the front and rear wheel motors while climbing. PID control is used to provide appropriate torque to both front and rear wheels as well as at to the wheelchair seat during climbing. Results show that the wheelchair movement can be controlled smoothly and the seat maintained at the desired position with the adapted approach.

  17. Comparative Effect of Forward and Backward Stair Climbing on ...

    African Journals Online (AJOL)

    olagbegi

    SUMMARY. Forward stair climbing (FSC) is associated with cardiovascular fitness benefits, but the training effects of backward stair climbing (BSC) have not been reported in the literature. This study compared the effects of 8 weeks of FSC and BSC on the cardiovascular parameters of apparently healthy young adults.

  18. Stair negotiation in women with fibromyalgia: A descriptive correlational study.

    Science.gov (United States)

    Collado-Mateo, Daniel; Domínguez-Muñoz, Francisco J; Olivares, Pedro R; Adsuar, José C; Gusi, Narcis

    2017-10-01

    Walking up and down stairs is a common and important activity of daily living. Women with fibromyalgia often show a reduced ability to perform this task.The objective of this study was to evaluate the test-retest reliability of stair negotiation tasks and to assess the impact of fibromyalgia symptoms on the ability to negotiate stairs.Forty-two women with fibromyalgia participated in this descriptive correlational study. The relevance of the stair negotiation (both walking up and down) was evaluated by assessing its association with the revised version of the fibromyalgia impact questionnaire (FIQ-R) and other health-related variables. Test-retest reliability was also analyzed. The main outcome measures were time spent walking up and down stairs and impact of fibromyalgia, quality of life, number of falls, weight, and lower limb strength and endurance.The intraclass correlation coefficient (ICC) for stair descent was 0.929 whereas that for ascent was 0.972. The score in these tests correlated significantly with the total score for the FIQ-R and the score for many of dimensions and symptoms: that is, physical function, overall impact of fibromyalgia, pain, energy, stiffness, restorative sleep, tenderness, self-perceived balance problems, and sensitivity.Given the importance of the stair negotiation as activity of daily living and the high reliability, both stair ascent and descent tasks may be useful as outcome measures in studies on patients with fibromyalgia.

  19. Comparative Effect of Forward and Backward Stair Climbing on ...

    African Journals Online (AJOL)

    Forward stair climbing (FSC) is associated with cardiovascular fitness benefits, but the training effects of backward stair climbing (BSC) have not been reported in the literature. This study compared the effects of 8 weeks of FSC and BSC on the cardiovascular parameters of apparently healthy young adults. Forty apparently ...

  20. Musical stairs: the impact of audio feedback during stair-climbing physical therapies for children.

    Science.gov (United States)

    Khan, Ajmal; Biddiss, Elaine

    2015-05-01

    Enhanced biofeedback during rehabilitation therapies has the potential to provide a therapeutic environment optimally designed for neuroplasticity. This study investigates the impact of audio feedback on the achievement of a targeted therapeutic goal, namely, use of reciprocal steps. Stair-climbing therapy sessions conducted with and without audio feedback were compared in a randomized AB/BA cross-over study design. Seventeen children, aged 4-7 years, with various diagnoses participated. Reports from the participants, therapists, and a blinded observer were collected to evaluate achievement of the therapeutic goal, motivation and enjoyment during the therapy sessions. Audio feedback resulted in a 5.7% increase (p = 0.007) in reciprocal steps. Levels of participant enjoyment increased significantly (p = 0.031) and motivation was reported by child participants and therapists to be greater when audio feedback was provided. These positive results indicate that audio feedback may influence the achievement of therapeutic goals and promote enjoyment and motivation in young patients engaged in rehabilitation therapies. This study lays the groundwork for future research to determine the long term effects of audio feedback on functional outcomes of therapy. Stair-climbing is an important mobility skill for promoting independence and activities of daily life and is a key component of rehabilitation therapies for physically disabled children. Provision of audio feedback during stair-climbing therapies for young children may increase their achievement of a targeted therapeutic goal (i.e., use of reciprocal steps). Children's motivation and enjoyment of the stair-climbing therapy was enhanced when audio feedback was provided.

  1. The stair-step approach in mathematics

    CERN Document Server

    Sedrakyan, Hayk

    2018-01-01

    This book is intended as a teacher’s manual and as an independent-study handbook for students and mathematical competitors. Based on a traditional teaching philosophy and a non-traditional writing approach (the stair-step method), this book consists of new problems with solutions created by the authors. The main idea of this approach is to start from relatively easy problems and “step-by-step” increase the level of difficulty toward effectively maximizing students' learning potential. In addition to providing solutions, a separate table of answers is also given at the end of the book. A broad view of mathematics is covered, well beyond the typical elementary level, by providing more in depth treatment of Geometry and Trigonometry, Number Theory, Algebra, Calculus, and Combinatorics.

  2. Boosting workplace stair utilization: a study of incremental reinforcement.

    Science.gov (United States)

    Schumacher, Joseph E; Utley, Janice; Sutton, Lindsay; Horton, Trudi; Hamer, Trey; You, Zhiying; Klapow, Joshua C

    2013-02-01

    This study was designed to determine whether engagement in stair taking can be increased in a worksite setting through the provision of an employer-sponsored, behavior-based incentive system in which employees (members) accumulate points that can be redeemed for merchandise. ChipRewards implemented stair utilization in one employer as a part of a larger health incentive engagement program. Using an AB (baseline-intervention) design, members (N = 216) were observed for 6 months (6.17.10 to 12.14.10 or 129 weekdays after excluding 52 weekend days) before the intervention (baseline) and after 6 months (1.1.11 to 6.30.11 with the same number of weekdays) of implementation. Members were 84% female, 51% Caucasian, 48% African American, 3% Hispanic, and 45 years average age. The number of total stair transactions for all members for all days monitored increased from 5,070 to 38,900, and the average number of stair transactions per day rose from 39 to 301, representing over a 600% increase. The overall cost of incentives for stair utilization was $3,739.30 or $17.55 per member on average. This study supports that stair usage in the workplace is a viable way to increase physical activity. This study adds to existing research that attempted to increase stair utilization through promotion only by adding a behavioral reinforcement strategy. Finally, this study demonstrates that a physical activity among employees at the worksite can be increased with minimal relative cost.

  3. Effect of dual task type on gait and dynamic stability during stair negotiation at different inclinations

    NARCIS (Netherlands)

    Madehkhaksar, F.; Egges, J.

    Stair gait is a common daily activity with great potential risk for falls. Stairs have varying inclinations and people may perform other tasks concurrently with stair gait. This study investigated dual-task interference in the context of complex gait tasks, such as stair gait at different

  4. Reliable Stair Climbing in the Simple Hexapod 'RHex'

    National Research Council Canada - National Science Library

    Moore, E. Z; Campbell, D; Grimminger, F; Buehler, M

    2002-01-01

    RHex is a hexapod with compliant legs and only six actuated degrees of freedom. Its ability to traverse highly fractured and unstable terrain, as well ascend and descend a particular flight of stairs has already been documented...

  5. Stair Descent in the Simple Hexapod ’RHex’

    Science.gov (United States)

    2003-01-01

    robots that successfully do so. Notable exceptions are the Honda bipeds - P2, P3 and Asimo, and Raibert’s tethered biped , yet no specific publications...Stair Descent in the Simple Hexapod ‘RHex’ D. Campbell and M. Buehler dcampb@cim.mcgill.ca, buehler@cim.mcgill.ca, Ambulatory Robotics ...first controller that allows our small hexapod robot , RHex, to descend a wide variety of regular sized, “real-world” stairs. After selecting one of

  6. Research on Dynamics and Stability in the Stairs-Climbing of a Tracked Mobile Robot

    Directory of Open Access Journals (Sweden)

    Weijun Tao

    2012-10-01

    Full Text Available Aiming at the functional requirement of climbing up the stairs, the dynamics and stability during a tracked mobile robot's climbing of stairs is studied. First, from the analysis of its cross-country performance, the mechanical structure of the tracked mobile robot is designed and the hardware composition of its control system is given. Second, based on the analysis to its stairs-climbing process, the dynamical model of stairs-climbing is established by using the classical mechanics method. Next, the stability conditions for its stairs-climbing are determined and an evaluation method of its stairs-climbing stability is proposed, based on a mechanics analysis on the robot's backwards tumbling during the stairs-climbing process. Through simulation and experiments, the effectiveness of the dynamical model and the stability evaluation method of the tracked mobile robot in stairs-climbing is verified, which can provide design and analysis foundations for the tracked mobile robots' stairs-climbing.

  7. Ground reaction forces and frictional demands during stair descent: effects of age and illumination.

    Science.gov (United States)

    Christina, Kathryn A; Cavanagh, Peter R

    2002-04-01

    Stair descent is an inherently risky and demanding task that older adults often encounter in everyday life. It is believed that slip between the foot or shoe sole and the stair surface may play a role in stair related falls, however, there are no reports on slip resistance requirements for stair descent. The aim of this study was to determine the required coefficient of friction (RCOF) necessary for safe stair descent in 12 young and 12 older adults, under varied illuminance conditions. The RCOF during stair descent was found to be comparable in magnitude and time to that for overground walking, and thus, with adequate footwear and dry stair surfaces, friction does not appear to be a major determinant of stair safety. Illuminance level had little effect on the dependent variables quantified in this study. However, the older participants demonstrated safer strategies than the young during stair descent, as reflected by differences in the ground reaction forces and lower RCOF.

  8. Balance control during stair negotiation in older adults.

    Science.gov (United States)

    Lee, Heng-Ju; Chou, Li-Shan

    2007-01-01

    Stair negotiation is among the most challenging and hazardous types of locomotion for older people. However, the effect of aging on balance control during stair negotiation has not been investigated. Instantaneous inclination angles between the center of mass (CoM) and center of pressure (CoP) have been reported to detect gait instability effectively in the elderly. The purpose of this study was to compare the CoM-CoP inclination angles between 12 healthy elderly and 13 healthy young adults when performing stair ascent (SA) and descent (SD) on a three-step staircase. Whole body motion data were collected with an eight-camera motion analysis system. Four force plates were mounted on the floor as well as the first two steps to measure ground reaction forces. No significant group differences were detected in any of the temporal-distance gait measures and CoM-CoP inclination angles during SA and SD. Compared to the floor-to-stair transition phase, both groups demonstrated a significantly greater CoM-CoP medial inclination angle while ascending the stairs. However, a significant reduction in medial inclination was only detected in young adults when transferring from SD to level ground walking. Elderly adults were found to demonstrate a significantly greater medial inclination angle during the stair-to-floor transition phase when compared to young adults. Age-related degenerations in the elderly could compromise their ability to regulate body sway during the stair-to-floor transition, which may subsequently increase the risk of falling.

  9. Novel knee joint mechanism of transfemoral prosthesis for stair ascent.

    Science.gov (United States)

    Inoue, Koh; Wada, Takahiro; Harada, Ryuchi; Tachiwana, Shinichi

    2013-06-01

    The stability of a transfemoral prosthesis when walking on flat ground has been established by recent advances in knee joint mechanisms and their control methods. It is, however, difficult for users of a transfemoral prosthesis to ascend stairs. This difficulty is mainly due to insufficient generation of extension moment around the knee joint of the prosthesis to lift the body to the next step on the staircase and prevent any unexpected flexion of the knee joint in the stance phase. Only a prosthesis with an actuator has facilitated stair ascent using a step-over-step gait (1 foot is placed per step). However, its use has issues associated with the durability, cost, maintenance, and usage environment. Therefore, the purpose of this research is to develop a novel knee joint mechanism for a prosthesis that generates an extension moment around the knee joint in the stance phase during stair ascent, without the use of any actuators. The proposed mechanism is based on the knowledge that the ground reaction force increases during the stance phase when the knee flexion occurs. Stair ascent experiments with the prosthesis showed that the proposed prosthesis can realize stair ascent without any undesirable knee flexion. In addition, the prosthesis is able to generate a positive knee joint moment power in the stance phase even without any power source.

  10. Investigating behavioural mimicry in the context of stair/escalator choice.

    Science.gov (United States)

    Webb, Oliver J; Eves, Frank F; Smith, Lee

    2011-05-01

    We investigated whether individuals mimic the stair/escalator choices of preceding pedestrians. Our methodology sought to separate cases where the 'model' and 'follower' were acquaintances or strangers. Natural experiment. Infrared monitors provided a second-by-second log of when pedestrians ascended adjacent stairs/escalators in a mall. Manual timings established that stair climbers spent ≥ 7 s on ascent, during which time they could act as models to following pedestrians. Thus, individuals who mounted the stairs/escalator ≤ 7 s after the previous stair climber were assigned to a 'stair model' condition. A 'no stair model' condition comprised individuals with a gap to the previous stair climber of ≥ 60 s. The stair model condition was subdivided, depending if the gap between model and follower was 1-2 s or 3-7 s. It was hypothesized that the former cohort may know the model. Percentage stair climbing was significantly higher in the 'stair model' versus 'no stair model' condition (odds ratio [OR]= 2.08). Subgroup analyses showed greater effects in the '1-2 s' cohort (OR = 3.33) than the '3-7 s' cohort (OR = 1.39). Individuals appear to mimic the stair/escalator choices of fellow pedestrians, with more modest effects between strangers. People exposed to message prompts at stair/escalator sites are known to take the stairs unprompted in subsequent situations. Our results suggest that these individuals could recruit a second generation of stair climbers via mimicry. Additionally, some of the immediate behavioural effects observed in interventions may be a product of mimicry, rather than a direct effect of the messages themselves. ©2010 The British Psychological Society.

  11. Stair-Walking Performance in Adolescents with Intellectual Disabilities

    Directory of Open Access Journals (Sweden)

    Wann-Yun Shieh

    2016-07-01

    Full Text Available Most individuals with intellectual disabilities (ID demonstrate problems in learning and movement coordination. Consequently, they usually have difficulties in activities such as standing, walking, and stair climbing. To monitor the physical impairments of these children, regular gross motor evaluation is crucial. Straight-line level walking is the most frequently used test of their mobility. However, numerous studies have found that unless the children have multiple disabilities, no significant differences can be found between the children with ID and typically-developed children in this test. Stair climbing presents more challenges than level walking because it is associated with numerous physical factors, including lower extremity strength, cardiopulmonary endurance, vision, balance, and fear of falling. Limited ability in those factors is one of the most vital markers for children with ID. In this paper, we propose a sensor-based approach for measuring stair-walking performance, both upstairs and downstairs, for adolescents with ID. Particularly, we address the problem of sensor calibration to ensure measurement accuracy. In total, 62 participants aged 15 to 21 years, namely 32 typically-developed (TD adolescents, 20 adolescents with ID, and 10 adolescents with multiple disabilities (MD, participated. The experimental results showed that stair-walking is more sensitive than straight-line level walking in capturing gait characteristics for adolescents with ID.

  12. Neuromuscular function during stair descent in meniscectomized patients and controls

    DEFF Research Database (Denmark)

    Thorlund, Jonas Bloch; Roos, Ewa M; Aagaard, Per

    2011-01-01

    The aim of this study was to identify differences in knee range of motion (ROM), movement speed, ground reaction forces (GRF) profile, neuromuscular activity, and muscle coactivation during the transition between stair descent and level walking in meniscectomized patients at high risk of knee...

  13. Mirror, Mirror by the Stairs: The Impact of Mirror Exposure on Stair versus Elevator Use in College Students.

    Science.gov (United States)

    Hodgin, Katie L; Graham, Dan J

    2016-01-01

    Previous research has indicated that self-awareness-inducing mirrors can successfully incite behaviors that align with one's personal values, such as helping others. Other research has found a large discrepancy between the high percentage of young adults who report valuing the healthfulness of physical activity (PA) and the low percentage who actually meet PA participation standards. However, few studies have examined how mirror exposure and both perceived and actual body size influence highly valued PA participation among college students. The present study assessed stair versus elevator use on a western college campus and hypothesized that mirror exposure would increase the more personally healthy transportation method of stair use. In accordance with previous research, it was also hypothesized that males and those with a lower body mass index (BMI) would be more likely to take the stairs, and that body size distorting mirrors would impact the stair-elevator decision. One hundred sixty-seven students (51% male) enrolled in an introductory psychology course were recruited to take a survey about their "transportation choices" at an indoor campus parking garage. Participants were individually exposed to either no mirror, a standard full-length mirror, or a full-length mirror manipulated to make the reflected body size appear either slightly thinner or slightly wider than normal before being asked to go to the fourth floor of the garage for a survey. Participants' choice of floor-climbing method (stairs or elevator) was recorded, and they were administered an Internet-based survey assessing demographic information, BMI, self-awareness, perceived body size, and other variables likely to be associated with stair use. Results from logistic regression analyses revealed that participants who were not exposed to a mirror [odds ratios (OR) = 0.37, 95% CI: 0.14-0.96], males (OR = 0.33, 95% CI: 0.13-0.85), those with lower BMI (OR = 0.84, 95% CI: 0.71-0.99), those

  14. Mastering MariaDB

    CERN Document Server

    Razzoli, Federico

    2014-01-01

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

  15. Instant InnoDB

    CERN Document Server

    Reid, Matt

    2013-01-01

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

  16. Risk and protective factors for falls on stairs in young children: multicentre case-control study.

    Science.gov (United States)

    Kendrick, D; Zou, K; Ablewhite, J; Watson, M; Coupland, C; Kay, B; Hawkins, A; Reading, R

    2016-10-01

    To investigate risk and protective factors for stair falls in children aged children with medically attended stair fall injuries. Controls were matched on age, sex, calendar time and study centre. A total of 610 cases and 2658 controls participated. Cases' most common injuries were bangs on the head (66%), cuts/grazes not requiring stitches (14%) and fractures (12%). Parents of cases were significantly more likely not to have stair gates (adjusted OR (AOR) 2.50, 95% CI 1.90 to 3.29; population attributable fraction (PAF) 21%) or to leave stair gates open (AOR 3.09, 95% CI 2.39 to 4.00; PAF 24%) both compared with having closed stair gates. They were more likely not to have carpeted stairs (AOR 1.52, 95% CI 1.09 to 2.10; PAF 5%) and not to have a landing part-way up their stairs (AOR 1.34, 95% CI 1.08 to 1.65; PAF 18%). They were more likely to consider their stairs unsafe to use (AOR 1.46, 95% CI 1.07 to 1.99; PAF 5%) or to be in need of repair (AOR 1.71, 95% CI 1.16 to 2.50; PAF 5%). Structural factors including having landings part-way up the stairs and keeping stairs in good repair were associated with reduced stair fall injury risk. Family factors including having stair gates, not leaving gates open and having stair carpets were associated with reduced injury risk. If these associations are causal, addressing these factors in housing policy and routine child health promotion could reduce stair fall injuries. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  17. Instant MongoDB

    CERN Document Server

    Nayak, Amol

    2013-01-01

    Get to grips with a new technology, understand what it is and what it can do for you, and then get to work with the most important features and tasks. MongoDB Starter is a fast and practical guide designed to help you start developing high-performance and scalable applications using MongoDB.MongoDB Starter is ideal for developers who are new to MongoDB and who need a no-nonsense guide on how to start working with it. No knowledge of MongoDB is required to follow this book, but some knowledge of C++ would be helpful.

  18. PNRI mutant variety: Freycinetia multi flora 'Golden Stairs'

    International Nuclear Information System (INIS)

    Aurigue, Fernando B.

    2010-01-01

    Ferricyanate multi flora 'Golden Stairs,' with the proposed common name Golden Stairs Ferricyanate, is a chlorophyll mutant of a selected female clone registered by the Philippine Nuclear Research Institute as Nic 2008 Or-67. The new mutant variety was developed by treating stem cuttings with acute gamma radiation from a Cobalt-60 source. It is similar to the original and control plants except for the leaf color. This shows that mutation induction by gamma radiation can alter only one characteristics (e.g., leaf color) without affecting the other good attributes of the plant. Propagation is by shoot-tip cutting, stem cutting and division of the clump or the rhizome. The plant may be used as potted ornamental, landscaping material or source of cut foliage and cut flower for flower arrangements. (author)

  19. A simple model of a Slinky walking down stairs

    Science.gov (United States)

    Hu, Ai-Ping

    2010-01-01

    The motion of a Slinky walking down a set of stairs is modeled by a simple dynamical system with two degrees of freedom undergoing inelastic collisions. Numerical integration of the model's equations of motion shows that the model's behavior is similar to observations of the motion of an actual Slinky. In particular, it is found that the model's motion exhibits a periodic gait, although subject to more restrictive launch conditions than an actual Slinky.

  20. Reliable Stair Climbing in the Simple Hexapod ’RHex’

    Science.gov (United States)

    2002-01-01

    legged robots have successfully climbed stairs – recently the Honda bipeds climbed quasi- statically.6 Raibert built a biped that could hop over...cim.mcgill.ca, fgrimminger@web.de, buehler@cim.mcgill.ca Ambulatory Robotics Laboratory, Centre for Intelligent Machines, McGill University Montreal, Quebec...this paper, we describe an open loop controller that enables our small robot (Length: 51 cm, Width: 20 cm, Height: 12.7 cm. Leg length: 16 cm), to

  1. Amount of balance necessary for the independence of transfer and stair-climbing in stroke inpatients.

    Science.gov (United States)

    Fujita, Takaaki; Sato, Atsushi; Ohashi, Yuji; Nishiyama, Kazutaka; Ohashi, Takuro; Yamane, Kazuhiro; Yamamoto, Yuichi; Tsuchiya, Kenji; Otsuki, Koji; Tozato, Fusae

    2018-05-01

    The purpose of this study was to clarify the amount of balance necessary for the independence of transfer and stair-climbing in stroke patients. This study included 111 stroke inpatients. Simple and multiple regression analyses were conducted to establish the association between the FIM ® instrument scores for transfer or stair-climbing and Berg Balance Scale. Furthermore, receiver operating characteristic curves were used to elucidate the amount of balance necessary for the independence of transfer and stair-climbing. Simple and multiple regression analyses showed that the FIM ® instrument scores for transfer and stair-climbing were strongly associated with Berg Balance Scale. On comparison of the independent and supervision-dependent groups, Berg Balance Scale cut-off values for transfer and stair-climbing were 41/40 and 54/53 points, respectively. On comparison of the independent-supervision and dependent groups, the cut-off values for transfer and stair-climbing were 30/29 and 41/40 points, respectively. The calculated cut-off values indicated the amount of balance necessary for the independence of transfer and stair-climbing, with and without supervision, in stroke patients. Berg Balance Scale has a good discriminatory ability and cut-off values are clinically useful to determine the appropriate independence levels of transfer and stair-climbing in hospital wards. Implications for rehabilitation The Berg Balance Scale's (BBS) strong association with transfer and stair-climbing independence and performance indicates that establishing cut-off values is vitally important for the established use of the BBS clinically. The cut-off values calculated herein accurately demonstrate the level of balance necessary for transfer and stair-climbing independence, with and without supervision, in stroke patients. These criteria should be employed clinically for determining the level of independence for transfer and stair-climbing as well as for setting balance training

  2. Scaling CouchDB

    CERN Document Server

    Holt, Bradley

    2011-01-01

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

  3. dbSNP

    Data.gov (United States)

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

  4. dbVar

    Data.gov (United States)

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

  5. A Concept Of Modification And Simulation Studies Of A Mechatronic Stair Transporter For The Disabled

    Directory of Open Access Journals (Sweden)

    Wudarczyk Sławomir

    2015-12-01

    Full Text Available A numerical model of existing stair climber with its passenger was built and its operation was analysed through simulations. A modification of the stair climber has been developed on a basis of the simulation studies. The modification depends on equipping the device with additional controllable mechanism the function of which is to change the position of the passenger’s centre of gravity. Comparative simulation studies were carried out for the standard version and the modified version of the stair transporter in a system for the dynamic.

  6. Scaling MongoDB

    CERN Document Server

    Chodorow, Kristina

    2011-01-01

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

  7. A common perceptual parameter for stair climbing for children, young and old adults.

    Science.gov (United States)

    Cesari, P; Formenti, F; Olivato, P

    2003-02-01

    In this paper we examine whether a common perceptual parameter is available for guiding old adults, young adults and children in climbing the highest stair mountable in a bipedal fashion. Previous works have shown that the ratio between the height of the stair and the hip height was the body-scaled invariance adopted as information for selecting the highest stair by young adults [Journal of Experimental Psychology: Human Perception and Performance 10 (1984) 683-703] but not by older adults [Journal of Experimental Psychology: Human Perception and Performance 3 (1992) 691-697]. Indeed, for older adults additional bio-mechanical parameters needed to be added to the model due to their decrease in leg strength and flexibility.Up to now, no perceptual invariant has been identified yet for determining the relevant information used for guiding the stair climbing action for normal healthy people. We propose a new parameter as the angle defined by the ratio between the height of the stair and the distance taken from the feet to the top edge of the stair before the initiation of the movement. We show that this angle is the same for children, young adults and older adults despite the different kinematics of the motion, the anthropometrics and the skill ability exhibit by the participants. In summary we show that even when the climbability judgments, based on the simple ratio leg length-stair height, are influenced by differences in age, participants use a common perceptual variable when they are coordinating their stair climbing action.

  8. ProteomicsDB.

    Science.gov (United States)

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

    2018-01-04

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

  9. MongoDB high availability

    CERN Document Server

    Mehrabani, Afshin

    2014-01-01

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

  10. Foot clearance strategy for step-over-step stair climbing in transfemoral amputees.

    Science.gov (United States)

    Hobara, Hiroaki; Kobayashi, Yoshiyuki; Nakamura, Takashi; Yamasaki, Nobuya; Ogata, Toru

    2014-08-01

    Stair ascent is a particularly challenging task for transfemoral amputees. The aim of this clinical note was to describe the kinematic features of foot clearance in transfemoral amputee who can ascend stairs using a step-over-step strategy. The marker trajectories of the first metatarsophalangeal joint (Mt1) and clearance height were measured in two transfemoral amputees who could (TF1) and could not (TF2) climb stairs using a step-over-step strategy. The Mt1 marker trajectories of the TF1 moved backward in the early swing phase, and the trajectory followed an off-centered parabolic arc to achieve a similar clearance height as able-bodied subjects. TF2 could not climb the stairs without tripping in each step. An effective compensatory strategy to avoid tripping during stair climbing may be to use the hip joint for a backward extension and rapid flexion of the prosthetic leg during the early swing phase. The foot clearance strategy in transfemoral amputees who can climb stairs using a step-over-step strategy will help us better understand adaptive prosthetic control and thus develop more effective gait rehabilitation programs. © The International Society for Prosthetics and Orthotics 2013.

  11. Markerless Knee Joint Position Measurement Using Depth Data during Stair Walking

    Directory of Open Access Journals (Sweden)

    Ami Ogawa

    2017-11-01

    Full Text Available Climbing and descending stairs are demanding daily activities, and the monitoring of them may reveal the presence of musculoskeletal diseases at an early stage. A markerless system is needed to monitor such stair walking activity without mentally or physically disturbing the subject. Microsoft Kinect v2 has been used for gait monitoring, as it provides a markerless skeleton tracking function. However, few studies have used this device for stair walking monitoring, and the accuracy of its skeleton tracking function during stair walking has not been evaluated. Moreover, skeleton tracking is not likely to be suitable for estimating body joints during stair walking, as the form of the body is different from what it is when it walks on level surfaces. In this study, a new method of estimating the 3D position of the knee joint was devised that uses the depth data of Kinect v2. The accuracy of this method was compared with that of the skeleton tracking function of Kinect v2 by simultaneously measuring subjects with a 3D motion capture system. The depth data method was found to be more accurate than skeleton tracking. The mean error of the 3D Euclidian distance of the depth data method was 43.2 ± 27.5 mm, while that of the skeleton tracking was 50.4 ± 23.9 mm. This method indicates the possibility of stair walking monitoring for the early discovery of musculoskeletal diseases.

  12. Semantics and technologies in modern design of interior stairs

    Science.gov (United States)

    Kukhta, M.; Sokolov, A.; Pelevin, E.

    2015-10-01

    Use of metal in the design of interior stairs presents new features for shaping, and can be implemented using different technologies. The article discusses the features of design and production technologies of forged metal spiral staircase considering the image semantics based on the historical and cultural heritage. To achieve the objective was applied structural- semantic method (to identify the organization of structure and semantic features of the artistic image), engineering methods (to justify the construction of the object), anthropometry method and ergonomics (to provide usability), methods of comparative analysis (to reveale the features of the way the ladder in different periods of culture). According to the research results are as follows. Was revealed the semantics influence on the design of interior staircase that is based on the World Tree image. Also was suggested rational calculation of steps to ensure the required strength. And finally was presented technology, providing the realization of the artistic image. In the practical part of the work is presented version of forged staircase.

  13. DB2 9 for Developers

    CERN Document Server

    Gunning, Philip K

    2008-01-01

    Written by an "in-the-trenches" consultant, this guide hails the newest version of DB2 as a major release, highlighting the large number of totally new features, most notably the addition of XML capabilities. Packed with the information DB2 developers and administrators need to know when implementing version 9, the discussion covers upgrading from prior releases of DB2, converting relational data to XML data, and how DB2 supports industry standard schemas. With detailed examples and useful scripts, users learn how to develop DB2 XML applications, design an XML database, and tune the

  14. MariaDB cookbook

    CERN Document Server

    Bartholomew, Daniel

    2014-01-01

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

  15. Reliability of electromyography parameters during stair deambulation in patellofemoral pain syndrome

    Directory of Open Access Journals (Sweden)

    Marcella Ferraz Pazzinatto

    2015-06-01

    Full Text Available Reliability is essential to all aspects of the measure, as it shows the quality of the information and allows rational conclusions with regard to the data. There has been controversial results regarding the reliability of electromyographic parameters assessed during stair ascent and descent in individuals with patellofemoral pain syndrome (PFPS. Therefore, this study aims to determine the reliability of time and frequency domain electromyographic parameters on both gestures in women with PFPS. Thirty-one women with PFPS were selected to participate in this study. Data from vastus lateralis and medialis were collected during stair deambulation. The selected parameters were: automatic onset, median frequency bands of low, medium and high frequency. Reliability was determined by intraclass correlation coefficient and the standard error of measurement. The frequency domain variables have shown good reliability, with the stair ascent presenting the best rates. On the other hand, onset has proved to be inconsistent in all measures. Our findings suggest that stair ascent is more reliable than stair descent to evaluate subjects with PFPS in the most cases.

  16. Umbrella Wheel - a stair-climbing and obstacle-handling wheel design concept

    DEFF Research Database (Denmark)

    Iversen, Simon; Jouffroy, Jerome

    This paper proposes a new design for stair-climbing using a wheel that can split into segments and walk up stairs or surmount other obstacles often found where humans traverse, while still being able to retain a perfectly round shape for traveling on smooth ground. Using this change of configurat......This paper proposes a new design for stair-climbing using a wheel that can split into segments and walk up stairs or surmount other obstacles often found where humans traverse, while still being able to retain a perfectly round shape for traveling on smooth ground. Using this change...... of configuration, staircases with a wide range of dimensions can be covered efficiently and safely. The design, named Umbrella Wheel, can consist of as many wheel segments as desired, and as few as two. A smaller or higher number of wheel segments has advantages and disadvantages depending on the specific...... situation. Modeling the trajectory of the wheel when as it ascends or descends stairs is given and the results are analyzed....

  17. Umbrella Wheel - a stair-climbing and obstacle-handling wheel design concept

    DEFF Research Database (Denmark)

    Iversen, Simon; Jouffroy, Jerome

    2017-01-01

    This paper proposes a new design for stair-climbing using a wheel that can split into segments and walk up stairs or surmount other obstacles often found where humans traverse, while still being able to retain a perfectly round shape for traveling on smooth ground. Using this change of configurat......This paper proposes a new design for stair-climbing using a wheel that can split into segments and walk up stairs or surmount other obstacles often found where humans traverse, while still being able to retain a perfectly round shape for traveling on smooth ground. Using this change...... of configuration, staircases with a wide range of dimensions can be covered efficiently and safely. The design, named Umbrella Wheel, can consist of as many wheel segments as desired, and as few as two. A smaller or higher number of wheel segments has advantages and disadvantages depending on the specific...... situation. Modeling the trajectory of the wheel when as it ascends or descends stairs is given and the results are analyzed....

  18. Effects of Descending Stair Walking on Health and Fitness of Elderly Obese Women.

    Science.gov (United States)

    Chen, Trevor C; Hsieh, Chung-Chan; Tseng, Kuo-Wei; Ho, Chih-Chiao; Nosaka, Kazunori

    2017-08-01

    Eccentric exercise training produces positive fitness and health outcomes, but whether this is also the case for descending stair walking (DSW) is unknown. This study investigated the hypothesis that DSW would improve insulin sensitivity, lipid profiles and physical fitness better than ascending stair walking (ASW). Elderly (≥60 yr) obese women were placed to either DSW or ASW group (n = 15 per group). An elevator was used to eliminate ascending stairs for DSW, and descending stairs for ASW. Descending stair walking and ASW were performed twice a week for 12 wk by increasing the repetitions gradually. Overnight fasting blood samples were taken 3 d before the first training session and 4 d after the last training session, and analyzed for insulin sensitivity and lipid profile markers. Resting HR, systolic blood pressure, and diastolic blood pressure, bone mineral density, knee extensor maximal voluntary isometric contraction strength and several functional physical fitness measures were taken before and after the intervention. Average HR during DSW (88.6 ± 7.8 bpm) was lower (P fitness measures showed greater (P health and fitness.

  19. Stairs or escalator? Using theories of persuasion and motivation to facilitate healthy decision making.

    Science.gov (United States)

    Suri, Gaurav; Sheppes, Gal; Leslie, Sara; Gross, James J

    2014-12-01

    To encourage an increase in daily activity, researchers have tried a variety of health-related communications, but with mixed results. In the present research-using the stair escalator choice context-we examined predictions derived from the Heuristic Systematic Model (HSM), Self Determination Theory (SDT), and related theories. Specifically, we tested whether (as predicted by HSM) signs that encourage heuristic processing ("Take the Stairs") would have greatest impact when placed at the stair/escalator point of choice (when processing time is limited), whereas signs that encourage systematic processing ("Will You Take the Stairs?") would have greatest impact when placed at some distance from the point of choice (when processing time is less limited). We also tested whether (as predicted by SDT) messages promoting autonomy would be more likely to result in sustained motivated behavior (i.e., stair taking at subsequent uncued choice points) than messages that use commands. A series of studies involving more than 9,000 pedestrians provided support for these predictions. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

  20. [Ose, Ieva. Livonijas pilu attēli no marķīza Pauluči albuma - Abbildungen der livländischen Burgen im Album des Marquis Paulucci] / Ivar Leimus

    Index Scriptorium Estoniae

    Leimus, Ivar, 1953-

    2011-01-01

    Arvustus: Livonijas pilu attēli no marķīza Pauluči albuma = Abbildungen der livländischen Burgen im Album des Marquis Paulucci. LU Latvijas vēstures institūts; Latvijas Akadēmiska biblioteka. (Rīga, 2008.) Kuramaa, Liivimaa ja Eestimaa pildialbumitest, mis tõenäoliselt on valminud aastatel 1827-1830, mis on nüüd välja antud ühiste kaante vahel. Tekst tõlgitud saksa keelde

  1. RavenDB high performance

    CERN Document Server

    Ritchie, Brian

    2013-01-01

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

  2. Stair evacuation simulation based on cellular automata considering evacuees’ walk preferences

    International Nuclear Information System (INIS)

    Ding Ning; Luh, Peter B.; Zhang Hui; Chen Tao

    2015-01-01

    As a physical model, the cellular automata (CA) model is widely used in many areas, such as stair evacuation. However, existing CA models do not consider evacuees’ walk preferences nor psychological status, and the structure of the basic model is unapplicable for the stair structure. This paper is to improve the stair evacuation simulation by addressing these issues, and a new cellular automata model is established. Several evacuees’ walk preference and how evacuee’s psychology influences their behaviors are introduced into this model. Evacuees’ speeds will be influenced by these features. To validate this simulation, two fire drills held in two high-rise buildings are video-recorded. It is found that the simulation results are similar to the fire drill results. The structure of this model is simple, and it is easy to further develop and utilize in different buildings with various kinds of occupants. (paper)

  3. Using a body sensor network to measure the effect of fatigue on stair climbing performance

    International Nuclear Information System (INIS)

    Bergmann, Jeroen H M; Smith, Ian C H; Mayagoitia, Ruth E

    2012-01-01

    In terms of self-rated health, the most important activities of daily living are those involving mobility. Of these activities stair climbing is regarded as the most strenuous. A loss of stair climbing ability with age is normally associated with a loss of muscle strength and power, while other factors that influence muscle function, such as fatigue, are often not taken into account. So far no research has been published on how long-lasting fatigue affects activities of daily living, despite the fact that it has been repeatedly proven, in laboratory settings, to influence muscle force production over long periods of time. Technological advances in body sensor networks (BSNs) now provide a method to measure performance during complex real-life situations. In this study the use of a BSN was explored to investigate the effects of long-lasting fatigue on stair climbing performance in 20 healthy adults. Stair climbing performance was measured before and after a fatiguing protocol using a BSN. Performance was defined by temporal and spatial parameters. Long-lasting fatigue was successfully induced in all participants using an exercise protocol. The BSN showed that post-exercise fatigue did not influence stair climbing times (p > 0.2) and no meaningful changes in joint angles were found. No effect on overall stair climbing performance was found, despite a clear presence of long-lasting fatigue. This study shows that physiological paradigms can be further explored using BSNs. Ecological validity of lab-based measurements can be increased by combining them with BSNs. (paper)

  4. Braking and propulsive impulses in individuals with patellofemoral pain syndrome when walking up and down stairs

    Directory of Open Access Journals (Sweden)

    Marcelo Camargo Saad

    2014-12-01

    Full Text Available Patellofemoral pain syndrome (PFPS is a prevalent clinical condition and it affects gait behavior. Braking and propulsive impulses are important biomechanical parameters obtained from ground reaction forces (GRF, which combine the amount of force applied over a period of time. The aim of this study was to evaluate these impulses while walking up and down stairs in healthy controls and PFPS individuals. The results did not reveal significant differences in braking and propulsive impulses between groups during these activities. Thus, the painful condition on a simple functional activity was insufficient to change the motor strategy to walking up or down the stairs.

  5. Increased Difficulties in Managing Stairs in Visually Impaired Older Adults: A Community-Based Survey.

    Directory of Open Access Journals (Sweden)

    Chen-Wei Pan

    Full Text Available Managing stairs is a challenging aspect of daily activities of living for older people. We assessed whether older adults with visual impairment (VI have greater difficulties of managing stairs in daily lives.The study was designed as a community-based cross-sectional study based on a Chinese cohort aged 60 years and older in rural China. Visual acuity (VA was measured in both eyes using a retro-illuminated Snellen chart with tumbling-E optotypes. VI (including blindness was defined as presenting VA of worse than 20/60 in either eye. Having any difficulties in managing stairs was self-reported based on a question drawn from the Barthel Index. Information on participants' socioeconomic status, lifestyle-related factors, diseases histories and medication intake was collected using a questionnaire.The Barthel Index, Activities of Daily Living questionnaire was completed by 4597 (99.7% participants including 2218 men and 2379 women. The age of the participants ranged from 60 to 93 years with a mean of 67.6 ± 6.3 years. In age and gender adjusted models, adults with VI had a higher likelihood of having difficulties in managing stairs (odds ratio [OR] = 2.7; 95% confidence interval [CI] 2.0, 3.7 compared with those without. The association of VI with the likelihood of having difficulties in managing stairs was stronger in older adults who lived alone (OR = 3.2; 95%CI 1.8, 4.5 compared with those who lived with other family members (OR = 2.0; 95%CI 1.3, 4.3. Compared with hypertension, diabetes, obesity and cognitive dysfunction, VI had the greatest impact on people's abilities of managing stairs.VI was associated with an increased likelihood of having difficulties in managing stairs, especially in those who lived alone. However, whether the finding could be extrapolated to other populations warrants further studies as different environmental exposures such as illumination and types of stairs may alter the association observed in this study.

  6. A multistage controlled intervention to increase stair climbing at work: effectiveness and process evaluation.

    Science.gov (United States)

    Bellicha, Alice; Kieusseian, Aurélie; Fontvieille, Anne-Marie; Tataranni, Antonio; Copin, Nane; Charreire, Hélène; Oppert, Jean-Michel

    2016-04-11

    Stair climbing helps to accumulate short bouts of physical activity throughout the day as a strategy for attaining recommended physical activity levels. There exists a need for effective long-term stair-climbing interventions that can be transferred to various worksite settings. The aims of this study were: 1) to evaluate short- and long-term effectiveness of a worksite stair-climbing intervention using an objective measurement of stair climbing and a controlled design; and 2) to perform a process evaluation of the intervention. We performed a controlled before-and-after study. The study was conducted in two corporate buildings of the same company located in Paris (France), between September, 2013 and September, 2014. The status of either "intervention site" or "control site" was assigned by the investigators. Participants were on-site employees (intervention site: n = 783; control site: n = 545 at baseline). Two one-month intervention phases using signs (intervention phase 1) and enhancement of stairwell aesthetics (intervention phase 2) were performed. The main outcome was the change in stair climbing, measured with automatic counters and expressed in absolute counts/day/100 employees and percent change compared to baseline. Qualitative outcomes were used to describe the intervention process. Stair climbing significantly increased at the intervention site (+18.7%) but decreased at the control site (-13.3%) during the second intervention phase (difference between sites: +4.6 counts/day/100 employees, p < 0.001). After the intervention and over the long term, stair climbing returned to baseline levels at the intervention site, but a significant difference between sites was found (intervention site vs. control site: +2.9 counts/day/100 employees, p < 0.05). Some important facets of the intervention were implemented as intended but other aspects had to be adapted. The main difficulty reported by the company's staff members lay in matching the internal

  7. Wa-Chair: A concept for development of economical stair-climbing wheelchair

    Science.gov (United States)

    Jyoti Baishya, Nayan; Ogai, Harutoshi

    2018-02-01

    In this paper, a concept for development of cost effective and reliable stair climbing wheelchair is being proposed. Slider-crank mechanism is being used to compensate for any variation in inclination angle of the wheelchair during ascent or descent on stairs. Controlling wheelchair’s inclination angle can reduce risk for the rider as it prevents the wheelchair from toppling. A prototype is being developed to validate proposed mechanism. Proposed mechanism allows rider to view in the direction of progress which adds additional safety to the rider.

  8. Stair Climbing Control for 4-DOF Tracked Vehicle Based on Internal Sensors

    Directory of Open Access Journals (Sweden)

    Daisuke Endo

    2017-01-01

    Full Text Available In search-and-rescue missions, multi-degrees-of-freedom (DOF tracked robots that are equipped with subtracks are commonly used. These types of robots have superior locomotion performance on rough terrain. However, in teleoperated missions, the performance of tracked robots depends largely on the operators’ ability to control every subtrack appropriately. Therefore, an autonomous traversal function can significantly help in the teleoperation of such robots. In this paper, we propose a planning and control method for 4-DOF tracked robots climbing up/down known stairs automatically based on internal sensors. Experimental results obtained using mockup stairs verify the effectiveness of the proposed method.

  9. Kinematic compensations as children reciprocally ascend and descend stairs with unilateral and bilateral solid AFOs.

    Science.gov (United States)

    Nahorniak, M T; Gorton GE3rd; Gannotti, M E; Masso, P D

    1999-07-01

    The aim of this study was to identify the compensations made when a child with normal motor control ascends and descends stairs while wearing a solid AFO. Ten healthy children were asked to ascend and descend stairs with shoes, right and bilateral AFOs. Repeated measures ANOVA identified differences in selected kinematic parameters. Peak-to-peak excursion of pelvic rotation, pelvic obliquity, and hip ab/adduction increased with AFO use (PAFO use (P<0.05). Compensations at the trunk and the pelvis facilitated limb advancement and clearance. This information may be helpful in developing strategies for training patients with motor planning difficulties.

  10. Point-of-Decision Signs and Stair Use in a University Worksite Setting: General Versus Specific Messages.

    Science.gov (United States)

    Eckhardt, Mary R; Kerr, Jacqueline; Taylor, Wendell C

    2015-01-01

    This study tested the effectiveness of two point-of-decision signs to increase stair use and investigated message content by comparing signs with general and specific messages. This study used a quasi-experimental time series design, including a 2-week baseline period: 2 weeks with a general message and 2 weeks with a specific message. The signs were placed in an eight-story university building. The subjects comprised all adults entering the building. During the study, 2997 observations of stair/elevator choice were made. A stair-prompt sign with a general message and a sign with a specific message served as the interventions. Observers measured stair/elevator choice, demographics, and traffic volume. Logistic regression analyses were employed, adjusting for covariates. The specific sign intervention showed significantly increased odds of stair use compared to baseline (odds ratio [OR] = 2.04, 95% confidence interval [CI] = 1.46-2.84). The odds of stair use were also significantly greater with the specific sign than the general sign (OR = 1.57, 95% CI = 1.13-2.20). Only the specific sign significantly increased stair use. The results indicate that a specific message may be more effective at promoting stair use.

  11. 49 CFR 214.519 - Floors, decks, stairs, and ladders of on-track roadway maintenance machines.

    Science.gov (United States)

    2010-10-01

    ... roadway maintenance machines. 214.519 Section 214.519 Transportation Other Regulations Relating to... SAFETY On-Track Roadway Maintenance Machines and Hi-Rail Vehicles § 214.519 Floors, decks, stairs, and ladders of on-track roadway maintenance machines. Floors, decks, stairs, and ladders of on-track roadway...

  12. Do older people with visual impairment and living alone in a rural developing country report greater difficulty in managing stairs?

    Science.gov (United States)

    Hairi, Noran N; Bulgiba, Awang; Peramalah, Devi; Mudla, Izzuna

    2013-01-01

    Managing stairs is a challenging activity of daily living (ADL) for older people. This study aims to examine the association between visual impairment and difficulty in managing stairs among older people living alone and those living with others. A population-based cross sectional study was conducted in rural Malaysia from 2007 till 2008. Seven hundred and sixty five older people aged 60 years and over underwent eye examination for visual impairment. Visual acuity criteria were used to define visual impairment. Presenting visual acuity was assessed using a standard metric Snellen Chart of E type. Difficulty in managing stairs was measured according to a question drawn from the Barthel Index which asks "do you need help in climbing stairs". Overall, the prevalence of difficulty in managing stairs among older people in our population was 135 (18.3%, 95% CI 15.7-21.2). After adjusting for important confounders the odds ratio (OR) for visual impairment and difficulty in managing stairs among older people living alone was 5.04 (95% CI 2.27, 10.62). Among older people living with others, the adjusted OR for visual impairment and difficulty in managing stairs was 3.10 (95% CI 1.52, 6.80). In a sample of older people aged 60 years and over, those living alone with visual impairment had greater difficulty in managing stairs than those living with others. Identification of these groups of older people is useful for targeting interventions. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. Construct Validity and Test-Retest Reliability of the Climbing Stairs Questionnaire in Lower-Limb Amputees

    NARCIS (Netherlands)

    de Laat, Fred A.; Rommers, Gerardus M.; Geertzen, Jan H.; Roorda, Leo D.

    de Laat FA, Rommers GM, Geertzen JH, Roorda LD. Construct validity and test-retest reliability of the Climbing Stairs Questionnaire in lower-limb amputees. Arch Phys Med Rehabil 2010;91:1396-401. Objective: To investigate the construct validity and test-retest reliability of the Climbing Stairs

  14. To Take the Stairs or Not to Take the Stairs? Employing the Reflective–Impulsive Model to Predict Spontaneous Physical Activity

    Directory of Open Access Journals (Sweden)

    Marcos Daou

    2017-09-01

    Full Text Available The reflective–impulsive model (RIM has been employed to explain various health behaviors. The present study used RIM to predict a spontaneous physical activity behavior. Specifically, 107 participants (75 females; Mage = 20.6 years, SD = 1.92 years completed measures of (1 reflections about spontaneous physical activity, as indexed by self-report questionnaire; (2 impulse toward physical activity, as indexed by the manikin task; and (3 (state self-control, as indexed by the Stroop task. The dependent variable was whether participants took the stairs or the elevator to the study laboratory. Results revealed reflections toward spontaneous physical activity positively predicted stair-taking. Further, a significant impulse toward physical activity × self-control interaction was observed. This interaction revealed that participants with high self-control who had a high impulse toward PA were more likely to take the stairs than their counterparts with a low impulse toward PA, whereas the opposite was the case for participants with low self-control. However, the impulse × self-control interaction was not significant when employing a self-report measure of trait self-control. Thus, RIM may be a good framework with which to consider spontaneous physical activity, but careful consideration must be given when examining variables within RIM (e.g., the boundary condition of self-control.

  15. And She's Buying a Stairway to Health: Signs and Participant Factors Influencing Stair Ascent at a Public Airport.

    Science.gov (United States)

    Bellettiere, John; Liles, Sandy; BenPorat, Yael; Bliss, Natasha; Hughes, Suzanne C; Bishop, Brent; Robusto, Kristi; Hovell, Melbourne F

    2017-12-01

    Several studies have demonstrated that point-of-choice prompts modestly increase stair use (i.e., incidental physical activity) in many public places, but evidence of effectiveness in airport settings is weak. Furthermore, evaluating the effects of past physical activity on stair use and on point-of-choice prompts to increase stair use is lacking. The purpose of this study was to evaluate the influence of sign prompts and participant factors including past physical activity on stair ascent in an airport setting. We used a quasi-experimental design, systematically introducing and removing sign prompts daily across 22 days at the San Diego International Airport. Intercept interviewers recruited stair and escalator ascenders (N = 1091; 33.0% interview refusal rate) of the only stairs/escalators providing access to Terminal 1 from the parking lot. A 13-item questionnaire about demographics, physical activity, health behavior, and contextual factors provided data not available in nearly all other stair use studies. We examined the effects of signs and self-reported covariates using multivariable logistic regression analyses, and tested whether physical activity and other covariates modified the intervention effect. Adjusting for all significant covariates, prompts increased the odds of stair use (odds ratio 3.67; p point-of-choice prompts are independent of past physical activity, making them effective interventions for active adults and the higher risk population of inactive adults. Signs can prompt stair use in an airport setting and might be employed at most public stairs to increase rates of incidental physical activity and contribute to overall improvements in population health.

  16. Mycophenolate Mofetil Ameliorates Diabetic Nephropathy in db/db Mice

    Directory of Open Access Journals (Sweden)

    Jung-Woo Seo

    2015-01-01

    Full Text Available Chronic low-grade inflammation is an important factor in the pathogenesis of diabetic complication. Mycophenolate mofetil (MMF has an anti-inflammatory effect, inhibiting lymphocyte proliferation. Previous studies showed attenuation of diabetic nephropathy with MMF, but the underlying mechanisms were unclear. This study aimed to identify the effect of MMF on diabetic nephropathy and investigate its action mechanisms in type 2 diabetic mice model. Eight-week-old db/db and control mice (db/m mice received vehicle or MMF at a dose of 30 mg/kg/day for 12 weeks. MMF-treated diabetic mice showed decreased albuminuria, attenuated mesangial expansion, and profibrotic mRNA expressions despite the high glucose level. The number of infiltrated CD4+ and CD8+ T cells in the kidney was significantly decreased in MMF-treated db/db mice and it resulted in attenuating elevated intrarenal TNF-α and IL-17. The renal chemokines expression and macrophages infiltration were also attenuated by MMF treatment. The decreased expression of glomerular nephrin and WT1 was recovered with MMF treatment. MMF prevented the progression of diabetic nephropathy in db/db mice independent of glycemic control. These results suggest that the effects of MMF in diabetic nephropathy are mediated by CD4+ T cell regulation and related cytokines.

  17. Stair ascent with an innovative microprocessor-controlled exoprosthetic knee joint.

    Science.gov (United States)

    Bellmann, Malte; Schmalz, Thomas; Ludwigs, Eva; Blumentritt, Siegmar

    2012-12-01

    Climbing stairs can pose a major challenge for above-knee amputees as a result of compromised motor performance and limitations to prosthetic design. A new, innovative microprocessor-controlled prosthetic knee joint, the Genium, incorporates a function that allows an above-knee amputee to climb stairs step over step. To execute this function, a number of different sensors and complex switching algorithms were integrated into the prosthetic knee joint. The function is intuitive for the user. A biomechanical study was conducted to assess objective gait measurements and calculate joint kinematics and kinetics as subjects ascended stairs. Results demonstrated that climbing stairs step over step is more biomechanically efficient for an amputee using the Genium prosthetic knee than the previously possible conventional method where the extended prosthesis is trailed as the amputee executes one or two steps at a time. There is a natural amount of stress on the residual musculoskeletal system, and it has been shown that the healthy contralateral side supports the movements of the amputated side. The mechanical power that the healthy contralateral knee joint needs to generate during the extension phase is also reduced. Similarly, there is near normal loading of the hip joint on the amputated side.

  18. Age affects the attentional demands of stair ambulation: evidence from a dual-task approach.

    Science.gov (United States)

    Ojha, Heidi A; Kern, Rebecca W; Lin, Chien-Ho Janice; Winstein, Carolee J

    2009-10-01

    Approximately 75% of all injury-producing falls on steps for people of all ages occur in people 65 years of age and older. Diminished attentional capacity contributes to fall risk in older adults, particularly when task demands are high. The purpose of this study was to compare the attentional demands of ascending and descending a set of stairs (stair ambulation) in older adults and younger adults. This was a nonblinded, prospective, single-site, observational cohort study. Ten older (>65 years of age) and 10 younger (21-33 years of age) adults without disabilities were recruited. A dual-task approach was used for 2 task conditions: the first task was standing and responding verbally to an unanticipated auditory tone as quickly as possible (probe task), and the second task was ascending or descending a set of stairs with the same probe task. A 2-factor (group x task) analysis of variance with repeated measures on task (standing and stair ambulation) was performed for voice response time (VRT). Significance for the analysis was set at Ptask interaction was significant for VRT. Post hoc analyses indicated that during stair ambulation, the VRT for older adults was significantly longer than that for younger adults. For the standing task, the VRTs (X+/-SD) were similar for younger (322+/-65 milliseconds) and older (306+/-22 milliseconds) participants. For stair ascent and descent, the average VRTs were more than 100 milliseconds longer for older participants (493+/-113 and 470+/-127 milliseconds, respectively) than for younger participants (365+/-56 and 356+/-67 milliseconds, respectively). Because of the small sample size and generally fit older group, generalization of findings to older people at risk for falls is not recommended until further research is done. The results demonstrated that although both older and younger adults required similar attentional resources for the standing task, older adults required significantly more resources during stair ambulation. The

  19. Stairs to Skałka. From Iconography of Martyrdom of Bishop Stanislaus

    Directory of Open Access Journals (Sweden)

    Tomasz Węcławowicz

    2003-12-01

    flights of stairs or ladders leading to the gates from the site where the hired assassins mutilate the body of the Saint. Moreover, nearly in every depiction figures can be seen mounting the stairs towards the open gates. These figures as well as stairs or ladders or gates are not to be found in the texts of The Life o f the Saint because painted and graphic renderings have primarily moralizing aim. The archetype of ‘the stairs to Heaven’ is substantiated in the iconography of the Martyrdom as stairs to the church on Skałka. The interpretation of the stairs to Skałka can therefore be resented as follows: L i t e r a l l y , stairs to the gates are indeed stairs leading to the church ‘Na Skałce’. I n a n a l l e g o r i c a l interpretation, they are the Cross of Christ, who enabled the faithful to ascend to Redemption. A typological unity of steps on Jacob’s ladder and the Cross of Christ has frequently been raised in exegesis, and St. Stanislaus appears here, like every martyr, as alter Christus. In a t r o p o l o g i c a l interpretation, ascending stairs indicate aspiring towards perfection through mounting the steps of deeds. I n a n a n a g o g i c interpretation, these stairs lead to the gates of heavenly Jerusalem.

  20. Longitudinal Evaluation of Stair Walking Biomechanics in Patients with ACL Injury.

    Science.gov (United States)

    Lepley, Adam S; Gribble, Phillip A; Thomas, Abbey C; Tevald, Michael A; Sohn, David H; Pietrosimone, Brian G

    2016-01-01

    After anterior cruciate ligament (ACL) injury and reconstruction, abnormal biomechanics during daily tasks may have prominent and detrimental long-term consequences on knee joint health. The purpose of this study was to longitudinally evaluate hip and knee joint biomechanics during stair ascent and descent in patients with acute ACL injury and at return to activity after ACL reconstruction. Twenty individuals with unilateral ACL injury (age, 20.9 ± 4.4 yr; height, 172.4 ± 7.5 cm; mass, 76.2 ± 12.2 kg) that were scheduled to undergo surgical reconstruction were compared with 20 healthy matched controls (age, 21.7 ± 3.7 yr; height, 173.7 ± 9.9 cm; mass, 76.1 ± 19.7 kg). Lower extremity biomechanics were recorded using three-dimensional motion analysis during stair ascent and descent at two testing sessions (before surgery and at approximately 6 months after surgery or when they were allowed to return to unrestricted physical activity). Time between sessions for healthy participants was matched on the basis of the ACL group. Peak sagittal and frontal plane knee and hip joint angles and moments, joint angles at initial contact, and joint excursions across stance phase were evaluated. The ACL-injured limb of patients experienced smaller knee extension moments than the uninjured limb and healthy controls during stair ascent and descent (P ACL reconstruction. During stair ascent, ACL patients experienced more extended knee joint positions and less sagittal plane knee joint excursions, coupled with greater frontal plane hip joint excursions (P ACL injury experience reductions in knee flexion angle and knee extension moments during stair walking. These alterations were observed both before and after reconstruction, suggesting that early gait retraining interventions may be beneficial in these patients.

  1. Performance of women with fibromyalgia in walking up stairs while carrying a load

    Directory of Open Access Journals (Sweden)

    Daniel Collado-Mateo

    2016-02-01

    Full Text Available Background. Fibromyalgia is a chronic disease characterized by widespread pain and other associated symptoms. It has a relevant impact on physical fitness and the ability to perform daily living tasks. The objective of the study was to analyze the step-by-step-performance and the trunk tilt of women with fibromyalgia in the 10-step stair climbing test compared with healthy controls. Methods. A cross-sectional study was carried out. Twelve women suffering from fibromyalgia and eight healthy controls were recruited from a local association. Participants were asked to climb 10 stairs without carrying a load and 10 stairs carrying a load of 5 kg in each hand. Mediolateral trunk tilt was assessed using the “Functional Assessment of Biomechanics (FAB” wireless motion capture device, and the time between steps was assessed via weight-bearing insoles. Results. Trunk tilt in the stair-climbing task carrying a load was significantly higher in women with fibromyalgia when compared to the healthy controls (2.31 (0.63 vs. 1.69 (0.51 respectively. The effect of carrying a load was significantly higher for women with fibromyalgia compared with healthy controls at the intermediate and final part of the task. Discussion. Trunk tilt during stair climbing while carrying a load was higher in women with FM, which could increase the risk of falling. Additionally, women with FM experienced a higher pace slowdown as a consequence of the load, which supports the need of including specific strength and resistance training to physical therapies for this population.

  2. Interface stress in socket/residual limb with transtibial prosthetic suspension systems during locomotion on slopes and stairs.

    Science.gov (United States)

    Eshraghi, Arezoo; Abu Osman, Noor Azuan; Gholizadeh, Hossien; Ali, Sadeeq; Abas, Wan Abu Bakar Wan

    2015-01-01

    This study aimed to compare the effects of different suspension methods on the interface stress inside the prosthetic sockets of transtibial amputees when negotiating ramps and stairs. Three transtibial prostheses, with a pin/lock system, a Seal-In system, and a magnetic suspension system, were created for the participants in a prospective study. Interface stress was measured as the peak pressure by using the F-socket transducers during stairs and ramp negotiation. Twelve individuals with transtibial amputation managed to complete the experiments. During the stair ascent and descent, the greatest peak pressure was observed in the prosthesis with the Seal-In system. The magnetic prosthetic suspension system caused significantly different peak pressure at the anterior proximal region compared with the pin/lock (P = 0.022) and Seal-In (P = 0.001) during the stair ascent. It was also observed during the stair descent and ramp negotiation. The prostheses exhibited varying pressure profiles during the stair and ramp ascent. The prostheses with the pin/lock and magnetic suspension systems exhibited lower peak pressures compared with the Seal-In system. The intrasystem pressure distribution at the anterior and posterior regions of the residual limb was fairly homogenous during the stair and ramp ascent and descent. Nevertheless, the intrasystem pressure mapping revealed a significant difference among the suspension types, particularly at the anterior and posterior sensor sites.

  3. Do lower-extremity joint dynamics change when stair negotiation is initiated with a self-selected comfortable gait speed?

    Science.gov (United States)

    Vallabhajosula, Srikant; Yentes, Jennifer M; Momcilovic, Mira; Blanke, Daniel J; Stergiou, Nicholas

    2012-02-01

    Previous research on the biomechanics of stair negotiation has ignored the effect of the approaching speed. We examined if initiating stair ascent with a comfortable self-selected speed can affect the lower-extremity joint moments and powers as compared to initiating stair ascent directly in front of the stairs. Healthy young adults ascended a custom-built staircase instrumented with force platforms. Kinematics and kinetics data were collected simultaneously for two conditions: starting from farther away and starting in front of the stairs and analyzed at the first and second ipsilateral steps. Results showed that for the first step, participants produced greater peak knee extensor moment, peak hip extensor and flexor moments and peak hip positive power while starting from farther away. Also, for both the conditions combined, participants generated lesser peak ankle plantiflexor, greater peak knee flexor moment, lesser peak ankle negative power and greater peak hip negative power while encountering the first step. These results identify the importance of the starting position in experiments dealing with biomechanics of stair negotiation. Further, these findings have important implications for studying stair ascent characteristics of other populations such as older adults. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. MongoDB and PHP

    CERN Document Server

    Francia, Steve

    2012-01-01

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

  5. Stair locomotion in children with spastic hemiplegia: the impact of three different ankle foot orthosis (AFOs) configurations.

    Science.gov (United States)

    Sienko Thomas, Susan; Buckon, Cathleen E; Jakobson-Huston, Sabrina; Sussman, Michael D; Aiona, Michael D

    2002-10-01

    The purpose of this study was to investigate the impact of three different ankle foot orthoses (AFO) configurations on the function and kinematics of stair locomotion in children with spastic hemiplegia. Nineteen children were evaluated barefoot and with a hinged, posterior leaf spring (PLS) and solid AFO during stair ascent and descent. Stair specific items from the Pediatric Evaluation of Disability Inventory (PEDI) were used to evaluate function, while a motion measurement system was used to evaluate kinematics. The PEDI revealed no significant differences between AFOs and barefoot, although a greater percentage of children were able to keep up with their peers while wearing a hinged AFO. At the ankle, the hinged AFO provided the greatest amount of dorsiflexion during stance. All AFOs reduced plantarflexion in comparison to barefoot. The results of this study indicate that for children with spastic hemiplegia the use of an AFO did not impair stair ambulation.

  6. nanoSTAIR: a new strategic proposal to impulse standardization in nanotechnology research

    International Nuclear Information System (INIS)

    De Ipiña, J M López; Salvi, O; Hazebrouck, B; Jovanovic, A; Carre, F; Saamanen, A; Brouwer, D; Schmitt, M; Martin, S

    2015-01-01

    Nanotechnology is considered one of the key technologies of the 21 st century within Europe and a Key-Enabling Technology (KET) by Horizon 2020. Standardization has been identified in H2020 as one of the innovation-support measures by bridging the gap between research and the market, and helping the fast and easy transfer of research results to the European and international market. The development of new and improved standards requires high quality technical information, creating a fundamental interdependency between the standardization and research communities. In the frame of project nanoSTAIR (GA 319092), the present paper describes the European scenario on research and standardization in nanotechnology and presents a proposal of a European strategy (nanoSTAIR) to impulse direct “pipelines” between research and standardization. In addition, strategic actions focused on integration of standardization in the R and D projects, from the early stages of the design of a future business (Project Proposal), are also described. (paper)

  7. Physiological responses to simulated stair climbing in professional firefighters wearing rubber and leather boots.

    Science.gov (United States)

    Huang, Chun-Jung; Garten, Ryan S; Wade, Chip; Webb, Heather E; Acevedo, Edmund O

    2009-09-01

    No studies have considered whether a firefighter's boots are a factor influencing physiological responses. The purpose of this study was to examine physiological responses to a fire simulation activity (stair climb) in professional firefighters wearing rubber boots (RB) and leather boots (LB). Twelve professional firefighters participated in two counterbalanced simulated firefighter stair climb (SFSC) sessions, one wearing RB and the other wearing LB. Heart rate, oxygen uptake (VO(2)), expiratory ventilation (V(E)), blood lactate (BLa), salivary cortisol (SCORT), and leg strength were assessed prior to and following a SFSC. LB elicited significantly greater SCORT values and knee flexion time to peak torque. Furthermore, RB revealed significantly greater ankle dorsiflexion peak torque after SFSC. BLa was positively related to knee flexion peak torque after SFSC in the RB. Firefighters when wearing the RB may be more effective at resisting fatigue and increase more force production.

  8. nanoSTAIR: a new strategic proposal to impulse standardization in nanotechnology research

    Science.gov (United States)

    López de Ipiña, J. M.; Salvi, O.; Hazebrouck, B.; Jovanovic, A.; Carre, F.; Saamanen, A.; Brouwer, D.; Schmitt, M.; Martin, S.

    2015-05-01

    Nanotechnology is considered one of the key technologies of the 21st century within Europe and a Key-Enabling Technology (KET) by Horizon 2020. Standardization has been identified in H2020 as one of the innovation-support measures by bridging the gap between research and the market, and helping the fast and easy transfer of research results to the European and international market. The development of new and improved standards requires high quality technical information, creating a fundamental interdependency between the standardization and research communities. In the frame of project nanoSTAIR (GA 319092), the present paper describes the European scenario on research and standardization in nanotechnology and presents a proposal of a European strategy (nanoSTAIR) to impulse direct “pipelines” between research and standardization. In addition, strategic actions focused on integration of standardization in the R&D projects, from the early stages of the design of a future business (Project Proposal), are also described.

  9. Stair walking is more energizing than low dose caffeine in sleep deprived young women.

    Science.gov (United States)

    Randolph, Derek D; O'Connor, Patrick J

    2017-05-15

    The acute energizing effect of exercise and caffeine has never been examined in a single study of adults with chronic sleep deprivation but evidence from a study of this type could help individuals choose between these two common alertness-enhancing options. The apriori primary aim of this experiment was to compare the influence of 10-min of low-to-moderate intensity stair walking to the consumption of capsules containing 50mg caffeine or flour (placebo) on feelings of energy in physically active, college female caffeine users with chronic insufficient sleep. Effects on secondary outcomes related to feelings of energy also were assessed. A repeated measures crossover experiment was conducted with 18 college women (18-23years) who reported (i) daily caffeine consumption that was not extreme (40-400mg), (ii) typical leisure time physical activity that was not extreme (at least 2 weekly mild 15-min or longer bouts and no >5 strenuous 15-min or longer bouts), and (iii) sleeping attention (CPT), simple reaction time (SRT), and motivation to complete the cognitive tasks were measured before and after a 10-min exercise condition (20min seated rest followed by 10min of low-to-moderate intensity stair walking) and compared to both a caffeine condition (50mg caffeine capsule followed by 30min of seated rest) and a similar flour (placebo) capsule condition. Condition (exercise, caffeine, placebo)×Time (Baseline, Post-1, Post-2, and for mood Post-3) ANCOVAs (controlling for Condition order) tested the hypothesized effects. Condition×Time interactions showed that stair walking increased POMS-BF vigor at Post-1 compared to both placebo and caffeine. Other interactions were not significant. A brief bout of low-to-moderate intensity stair walking has transient energizing effects that exceed a low dose of caffeine for active young women with chronic insufficient sleep. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Kinematics and kinetics during stair ascent in individuals with Gluteal Tendinopathy.

    Science.gov (United States)

    Allison, Kim; Vicenzino, Bill; Bennell, Kim L; Wrigley, Tim V; Grimaldi, Alison; Hodges, Paul W

    2016-12-01

    Individuals with gluteal tendinopathy commonly report lateral hip pain and disability during stair ascent. This study aimed to compare kinematics and kinetics between individuals with and without gluteal tendinopathy during a step up task. 35 individuals with unilateral gluteal tendinopathy and 35 pain-free controls underwent three-dimensional motion analysis of stance phase during stair ascent. An analysis of covariance was performed to compare hip, pelvis and trunk kinematic and kinetic variables between groups. A K-means cluster analysis was performed to identify subgroups from the entire group (n=70) based on the characteristics of the external hip adduction moment. Finally, a Newcombe-Wilson test was performed to evaluate the relationship between group and cluster codes and a 3×2 ANOVA to investigate the differences in kinematics between groups and cluster codes. Individuals with gluteal tendinopathy exhibited a greater hip adduction moment impulse during stair ascent (ES=0.83), greater internal rotation impulse during the first 50% stance phase (ES=0.63) and greater contralateral trunk lean throughout stance than controls (ranging from ES=0.67-0.93). Three subgroups based on hip adduction moment characteristics were identified. Individuals with GT were 4.5 times more likely to have a hip adduction moment characteristic of a large impulse and greater lateral pelvic translation at heel strike than the subgroup most likely to contain controls. Individuals with GT exhibit greater hip adduction moment impulse and alterations in trunk and pelvic kinematics during stair ascent. Findings provide a basis to consider frontal plane trunk and pelvic control in the management of gluteal tendinopathy. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. The effects of stair gait training using proprioceptive neuromuscular facilitation on stroke patients' dynamic balance ability.

    Science.gov (United States)

    Seo, KyoChul; Park, Seung Hwan; Park, KwangYong

    2015-05-01

    [Purpose] This study aims to examine stroke patients' changes in dynamic balance ability through stair gait training where in proprioceptive neuromuscular facilitation (PNF) was applied. [Subjects and Methods] In total 30 stroke patients participated in this experiment and were randomly and equally allocated to an experimental group and a control group. The experimental group received exercise treatment for 30 min and stair gait training where in PNF was applied for 30 min and the control group received exercise treatment for 30 min and ground gait training where in PNF was applied for 30 min. For the four weeks of the experiment, each group received training three times per week, for 30 min each time. Berg Balance Scale (BBS) values were measured and a time up and go (TUG) test and a functional reach test (FRT) were performed for a comparison before and after the experiment. [Results] According to the result of the stroke patients' balance performance through stair gait training, the BBS and FRT results significantly increased and the TUG test result significantly decreased in the experimental group. On the contrary, BBS and FRT results did not significantly increase and the TUG test result did not significantly decrease in the control group. According to the result of comparing differences between before and after training in each group, there was a significant change in the BBS result of the experimental group only. [Conclusions] In conclusion, the gait training group to which PNF was applied saw improvements in their balance ability, and a good result is expected when neurological disease patients receive stair gait training applying PNF.

  12. The effects of stair gait training using proprioceptive neuromuscular facilitation on stroke patients’ dynamic balance ability

    Science.gov (United States)

    Seo, KyoChul; Park, Seung Hwan; Park, KwangYong

    2015-01-01

    [Purpose] This study aims to examine stroke patients’ changes in dynamic balance ability through stair gait training where in proprioceptive neuromuscular facilitation (PNF) was applied. [Subjects and Methods] In total 30 stroke patients participated in this experiment and were randomly and equally allocated to an experimental group and a control group. The experimental group received exercise treatment for 30 min and stair gait training where in PNF was applied for 30 min and the control group received exercise treatment for 30 min and ground gait training where in PNF was applied for 30 min. For the four weeks of the experiment, each group received training three times per week, for 30 min each time. Berg Balance Scale (BBS) values were measured and a time up and go (TUG) test and a functional reach test (FRT) were performed for a comparison before and after the experiment. [Results] According to the result of the stroke patients’ balance performance through stair gait training, the BBS and FRT results significantly increased and the TUG test result significantly decreased in the experimental group. On the contrary, BBS and FRT results did not significantly increase and the TUG test result did not significantly decrease in the control group. According to the result of comparing differences between before and after training in each group, there was a significant change in the BBS result of the experimental group only. [Conclusions] In conclusion, the gait training group to which PNF was applied saw improvements in their balance ability, and a good result is expected when neurological disease patients receive stair gait training applying PNF. PMID:26157240

  13. Eye Movement Patterns of the Elderly during Stair Descent:Effect of Illumination

    Science.gov (United States)

    Kasahara, Satoko; Okabe, Sonoko; Nakazato, Naoko; Ohno, Yuko

    The relationship between the eye movement pattern during stair descent and illumination was studied in 4 elderly people in comparison with that in 5 young people. The illumination condition was light (85.0±30.9 lx) or dark (0.7±0.3 lx), and data of eye movements were obtained using an eye mark recorder. A flight of 15 steps was used for the experiment, and data on 3 steps in the middle, on which the descent movements were stabilized, were analyzed. The elderly subjects pointed their eyes mostly directly in front in the facial direction regardless of the illumination condition, but the young subjects tended to look down under the light condition. The young subjects are considered to have confirmed the safety of the front by peripheral vision, checked the stepping surface by central vision, and still maintained the upright position without leaning forward during stair descent. The elderly subjects, in contrast, always looked at the visual target by central vision even under the light condition and leaned forward. The range of eye movements was larger vertically than horizontally in both groups, and a characteristic eye movement pattern of repeating a vertical shuttle movement synchronous with descent of each step was observed. Under the dark condition, the young subjects widened the range of vertical eye movements and reduced duration of fixation. The elderly subjects showed no change in the range of eye movements but increased duration of fixation during stair descent. These differences in the eye movements are considered to be compensatory reactions to narrowing of the vertical visual field, reduced dark adaptation, and reduced dynamic visual acuity due to aging. These characteristics of eye movements of the elderly lead to an anteriorly leaned posture and lack of attention to the front during stair descent.

  14. Autonomous motivation is not enough: the role of compensatory health beliefs for the readiness to change stair and elevator use.

    Science.gov (United States)

    Radtke, Theda; Rackow, Pamela

    2014-11-28

    Compensatory health beliefs (CHBs) are beliefs that an unhealthy behavior can be compensated with a healthy behavior. In line with the CHBs model, the aim of this study was twofold. First, the study investigated the relationship between autonomous motivation and CHBs that physical inactivity can be compensated by taking the stairs instead of the elevator. Second, the study focused on the associations between CHBs and readiness to use the stairs more often and stair and elevator use. Thus, a cross-sectional online questionnaire was designed that was filled out by 135 participants. Path analysis showed that individuals with stronger autonomous motivation to use the stairs strongly agreed that sedentary behavior could be compensated by taking the stairs instead of the elevator. Moreover, CHBs were positively related to readiness to change behavior, but not to self-reported stair and elevator use. Even though future research is necessary to replicate these findings, autonomous motivation seems to have a positive impact on CHBs which, in turn, might boost an intended behavior change. Thus, promoting possible compensation of physical inactivity might foster the readiness to change the unhealthy behavior.

  15. Autonomous Motivation Is Not Enough: The Role of Compensatory Health Beliefs for the Readiness to Change Stair and Elevator Use

    Directory of Open Access Journals (Sweden)

    Theda Radtke

    2014-11-01

    Full Text Available Compensatory health beliefs (CHBs are beliefs that an unhealthy behavior can be compensated with a healthy behavior. In line with the CHBs model, the aim of this study was twofold. First, the study investigated the relationship between autonomous motivation and CHBs that physical inactivity can be compensated by taking the stairs instead of the elevator. Second, the study focused on the associations between CHBs and readiness to use the stairs more often and stair and elevator use. Thus, a cross-sectional online questionnaire was designed that was filled out by 135 participants. Path analysis showed that individuals with stronger autonomous motivation to use the stairs strongly agreed that sedentary behavior could be compensated by taking the stairs instead of the elevator. Moreover, CHBs were positively related to readiness to change behavior, but not to self-reported stair and elevator use. Even though future research is necessary to replicate these findings, autonomous motivation seems to have a positive impact on CHBs which, in turn, might boost an intended behavior change. Thus, promoting possible compensation of physical inactivity might foster the readiness to change the unhealthy behavior.

  16. Kinetic comparison of older men and women during walk-to-stair descent transition.

    Science.gov (United States)

    Singhal, Kunal; Kim, Jemin; Casebolt, Jeffrey; Lee, Sangwoo; Han, Ki Hoon; Kwon, Young-Hoo

    2014-09-01

    Stair walking is one of the most challenging tasks for older adults, with women reporting higher incidence of falls. The purpose of this study was to investigate the gender differences in kinetics during stair descent transition. Twenty-eight participants (12 male and 16 female; 68.5 and 69.0 years of mean age, respectively) performed stair descent from level walking in a step-over-step manner at a self-selected speed over a custom-made three-step staircase with embedded force plates. Kinematic and force data were combined using inverse dynamics to generate kinetic data for gender comparison. The top and the first step on the staircase were chosen for analysis. Women showed a higher trail leg peak hip abductor moment (-1.0 Nm/kg), lower trail leg peak knee extensor moment and eccentric power (0.74 Nm/kg and 3.15 W/kg), and lower peak concentric power at trail leg ankle joint (1.29 W/kg) as compared to men (ppredispose women to a higher risk of fall. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Stair negotiation time in community-dwelling older adults: normative values and association with functional decline.

    Science.gov (United States)

    Oh-Park, Mooyeon; Wang, Cuiling; Verghese, Joe

    2011-12-01

    To establish reference values for stair ascent and descent times in community-dwelling, ambulatory older adults, and to examine their predictive validity for functional decline. Longitudinal cohort study. Mean follow-up time was 1.8 years (maximum, 3.2y; total, 857.9 person-years). Community sample. Adults 70 years and older (N=513; mean age, 80.8 ± 5.1y) without disability or dementia. Not applicable. Time to ascend and descend 3 steps measured at baseline. A 14-point disability scale assessed functional status at baseline and at follow-up interviews every 2 to 3 months. Functional decline was defined as an increase in the disability score by 1 point during the follow-up period. The mean±SD stair ascent and descent times for 3 steps were 2.78 ± 1.49 and 2.83 ± 1.61 seconds, respectively. The proportion of self-reported and objective difficulty was higher with longer stair ascent and descent times (PRehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  18. [How to make your own custom cutting guides for both mandibular and fibular stair step osteotomies?

    Science.gov (United States)

    Rem, K; Bosc, R; De Kermadec, H; Hersant, B; Meningaud, J-P

    2017-12-01

    Using tailored cutting guides for osteocutaneous free fibula flap in complex mandibular reconstruction after cancer resection surgery constitutes a substantial improvement. Autonomously conceiving and manufacturing the cutting guides within a plastic surgery department with computer-aided design (CAD) and three-dimensional (3D) printing allows planning more complex osteotomies, such as stair-step osteotomies, in order to achieve more stable internal fixations. For the past three years, we have been producing by ourselves patient-tailored cutting guides using CAD and 3D printing. Osteotomies were virtually planned, making the cutting lines more complex in order to optimize the internal fixation stability. We also printed reconstructed mandible templates and shaped the reconstruction plates on them. We recorded data including manufacturing techniques and surgical outcomes. Eleven consecutive patients were operated on for an oral cavity cancer. For each patient, we planned the fibular and mandibular stair-step osteotomies and we produced tailored cutting guides. In all patients, we achieved to get immediately stable internal fixations and in 10 patients, a complete bone consolidation after 6 months. Autonomously manufacturing surgical cutting guides for mandibular reconstruction by free fibula flap is a significant improvement, regarding ergonomics and precision. Planning stair-step osteotomies to perform complementary internal fixation increases contact surface and congruence between the bone segments, thus improving the reconstructed mandible stability. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  19. Walking and stair climbing abilities in individuals after chronic stroke with and without mental health problem.

    Science.gov (United States)

    Prasomsri, Jaruwan; Jalayondeja, Chutima; Bovonsunthonchai, Sunee; Khemthong, Supalak

    2014-07-01

    To compare muscle strength, balance, walking and stair climbing abilities among individuals after chronic stroke with or without mental health problems; to describe their physiological response after stress stimulation. Subjects who had their first stroke more than one year ago were classified for mental health problems according to the Depression Anxiety Stress Scale-21. Lower extremity muscle strength of the quadriceps and plantar flexors, was measured by dynamometer Balance and walking performance was measured by the Berg Balance Scale (BBS), 10-m walk test and timing of stair climbing. Community participation and spiritual well-being were measured. The physiological response of stress stimulation was assessed by the long stress test protocol of the biofeedback device. Forty-five subjects with chronic stroke aged 40-80 years were grouped by with (n = 25) and without mental health problems (n = 20). Significant differences were found in quadriceps muscle strength, BBS, walking and stair climbing speed, community participation and spiritual well-being between two groups. In the stress stimulus phase, the electromyography and heart rate variability demonstrated significant difference between those with and without stress. Individuals with chronic stroke with mental health problems demonstrated decreased quadriceps muscle strength, balance and locomotor performances.

  20. Kinematic characteristics of anterior cruciate ligament deficient knees with concomitant meniscus deficiency during ascending stairs.

    Science.gov (United States)

    Zhang, Yu; Huang, Wenhan; Ma, Limin; Lin, Zefeng; Huang, Huayang; Xia, Hong

    2017-02-01

    It is commonly believed that a torn ACL or a damaged meniscus may be associated with altered knee joint movements. The purpose of this study was to measure the tibiofemoral kinematics of ACL deficiency with concomitant meniscus deficiency. Unilateral knees of 28 ACL deficient participants were studied while ascending stairs. Among these patients, 6 had isolated ACL injuries (group I), 8 had combined ACL and medial meniscus injuries (group II), 8 had combined ACL and lateral meniscus injuries (group III) and 6 had combined ACL and medial-lateral meniscus injuries (group IV). Both knees were then scanned during a stair climb activity using single fluoroscopic image system. Knee kinematics were measured at 0°, 5°, 10°, 15°, 30° and 60° of flexion during ascending stairs. At 0°, 15° and 30° flexion of the knee, the tibia rotated externally by 13.9 ± 6.1°,13.8 ± 9.5° and 15.9 ± 9.8° in Group I. Group II and III exhibited decreased external rotation from 60° to full extension. Statistical differences were found in 0°, 15°and 30° of flexion for the 2 groups compared with Group I. In general, the tibia showed anterior translation with respect to the femur during ascending stairs. It was further determined that Group III had larger anterior translation compared with Group IV at 0° and 5° of flexion (-6.9 ± 1.7 mm vs. 6.2 ± 11.3 mm, P = 0.041; -9.0 ± 1.8 mm vs. 8.1 ± 13.4 mm, P = 0.044). During ascending stairs the ACL deficient knee with different deficiencies in the meniscus will show significantly different kinematics compared with that of uninjured contralateral knee. Considering the varying effect of meniscus injuries on knee joint kinematics, future studies should concentrate on specific treatment of patients with combined ACL and meniscus injuries to protect the joint from abnormal kinematics and subsequent postoperative degeneration.

  1. Innovative gait robot for the repetitive practice of floor walking and stair climbing up and down in stroke patients

    Science.gov (United States)

    2010-01-01

    Background Stair climbing up and down is an essential part of everyday's mobility. To enable wheelchair-dependent patients the repetitive practice of this task, a novel gait robot, G-EO-Systems (EO, Lat: I walk), based on the end-effector principle, has been designed. The trajectories of the foot plates are freely programmable enabling not only the practice of simulated floor walking but also stair climbing up and down. The article intended to compare lower limb muscle activation patterns of hemiparetic subjects during real floor walking and stairs climbing up, and during the corresponding simulated conditions on the machine, and secondly to demonstrate gait improvement on single case after training on the machine. Methods The muscle activation pattern of seven lower limb muscles of six hemiparetic patients during free and simulated walking on the floor and stair climbing was measured via dynamic electromyography. A non-ambulatory, sub-acute stroke patient additionally trained on the G-EO-Systems every workday for five weeks. Results The muscle activation patterns were comparable during the real and simulated conditions, both on the floor and during stair climbing up. Minor differences, concerning the real and simulated floor walking conditions, were a delayed (prolonged) onset (duration) of the thigh muscle activation on the machine across all subjects. Concerning stair climbing conditions, the shank muscle activation was more phasic and timely correct in selected patients on the device. The severely affected subject regained walking and stair climbing ability. Conclusions The G-EO-Systems is an interesting new option in gait rehabilitation after stroke. The lower limb muscle activation patterns were comparable, a training thus feasible, and the positive case report warrants further clinical studies. PMID:20584307

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    for cerebral glucose hypometabolism and unravel the functionality of cerebral mitochondria in type 2 diabetes mellitus. Acutely isolated cerebral cortical and hippocampal slices of db/db mice were incubated in media containing [U-(13)C]glucose, [1,2-(13)C]acetate or [U-(13)C]β-hydroxybutyrate and tissue...... extracts were analysed by mass spectrometry. Oxygen consumption and ATP synthesis of brain mitochondria of db/db mice were assessed by Seahorse XFe96 and luciferin-luciferase assay, respectively. Glucose hypometabolism was observed for both cerebral cortical and hippocampal slices of db/db mice....... Significant increased metabolism of [1,2-(13)C]acetate and [U-(13)C]β-hydroxybutyrate was observed for hippocampal slices of db/db mice. Furthermore, brain mitochondria of db/db mice exhibited elevated oxygen consumption and ATP synthesis rate. This study provides evidence of several changes in brain energy...

  3. Dicty_cDB: SLA124 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available FP_125701 Acyrthosiphon pisum, Pea Aphid Acyrthosiphon pisum cDNA clone WHAP020_G...AA22DB11 5', mRNA sequence. 202 2e-49 2 CF588057 |CF588057.1 USDA-FP_121200-058 Acyrthosiphon pisum, Pea Aphid...86814 |CN586814.1 USDA-FP_129886 Acyrthosiphon pisum, Pea Aphid Acyrthosiphon pisum cDNA clone WHAP090_B10,

  4. How to monitor and mitigate stair-casing in l1 trend filtering

    OpenAIRE

    Rojas, Cristian R.; Wahlberg, Bo

    2014-01-01

    In this paper we study the estimation of changing trends in time-series using $\\ell_1$ trend filtering. This method generalizes 1D Total Variation (TV) denoising for detection of step changes in means to detecting changes in trends, and it relies on a convex optimization problem for which there are very efficient numerical algorithms. It is known that TV denoising suffers from the so-called stair-case effect, which leads to detecting false change points. The objective of this paper is to show...

  5. Taking the stairs instead: The impact of workplace design standards on health promotion strategies

    Directory of Open Access Journals (Sweden)

    Marian Tye

    2013-01-01

    Full Text Available AbstractBackground Comprehensive health promotion in Western Australia has been conducted from the point of views of policy development, promotion, education and service delivery. Much of this recent work has been focused on supporting workplaces – but there has yet to be any real focus on the design of the actual physical workplace environment from a health promotion perspective. Aims This paper is aimed at highlighting the gap in health promotion knowledge by addressing how the disciplines of architecture and health promotion can work together to challenge the regulations that dictate design practice and ultimately bridge that gap for long-term change. The overarching aim is to undertake further evidenced-based research that will inform best practice in the planning and design of workplaces to reduce sedentary behaviour and increase opportunities for physical activity. Method Within this wide objective this paper focuses in particular on the idea of stairs-versus-lift movement strategies within office buildings. By examining building design guidelines from a health promotion perspective we expose a central dichotomy, where health promotion posters say “Take the stairs instead” whereas the language of building design suggests that the lift is best. Results From a design point of view, the National Codes of Construction (NCC, formally known as the Building Codes of Australia (BCA, the essential technical regulation for all building design and construction, primarily addresses the concepts of ‘egress’ and ‘travel distance’ for escape in the event of fire, and building access in terms of universal access. Additionally, The Property Council of Australia’s Guide to Office Building Quality prioritises lift performance criteria along with the quality and experience of lift use as a major grading factor. There is no provision in either set of standards for staircase quality and experience. Conclusion The stairs, despite being promoted

  6. Perceptual Modification of the Built Environment to Influence Behavior Associated with Physical Activity: Quasi-Experimental Field Studies of a Stair Banister Illusion.

    Science.gov (United States)

    Masters, Rich; Capio, Catherine; Poolton, Jamie; Uiga, Liis

    2018-02-15

    Re-engineering the built environment to influence behaviors associated with physical activity potentially provides an opportunity to promote healthier lifestyles at a population level. Here we present evidence from two quasi-experimental field studies in which we tested a novel, yet deceptively simple, intervention designed to alter perception of, and walking behavior associated with, stairs in an urban area. Our objectives were to examine whether adjusting a stair banister has an influence on perceptions of stair steepness or on walking behavior when approaching the stairs. In study 1, we asked participants (n = 143) to visually estimate the steepness of a set of stairs viewed from the top, when the stair banister was adjusted so that it converged with or diverged from the stairs (± 1.91°) or remained neutral (± 0°). In study 2, the walking behavior of participants (n = 36) was filmed as they approached the stairs to descend, unaware of whether the banister converged, diverged, or was neutral. In study 1, participants estimated the stairs to be steeper if the banister diverged from, rather than converged with, the stairs. The effect was greater when participants were unaware of the adjustment. In study 2, walking speed was significantly slower when the banister diverged from, rather than converged with, the stairs. These findings encourage us to speculate about the potential to economically re-engineer features of the built environment to provide opportunities for action (affordances) that invite physical activity behavior or even promote safer navigation of the environment.

  7. The IRPVM-DB database

    International Nuclear Information System (INIS)

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

    1997-01-01

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

  8. Knee Joint Loads and Surrounding Muscle Forces during Stair Ascent in Patients with Total Knee Replacement

    Science.gov (United States)

    Rasnick, Robert; Standifird, Tyler; Reinbolt, Jeffrey A.; Cates, Harold E.

    2016-01-01

    Total knee replacement (TKR) is commonly used to correct end-stage knee osteoarthritis. Unfortunately, difficulty with stair climbing often persists and prolongs the challenges of TKR patents. Complete understanding of loading at the knee is of great interest in order to aid patient populations, implant manufacturers, rehabilitation, and future healthcare research. Musculoskeletal modeling and simulation approximates joint loading and corresponding muscle forces during a movement. The purpose of this study was to determine if knee joint loadings following TKR are recovered to the level of healthy individuals, and determine the differences in muscle forces causing those loadings. Data from five healthy and five TKR patients were selected for musculoskeletal simulation. Variables of interest included knee joint reaction forces (JRF) and the corresponding muscle forces. A paired samples t-test was used to detect differences between groups for each variable of interest (pknee extension moment and muscle forces during the loading response phase indicates the presence of deficits in TKR in quadriceps muscle force production during stair ascent. This result combined with greater flexor muscle forces resulted in similar compressive JRF during loading response between groups. PMID:27258086

  9. The detailed measurement of foot clearance by young adults during stair descent.

    Science.gov (United States)

    Telonio, A; Blanchet, S; Maganaris, C N; Baltzopoulos, V; McFadyen, B J

    2013-04-26

    Foot clearance is an important variable for understanding safe stair negotiation, but few studies have provided detailed measures of it. This paper presents a new method to calculate minimal shoe clearance during stair descent and compares it to previous literature. Seventeen healthy young subjects descended a five step staircase with step treads of 300 mm and step heights of 188 mm. Kinematic data were collected with an Optotrak system (model 3020) and three non-colinear infrared markers on the feet. Ninety points were digitized on the foot sole prior to data collection using a 6 marker probe and related to the triad of markers on the foot. The foot sole was reconstructed using the Matlab (version 7.0) "meshgrid" function and minimal distance to each step edge was calculated for the heel, toe and foot sole. Results showed significant differences in minimum clearance between sole, heel and toe, with the shoe sole being the closest and the toe the furthest. While the hind foot sole was closest for 69% of the time, the actual minimum clearance point on the sole did vary across subjects and staircase steps. This new method, and the findings on healthy young subjects, can be applied to future studies of other populations and staircase dimensions. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Effect of health-promoting posters placed on the platforms of two train stations in Copenhagen, Denmark, on the choice between taking the stairs or the escalators

    DEFF Research Database (Denmark)

    Iversen, Mette Kathrine; Händel, M N; Nydal Jensen, Eva

    2007-01-01

    OBJECTIVE: The purpose of this study was to determine whether posters placed on the platforms of two train stations in Copenhagen, promoting use of the stairs, would encourage people to use the stairs rather than the adjacent escalator. An additional purpose was to see if the effect...

  11. Getting started with MariaDB

    CERN Document Server

    Bartholomew, Daniel

    2013-01-01

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

  12. CouchDB the definitive guide

    CERN Document Server

    Anderson, J; Slater, Noah

    2010-01-01

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

  13. Association between body composition and stair negotiation ability among individuals >55 years of age: a cross-sectional study

    Directory of Open Access Journals (Sweden)

    Dip RM

    2017-08-01

    Full Text Available Renata Maciulis Dip, Marcos AS Cabrera, Sabrina Ferrari Prato Department of Public Health, Postgraduate Program in Public Health, State University of Londrina (UEL, Londrina, Paraná, Brazil Background: Loss of muscle strength exerts a considerable impact on the quality of life and mortality of older adults. The present household survey study measured body composition and muscle strength with the aim of analyzing the roles of low lean mass, low muscle strength and obesity in stair negotiation ability and the effect of comorbidities on the relationship between body composition and functional capacity.Methods: Body composition was assessed using bioelectrical impedance analysis and muscle strength was assessed with a hand grip dynamometer. The study population comprised individuals >55 years of age from a medium-sized Brazilian municipality. The sample included 451 participants.Results: A total of 368 subjects were interviewed; their ages varied from 56 to 91 years. Among males, low muscle strength was associated with stair negotiation difficulty independent of muscle mass, age and obesity but muscle mass was not. However, when we analyzed comorbidities and body composition jointly, chronic lower limb pain and obesity were independently associated with stair negotiation difficulty but body composition and age were not. Among women, after comorbidities were included into the model, low muscle strength and obesity remained associated with stair negotiation difficulty as chronic lower limb pain and depression. The relationship between muscle function and comorbidities is discussed in this article. Keywords: sarcopenia, obesity, depression, older people

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

    Science.gov (United States)

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

    2012-01-01

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

  15. Dynamic stability control in younger and older adults during stair descent.

    Science.gov (United States)

    Bosse, Iris; Oberländer, Kai Daniel; Savelberg, Hans Hubert; Meijer, Kenneth; Brüggemann, Gert-Peter; Karamanidis, Kiros

    2012-12-01

    The purpose of this study was to examine dynamic stability control in older and younger adults while descending stairs. Thirteen older (aged 64-77 years) and 13 younger (aged 22-29 years) adults descended a staircase at their preferred speed. A motion capture system and three force plates were used to determine locomotion mechanics. Dynamic stability was investigated by using the margin of stability, calculated as the instantaneous difference between anterior boundary of the base of support and extrapolated centre of mass. At the initiation of the single support phase, older adults demonstrated a more negative (pelderly was the higher velocity of the centre of mass (pcontrol the motion of the body's centre of mass while stepping down. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Stair-Step Particle Flux Spectra on the Lunar Surface: Evidence for Nonmonotonic Potentials?

    Science.gov (United States)

    Collier, Michael R.; Newheart, Anastasia; Poppe, Andrew R.; Hills, H. Kent; Farrell, William M.

    2016-01-01

    We present examples of unusual "stair-step" differential flux spectra observed by the Apollo 14 Suprathermal Ion Detector Experiment on the lunar dayside surface in Earth's magnetotail. These spectra exhibit a relatively constant differential flux below some cutoff energy and then drop off precipitously, by about an order of magnitude or more, at higher energies. We propose that these spectra result from photoions accelerated on the lunar dayside by nonmonotonic potentials (i.e.,potentials that do not decay to zero monotonically) and present a model for the expected differential flux. The energy of the cutoff and the magnitude of the differential flux are related to the properties of the local space environment and are consistent with the observed flux spectra. If this interpretation is correct, these surface-based ion observations provide a unique perspective that both complements and enhances the conclusions obtained by remote-sensing orbiter observations on the Moon's exospheric and electrostatic properties.

  17. IBM DB2 97 Advanced Administration Cookbook

    CERN Document Server

    Neagu, Adrian

    2012-01-01

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

  18. Getting started with OrientDB

    CERN Document Server

    Tesoriero, Claudio

    2013-01-01

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

  19. A multi-component stair climbing promotional campaign targeting calorific expenditure for worksites; a quasi-experimental study testing effects on behaviour, attitude and intention

    Directory of Open Access Journals (Sweden)

    Eves Frank F

    2012-06-01

    Full Text Available Abstract Background Accumulation of lifestyle physical activity is a current aim of health promotion, with increased stair climbing one public health target. While the workplace provides an opportunity for regular stair climbing, evidence for effectiveness of point-of-choice interventions is equivocal. This paper reports a new approach to worksite interventions, aimed at changing attitudes and, hence, behaviour. Methods Pre-testing of calorific expenditure messages used structured interviews with members of the public (n = 300. Effects of multi-component campaigns on stair climbing were tested with quasi-experimental, interrupted time-series designs. In one worksite, a main campaign poster outlining the amount of calorific expenditure obtainable from stair climbing and a conventional point-of-choice prompt were used (Poster alone site. In a second worksite, additional messages in the stairwell about calorific expenditure reinforced the main campaign (Poster + Stairwell messages site. The outcome variables were automated observations of stair and lift ascent (28,854 and descent (29,352 at baseline and for three weeks after the intervention was installed. Post-intervention questionnaires for employees at the worksites assessed responses to the campaign (n = 253. Analyses employed Analysis of Variance with follow-up Bonferroni t-tests (message pre-testing, logistic regression of stair ascent and descent (campaign testing, and Bonferroni t-tests and multiple regression (follow-up questionnaire. Results Pre-testing of messages based on calorific expenditure suggested they could motivate stair climbing if believed. The new campaign increased stair climbing, with greater effects at the Poster + Stairwell messages site (OR = 1.52, 95% CI = 1.40-1.66 than Posters alone (OR = 1.24, 95% CI = 1.15-1.34. Follow-up revealed higher agreement with two statements about calorific outcomes of stair climbing in the site where they

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

    Directory of Open Access Journals (Sweden)

    Francesco Faita

    2018-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Mai-Huong Nguyen

    2011-01-01

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

  2. The BIOSIS data base: Evaluation of its indexes and the STRATBLDR, CHEMFILE, STAIRS and DIALOG systems for on-line searching

    Science.gov (United States)

    Nees, M.; Green, H. O.

    1977-01-01

    An IBM-developed program, STAIRS, was selected for performing a search on the BIOSIS file. The evaluation of the hardware and search systems and the strategies used are discussed. The searches are analyzed by type of end user.

  3. The effects of container design and stair climbing on maximal acceptable lift weight, wrist posture, psychophysical, and physiological responses in wafer-handling tasks.

    Science.gov (United States)

    Chung, H C; Wang, M J

    2001-12-01

    Despite the high level of automation in semiconductor manufacturing processes, many manual operations are still involved in the workplace. Due to inadequate human-machine interface design, stairs are frequently used to help operators perform wafer-handling tasks. This study was designed to evaluate the effects of climbing stairs and carrying wafer containers (pods) on psychophysical responses (maximal acceptable weight of lift--MAWL, and ratings of perceived exertion--RPE), physiological responses (oxygen consumption--VO2, and heart rate--HR), and wrist posture (ulnar and radial deviations). Each of 12 subjects (six males and six females) performed six sessions (3 climbing stairs x 2 pods types). The results indicate that climbing stairs had a significant influence on MAWL and VO2 (pJob design implications are discussed.

  4. MongoDB the definitive guide

    CERN Document Server

    Chodorow, Kristina

    2010-01-01

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

  5. A business plan for SylvaDB

    OpenAIRE

    Suárez Sánchez de León, Juan Luis

    2014-01-01

    Pla de negoci i descripció de producte per SylvaDB, un sistema de gestió de base de dades orientada a grafs desenvolupada al CulturePlex Lab, al Canadà. Plan de negocio y descripción de producto para SylvaDB, un sistema de gestión de base de datos orientada a grafos desarrollada en el CulturePlex Lab, en Canadá. A business plan and product description for SylvaDB, a graph database management system developed in the CulturePlex Lab, Canada.

  6. Falling up the stairs: the equivalent of 'bashing it with a bible' for an ACL ganglion cyst of the knee.

    Science.gov (United States)

    Dacombe, Peter Jonathan; Robinson, James

    2012-03-27

    Intra-articular anterior cruciate ligament (ACL) cysts are rare, the pathogenesis remains unknown, with trauma often implicated. Often asymptomatic, incidental MRI findings, 11% produce symptoms such as pain, locking or instability. Treatment of intra-articular ganglia differs from the traditional 'bash it with a bible' mantra for ganglia elsewhere with surgical debridement generally indicated for symptomatic cases. This case report describes a 43-year-old male car mechanic who presented with a symptomatic ACL cyst diagnosed on MRI. While waiting for surgery the patient fell up his stairs at home, causing forced hyperflexion of his knee. After an initial sharp pain, within 24 h the patient experienced complete resolution of symptoms. Postfall MRI showed no evidence of the initial lesion, leading to our conclusion that for this patient, a fall up the stairs was the equivalent of 'bashing it with a bible' for an ACL ganglion cyst of the knee.

  7. Stair-rod dislocation cores acting as one-dimensional charge channels in GaAs nanowires

    Science.gov (United States)

    Bologna, Nicolas; Agrawal, Piyush; Campanini, Marco; Knödler, Moritz; Rossell, Marta D.; Erni, Rolf; Passerone, Daniele

    2018-01-01

    Aberration-corrected scanning transmission electron microscopy and density-functional theory calculations have been used to investigate the atomic and electronic structure of stair-rod dislocations connected via stacking faults in GaAs nanowires. At the apexes, two distinct dislocation cores consisting of single-column pairs of either gallium or arsenic were identified. Ab initio calculations reveal an overall reduction in the energy gap with the development of two bands of filled and empty localized states at the edges of valence and conduction bands in the Ga core and in the As core, respectively. Our results suggest the behavior of stair-rod dislocations along the nanowire as one-dimensional charge channels, which could host free carriers upon appropriate doping.

  8. Single-leg squats identify independent stair negotiation ability in older adults referred for a physiotherapy mobility assessment at a rural hospital.

    Science.gov (United States)

    Hockings, Rowena L; Schmidt, David D; Cheung, Christopher W

    2013-07-01

    To determine whether single-leg squats identify ability to negotiate stairs in older adults at a rural hospital. Cross-sectional analytical study. Acute wards and emergency department of a rural hospital in Australia. A systematic sample of 143 older adults (72 men, 71 women, 80.0 ± 6.8 years) from the emergency department or acute wards of Shoalhaven Hospital referred for a physiotherapy mobility assessment. Ability to complete up to three single-leg squats and negotiate up to three steps were measured. Covariates and demographic variables were collected. The squat test had 86% sensitivity, 100% specificity, 100% positive predictive value, and 49% negative predictive value in correctly identifying stair negotiation ability. Participants who could complete single-leg squats were 57 times more likely to be able to independently negotiate stairs than participants who could not complete squats. Multivariate regression analysis indicated that walker use, pain severity and whether participants lived alone were significant and independent predictors of ability to negotiate stairs independently. Single-leg squats may be an accurate identifier of stair negotiation ability in older adults admitted to the hospital for an acute illness or injury. A traditional stairs assessment would be required if older adults were unable to complete the squat test or had moderate to severe pain, used a walker to ambulate, or did not live alone. The squat test is a potentially more-efficient assessment tool than traditional stair assessments in determining an individual's ability to negotiate stairs and suitability for discharge where poor mobility is a problem. © 2013, Copyright the Authors Journal compilation © 2013, The American Geriatrics Society.

  9. 〈Original Papers〉A Design of Stair-climbing Personal Mobility Robot Based on Inverted Pendulum Mechanism

    OpenAIRE

    友國, 伸保

    2012-01-01

    [synopsis] In this paper, an inverted pendulum type personal mobility robot with virtual wheel is described. The robot enables to climb a stairs only with two virtual wheels consist of one rotary link and two wheels which are attached to the both ends of the rotary link. The mechanical dimensions of the rotary link and tire restrict applicable step size. Therefore these mechanical dimensions are delivered by an analysis based on Building Code.

  10. Development of a Stair-Step Multifrequency Synchronized Excitation Signal for Fast Bioimpedance Spectroscopy

    Science.gov (United States)

    Bian, He; Du, Fangling; Sun, Qiang

    2014-01-01

    Wideband excitation signal with finite prominent harmonic components is desirable for fast bioimpedance spectroscopy (BIS) measurements. This work introduces a simple method to synthesize and realize a type of periodical stair-step multifrequency synchronized (MFS) signal. The Fourier series analysis shows that the p-order MFS signal f(p, t) has constant 81.06% energy distributed equally on its p  2nth primary harmonics. The synthesis principle is described firstly and then two examples of the 4-order and 5-order MFS signals, f(4, t) and f(5, t), are synthesized. The method to implement the MFS waveform based on a field-programmable gate array (FPGA) and a digital to analog converter (DAC) is also presented. Both the number and the frequencies of the expected primary harmonics can be adjusted as needed. An impedance measurement experiment on a RC three-element equivalent model is performed, and results show acceptable precision, which validates the feasibility of the MFS excitation. PMID:24701563

  11. Development of a Stair-Step Multifrequency Synchronized Excitation Signal for Fast Bioimpedance Spectroscopy

    Directory of Open Access Journals (Sweden)

    Yuxiang Yang

    2014-01-01

    Full Text Available Wideband excitation signal with finite prominent harmonic components is desirable for fast bioimpedance spectroscopy (BIS measurements. This work introduces a simple method to synthesize and realize a type of periodical stair-step multifrequency synchronized (MFS signal. The Fourier series analysis shows that the p-order MFS signal f(p,t has constant 81.06% energy distributed equally on its p  2nth primary harmonics. The synthesis principle is described firstly and then two examples of the 4-order and 5-order MFS signals, f(4,t and f(5,t, are synthesized. The method to implement the MFS waveform based on a field-programmable gate array (FPGA and a digital to analog converter (DAC is also presented. Both the number and the frequencies of the expected primary harmonics can be adjusted as needed. An impedance measurement experiment on a RC three-element equivalent model is performed, and results show acceptable precision, which validates the feasibility of the MFS excitation.

  12. Feedback control of the neuromusculoskeletal system in a forward dynamics simulation of stair locomotion.

    Science.gov (United States)

    Selk Ghafari, A; Meghdari, A; Vossoughi, G

    2009-08-01

    The aim of this study is to employ feedback control loops to provide a stable forward dynamics simulation of human movement under repeated position constraint conditions in the environment, particularly during stair climbing. A ten-degrees-of-freedom skeletal model containing 18 Hill-type musculotendon actuators per leg was employed to simulate the model in the sagittal plane. The postural tracking and obstacle avoidance were provided by the proportional-integral-derivative controller according to the modulation of the time rate change of the joint kinematics. The stability of the model was maintained by controlling the velocity of the body's centre of mass according to the desired centre of pressure during locomotion. The parameters of the proposed controller were determined by employing the iterative feedback tuning approach to minimize tracking errors during forward dynamics simulation. Simultaneously, an inverse-dynamics-based optimization was employed to compute a set of desired musculotendon forces in the closed-loop simulation to resolve muscle redundancy. Quantitative comparisons of the simulation results with the experimental measurements and the reference muscles' activities illustrate the accuracy and efficiency of the proposed method during the stable ascending simulation.

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

    Science.gov (United States)

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

    2011-01-01

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

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    (-/-) were studied. In AMPKa2(-/-) resistance arteries, insulin caused vasoconstriction in the presence of PVAT, and AMPKa2(+/+) resistance arteries showed a neutral response. On the other hand, inhibition of the inflammatory kinase Jun NH(2)-terminal kinase (JNK) in db/db PVAT restored insulin...... in muscle, the underlying mechanisms, and how obesity disturbs this vasodilation. Insulin-induced vasoreactivity of resistance arteries was studied with PVAT from C57BL/6 or db/db mice. PVAT weight in muscle was higher in db/db mice compared with C57BL/6 mice. PVAT from C57BL/6 mice uncovered insulin......-induced vasodilation; this vasodilation was abrogated with PVAT from db/db mice. Blocking adiponectin abolished the vasodilator effect of insulin in the presence of C57BL/6 PVAT, and adiponectin secretion was lower in db/db PVAT. To investigate this interaction further, resistance arteries of AMPKa2(+/+) and AMPKa2...

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

    Directory of Open Access Journals (Sweden)

    Mei-Ling Su

    2016-07-01

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

  16. The Marquis de Condorcet goes to Bern

    DEFF Research Database (Denmark)

    Bochsler, Daniel

    2010-01-01

    JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about...

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

    Science.gov (United States)

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

    2016-06-01

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

  18. Electrocortical correlates of human level-ground, slope, and stair walking.

    Directory of Open Access Journals (Sweden)

    Trieu Phat Luu

    Full Text Available This study investigated electrocortical dynamics of human walking across different unconstrained walking conditions (i.e., level ground (LW, ramp ascent (RA, and stair ascent (SA. Non-invasive active-electrode scalp electroencephalography (EEG signals were recorded and a systematic EEG processing method was implemented to reduce artifacts. Source localization combined with independent component analysis and k-means clustering revealed the involvement of four clusters in the brain during the walking tasks: Left and Right Occipital Lobe (LOL, ROL, Posterior Parietal Cortex (PPC, and Central Sensorimotor Cortex (SMC. Results showed that the changes of spectral power in the PPC and SMC clusters were associated with the level of motor task demands. Specifically, we observed α and β suppression at the beginning of the gait cycle in both SA and RA walking (relative to LW in the SMC. Additionally, we observed significant β rebound (synchronization at the initial swing phase of the gait cycle, which may be indicative of active cortical signaling involved in maintaining the current locomotor state. An increase of low γ band power in this cluster was also found in SA walking. In the PPC, the low γ band power increased with the level of task demands (from LW to RA and SA. Additionally, our results provide evidence that electrocortical amplitude modulations (relative to average gait cycle are correlated with the level of difficulty in locomotion tasks. Specifically, the modulations in the PPC shifted to higher frequency bands when the subjects walked in RA and SA conditions. Moreover, low γ modulations in the central sensorimotor area were observed in the LW walking and shifted to lower frequency bands in RA and SA walking. These findings extend our understanding of cortical dynamics of human walking at different level of locomotion task demands and reinforces the growing body of literature supporting a shared-control paradigm between spinal and

  19. Electrocortical correlates of human level-ground, slope, and stair walking.

    Science.gov (United States)

    Luu, Trieu Phat; Brantley, Justin A; Nakagome, Sho; Zhu, Fangshi; Contreras-Vidal, Jose L

    2017-01-01

    This study investigated electrocortical dynamics of human walking across different unconstrained walking conditions (i.e., level ground (LW), ramp ascent (RA), and stair ascent (SA)). Non-invasive active-electrode scalp electroencephalography (EEG) signals were recorded and a systematic EEG processing method was implemented to reduce artifacts. Source localization combined with independent component analysis and k-means clustering revealed the involvement of four clusters in the brain during the walking tasks: Left and Right Occipital Lobe (LOL, ROL), Posterior Parietal Cortex (PPC), and Central Sensorimotor Cortex (SMC). Results showed that the changes of spectral power in the PPC and SMC clusters were associated with the level of motor task demands. Specifically, we observed α and β suppression at the beginning of the gait cycle in both SA and RA walking (relative to LW) in the SMC. Additionally, we observed significant β rebound (synchronization) at the initial swing phase of the gait cycle, which may be indicative of active cortical signaling involved in maintaining the current locomotor state. An increase of low γ band power in this cluster was also found in SA walking. In the PPC, the low γ band power increased with the level of task demands (from LW to RA and SA). Additionally, our results provide evidence that electrocortical amplitude modulations (relative to average gait cycle) are correlated with the level of difficulty in locomotion tasks. Specifically, the modulations in the PPC shifted to higher frequency bands when the subjects walked in RA and SA conditions. Moreover, low γ modulations in the central sensorimotor area were observed in the LW walking and shifted to lower frequency bands in RA and SA walking. These findings extend our understanding of cortical dynamics of human walking at different level of locomotion task demands and reinforces the growing body of literature supporting a shared-control paradigm between spinal and cortical

  20. Timed Stair Climbing is the Single Strongest Predictor of Perioperative Complications in Patients Undergoing Abdominal Surgery

    Science.gov (United States)

    Reddy, Sushanth; Contreras, Carlo M; Singletary, Brandon; Bradford, T Miller; Waldrop, Mary G; Mims, Andrew H; Smedley, W Andrew; Swords, Jacob A; Thomas N, Wang; Martin J, Heslin

    2016-01-01

    Background Current methods to predict patients' peri-operative morbidity utilize complex algorithms with multiple clinical variables focusing primarily on organ-specific compromise. The aim of the present study is to determine the value of a timed stair climb (SC) in predicting peri-operative complications for patients undergoing abdominal surgery. Study Design From March 2014 to July 2015, 362 patients attempted SC while being timed prior to undergoing elective abdominal surgery. Vital signs were measured before and after SC. Ninety day post-operative complications were assessed by the Accordion Severity Grading System. The prognostic value of SC was compared to the ACS NSQIP risk calculator. Results A total of 264 (97.4%) patients were able to complete SC. SC time directly correlated to changes in both mean arterial pressure and heart rate as an indicator of stress. An Accordion grade 2 or higher complication occurred in 84 (25%) patients. There were 8 mortalities (2.4%). Patients with slower SC times had an increased complication rate (P<0.0001). In multivariable analysis SC time was the single strongest predictor of complications (OR=1.029, P<0.0001), and no other clinical co-morbidity reached statistical significance. Receiver operative characteristic curves predicting post-operative morbidity by SC time was superior to that of the ACS risk calculator (AUC 0.81 vs. 0.62, P<0.0001). Additionally slower patients had a greater deviation from predicted length of hospital stay (P=0.034) Conclusions SC provides measurable stress, accurately predicts post-operative complications, and is easy to administer in patients undergoing abdominal surgery. Larger patient populations with a diverse group of operations will be needed to further validate the use of SC in risk prediction models. PMID:26920993

  1. Stairs instead of elevators at the workplace decreases PCSK9 levels in a healthy population.

    Science.gov (United States)

    Kamani, Christel H; Gencer, Baris; Montecucco, Fabrizio; Courvoisier, Delphine; Vuilleumier, Nicolas; Meyer, Philippe; Mach, François

    2015-10-01

    Regular physical activity is recommended to lower low-density lipoprotein cholesterol (LDL-C) in a healthy population. Inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9) was shown to reduce (LDL-C) levels; however, the impact of physical exercise on PCSK9 levels remains unclear. We used data from 67 healthy hospital employees who participated in a 6-month intervention promoting active use of stairs instead of elevators during 3 months, followed by 3 months without recommendation. We confirmed the degree of physical activity with estimated aerobic capacity (VO2 max ) and measured serum PCSK9 levels at baseline, 3 and 6 month. Using a multilevel regression model, we analysed changes of PCSK9 levels over time adjusting for age, gender, aerobic capacity, baseline LDL-C, and LDL-C and body mass index (BMI) changes. At baseline, PCSK9 levels were associated with higher aerobic capacity (P-value = 0·024). At 3 months, we observed a significant decrease in mean PCSK9 levels from 403·6 to 324·3 ng/mL (P-value = 0·001), as well a significant decrease in mean LDL-C levels from 3·5 to 3·3 mM (P-value = 0·01). During this period, mean aerobic capacity (VO2 max ) increased from 37·0 to 40·4 mL/kg/min (P-value < 0·001). Physical activity was independently associated with a decrease in PCSK9 levels after adjustment for age, gender, baseline aerobic capacity, and LDL-C and BMI changes. Daily physical activity at the work place is independently associated with a decrease in PCSK9 levels over time. © 2015 Stichting European Society for Clinical Investigation Journal Foundation.

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

    Directory of Open Access Journals (Sweden)

    Shudong Wang

    2017-03-01

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

  3. The effects of hip external rotator exercises and toe-spread exercises on lower extremity muscle activities during stair-walking in subjects with pronated foot.

    Science.gov (United States)

    Goo, Young-Mi; Kim, Da-Yeon; Kim, Tae-Ho

    2016-03-01

    [Purpose] The purpose of the present study was to examine the effects of toe-spread (TS) exercises and hip external rotator strengthening exercises for pronated feet on lower extremity muscle activities during stair-walking. [Subjects and Methods] The participants were 20 healthy adults with no present or previous pain, no past history of surgery on the foot or the ankle, and no foot deformities. Ten subjects performed hip external rotator strengthening exercises and TS exercises and the remaining ten subjects performed only TS exercises five times per week for four weeks. [Results] Less change in navicular drop height occurred in the group that performed hip external rotator exercises than in the group that performed only TS exercises. The group that performed only TS exercises showed increased abductor hallucis muscle activity during both stair-climbing and -descending, and the group that performed hip external rotator exercises showed increased muscle activities of the vastus medialis and abductor hallucis during stair-climbing and increased muscle activity of only the abductor hallucis during stair-descending after exercise. [Conclusion] Stair-walking can be more effectively performed if the hip external rotator muscle is strengthened when TS exercises are performed for the pronated foot.

  4. Getting started with LevelDB

    CERN Document Server

    Dent, Andy

    2013-01-01

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

  5. Transcriptional Profile of Kidney from Type 2 Diabetic db/db Mice

    Directory of Open Access Journals (Sweden)

    Haojun Zhang

    2017-01-01

    Full Text Available Diabetic nephropathy (DN, a common diabetic microvascular complication, is characterized by progressive glomerular sclerosis and tubulointerstitial fibrosis. However, the underlying mechanisms involved in DN remain to be elucidated. We explored changes in the transcriptional profile in spontaneous type 2 diabetic db/db mice by using the cDNA microarray. Compared with control db/m mice, the db/db mice exhibited marked increases in body weight, kidney weight, and urinary albumin excretion. Renal histological analysis revealed mesangial expansion and thickness of the basement membrane in the kidney of the db/db mice. A total of 355 differentially expressed genes (DEGs were identified by microarray analysis. Pathway enrichment analysis suggested that biological oxidation, bile acid metabolism, and steroid hormone synthesis were the 3 major significant pathways. The top 10 hub genes were selected from the constructed PPI network of DEGs, including Ccnb2 and Nr1i2, which remained largely unclear in DN. We believe that our study can help elucidate the molecular mechanisms underlying DN.

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

    Directory of Open Access Journals (Sweden)

    Yuzhi Ding

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

  7. Long-term Tai Chi exercise increases body stability of the elderly during stair ascent under high and low illumination.

    Science.gov (United States)

    Song, Qipeng; Wang, Shen; Wong, Del P; Zhou, Jingyi; Sun, Wei; Zhang, Cui; Gu, Houxin; Mao, Dewei

    2017-09-07

    The effects of long-term Tai Chi exercise on body stability of the elderly during stair ascent under high and low illumination were investigated. Forty-five healthy elderly women were divided into three groups, namely, Tai Chi exercise group, brisk walking group and no-exercise control group. All the participants ascended a staircase, during which force platforms and a motion capture system collected the data. Under the high illumination, Tai Chi exercise participants exhibited higher loading rate and anteroposterior centre of pressure (COP ap ) displacement as well as a lower braking impulse than no-exercise group. Under the low illumination, Tai Chi exercise participants demonstrated higher COP ap and mediolateral centre of pressure (COP ml ) displacements as well as lower braking and lateral impulses compared with no-exercise participants. The centre of mass (COM) ml sway in Tai Chi and no exercise participants were higher, the loading rates in Tai Chi and walking participants were higher, and the lateral impulse in no exercise participants was higher under low illumination than under high illumination. Thus, low illumination increases the risk of falling. Tai Chi participants increased their foot clearance, head inclination angle and COP ap displacement under low illumination to increase their stability during stair ascent.

  8. Diabetic patients with and without peripheral neuropathy reveal different hip and ankle biomechanical strategies during stair descent

    Directory of Open Access Journals (Sweden)

    Andreja P. Picon

    Full Text Available BACKGROUND: The progression of diabetes and the challenge of daily tasks may result in changes in biomechanical strategies. Descending stairs is a common task that patients have to deal with, however it still has not been properly studied in this population. OBJECTIVES: We describe and compare the net joint moments and kinematics of the lower limbs in diabetic individuals with and without peripheral neuropathy and healthy controls during stair descent. METHOD: Forty-two adults were assessed: control group (13, diabetic group (14, and neuropathic diabetic group (15. The flexor and extensor net moment peaks and joint angles of the hip, knee, and ankle were described and compared in terms of effect size and ANOVAs (p<0.05. RESULTS: Both diabetic groups presented greater dorsiflexion [large effect size] and a smaller hip extensor moment [large effect size] in the weight acceptance phase. In the propulsion phase, diabetics with and without neuropathy showed a greater hip flexor moment [large effect size] and smaller ankle extension [large effect size]. CONCLUSION: Diabetic patients, even without neuropathy, revealed poor eccentric control in the weight acceptance phase, and in the propulsion phase, they showed a different hip strategy, where they chose to take the leg off the ground using more flexion torque at the hip instead of using a proper ankle extension function.

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

    Science.gov (United States)

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

    2017-02-01

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

  10. Using SciDB to Support Photon Science Data Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Becla, Jack; Wang, Daniel; lim, Kian-Tat; /SLAC

    2012-02-15

    Array data analytic systems like SciDB hold great potential to accelerate processing data from SLAC's Linac Coherent Light Source and other experiments. SciDB is unique in its ability to integrate storage and processing of array data efficiently, providing both space-efficient storage and out-of-memory efficient parallel array processing. We describe a recent effort to leverage SciDB to store and process LCLS data. The work includes development of software to import data into SciDB, subsequent benchmarks, and interactive manipulation of data in SciDB.

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

    Directory of Open Access Journals (Sweden)

    Patricia Bogdanov

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

  12. Interpretation of movement during stair ascent for predicting severity and prognosis of knee osteoarthritis in elderly women using support vector machine.

    Science.gov (United States)

    Yoo, Tae Keun; Kim, Sung Kean; Choi, Soo Beom; Kim, Deog Young; Kim, Deok Won

    2013-01-01

    Several studies have demonstrated that pathologic movement changes in knee osteoarthritis (OA) may contribute to disease progression. The aim of this study was to investigate the association between movement changes during stair ascent and pain, radiographic severity, and prognosis of knee OA in the elderly women using machine learning (ML) over a seven-year follow-up period. Eighteen elderly female patients with knee OA and 20 healthy controls were enrolled. Kinematic data for stair ascent were obtained using a 3D-motion analysis system at baseline. Kinematic factors were analyzed based on one of the popular ML methods, support vector machines (SVM). SVM was used to search kinematic predictors associated with pain, radiographic severity of knee OA, and unfavorable outcomes, which were defined as persistent knee pain as reported at the seven-year follow-up or as having undergone total knee replacement during the follow-up period. Six patients (46.2%) had unfavorable outcomes at the seven-year follow-up. SVM showed accuracy of detection of knee OA (97.4%), prediction of pain (83.3%), radiographic severity (83.3%), and unfavorable outcomes (69.2%). The predictors with SVM included the time of stair ascent, maximal anterior pelvis tilting, knee flexion at initial foot contact, and ankle dorsiflexion at initial foot contact. The interpretation of movement during stair ascent using ML may be helpful for physicians not only in detecting knee OA, but also in evaluating pain and radiographic severity.

  13. RavenDB 2.x beginner's guide

    CERN Document Server

    Tannir, Khaled

    2013-01-01

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

  14. Radial pulsations in DB white dwarfs?

    Science.gov (United States)

    Kawaler, Steven D.

    1993-01-01

    Theoretical models of DB white dwarfs are unstable against radial pulsation at effective temperatures near 20,000-30,000 K. Many high-overtone modes are unstable, with periods ranging from 12 s down to the acoustic cutoff period of approximately 0.1 s. The blue edge for radial instability lies at slightly higher effective temperatures than for nonradial pulsations, with the temperature of the blue edge dependent on the assumed efficiency of convection. Models with increased convective efficiency have radial blue edges that are increasingly closer to the nonradial blue edge; in all models the instability persists into the nonradial instability strip. Radial pulsations therefore may exist in the hottest DB stars that lie below the DB gap; the greatest chance for detection would be observations in the ultraviolet. These models also explain why searches for radial pulsations in DA white dwarfs have failed: the efficient convection needed to explain the blue edge for nonradial DA pulsation means that the radial instability strip is 1000 K cooler than found in previous investigations. The multiperiodic nature of the expected pulsations can be used to advantage to identify very low amplitude modes using the uniform spacing of the modes in frequency. This frequency spacing is a direct indicator of the mass of the star.

  15. Effect of pioglitazone on metabolic features in endotoxemia model in obese diabetic db/db mice.

    Science.gov (United States)

    Sharma, Manoranjan; Mohapatra, Jogeswar; Malik, Umar; Nagar, Jignesh; Chatterjee, Abhijit; Ramachandran, Balaraman; Jain, Mukul R

    2017-06-01

    Infectious diseases are more frequent in diabetic patients, leading to increased morbidity and mortality. Endotoxemia affects glucose metabolism and lipolytic capacity. The aims of the present study were to determine whether endotoxemia exacerbates metabolic features (adipose inflammation, adipogenesis, and insulin resistance [IR]) in an animal model of diabetes (i.e. db/db mice) after acute infection and the effects of pioglitazone. Female db/db mice treated with pioglitazone (3 and 30 mg/kg, p.o.) for 14 days were challenged with lipopolysaccharide (LPS; 200 μg/kg), followed by an oral glucose tolerance test (OGTT). Quantitative real-time polymerase chain reaction (PCR) was used to evaluate the expression of genes in white adipose tissue (WAT) involved in: (i) adipogenesis (lipoprotein lipase [Lpl], fatty acid binding protein-4 [Ap2] and adiponectin [Adipoq]); (ii) insulin signaling (peroxisome proliferator-activated receptor gamma [Pparg], suppressor of cytokine signaling 3 [Socs3], solute carrier family 2 [facilitated glucose transporter], member 4 [Slc2a4]); and (iii) inflammation (tumor necrosis factor [Tnf], interleukin-6 [Il6], monocyte chemoattractant protein-1 [Ccl2], cyclo-oxygenase-2 [prostaglandin-endoperoxide synthase 2; Ptgs2]). Experimental endotoxemia downregulated mRNA expression of Pparg, Slc2a4, Adipoq, Lpl, and Ap2, which coincided with upregulation of Il6, Tnf, Ccl2, Ptgs2, and Socs3 expression. Pioglitazone dose-dependently decreased Tnf, Il6, Ccl2, Ptgs2, and Socs3 expression in WAT, in association with upregulation of Lpl, Ap2, Slc2a4, and Adipoq expression, indicating improvement in endotoxin-induced IR. The findings suggest that LPS challenge exacerbates IR in db/db mice by altering the expression of genes in WAT involved in adipogenesis and inflammation, which is effectively controlled by pioglitazone treatment. © 2016 Ruijin Hospital, Shanghai Jiaotong University School of Medicine and John Wiley & Sons Australia, Ltd.

  16. Novel small-molecule AMPK activator orally exerts beneficial effects on diabetic db/db mice

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yuan-Yuan; Yu, Li-Fang; Zhang, Li-Na; Qiu, Bei-Ying; Su, Ming-Bo; Wu, Fang; Chen, Da-Kai; Pang, Tao; Gu, Min; Zhang, Wei; Ma, Wei-Ping; Jiang, Hao-Wen; Li, Jing-Ya, E-mail: jyli@mail.shcnc.ac.cn; Nan, Fa-Jun, E-mail: fjnan@mail.shcnc.ac.cn; Li, Jia, E-mail: jli@mail.shcnc.ac.cn

    2013-12-01

    AMP-activated protein kinase (AMPK), which is a pivotal guardian of whole-body energy metabolism, has become an attractive therapeutic target for metabolic syndrome. Previously, using a homogeneous scintillation proximity assay, we identified the small-molecule AMPK activator C24 from an optimization based on the original allosteric activator PT1. In this paper, the AMPK activation mechanism of C24 and its potential beneficial effects on glucose and lipid metabolism on db/db mice were investigated. C24 allosterically stimulated inactive AMPK α subunit truncations and activated AMPK heterotrimers by antagonizing autoinhibition. In primary hepatocytes, C24 increased the phosphorylation of AMPK downstream target acetyl-CoA carboxylase dose-dependently without changing intracellular AMP/ATP ratio, indicating its allosteric activation in cells. Through activating AMPK, C24 decreased glucose output by down-regulating mRNA levels of phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) in primary hepatocytes. C24 also decreased the triglyceride and cholesterol contents in HepG2 cells. Due to its improved bioavailability, chronic oral treatment with multiple doses of C24 significantly reduced blood glucose and lipid levels in plasma, and improved the glucose tolerance of diabetic db/db mice. The hepatic transcriptional levels of PEPCK and G6Pase were reduced. These results demonstrate that this orally effective activator of AMPK represents a novel approach to the treatment of metabolic syndrome. - Highlights: • C24 activates AMPK through antagonizing autoinhibition within α subunit. • C24 activates AMPK in hepatocytes and decreases glucose output via AMPK. • C24 exerts beneficial effects on diabetic db/db mice. • C24 represents a novel therapeutic for treatment of metabolic syndrome.

  17. Novel small-molecule AMPK activator orally exerts beneficial effects on diabetic db/db mice

    International Nuclear Information System (INIS)

    Li, Yuan-Yuan; Yu, Li-Fang; Zhang, Li-Na; Qiu, Bei-Ying; Su, Ming-Bo; Wu, Fang; Chen, Da-Kai; Pang, Tao; Gu, Min; Zhang, Wei; Ma, Wei-Ping; Jiang, Hao-Wen; Li, Jing-Ya; Nan, Fa-Jun; Li, Jia

    2013-01-01

    AMP-activated protein kinase (AMPK), which is a pivotal guardian of whole-body energy metabolism, has become an attractive therapeutic target for metabolic syndrome. Previously, using a homogeneous scintillation proximity assay, we identified the small-molecule AMPK activator C24 from an optimization based on the original allosteric activator PT1. In this paper, the AMPK activation mechanism of C24 and its potential beneficial effects on glucose and lipid metabolism on db/db mice were investigated. C24 allosterically stimulated inactive AMPK α subunit truncations and activated AMPK heterotrimers by antagonizing autoinhibition. In primary hepatocytes, C24 increased the phosphorylation of AMPK downstream target acetyl-CoA carboxylase dose-dependently without changing intracellular AMP/ATP ratio, indicating its allosteric activation in cells. Through activating AMPK, C24 decreased glucose output by down-regulating mRNA levels of phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) in primary hepatocytes. C24 also decreased the triglyceride and cholesterol contents in HepG2 cells. Due to its improved bioavailability, chronic oral treatment with multiple doses of C24 significantly reduced blood glucose and lipid levels in plasma, and improved the glucose tolerance of diabetic db/db mice. The hepatic transcriptional levels of PEPCK and G6Pase were reduced. These results demonstrate that this orally effective activator of AMPK represents a novel approach to the treatment of metabolic syndrome. - Highlights: • C24 activates AMPK through antagonizing autoinhibition within α subunit. • C24 activates AMPK in hepatocytes and decreases glucose output via AMPK. • C24 exerts beneficial effects on diabetic db/db mice. • C24 represents a novel therapeutic for treatment of metabolic syndrome

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2003-05-01

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

  19. Database design and SQL for DB2

    CERN Document Server

    Cooper, James

    2013-01-01

    Thorough and updated coverage of database design and SQL for DB2 are the focus of this guide for the relational database-management system used on IBM i computer systems. Suitable for classroom instruction or self-study, this book explains the most widely used database language and the way that language is implemented on a variety of computer platforms. Topics covered include database concepts, SQL inquiries, web applications, and database security, and the material is reinforced by numerous illustrations, examples, and exercises.

  20. Klaim-DB: A Modeling Language for Distributed Database Applications

    DEFF Research Database (Denmark)

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

    2015-01-01

    We present the modelling language, Klaim-DB, for distributed database applications. Klaim-DB borrows the distributed nets of the coordination language Klaim but essentially re-incarnates the tuple spaces of Klaim as databases, and provides high-level language abstractions for the access and manip......We present the modelling language, Klaim-DB, for distributed database applications. Klaim-DB borrows the distributed nets of the coordination language Klaim but essentially re-incarnates the tuple spaces of Klaim as databases, and provides high-level language abstractions for the access...

  1. Patients with chronic peripheral vestibular hypofunction compared to healthy subjects exhibit differences in gaze and gait behaviour when walking on stairs and ramps

    Science.gov (United States)

    Swanenburg, Jaap; Bäbler, Edith; Adelsberger, Rolf; Straumann, Dominik

    2017-01-01

    Objective The aim of this study was to compare gaze behaviour during stair and ramp walking between patients with chronic peripheral vestibular hypofunction and healthy human subjects. Methods Twenty four (24) patients with chronic peripheral vestibular hypofunction (14 unilateral and 10 bilateral) and 24 healthy subjects performed stair and ramp up and down walks at self-selected speed. The walks were repeated five times. A mobile eye tracker was used to record gaze behaviour (defined as time directed to pre-defined areas) and an insole measurement device assessed gait (speed, step time, step length). During each walk gaze behaviour relative to i) detection of first transition area “First TA”, ii) detection of steps of the mid-staircase area and the handrail “Structure”, iii) detection of second transition area “Second TA”, and iv) looking elsewhere “Elsewhere” was assessed and expressed as a percentage of the walk duration. For all variables, a one-way ANOVA followed by contrast tests was conducted. Results Patients looked significantly longer at the “Structure” (p<0.001) and “Elsewhere” (p<0.001) while walking upstairs compared to walking downstairs (p<0.013). Patients looked significantly longer at the “Structure” (p<0.001) and “Elsewhere” (p<0.001) while walking upstairs compared to walking downstairs (p<0.013). No differences between groups were observed for the transition areas with exception of stair ascending. Patients were also slower going downstairs (p = 0.002) and presented with an increased step time (p = 0.003). Patients were walking faster up the ramp (p = 0.014) with longer step length (p = 0.008) compared to walking down the ramp (p = 0.050) with shorter step length (p = 0.024). Conclusions Patients with chronic peripheral vestibular hypofunction differed in time directed to pre-defined areas during stair and ramp walking and looked longer at stair and ramp areas of interest during walking compared to healthy

  2. Patients with chronic peripheral vestibular hypofunction compared to healthy subjects exhibit differences in gaze and gait behaviour when walking on stairs and ramps.

    Directory of Open Access Journals (Sweden)

    Jaap Swanenburg

    Full Text Available The aim of this study was to compare gaze behaviour during stair and ramp walking between patients with chronic peripheral vestibular hypofunction and healthy human subjects.Twenty four (24 patients with chronic peripheral vestibular hypofunction (14 unilateral and 10 bilateral and 24 healthy subjects performed stair and ramp up and down walks at self-selected speed. The walks were repeated five times. A mobile eye tracker was used to record gaze behaviour (defined as time directed to pre-defined areas and an insole measurement device assessed gait (speed, step time, step length. During each walk gaze behaviour relative to i detection of first transition area "First TA", ii detection of steps of the mid-staircase area and the handrail "Structure", iii detection of second transition area "Second TA", and iv looking elsewhere "Elsewhere" was assessed and expressed as a percentage of the walk duration. For all variables, a one-way ANOVA followed by contrast tests was conducted.Patients looked significantly longer at the "Structure" (p<0.001 and "Elsewhere" (p<0.001 while walking upstairs compared to walking downstairs (p<0.013. Patients looked significantly longer at the "Structure" (p<0.001 and "Elsewhere" (p<0.001 while walking upstairs compared to walking downstairs (p<0.013. No differences between groups were observed for the transition areas with exception of stair ascending. Patients were also slower going downstairs (p = 0.002 and presented with an increased step time (p = 0.003. Patients were walking faster up the ramp (p = 0.014 with longer step length (p = 0.008 compared to walking down the ramp (p = 0.050 with shorter step length (p = 0.024.Patients with chronic peripheral vestibular hypofunction differed in time directed to pre-defined areas during stair and ramp walking and looked longer at stair and ramp areas of interest during walking compared to healthy subjects. Patients did not differ in time directed to pre-defined areas during

  3. Carnosine enhances diabetic wound healing in the db/db mouse model of type 2 diabetes.

    Science.gov (United States)

    Ansurudeen, Ishrath; Sunkari, Vivekananda Gupta; Grünler, Jacob; Peters, Verena; Schmitt, Claus Peter; Catrina, Sergiu-Bogdan; Brismar, Kerstin; Forsberg, Elisabete Alcantara

    2012-07-01

    Diabetes mellitus (DM) is a progressive disorder with severe late complications. Normal wound healing involves a series of complex and well-orchestrated molecular events dictated by multiple factors. In diabetes, wound healing is grossly impaired due to defective, and dysregulated cellular and molecular events at all phases of wound healing resulting in chronic wounds that fail to heal. Carnosine, a dipeptide of alanine and histidine and an endogenous antioxidant is documented to accelerate healing of wounds and ulcers. However, not much is known about its role in wound healing in diabetes. Therefore, we studied the effect of carnosine in wound healing in db/db mice, a mice model of Type 2 DM. Six millimeter circular wounds were made in db/db mice and analyzed for wound healing every other day. Carnosine (100 mg/kg) was injected (I.P.) every day and also applied locally. Treatment with carnosine enhanced wound healing significantly, and wound tissue analysis showed increased expression of growth factors and cytokines genes involved in wound healing. In vitro studies with human dermal fibroblasts and microvascular-endothelial cells showed that carnosine increases cell viability in presence of high glucose. These effects, in addition to its known role as an antioxidant and a precursor for histamine synthesis, provide evidence for a possible therapeutic use of carnosine in diabetic wound healing.

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    in the db/db mouse model of T2DM. Glutamate and glutamine are both substrates for mitochondrial oxidation, and oxygen consumption was assessed in isolated brain mitochondria by Seahorse XFe96 analysis. In addition, acutely isolated cerebral cortical and hippocampal slices were incubated with [U-13C......]glutamate and [U-13C]glutamine, and tissue extracts were analyzed by gas chromatography-mass spectrometry. The oxygen consumption rate using glutamate and glutamine as substrates was not different in isolated cerebral mitochondria of db/db mice compared to controls. Hippocampal slices of db/db mice exhibited......Type 2 diabetes mellitus (T2DM) is a risk factor for the development of Alzheimer's disease, and changes in brain energy metabolism have been suggested as a causative mechanism. The aim of this study was to investigate the cerebral metabolism of the important amino acids glutamate and glutamine...

  5. Relationship between the climbing up and climbing down stairs domain scores on the FES-DMD, the score on the Vignos Scale, age and timed performance of functional activities in boys with Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    Lilian A. Y. Fernandes

    2014-12-01

    Full Text Available BACKGROUND: Knowing the potential for and limitations of information generated using different evaluation instruments favors the development of more accurate functional diagnoses and therapeutic decision-making. OBJECTIVE: To investigate the relationship between the number of compensatory movements when climbing up and going down stairs, age, functional classification and time taken to perform a tested activity (TA of going up and down stairs in boys with Duchenne muscular dystrophy (DMD. METHOD: A bank of movies featuring 30 boys with DMD performing functional activities was evaluated. Compensatory movements were assessed using the climbing up and going down stairs domain of the Functional Evaluation Scale for Duchenne Muscular Dystrophy (FES-DMD; age in years; functional classification using the Vignos Scale (VS, and TA using a timer. Statistical analyses were performed using the Spearman correlation test. RESULTS: There is a moderate relationship between the climbing up stairs domain of the FES-DMD and age (r=0.53, p=0.004 and strong relationships with VS (r=0.72, p=0.001 and TA for this task (r=0.83, p<0.001. There were weak relationships between the going down stairs domain of the FES-DMD-going down stairs with age (r=0.40, p=0.032, VS (r=0.65, p=0.002 and TA for this task (r=0.40, p=0.034. CONCLUSION: These findings indicate that the evaluation of compensatory movements used when climbing up stairs can provide more relevant information about the evolution of the disease, although the activity of going down stairs should be investigated, with the aim of enriching guidance and strengthening accident prevention. Data from the FES-DMD, age, VS and TA can be used in a complementary way to formulate functional diagnoses. Longitudinal studies and with broader age groups may supplement this information.

  6. Comparing MongoDB to SQL Server, Replicated

    NARCIS (Netherlands)

    K. Azizi

    2014-01-01

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

  7. CandidaDB: a genome database for Candida albicans pathogenomics.

    Science.gov (United States)

    d'Enfert, C; Goyard, S; Rodriguez-Arnaveilhe, S; Frangeul, L; Jones, L; Tekaia, F; Bader, O; Albrecht, Antje; Castillo, L; Dominguez, A; Ernst, J F; Fradin, C; Gaillardin, C; Garcia-Sanchez, S; de Groot, P; Hube, B; Klis, F M; Krishnamurthy, S; Kunze, D; Lopez, M-C; Mavor, A; Martin, N; Moszer, I; Onésime, D; Perez Martin, J; Sentandreu, R; Valentin, E; Brown, A J P

    2005-01-01

    CandidaDB is a database dedicated to the genome of the most prevalent systemic fungal pathogen of humans, Candida albicans. CandidaDB is based on an annotation of the Stanford Genome Technology Center C.albicans genome sequence data by the European Galar Fungail Consortium. CandidaDB Release 2.0 (June 2004) contains information pertaining to Assembly 19 of the genome of C.albicans strain SC5314. The current release contains 6244 annotated entries corresponding to 130 tRNA genes and 5917 protein-coding genes. For these, it provides tentative functional assignments along with numerous pre-run analyses that can assist the researcher in the evaluation of gene function for the purpose of specific or large-scale analysis. CandidaDB is based on GenoList, a generic relational data schema and a World Wide Web interface that has been adapted to the handling of eukaryotic genomes. The interface allows users to browse easily through genome data and retrieve information. CandidaDB also provides more elaborate tools, such as pattern searching, that are tightly connected to the overall browsing system. As the C.albicans genome is diploid and still incompletely assembled, CandidaDB provides tools to browse the genome by individual supercontigs and to examine information about allelic sequences obtained from complementary contigs. CandidaDB is accessible at http://genolist.pasteur.fr/CandidaDB.

  8. Resistance exercise training increases lower limb speed of strength generation during stair ascent and descent in people with diabetic peripheral neuropathy.

    Science.gov (United States)

    Handsaker, J C; Brown, S J; Bowling, F L; Maganaris, C N; Boulton, A J M; Reeves, N D

    2016-01-01

    To examine the effects of a 16-week resistance exercise training intervention on the speed of ankle and knee strength generation during stair ascent and descent, in people with neuropathy. A total of 43 people: nine with diabetic peripheral neuropathy, 13 with diabetes but no neuropathy and 21 healthy control subjects ascended and descended a custom-built staircase. The speed at which ankle and knee strength were generated, and muscle activation patterns of the ankle and knee extensor muscles were analysed before and after a 16-week intervention period. Ankle and knee strength generation during both stair ascent and descent were significantly higher after the intervention than before the intervention in the people with diabetes who undertook the resistance exercise intervention (P strength generation observed after the intervention would be expected to improve stability during the crucial weight acceptance phase of stair ascent and descent, and ultimately contribute towards reducing the risk of falling. Improvements in muscle strength as a result of the resistance exercise training intervention are likely to be the most influential factor for increasing the speed of strength generation. It is recommended that these exercises could be incorporated into a multi-faceted exercise programme to improve safety in people with diabetes and neuropathy. © 2015 The Authors. Diabetic Medicine © 2015 Diabetes UK.

  9. Effects of mid-foot contact area ratio on lower body kinetics/kinematics in sagittal plane during stair descent in women.

    Science.gov (United States)

    Lee, Jinkyu; Hong, Yoon No Gregory; Shin, Choongsoo S

    2016-07-01

    The mid-foot contact area relative to the total foot contact area can facilitate foot arch structure evaluation. A stair descent motion consistently provides initial fore-foot contact and utilizes the foot arch more actively for energy absorption. The purpose of this study was to compare ankle and knee joint angle, moment, and work in sagittal plane during stair descending between low and high Mid-Foot-Contact-Area (MFCA) ratio group. The twenty-two female subjects were tested and classified into two groups (high MFCA and low MFCA) using their static MFCA ratios. The ground reaction force (GRF) and kinematics of ankle and knee joints were measured while stair descending. During the period between initial contact and the first peak in vertical GRF (early absorption phase), ankle negative work for the low MFCA ratio group was 33% higher than that for the high MFCA ratio group (pfoot differs depending upon foot arch types classified by MFCA. The low MFCA ratio group seemed to absorb more impact energy using strain in the planar fascia during early absorption phase, whereas the high MFCA ratio group absorbed more impact energy using increased dorsiflexion during late absorption phase. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Populismo municipal y nacionalcatolicismo en la Valencia del general Primo de Rivera: el marqués de Sotelo (1923-1930 = Populism and Municipal Propaganda in Valencia during Primo de Rivera’s Dictatorship: the Marquis of Sotelo (1923-1930.

    Directory of Open Access Journals (Sweden)

    Julio López Iñíguez

    2016-05-01

    Full Text Available El presente trabajo pretende explicar las principales características políticas del régimen de Primo de Rivera en la ciudad de Valencia. Desde un análisis de la política municipal, el populismo y la publicidad de la construcción de obras públicas se presentan como los principales pilares para la consolidación del régimen en Valencia. La praxis política del marqués de Sotelo supuso para la ciudad el primer contacto con el nacionalcatolicismo. La figura de este alcalde, además, ocupa buena parte del texto al ser un fiel exponente de las prácticas políticas nacidas tras el golpe de septiembre de 1923.This paper aims to explain the main features of the political regime of Primo de Rivera in the city of Valencia. From an analysis of municipal politics, populism and advertising public works construction are presented as the main supports for the consolidation of the regime in Valencia. The political praxis of the Marquis of Sotelo assumed for the city’s first contact with the National Catholicism. The figure of the mayor, also occupies much of the text to be a faithful exponent of political practices born after the September 1923 coup.

  11. Altered control strategy between leading and trailing leg increases knee adduction moment in the elderly while descending stairs.

    Science.gov (United States)

    Karamanidis, Kiros; Arampatzis, Adamantios

    2011-02-24

    The aim of the study was to examine the external knee adduction moments in a group of older and younger adults while descending stairs and thus the possibility of an increased risk of knee osteoarthritis due to altered knee joint loading in the elderly. Twenty-seven older and 16 younger adults descended a purpose-built staircase. A motion capture system and a force plate were used to determine the subjects' 3D kinematics and ground reaction forces (GRF) during locomotion. Calculation of the leg kinematics and kinetics was done by means of a rigid, three-segment, 3D leg model. In the initial portion of the support phase, older adults showed a more medio-posterior GRF vector relative to the ankle joint, leading to lower ankle joint moments (Pelderly (Pcontrol strategy while stepping down is a more medially directed GRF vector increasing the magnitude of external knee adduction moment in the elderly. The observed changes between leading and trailing leg in the elderly may cause a redistribution of the mechanical load at the tibiofemoral joint, affecting the initiation and progression of knee osteoarthritis in the elderly. Copyright © 2010 Elsevier Ltd. All rights reserved.

  12. Frontal Plane Tibiofemoral Alignment is Strongly Related to Compartmental Knee Joint Contact Forces and Muscle Control Strategies during Stair Ascent.

    Science.gov (United States)

    Bennett, Hunter J; Weinhandl, Joshua T; Fleenor, Kristina; Zhang, Songning

    2018-03-12

    Static frontal plane tibiofemoral alignment is an important factor in dynamic knee alignment and knee adduction moments. However, little is known about the relationship between alignment and compartment contact forces or muscle control strategies. The purpose of this study was to estimate medial (MCF) and lateral (LCF) compartment knee joint contact forces and muscle forces during stair ascent using a musculoskeletal model implementing subject specific knee alignments. Kinematic and kinetic data from 20 healthy individuals with radiographically confirmed varus or valgus knee alignments were simulated using alignment specific models to predict MCFs and LCFs. Muscle forces were determined using static optimization. Independent samples t-tests compared contact and knee and frontal plane hip muscle forces between groups during weight acceptance and during pushoff. The varus group exhibited increased weight acceptance peak MCFs, while the valgus group exhibited increased pushoff peak LCFs. The varus group utilized increased vasti muscle forces during weight acceptance and hip adductor forces during pushoff. The valgus group utilized increased hip abductor forces during pushoff. The alignment dependent contact forces provide evidence of the significance of frontal plane knee alignment in healthy individuals, which may be important in considering future knee joint health. The differing muscle control strategies between alignments detail specific neuromuscular responses to control frontal plane knee loads.

  13. The effects of stair climbing on arterial stiffness, blood pressure, and leg strength in postmenopausal women with stage 2 hypertension.

    Science.gov (United States)

    Wong, Alexei; Figueroa, Arturo; Son, Won-Mok; Chernykh, Oksana; Park, Song-Young

    2018-02-12

    Menopause is accompanied by a progressive arterial stiffening associated with increases in blood pressure (BP) and decline in muscular function. It is crucial to prevent or reduce the negative effects of menopause on vascular and muscular function by implementing appropriate lifestyle interventions, such as exercise training. We examined the effects of a stair climbing (SC) regimen on arterial stiffness (pulse wave velocity [PWV]), BP, and leg strength in postmenopausal women with stage 2 hypertension. Using a parallel experimental design, participants were randomly assigned to either SC (n = 21) or nonexercising control group (n = 20) for 12 weeks. Participants in the SC group trained 4 d/wk, climbing 192 steps 2 to 5 times/d. Participants' brachial-to-ankle PWV (baPWV), BP, and leg strength were measured at baseline and after 12 weeks of their assigned intervention. There was a significant group by time interaction (P hypertensive postmenopausal women. The decrease in arterial stiffness partially explained the improvements in SBP and leg strength. SC may be an effective intervention in the prevention and treatment of menopause/aging-related vascular complications and muscle weakness.

  14. High-Order Sliding Mode-Based Synchronous Control of a Novel Stair-Climbing Wheelchair Robot

    Directory of Open Access Journals (Sweden)

    Juanxiu Liu

    2015-01-01

    Full Text Available For the attitude control of a novel stair-climbing wheelchair with inertial uncertainties and external disturbance torques, a new synchronous control method is proposed via combing high-order sliding mode control techniques with cross-coupling techniques. For this purpose, a proper controller is designed, which can improve the performance of the system under conditions of uncertainties and torque perturbations and also can guarantee the synchronization of the system. Firstly, a robust high-order sliding mode control law is designed to track the desired position trajectories effectively. Secondly, considering the coordination of the multiple joints, a high-order sliding mode synchronization controller is designed to reduce the synchronization errors and tracking errors based on the controller designed previously. Stability of the closed-loop system is proved by Lyapunov theory. The simulation is performed by MATLAB to verify the effectiveness of the proposed controller. By comparing the simulation results of two controllers, it is obvious that the proposed scheme has better performance and stronger robustness.

  15. Red raspberry (Rubus idaeus L.) intake decreases oxidative stress in obese diabetic (db/db) mice.

    Science.gov (United States)

    Noratto, Giuliana D; Chew, Boon P; Atienza, Liezl M

    2017-07-15

    Red raspberry fruit intake was investigated on obese diabetic (db/db) mice for 8weeks. Animals fed isocaloric diets (5.3% freeze-dried raspberry, or control) were assessed for obesity-diabetes-disease risk biomarkers. Results showed that raspberry intake improved antioxidant status and lessened plasma interleukin (IL)-6 (0.3-fold of control, p0.05). Plasma levels of total cholesterol (T-CHL), low density lipoprotein-cholesterol (LDL-CHL), and resistin were higher in the raspberry group. Overall, the enhanced detoxifying cell defenses exerted by raspberry intake might be due to its polyphenolics and fibre. This study demonstrates in vivo that raspberry intake, at a dose that can be achieved by human consumption, might protect against diabetes-induced oxidative stress. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    María G Soto-Urquieta

    2014-01-01

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

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

    Science.gov (United States)

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

  18. Modeling Solar Atmospheric Phenomena with AtomDB and PyAtomDB

    Science.gov (United States)

    Dupont, Marcus; Foster, Adam

    2018-01-01

    Taking advantage of the modeling tools made available by PyAtomDB (Foster 2015), we evaluated the impact of changing atomic data on solar phenomena, in particular their effects on models of coronal mass ejections (CME). Intitially, we perform modifications to the canonical SunNEI code (Murphy et al. 2011) in order to include non-equilibrium ionization (NEI) processes that occur in the CME modeled in SunNEI. The methods used involve the consideration of radiaitive cooling as well as ion balance calculations. These calculations were subsequently implemented within the SunNEI simulation. The insertion of aforementioned processes and parameter customizaton produced quite similar results of the original except for the case of iron. These differences were traced to inconsistencies in the recombination rates for Argon-like iron ions between the CHIANTI and AtomDB databases, even though they in theory use the same data. The key finding was that theoretical models are greatly impacted by the relative atomic database update cycles.Following the SunNEI comparison, we then use the AtomDB database to model the time depedencies of intensity flux spikes produced by a coronal shock wave (Ma et al. 2011). We produced a theretical representation for an ionizing plasma that interpolated over the intensity in four Astronomical Imaging Assembly (AIA) filters. Specifically, the 171 A (Fe IX) ,193 A (Fe XII, FeXXIV),211 A (Fe XIV),and 335 A (Fe XVI) wavelengths in order to assess the comparative spectral emissions between AtomDB and the observed data. The results of the theoretical model, in principle, shine light on both the equilibrium conditions before the shock and the non-equilibrium response to the shock front, as well as discrepancies introduced by changing the atomic data.

  19. Salvianolic Acid B Ameliorates Hyperglycemia and Dyslipidemia in db/db Mice through the AMPK Pathway

    Directory of Open Access Journals (Sweden)

    Ming-Qing Huang

    2016-12-01

    Full Text Available Background/Aims: Salvianolic acid B (Sal B, a major polyphenolic compound of Salvia miltiorrhiza Bunge, has been shown to possess potential antidiabetic activities. However, the action mechanism of SalB in type 2 diabetes has not been investigated extensively. The present study was designed to investigate the effects of Sal B on diabetes-related metabolic changes in a spontaneous model of type 2 diabetes, as well as its potential molecular mechanism. Methods: Male C57BL/KsJ-db/db mice were orally treated with Sal B (50 and 100 mg/kg or metformin (positive drug, 300 mg/kg for 6 weeks. Results: Both doses of Sal B significantly decreased fasting blood glucose, serum insulin, triglyceride and free fatty acid levels, reduced hepatic gluconeogenic gene expression and improved insulin intolerance in db/db mice. High dose Sal B also significantly improved glucose intolerance, increased hepatic glycolytic gene expression and muscle glycogen content, and ameliorated histopathological alterations of pancreas, similar to metformin. Sal B treatment resulted in increased phosphorylated AMP-activated protein kinase (p-AMPK protein expression in skeletal muscle and liver, increased glucose transporter 4 (GLUT4 and glycogen synthase protein expressions in skeletal muscle, and increased peroxisome proliferator-activated receptor alpha (PPARα and phosphorylated acetyl CoA carboxylase (p-ACC protein expressions in liver. Conclusion: Our data suggest that Sal B displays beneficial effects in the prevention and treatment of type 2 diabetes at least in part via modulation of the AMPK pathway.

  20. Dicty_cDB: Contig-U05902-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available _CD102_063 SV5 Solanum chacoense cDNA, mRN... 46 1.4 1 ( DN922450 ) 42800.2 Common Scab-Challenge...L1065DB01, 5... 46 1.4 1 ( CV471779 ) 44996.1 Common Scab-Challenged Tubers Solan...um tub... 46 1.4 1 ( CV470021 ) 42800.1 Common Scab-Challenged Tubers Solanum tub... 46 1.4 1 ( CK276538 ) E

  1. The Effect of Microporous Polysaccharide Hemospheres on Wound Healing and Scarring in Wild-Type and db/db Mice.

    Science.gov (United States)

    Miller, Kyle J; Cao, Wei; Ibrahim, Mohamed M; Levinson, Howard

    2017-04-01

    Hemostasis, the initial phase of wound healing, sets the stage for tissue repair. Microporous polysaccharide hemosphere powder (MPH) is an FDA-approved hemostatic agent that may impact the wound-healing process. This study examined the role of MPH in murine wild-type and diabetic (db/db) wound-healing models and a foreign body response scarring model. The powder was topically applied to excisional wounds in wild-type C57BL/6 mice and db/db mice. The effect of MPH on scarring was evaluated by applying it to the expanded polytetrafluoroethylene tube implantation model. In wild-type mice, topically applied MPH increased epithelial thickness. Levels of α-smooth muscle actin (α-SMA) were decreased in MPH-treated wild-type wounds, whereas Rho-associated protein kinase 2 (ROCK2) and transforming growth factor β levels were increased. In db/db mice, topical wound MPH application decreased epithelial thickness and delayed wound closure. The db/db wounds displayed an increased collagen index. The ROCK2 was increased in a similar manner to wild-type mice, whereas α-SMA and transforming growth factor β levels were decreased. The MPH-treated expanded polytetrafluoroethylene tube mice showed increased α-SMA levels and depressed ROCK2 levels. There were no changes in histologic parameters of the foreign body response. The results suggest that MPH does not adversely impact wound healing in wild-type mice, both topically and around implants, but prolongs time to closure and diminishes thickness in db/db wounds. The MPH application alters contractile proteins in all wound models. These changes could have downstream effects on the wound healing process, and further investigation into the use of MPH in altered or impaired states of wound healing is warranted.

  2. iPhone Sensors in Tracking Outcome Variables of the 30-Second Chair Stand Test and Stair Climb Test to Evaluate Disability: Cross-Sectional Pilot Study.

    Science.gov (United States)

    Adusumilli, Gautam; Joseph, Solomon Eben; Samaan, Michael A; Schultz, Brooke; Popovic, Tijana; Souza, Richard B; Majumdar, Sharmila

    2017-10-27

    Performance tests are important to characterize patient disabilities and functional changes. The Osteoarthritis Research Society International and others recommend the 30-second Chair Stand Test and Stair Climb Test, among others, as core tests that capture two distinct types of disability during activities of daily living. However, these two tests are limited by current protocols of testing in clinics. There is a need for an alternative that allows remote testing of functional capabilities during these tests in the osteoarthritis patient population. Objectives are to (1) develop an app for testing the functionality of an iPhone's accelerometer and gravity sensor and (2) conduct a pilot study objectively evaluating the criterion validity and test-retest reliability of outcome variables obtained from these sensors during the 30-second Chair Stand Test and Stair Climb Test. An iOS app was developed with data collection capabilities from the built-in iPhone accelerometer and gravity sensor tools and linked to Google Firebase. A total of 24 subjects performed the 30-second Chair Stand Test with an iPhone accelerometer collecting data and an external rater manually counting sit-to-stand repetitions. A total of 21 subjects performed the Stair Climb Test with an iPhone gravity sensor turned on and an external rater timing the duration of the test on a stopwatch. App data from Firebase were converted into graphical data and exported into MATLAB for data filtering. Multiple iterations of a data processing algorithm were used to increase robustness and accuracy. MATLAB-generated outcome variables were compared to the manually determined outcome variables of each test. Pearson's correlation coefficients (PCCs), Bland-Altman plots, intraclass correlation coefficients (ICCs), standard errors of measurement, and repeatability coefficients were generated to evaluate criterion validity, agreement, and test-retest reliability of iPhone sensor data against gold-standard manual

  3. SciDB: Open Source DMAS for Scientific Research

    Science.gov (United States)

    SciDB Team

    2013-11-01

    SciDB is a DMAS (Data Management and Analytics Software System) optimized for data management of big data and for big analytics. SciDB is organized around multidimensional array storage, a generalization of relational tables, and is designed to be scalable up to petabytes and beyond. Complex analytics are simplified with SciDB because arrays and vectors are first-class objects with built-in optimized operations. Spatial operators and time-series analysis are easy to express. Interfaces to common scientific tools like R as well as programming languages like C++ and Python are provided.

  4. Molecular signatures database (MSigDB) 3.0.

    Science.gov (United States)

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

    2011-06-15

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

  5. Relationship between the climbing up and climbing down stairs domain scores on the FES-DMD, the score on the Vignos Scale, age and timed performance of functional activities in boys with Duchenne muscular dystrophy.

    Science.gov (United States)

    Fernandes, Lilian A Y; Caromano, Fátima A; Assis, Silvana M B; Hukuda, Michele E; Voos, Mariana C; Carvalho, Eduardo V

    2014-01-01

    Knowing the potential for and limitations of information generated using different evaluation instruments favors the development of more accurate functional diagnoses and therapeutic decision-making. To investigate the relationship between the number of compensatory movements when climbing up and going down stairs, age, functional classification and time taken to perform a tested activity (TA) of going up and down stairs in boys with Duchenne muscular dystrophy (DMD). A bank of movies featuring 30 boys with DMD performing functional activities was evaluated. Compensatory movements were assessed using the climbing up and going down stairs domain of the Functional Evaluation Scale for Duchenne Muscular Dystrophy (FES-DMD); age in years; functional classification using the Vignos Scale (VS), and TA using a timer. Statistical analyses were performed using the Spearman correlation test. There is a moderate relationship between the climbing up stairs domain of the FES-DMD and age (r=0.53, p=0.004) and strong relationships with VS (r=0.72, p=0.001) and TA for this task (r=0.83, pDMD-going down stairs with age (r=0.40, p=0.032), VS (r=0.65, p=0.002) and TA for this task (r=0.40, p=0.034). These findings indicate that the evaluation of compensatory movements used when climbing up stairs can provide more relevant information about the evolution of the disease, although the activity of going down stairs should be investigated, with the aim of enriching guidance and strengthening accident prevention. Data from the FES-DMD, age, VS and TA can be used in a complementary way to formulate functional diagnoses. Longitudinal studies and with broader age groups may supplement this information.

  6. Biomechanical demands of the 2-step transitional gait cycles linking level gait and stair descent gait in older women.

    Science.gov (United States)

    Alcock, Lisa; O'Brien, Thomas D; Vanicek, Natalie

    2015-12-16

    Stair descent is an inherently complex form of locomotion posing a high falls risk for older adults, specifically when negotiating the transitional gait cycles linking level gait and descent. The aim of this study was to enhance our understanding of the biomechanical demands by comparing the demands of these transitions. Lower limb kinematics and kinetics of the 2-step transitions linking level and descent gait at the top (level-to-descent) and the bottom (descent-to-level) of the staircase were quantified in 36 older women with no falls history. Despite undergoing the same vertical displacement (2-steps), the following significant (pvelocity; reduced hip extension and increased ankle dorsiflexion (late stance/pre-swing); reduced ground reaction forces, larger knee extensor moments and powers (absorption; late stance); reduced ankle plantarflexor moments (early and late stance) and increased ankle powers (mid-stance). Top transition biomechanics were similar to those reported previously for continuous descent. Kinetic differences at the knee and ankle signify the contrasting and prominent functions of controlled lowering during the top transition and forward continuance during the bottom transition. The varying musculoskeletal demands encountered during each functional sub-task should be addressed in falls prevention programmes with elderly populations where the greatest clinical impact may be achieved. Knee extensor eccentric power through flexion exercises would facilitate a smooth transition at the top and improving ankle plantarflexion strength during single and double limb stance activities would ease the transition into level gait following continuous descent. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. The business value of DB2 for z/OS IBM DB2 analytics accelerator and optimizer

    CERN Document Server

    Campbell, John; Li, Ruiping; Parekh, Surekha; Purcell, Terry

    2013-01-01

    Celebrating the 30th anniversary of the first release of DB2, this book highlights the important milestones, capabilities, and impacts of the database management software for IBM's mainframe operating system. Special focus is given to IBM DB2 Analytics Accelerator, covering the key design and operational aspects that enable IBM DB2 for z/OS clients to benefit from faster performance, reduced CPU usage, and lower costs. The second half of the book discusses performance enhancements and cost-saving measures in the version 10 release and is rich with hints and tips for a successful upgrade. A spe

  8. StarDB: a large-scale DBMS for strings

    KAUST Repository

    Sahli, Majed

    2015-08-01

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

  9. Eukaryotic Pathogen Database Resources (EuPathDB)

    Data.gov (United States)

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

  10. Dicty_cDB: Contig-U04605-1 [Dicty_cDB

    Lifescience Database Archive (English)

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

  11. DB2 10.1 fundamentals certification study guide

    CERN Document Server

    Sanders, Roger E

    2014-01-01

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

  12. GigaDB: announcing the GigaScience database

    Directory of Open Access Journals (Sweden)

    Sneddon Tam P

    2012-07-01

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

  13. LocSigDB: a database of protein localization signals

    Science.gov (United States)

    Negi, Simarjeet; Pandey, Sanjit; Srinivasan, Satish M.; Mohammed, Akram; Guda, Chittibabu

    2015-01-01

    LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in a eukaryotic cell with brief coverage of bacterial proteins. Proteins must be localized at their appropriate subcellular compartment to perform their desired function. Mislocalization of proteins to unintended locations is a causative factor for many human diseases; therefore, collection of known sorting signals will help support many important areas of biomedical research. By performing an extensive literature study, we compiled a collection of 533 experimentally determined localization signals, along with the proteins that harbor such signals. Each signal in the LocSigDB is annotated with its localization, source, PubMed references and is linked to the proteins in UniProt database along with the organism information that contain the same amino acid pattern as the given signal. From LocSigDB webserver, users can download the whole database or browse/search for data using an intuitive query interface. To date, LocSigDB is the most comprehensive compendium of protein localization signals for eight distinct subcellular locations. Database URL: http://genome.unmc.edu/LocSigDB/ PMID:25725059

  14. Effects of unilateral and bilateral experimental low-back pain on trunk muscle activity during stair walking in healthy and recurrent low-back pain patients

    DEFF Research Database (Denmark)

    Larsen, Lars Henrik; Hirata, Rogerio Pessoto; Graven-Nielsen, Thomas

    with recurrent mild to moderate LBP were included. All participants completed questionnaires on personal and functional status and Oswestry disability index scoring (ODI). The participants performed maximal voluntary contraction (MVC) and series of 10 stair ascent and descent motor tasks, initiated...... by the dominant side foot. Bilateral footswitch data and electromyography (EMG) from the dominant side m. iliocostalis, m. multifidus, m. longissimus, m. rectus abdominis and externus and internus obliquus muscles were recorded before and during experimental unilateral and bilateral LBP were induced in randomized...

  15. Case Study: A Bio-Inspired Control Algorithm for a Robotic Foot-Ankle Prosthesis Provides Adaptive Control of Level Walking and Stair Ascent

    Directory of Open Access Journals (Sweden)

    Uzma Tahir

    2018-04-01

    Full Text Available Powered ankle-foot prostheses assist users through plantarflexion during stance and dorsiflexion during swing. Provision of motor power permits faster preferred walking speeds than passive devices, but use of active motor power raises the issue of control. While several commercially available algorithms provide torque control for many intended activities and variations of terrain, control approaches typically exhibit no inherent adaptation. In contrast, muscles adapt instantaneously to changes in load without sensory feedback due to the intrinsic property that their stiffness changes with length and velocity. We previously developed a “winding filament” hypothesis (WFH for muscle contraction that accounts for intrinsic muscle properties by incorporating the giant titin protein. The goals of this study were to develop a WFH-based control algorithm for a powered prosthesis and to test its robustness during level walking and stair ascent in a case study of two subjects with 4–5 years of experience using a powered prosthesis. In the WFH algorithm, ankle moments produced by virtual muscles are calculated based on muscle length and activation. Net ankle moment determines the current applied to the motor. Using this algorithm implemented in a BiOM T2 prosthesis, we tested subjects during level walking and stair ascent. During level walking at variable speeds, the WFH algorithm produced plantarflexion angles (range = −8 to −19° and ankle moments (range = 1 to 1.5 Nm/kg similar to those produced by the BiOM T2 stock controller and to people with no amputation. During stair ascent, the WFH algorithm produced plantarflexion angles (range −15 to −19° that were similar to persons with no amputation and were ~5 times larger on average at 80 steps/min than those produced by the stock controller. This case study provides proof-of-concept that, by emulating muscle properties, the WFH algorithm provides robust, adaptive control of level walking at

  16. Antihyperglycemic and Antiobesity Effects of JAL2 on db/db Mice

    Directory of Open Access Journals (Sweden)

    In-Seung Lee

    2016-01-01

    Full Text Available Lonicera japonica Thunb. (LJT and Rehmannia glutinosa Libosch. (RGL have been used traditionally as a herbal medicine in Korean medicine. Using LC/Q-TOF was performed to profile the two herbal medicines and the mixture of LJR and RGL (JAL2, ratio 1 : 1. We performed oral glucose tolerance test (OGTT and plasma GLP-1 and insulin secretion by multiplex assays to investigate antidiabetic effects of LJT, RGL, and JAL2 in db/db mice, the mice model of type 2 diabetes mellitus (T2DM. Also, the antiobesity-related factors such as plasma peptide YY (PYY, triglyceride, total cholesterol, HDL, LDL, and weight of liver, epididymal, and retroperitoneal fat tissue were investigated. Through the multiplex assay, it was found that JAL2 treatment more efficiently attenuated high levels of blood glucose by stimulating GLP-1 secretion and reduced LDL concentration and weight of liver and retroperitoneal fat tissue compared to LJT or RGL treated separately. These results suggest that the JAL2 has antidiabetes and antiobesity effects in T2DM mice model.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-09-09

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

  18. DPP-4 inhibitor des-F-sitagliptin treatment increased insulin exocytosis from db/db mice β cells

    International Nuclear Information System (INIS)

    Nagamatsu, Shinya; Ohara-Imaizumi, Mica; Nakamichi, Yoko; Aoyagi, Kyota; Nishiwaki, Chiyono

    2011-01-01

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

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  20. Anti-diabetic effect of amorphastilbol through PPARα/γ dual activation in db/db mice

    International Nuclear Information System (INIS)

    Lee, Woojung; Ham, Jungyeob; Kwon, Hak Cheol; Kim, Yong Kee; Kim, Su-Nam

    2013-01-01

    Highlights: ► Amorphastilbol stimulates the transcriptional activities of both PPARα and PPARγ. ► Amorphastilbol improves glucose and lipid impairment in db/db mice. ► There are no side effects, such as hepatomegaly, in amorphastilbol-treated mice. ► Amorphastilbol can be used as a potential therapeutic agent against T2DM. - Abstract: Peroxisome proliferator-activated receptors (PPARs) have been considered as desirable targets for metabolic syndrome treatments, even though their specific agonists have several side effects, including body weight gain, edema, and tissue failure. The effects of amorphastilbol (APH) on glucose- and lipid metabolism were investigated with in vitro 3T3-L1 adipocyte systems and in vivo db/db mice model. APH selectively stimulates the transcriptional activities of both PPARα and PPARγ, which are able to enhance fatty acid oxidation and glucose utilization. Furthermore, APH improves glucose and lipid impairment in db/db mice. More importantly, there are no significant side effects, such as weight gain or hepatomegaly, in APH-treated animals, implying that APH do not adversely affect liver or lipid metabolism. All our data suggest that APH can be used as potential therapeutic agents against type 2 diabetes and related metabolic disorders, including obesity, by enhancing glucose and lipid metabolism

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

    Science.gov (United States)

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

    2009-01-01

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

  2. Anti-diabetic effect of amorphastilbol through PPARα/γ dual activation in db/db mice

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woojung; Ham, Jungyeob; Kwon, Hak Cheol [Natural Medicine Center, KIST Gangneung Institute, Gangneung 210-340 (Korea, Republic of); Kim, Yong Kee, E-mail: yksnbk@sookmyung.ac.kr [College of Pharmacy, Sookmyung Women’s University, Seoul 140-742 (Korea, Republic of); Kim, Su-Nam, E-mail: snkim@kist.re.kr [Natural Medicine Center, KIST Gangneung Institute, Gangneung 210-340 (Korea, Republic of)

    2013-03-01

    Highlights: ► Amorphastilbol stimulates the transcriptional activities of both PPARα and PPARγ. ► Amorphastilbol improves glucose and lipid impairment in db/db mice. ► There are no side effects, such as hepatomegaly, in amorphastilbol-treated mice. ► Amorphastilbol can be used as a potential therapeutic agent against T2DM. - Abstract: Peroxisome proliferator-activated receptors (PPARs) have been considered as desirable targets for metabolic syndrome treatments, even though their specific agonists have several side effects, including body weight gain, edema, and tissue failure. The effects of amorphastilbol (APH) on glucose- and lipid metabolism were investigated with in vitro 3T3-L1 adipocyte systems and in vivo db/db mice model. APH selectively stimulates the transcriptional activities of both PPARα and PPARγ, which are able to enhance fatty acid oxidation and glucose utilization. Furthermore, APH improves glucose and lipid impairment in db/db mice. More importantly, there are no significant side effects, such as weight gain or hepatomegaly, in APH-treated animals, implying that APH do not adversely affect liver or lipid metabolism. All our data suggest that APH can be used as potential therapeutic agents against type 2 diabetes and related metabolic disorders, including obesity, by enhancing glucose and lipid metabolism.

  3. Effects of low-intensity pulsed electromagnetic fields on bone microarchitecture, mechanical strength and bone turnover in type 2 diabetic db/db mice.

    Science.gov (United States)

    Li, Jianjun; Zeng, Zhaobin; Zhao, Yantao; Jing, Da; Tang, Chuhua; Ding, Yin; Feng, Xue

    2017-09-07

    Type 2 diabetic patients have impaired bone quality, leading to increased fracture risk. Substantial evidence demonstrates that pulsed electromagnetic fields (PEMF) could resist osteopenia/osteoporosis induced by estrogen deficiency and disuse. However, the effects of PEMF on osteopenia/osteoporosis associated with diabetes, especially for more prevalent type 2 diabetes, remain poorly understood. We herein investigated the skeletal effects and mechanisms of PEMF (15 Hz, 20 Gs) on leptin receptor-deficient db/db mice with typical type 2 diabetic symptoms. Our µCT results showed that 12-week PEMF exposure significantly improved both cancellous and cortical bone microarchitecture in db/db mice. Three-point bending and biomechanical indentation testing demonstrated that PEMF improved whole-bone structural properties and tissue-level material properties in db/db mice. PEMF significantly promoted bone formation in db/db mice evidenced by increased serum osteocalcin and bone mineral apposition rate, whereas PEMF exerted no observable alteration in bone resorption. Real-time PCR showed that PEMF upregulated tibial gene expression of osteoblastogenesis-related of canonical Wnt/β-catenin signaling but not osteoclastogenesis-related RANKL-RANK signaling in db/db mice. Our findings demonstrate that PEMF improved bone quantity and quality with obvious anabolic activities in db/db mice, and imply that PEMF might become a clinically applicable treatment modality for improving bone quality in type 2 diabetic patients.

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

    Lifescience Database Archive (English)

    Full Text Available e Site Policy | Contact Us Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  5. Crutches and children - stairs

    Science.gov (United States)

    ... Edelstein JE. Canes, crutches, and walkers. In: Hsu JD, Michael JW, Fisk JR, eds. AAOS Atlas of ... Ma, MD, Professor, Chief, Sports Medicine and Shoulder Service, UCSF Department of Orthopaedic ...

  6. Canted antiferromagnetism in KNi3[PO3(F,OH)]2[PO2(OH)2]F2 with a stair-case Kagomé lattice

    Science.gov (United States)

    Liu, Li-Chen; Ren, Wei-Jian; Huang, Ya-Xi; Pan, Yuanming; Mi, Jin-Xiao

    2017-10-01

    A new nickel phosphate KNi3[PO3(F,OH)]2[PO2(OH)2]F2 has been synthesized using a modified hydrothermal method. Structural characterizations show that it adopts a 3D framework structure with 2D layers of Ni octahedra in a stair-case Kagomé lattice. The Ni2 octahedron at the inversion center shares two trans-faces with Ni1 octahedra to form a linear trimer (Ni3O8F6) as the basic structural unit. The Ni-trimers are linked between themselves by sharing F-corners and to [PO3(F,OH)] tetrahedral groups by sharing O-corners to form 2D stair-case Kagomé layers, which are parallel to the (100) plane and are stacked along the a-axis. Successive Kagomé layers are combined together by [PO2(OH)2] tetrahedral groups and interstice cations K+. Magnetic measurements reveal that KNi3[PO3(F,OH)]2[PO2(OH)2]F2 exhibits a canted antiferromagnetic ordering with a ferromagnetic component at low temperatures.

  7. Dicty_cDB: Contig-U15891-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available :none) Candida dubliniensis CD36 chromo... 122 5e-26 AM270139_47( AM270139 |pid:none) Aspergillus niger...-04 FM992692_190( FM992692 |pid:none) Candida dubliniensis CD36 chromo... 51 1e-04 BT051683_1( BT051683 |pid:none) Medic... dubliniensis CD36 chromo... 224 7e-57 AM042543_1( AM042543 |pid:none) Sordaria macrospora partial kbp ge...zed and subtracted western ... 52 7e-16 3 ( DB751149 ) Apis mellifera head cDNA, RIKEN full-length enric...s tropicalis EST, clone TGas138l22 3'. 46 8e-15 5 ( FE260864 ) CAZO1635.rev CAZO Naegleria gruberi Flagella

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-08-10

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

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2018-02-02

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

  11. Transcriptional profiling of diabetic neuropathy in the BKS db/db mouse: a model of type 2 diabetes.

    Science.gov (United States)

    Pande, Manjusha; Hur, Junguk; Hong, Yu; Backus, Carey; Hayes, John M; Oh, Sang Su; Kretzler, Matthias; Feldman, Eva L

    2011-07-01

    A better understanding of the molecular mechanisms underlying the development and progression of diabetic neuropathy (DN) is essential for the design of mechanism-based therapies. We examined changes in global gene expression to define pathways regulated by diabetes in peripheral nerve. Microarray data for 24-week-old BKS db/db and db/+ mouse sciatic nerve were analyzed to define significantly differentially expressed genes (DEGs); DEGs were further analyzed to identify regulated biological processes and pathways. Expression profile clustering was performed to identify coexpressed DEGs. A set of coexpressed lipid metabolism genes was used for promoter sequence analysis. Gene expression changes are consistent with structural changes of axonal degeneration. Pathways regulated in the db/db nerve include lipid metabolism, carbohydrate metabolism, energy metabolism, peroxisome proliferator-activated receptor signaling, apoptosis, and axon guidance. Promoter sequences of lipid metabolism-related genes exhibit evidence of coregulation of lipid metabolism and nervous system development genes. Our data support existing hypotheses regarding hyperglycemia-mediated nerve damage in DN. Moreover, our analyses revealed a possible coregulation mechanism connecting hyperlipidemia and axonal degeneration. © 2011 by the American Diabetes Association.

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

    CERN Document Server

    Sanders, Roger E

    2007-01-01

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

  13. NGSmethDB 2017: enhanced methylomes and differential methylation.

    Science.gov (United States)

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

    2017-01-04

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

  14. 50 tips and tricks for MongoDB developers

    CERN Document Server

    Chodorow, Kristina

    2011-01-01

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

  15. SilkDB: a knowledgebase for silkworm biology and genomics

    DEFF Research Database (Denmark)

    Wang, Jing; Xia, Qingyou; He, Ximiao

    2005-01-01

    of the large-scale, genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set...... by using B.mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies...

  16. PHP and MongoDB Web Development Beginner's Guide

    CERN Document Server

    Islam, Rubayeet

    2011-01-01

    The book follows a "Code first, explain later" approach, using practical examples in PHP to demonstrate unique features of MongoDB. This book is packed with step-by-step instructions and practical examples, along with challenges to test and improve your knowledge. This book assumes that you are experienced in web application development using PHP, HTML, and CSS. Having working knowledge of using a relational database system such as MySQL will help you grasp some of the concepts quicker, but it is not strictly mandatory. No prior knowledge of MongoDB is required.

  17. La rebelión del Marqués del Valle: un examen del gobierno virreinal en Nueva España en 1566 = The Rebellion of the Marquis of the Valley: A Test for the Viceregal Government in New Spain at 1566

    Directory of Open Access Journals (Sweden)

    Reiko Tateiwa Igarashi

    2016-12-01

    Full Text Available ResumenEl presente trabajo analiza las diversas fuerzas políticas (visitador, virrey, Audiencia y Consejo de Indias, que actuaron e intervinieron durante los primeros gobiernos virreinales de Nueva España en el siglo XVI, a través de la rebelión del marqués del Valle, Martín Cortés, hijo y heredero del conquistador Hernán Cortés a quien consideraron como líder natural los criollos, descendientes de los conquistadores que reclamaban al rey su derecho de sucesión en las encomiendas, el cual se había visto limitado por las Leyes Nuevas. Lejos de responder a la reclamación de estos criollos, las autoridades real y virreinal revelaron su dificultad para comprender la realidad novohispana y la falta de coordinación política entre la metrópoli y la capital mexicana. Finalmente, se decidieron a introducir cambios en su política, entre ellos, la posibilidad de enviar al príncipe heredero Felipe a las Indias con el fin de establecer el orden. AbstractThis paper analyses the attitude of viceregal political institutions –such as the royal visitador, the Viceroy, the royal Audiencia, the Council of Indies–, during the first governments of New Spain in the 16th century through the rebellion of the Marquis of the Valley, Martín Cortés, conqueror Hernán Cortés’ son, natural leader of the second generation of the conquerors who demanded the King their right to the encomienda, limited by the New Laws. Far from giving a response to the criollos, the real and viceregal authorities showed their difficulties to understand the reality of the Indies and lack of coordination on its policies between the metropolis and its colony. Finally, they started to introduce changes, including the possibility to send prince Felipe to the Indies in order to establish the royal authority.

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

    Directory of Open Access Journals (Sweden)

    Ortsäter Henrik

    2012-02-01

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

  19. Reliability and Minimal Detectable Change Values for Predictions of Knee Forces during Gait and Stair Ascent Derived from the FreeBody Musculoskeletal Model of the Lower Limb

    Directory of Open Access Journals (Sweden)

    Phil D. B. Price

    2017-12-01

    Full Text Available FreeBody is a musculoskeletal model of the lower limb used to calculate predictions of muscle and joint contact forces. The validation of FreeBody has been described in a number of publications; however, its reliability has yet to be established. The purpose of this study was, therefore, to establish the test–retest reliability of FreeBody in a population of healthy adults in order to add support to previous and future research using FreeBody that demonstrates differences between cohorts after an intervention. We hypothesized that test–retest estimations of knee contact forces from FreeBody would demonstrate a high intra-class correlation. Kinematic and kinetic data from nine older participants (4 men: mean age = 63 ± 11 years; 5 women: mean age = 49 ± 4 years performing level walking and stair ascent was collected on consecutive days and then analyzed using FreeBody. There was a good level of intra-session agreement between the waveforms for the individual trials of each activity during testing session 1 (R = 0.79–0.97. Similarly, overall there was a good inter-session agreement within subjects (R = 0.69–0.97 although some subjects showed better agreement than others. There was a high level of agreement between the group mean waveforms of the two sessions for all variables (R = 0.882–0.997. The intra-class correlation coefficients (ICC were very high for peak tibiofemoral joint contact forces (TFJ and hamstring forces during gait, for peak patellofemoral joint contact forces and quadriceps forces during stair ascent and for peak lateral TFJ and the proportion of TFJ accounted for by the medial compartment during both tasks (ICC = 0.86–0.96. Minimal detectable change (MDC of the peak knee forces during gait ranged between 0.43 and 1.53 × body weight (18–170% of the mean peak values. The smallest MDCs were found for medial TFJ share (4.1 and 5.8% for walking and stair ascent, respectively

  20. MiR?30c protects diabetic nephropathy by suppressing epithelial?to?mesenchymal transition in db/db mice

    OpenAIRE

    Zhao, Yanru; Yin, Zhongwei; Li, Huaping; Fan, Jiahui; Yang, Shenglan; Chen, Chen; Wang, Dao Wen

    2017-01-01

    Summary Epithelial?to?mesenchymal transition (EMT) plays a significant role in tubulointerstitial fibrosis, which is a hallmark of diabetic nephropathy. Thus, identifying the mechanisms of EMT activation could be meaningful. In this study, loss of miR?30c accompanied with increased EMT was observed in renal tubules of db/db mice and cultured HK2 cells exposed to high glucose. To further explore the roles of miR?30c in EMT and tubulointerstitial fibrosis, recombinant adeno?associated viral vec...

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

    International Nuclear Information System (INIS)

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

    1986-01-01

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

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

    Lifescience Database Archive (English)

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

  3. Web development with MongoDB and Node.js

    CERN Document Server

    Krol, Jason

    2014-01-01

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

  4. ProOpDB: Prokaryotic Operon DataBase.

    Science.gov (United States)

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

    2012-01-01

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

  5. SolveDB: Integrating Optimization Problem Solvers Into SQL Databases

    DEFF Research Database (Denmark)

    Siksnys, Laurynas; Pedersen, Torben Bach

    2016-01-01

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

  6. Associations of the stair climb power test with muscle strength and functional performance in people with COPD: A cross-sectional study

    DEFF Research Database (Denmark)

    Roig, Marc; Eng, Janice J.; MacIntyre, Donna L.

    2010-01-01

    BACKGROUND: The Stair Climb Power Test (SCPT) is a functional test associated with leg muscle power in older people. OBJECTIVE: The purposes of this study were to compare the results of the SCPT in people with chronic obstructive pulmonary disease (COPD) and people who were healthy and to explore...... associations of the SCPT with muscle strength (force-generating capacity) and functional performance. DESIGN: The study was a cross-sectional investigation. METHODS: Twenty-one people with COPD and a predicted mean (SD) percentage of forced expiratory volume in 1 second of 47.2 (12.9) and 21 people who were...... healthy and matched for age, sex, and body mass were tested with the SCPT. Knee extensor and flexor muscle torque was assessed with an isokinetic dynamometer. Functional performance was assessed with the Timed "Up & Go" Test (TUG) and the Six-Minute Walk Test (6MWT). RESULTS: People with COPD showed lower...

  7. Effects of unilateral and bilateral experimental low back pain on trunk muscle activity during stair walking in healthy and recurrent low back pain patients

    DEFF Research Database (Denmark)

    Larsen, Lars Henrik; Hirata, Rogerio Pessoto; Graven-Nielsen, Thomas

    Aim To explore the trunk muscle activity in healthy and recurrent low back pain (R-LBP) patients with no present pain during stair ascent and descent before and after unilateral and bilateral experimental low back pain (LBP). Methods Twenty-five healthy controls and 25 pain-free R-LBP patients...... in m. rectus abdominis during all phases, with larger decrease during bilateral compared with unilateral pain (Ppain in the back muscles (P....04). Conclusions The impact of unilateral and bilateral experimental LBP on trunk muscle activity was different between healthy participants and R-LBP patients. Pain resulted in increased trunk muscle activity in healthy, while R-LBP patients decreased the back and increased the abdominal muscle activity. However...

  8. Comparative Evaluation of Core and Knee Extensor Mechanism Muscle Activation Patterns in a Stair Stepping Task in Healthy Controls and Patellofemoral Pain Patients

    Directory of Open Access Journals (Sweden)

    Alireza Motealleh

    2014-12-01

    Full Text Available Background: Patellofemoral pain (PFP is a common affliction and complex clinical entity. Deficit in neuromotor control of the core may be a remote contributing factor to the development of PFPS. Comparative evaluation of core and extensor mechanism muscle activation patterns between healthy group and patients involved by patellofemoral pain syndrome (PFPS in a stair stepping task is the aim of this study. Methods: In this non-randomized interventional study fifteen males with PFPS and fifteen asymptomatic controls participated. Electromyographic (EMG activity of Vastusmedialisobliquus (VMO, Vastuslateralis (VL, Gluteus medius (GMED, Gluteus Maximus (GMAX, Internal oblique (IO and Erector spinae (ES were recorded and EMG onsets were assessed in both stepping up (SU and down (SD. The time of foot contact determined by a foot switch. Results: During SU: Onset times of all muscles except, VL and ES in the controls were significantly less than PFPS group (P<0.05. In PFPS group the temporal sequence of ES, VL and VMO were different from control groups. During SD: Onset times of all muscles except, GMAX and ES in the control group were significantly less than PFP group (P<0.05. The sequence of muscle activity in both healthy and PFP groups were the same. Conclusion: Our findings are in line with previous researches about the effects of core on function and control of lower extremity. Activation patterns of core and vasti muscles are different between control and PFPS group during stair stepping task. Designing exercises to correct inappropriate timing of core muscles may have a role in management of PFPS and it needs more future researches.

  9. Toward a clinical definition of early osteoarthritis: onset of patient-reported knee pain begins on stairs. Data from the osteoarthritis initiative.

    Science.gov (United States)

    Hensor, Elizabeth M A; Dube, Bright; Kingsbury, Sarah R; Tennant, Alan; Conaghan, Philip G

    2015-01-01

    Early detection of osteoarthritis (OA) would increase the chances of effective intervention. We aimed to investigate which patient-reported activity is first associated with knee pain. We hypothesized that pain would occur first during activities requiring weight bearing and knee bending. Data were obtained from the Osteoarthritis Initiative (OAI), a multicenter, longitudinal prospective observational cohort of people who have or are at high risk of OA. Participants completed the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC; Likert scale) annually for up to 7 years. Rasch analysis was used to rank the WOMAC pain questions (activities) in order of affirmation as the pain score increased from 0. For each total WOMAC score category (0-20) we selected 25 individuals at random based on their maximum score across all visits. Fit to the Rasch model was assessed in this subset; stability of question ranking over successive visits was confirmed in the full OAI. WOMAC data on 4,673 people were included, with 491 selected for subset analysis. The subset data showed good fit to the Rasch model (χ(2) = 43.31, P = 0.332). In the full OAI, the "using stairs" question was the first to score points as the total pain score increased from 0 (baseline logit score ± 95% confidence interval -4.74 ± 0.07), then "walking" (-2.94 ± 0.07), "standing" (-2.65 ± 0.07), "lying/sitting" (-2.00 ± 0.08), and finally "in bed" (-1.32 ± 0.09). This ordering was consistent over successive visits. Knee pain is most likely to first appear during weight-bearing activities involving bending of the knee, such as using stairs. First appearance of this symptom may identify a group suitable for early intervention strategies. © 2015 The Authors. Arthritis Care & Research is published by Wiley Periodicals, Inc. on behalf of the American College of Rheumatology.

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

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us dbQSNP Update History of This Database Date Update contents 2017/02/16 dbQSNP English archiv...e Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - dbQSNP | LSDB Archive ...

  11. Update History of This Database - DB-SPIRE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us DB-SPIRE Update History of This Database Date Update contents 2017/02/16 DB-SPIRE English ar...ase Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - DB-SPIRE | LSDB Archive ...

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

    NARCIS (Netherlands)

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

    2013-01-01

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

  13. Dissection of metabolic pathways in the Db/Db mouse model by integrative proteome and acetylome analysis.

    Science.gov (United States)

    Hölper, Soraya; Nolte, Hendrik; Bober, Eva; Braun, Thomas; Krüger, Marcus

    2015-03-01

    Insulin resistance is often associated with excessive caloric intake and metabolic syndrome (MS) favours the development of Diabetes Mellitus Type II (T2DM). T2DM is a chronic disease with severe long-term consequences, such as dyslipidemia, retinopathy, kidney failure, and cardiovascular diseases. Although studied extensively, several aspects of T2DM remain poorly understood. Liver is the leading organ in the maintenance of metabolic fitness serving as the first relay station for processing dietary information in a direct response to nutritional input and changes in insulin and other endocrine signals. Evidence from several murine models suggests a unique function of the liver in the development of MS and T2DM. Here, we utilised Db/Db mice to understand the impact of T2DM on the proteome of liver cells. Global analysis of the liver proteome using a SILAC approach identified 407 significantly regulated proteins under diabetic conditions out of 8500 identified liver proteins. Furthermore, we mapped 1604 different acetylation sites in liver proteins. After normalization of the protein level, we identified 34 regulated acetyl lysine residues on 21 individual proteins, which were significantly altered in Db/Db compared to wild-type livers. We reason that the dataset provides a versatile resource for functional studies aiming to understand consequences of changes in protein abundances and acetylation in livers of diabetic animals.

  14. Reversibility of β-Cell-Specific Transcript Factors Expression by Long-Term Caloric Restriction in db/db Mouse

    Directory of Open Access Journals (Sweden)

    Chunjun Sheng

    2016-01-01

    Full Text Available Type 2 diabetes (T2D is characterized by β-cell dedifferentiation, but underlying mechanisms remain unclear. The purpose of the current study was to explore the mechanisms of β-cell dedifferentiation with and without long-term control of calorie intake. We used a diabetes mouse model (db/db to analyze the changes in the expression levels of β-cell-specific transcription factors (TFs and functional factors with long-term caloric restriction (CR. Our results showed that chronic euglycemia was maintained in the db/db mice with long-term CR intervention, and β-cell dedifferentiation was significantly reduced. The expression of Glut2, Pdx1, and Nkx6.1 was reversed, while MafA expression was significantly increased with long-term CR. GLP-1 pathway was reactivated with long-term CR. Our work showed that the course of β-cell dedifferentiation can intervene by long-term control of calorie intake. Key β-cell-specific TFs and functional factors play important roles in maintaining β-cell differentiation. Targeting these factors could optimize T2D therapies.

  15. Acceleration of biliary cholesterol secretion restores glycemic control and alleviates hypertriglyceridemia in obese db/db mice.

    Science.gov (United States)

    Su, Kai; Sabeva, Nadezhda S; Wang, Yuhuan; Liu, Xiaoxi; Lester, Joshua D; Liu, Jingjing; Liang, Shuang; Graf, Gregory A

    2014-01-01

    Recent studies support a role for cholesterol in the development of obesity and nonalcoholic fatty liver disease. Mice lacking the ABCG5 ABCG8 (G5G8) sterol transporter have reduced biliary cholesterol secretion and are more susceptible to steatosis, hepatic insulin resistance, and loss of glycemic control when challenged with a high-fat diet. We hypothesized that accelerating G5G8-mediated biliary cholesterol secretion would correct these phenotypes in obese mice. Obese (db/db) male and their lean littermates were administered a cocktail of control adenovirus or adenoviral vectors encoding ABCG5 and ABCG8 (AdG5G8). Three days after viral administration, measures of lipid and glucose homeostasis were determined, and tissues were collected for biochemical analyses. AdG5G8 increased biliary cholesterol and fecal sterol elimination. Fasting glucose and triglycerides declined, and glucose tolerance improved in obese mice expressing G5G8 compared with mice receiving control adenovirus. These changes were associated with a reduction in phosphorylated eukaryotic initiation factor 2α and c-Jun N-terminal kinase in liver, suggesting alleviation of endoplasmic reticulum stress. Phosphorylated insulin receptor and protein kinase B were increased, indicating restored hepatic insulin signaling. However, there was no reduction in hepatic triglycerides after the 3-day treatment period. Accelerating biliary cholesterol secretion restores glycemic control and reduces plasma triglycerides in obese db/db mice.

  16. Sodium fluorocitrate having protective effect on palmitate-induced beta cell death improves hyperglycemia in diabetic db/db mice.

    Science.gov (United States)

    Jung, Ik-Rak; Choi, Sung-E; Hong, Seung A; Hwang, Yoonjung; Kang, Yup

    2017-10-10

    Beta cell loss and insulin resistance play roles in the pathogenesis of type 2 diabetes. Elevated levels of free fatty acids in plasma might contribute to the loss of beta cells. The objective of this study was to find a chemical that could protect against palmitate-induced beta cell death and investigate whether such chemical could improve hyperglycemia in mouse model of type 2 diabetes. Sodium fluorocitrate (SFC), an aconitase inhibitor, was found to be strongly and specifically protective against palmitate-induced INS-1 beta cell death. However, the protective effect of SFC on palmitate-induced cell death was not likely to be due to its inhibitory activity for aconitase since inhibition or knockdown of aconitase failed to protect against palmitate-induced cell death. Since SFC inhibited the uptake of palmitate into INS-1 cells, reduced metabolism of fatty acids was thought to be involved in SFC's protective effect. Ten weeks of treatment with SFC in db/db diabetic mice reduced glucose level but remarkably increased insulin level in the plasma. SFC improved impairment of glucose-stimulated insulin release and also reduced the loss of beta cells in db/db mice. Conclusively, SFC possessed protective effect against palmitate-induced lipotoxicity and improved hyperglycemia in mouse model of type 2 diabetes.

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

    Science.gov (United States)

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

    2013-06-01

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

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2016-09-01

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

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

    CERN Document Server

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

    2014-01-01

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

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

    International Nuclear Information System (INIS)

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

    2003-03-01

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

  2. Getting Started with GEO, CouchDB, and Nodejs

    CERN Document Server

    Thompson, Mick

    2011-01-01

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

  3. Analyzing GAIAN Database (GaianDB) on a Tactical Network

    Science.gov (United States)

    2015-11-30

    we connected 3 Raspberry Pi’s running GaianDB and our augmented version of splatform to a network of 3 CSRs. The Raspberry Pi is a low power, low...based on Debian from a connected secure digital high capacity (SDHC) card or a universal serial bus (USB) device. The Raspberry Pi comes equipped with...requirements, capabilities, and cost make the Raspberry Pi a useful device for sensor experimentation. From there, we performed 3 types of benchmarks

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    protein (BMP) ligands, such as Gremlin1, USAG1 and Sclerostin, were strongly up-regulated suggesting a dampening effect on BMP pathways. Together, these results indicate a lack of translation from T2D patient kidneys to the db/db model with regards to Smad signaling pathway. It is plausible that a strong...

  5. Jejunal proteins secreted by db/db mice or insulin-resistant humans impair the insulin signaling and determine insulin resistance.

    Directory of Open Access Journals (Sweden)

    Serenella Salinari

    Full Text Available Two recent studies demonstrated that bariatric surgery induced remission of type 2 diabetes very soon after surgery and far too early to be attributed to weight loss. In this study, we sought to explore the mechanism/s of this phenomenon by testing the effects of proteins from the duodenum-jejunum conditioned-medium (CM of db/db or Swiss mice on glucose uptake in vivo in Swiss mice and in vitro in both Swiss mice soleus and L6 cells. We studied the effect of sera and CM proteins from insulin resistant (IR and insulin-sensitive subjects on insulin signaling in human myoblasts.db/db proteins induced massive IR either in vivo or in vitro, while Swiss proteins did not. In L6 cells, only db/db proteins produced a noticeable increase in basal (473Ser-Akt phosphorylation, lack of GSK3β inhibition and a reduced basal (389Thr-p70-S6K1 phosphorylation. Human IR serum markedly increased basal (473Ser-Akt phosphorylation in a dose-dependent manner. Human CM IR proteins increased by about twofold both basal and insulin-stimulated (473Ser-Akt. Basal (9Ser-GSK3β phosphorylation was increased by IR subjects serum with a smaller potentiating effect of insulin.These findings show that jejunal proteins either from db/db mice or from insulin resistant subjects impair muscle insulin signaling, thus inducing insulin resistance.

  6. Molecular hydrogen improves obesity and diabetes by inducing hepatic FGF21 and stimulating energy metabolism in db/db mice.

    Science.gov (United States)

    Kamimura, Naomi; Nishimaki, Kiyomi; Ohsawa, Ikuroh; Ohta, Shigeo

    2011-07-01

    Recent extensive studies have revealed that molecular hydrogen (H(2)) has great potential for improving oxidative stress-related diseases by inhaling H(2) gas, injecting saline with dissolved H(2), or drinking water with dissolved H(2) (H(2)-water); however, little is known about the dynamic movement of H(2) in a body. First, we show that hepatic glycogen accumulates H(2) after oral administration of H(2)-water, explaining why consumption of even a small amount of H(2) over a short span time efficiently improves various disease models. This finding was supported by an in vitro experiment in which glycogen solution maintained H(2). Next, we examined the benefit of ad libitum drinking H(2)-water to type 2 diabetes using db/db obesity model mice lacking the functional leptin receptor. Drinking H(2)-water reduced hepatic oxidative stress, and significantly alleviated fatty liver in db/db mice as well as high fat-diet-induced fatty liver in wild-type mice. Long-term drinking H(2)-water significantly controlled fat and body weights, despite no increase in consumption of diet and water. Moreover, drinking H(2)-water decreased levels of plasma glucose, insulin, and triglyceride, the effect of which on hyperglycemia was similar to diet restriction. To examine how drinking H(2)-water improves obesity and metabolic parameters at the molecular level, we examined gene-expression profiles, and found enhanced expression of a hepatic hormone, fibroblast growth factor 21 (FGF21), which functions to enhance fatty acid and glucose expenditure. Indeed, H(2) stimulated energy metabolism as measured by oxygen consumption. The present results suggest the potential benefit of H(2) in improving obesity, diabetes, and metabolic syndrome.

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

    Science.gov (United States)

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

    2017-12-01

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

  8. Differential response of bone and kidney to ACEI in db/db mice: A potential effect of captopril on accelerating bone loss.

    Science.gov (United States)

    Zhang, Yan; Li, Xiao-Li; Sha, Nan-Nan; Shu, Bing; Zhao, Yong-Jian; Wang, Xin-Luan; Xiao, Hui-Hui; Shi, Qi; Wong, Man-Sau; Wang, Yong-Jun

    2017-04-01

    The components of renin-angiotensin system (RAS) are expressed in the kidney and bone. Kidney disease and bone injury are common complications associated with diabetes. This study aimed to investigate the effects of an angiotensin-converting enzyme inhibitor, captopril, on the kidney and bone of db/db mice. The db/db mice were orally administered by gavage with captopril for 8weeks with db/+ mice as the non-diabetic control. Serum and urine biochemistries were determined by standard colorimetric methods or ELISA. Histological measurements were performed on the kidney by periodic acid-schiff staining and on the tibial proximal metaphysis by safranin O and masson-trichrome staining. Trabecular bone mass and bone quality were analyzed by microcomputed tomography. Quantitative polymerase chain reaction and immunoblotting were applied for molecular analysis on mRNA and protein expression. Captopril significantly improved albuminuria and glomerulosclerosis in db/db mice, and these effects might be attributed to the down-regulation of angiotensin II expression and the expression of its down-stream profibrotic factors in the kidney, like connective tissue growth factor and vascular endothelial growth factor. Urinary excretion of calcium and phosphorus markedly increased in db/db mice in response to captopril. Treatment with captopril induced a decrease in bone mineral density and deterioration of trabecular bone at proximal metaphysis of tibia in db/db mice, as shown in the histological and reconstructed 3-dimensional images. Even though captopril effectively reversed the diabetes-induced changes in calcium-binding protein 28-k and vitamin D receptor expression in the kidney as well as the expression of RAS components and bradykinin receptor-2 in bone tissue, treatment with captopril increased the osteoclast-covered bone surface, reduced the osteoblast-covered bone surface, down-regulated the expression of type 1 collagen and transcription factor runt-related transcription

  9. A moving fluoroscope to capture tibiofemoral kinematics during complete cycles of free level and downhill walking as well as stair descent.

    Directory of Open Access Journals (Sweden)

    Renate List

    Full Text Available Videofluoroscopy has been shown to provide essential information in the evaluation of the functionality of total knee arthroplasties. However, due to the limitation in the field of view, most systems can only assess knee kinematics during highly restricted movements. To avoid the limitations of a static image intensifier, a moving fluoroscope has been presented as a standalone system that allows tracking of the knee during multiple complete cycles of level- and downhill-walking, as well as stair descent, in combination with the synchronous assessment of ground reaction forces and whole body skin marker measurements. Here, we assess the ability of the system to keep the knee in the field of view of the image intensifier. By measuring ten total knee arthroplasty subjects, we demonstrate that it is possible to maintain the knee to within 1.8 ± 1.4 cm vertically and 4.0 ± 2.6 cm horizontally of the centre of the intensifier throughout full cycles of activities of daily living. Since control of the system is based on real-time feedback of a wire sensor, the system is not dependent on repeatable gait patterns, but is rather able to capture pathological motion patterns with low inter-trial repeatability.

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

    Science.gov (United States)

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

    2013-09-01

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

  11. SU-PhysioDB: a physiological signals database for body area network security

    OpenAIRE

    Karaoğlan Altop, Duygu; Karaoglan Altop, Duygu; Levi, Albert; Tuzcu, Volkan

    2017-01-01

    This paper presents a new physiological signals database, SU-PhysioDB, that contains simultaneous measurements of electrocardiogram (ECG), blood pressure (BP) and body temperature (BT) signals. SU-PhysioDB can be used to evaluate the performance of the security mechanisms designed for the communication among the biosensors within Body Area Networks (BANs). We present a detailed description of our SU-PhysioDB database along with providing a performance comparison of two specific physiological ...

  12. License - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available database as follows: PGDBj - Ortholog DB © Akihiro Nakaya (Osaka University) licensed under CC Attribution-...ice. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us License - PGDBj - Ortholog DB | LSDB Archive ... ...List Contact us PGDBj - Ortholog DB License License to Use This Database Last updated : 2017/03/07 You may u...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

  13. Scalable Web Application using Node.JS and CouchDB

    OpenAIRE

    Paudyal, Umesh

    2011-01-01

    This report presents design and implementation of a protoype application using server side javascript programming language, node.JS and couchDB as backend database. It scales and evaluates the developed prototype application and the couchDB for their scalability and performance. The report concludes that node.JS is a suitable framework for development of scalable web servers and couchDB as a backend database, though natively not distributed and scalable, can be scaled and distributed across m...

  14. cuticleDB: a relational database of Arthropod cuticular proteins

    Directory of Open Access Journals (Sweden)

    Willis Judith H

    2004-09-01

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

  15. ProCarDB: a database of bacterial carotenoids.

    Science.gov (United States)

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

    2016-05-26

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

  16. 60-dB Bragg gratings in planar waveguides

    DEFF Research Database (Denmark)

    Jouanno, Jean-Marc; Hübner, Jörg; Kristensen, M.

    1997-01-01

    Bragg gratings are widely used as wavelength-selective elements in fiber devices. Integrated optics is a very attractive alternative for realizing such components. This way, multifunctional devices with high mechanical and thermal stability can be made using a technology with potential for mass-production....... The main limitation until now was the quality of the gratings written in planar waveguides. We report here 60-dB transmission dips obtained with 6-mm-long Bragg gratings written in Ge-doped planar waveguides...

  17. FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

    Directory of Open Access Journals (Sweden)

    Evelina Y. Basenko

    2018-03-01

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

  18. Update History of This Database - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj - Ortholog DB Update History of This Database Date Update contents 2017/03/07 PGDBj Orth...L of the Whole data download The URL of The original website information 2014/05/12 PGDBj Ortholog DB (Relea...se57 ver.) English archive site is opened. (Archive V1) 2012/08/01 PGDBj Ortholog DB ( http://pgdbj.jp/ortho...e Update History of This Database Site Policy | Contact Us Update History of This Database - PGDBj - Ortholog DB | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

  19. Database Description - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj - Ortholog DB Database Description General information of database Database name PGDBj - Orth...olog DB Alternative name Plant Genome Database Japan - Ortholog Database DOI 10.18908/lsdba.nbdc01194...teria Taxonomy ID: 1117 Database description Orthology is a homologous relationship among genes derived from...o predict the divergence of gene function based on syntenic relationships among species. PGDBj Ortholog DB i...f utilization of database PGDBj Ortholog DB is hierarchically organized to reflect evolutionary relationship

  20. Inhibition of miR-92a Suppresses Oxidative Stress and Improves Endothelial Function by Upregulating Heme Oxygenase-1 in db/db Mice.

    Science.gov (United States)

    Gou, Lingshan; Zhao, Lei; Song, Wencong; Wang, Li; Liu, Jian; Zhang, Hongsong; Huang, Yuhong; Lau, Chi Wai; Yao, Xiaoqiang; Tian, Xiao Yu; Wong, Wing Tak; Luo, Jiang-Yun; Huang, Yu

    2018-02-10

    Inhibition of microRNA-92a (miR-92a) is reported to suppress endothelial inflammation and delay atherogenesis. We hypothesize that miR-92a inhibition protects endothelial function through suppressing oxidative stress in diabetic db/db mice. In this study, we found elevated expression of miR-92a in aortic endothelium from db/db mice and in renal arteries from diabetic subjects. Endothelial cells (ECs) exposed to advanced glycation end products (AGEs) and oxidized low-density lipoprotein express higher level of miR-92a. Overexpression of miR-92a impairs endothelium-dependent relaxations (EDRs) in C57BL/6 mouse aortas. Overexpression of miR-92a suppresses expression of heme oxygenase-1 (HO-1), a critical cytoprotective enzyme, whereas inhibition of miR-92a increases HO-1 expression in human umbilical vein ECs (HUVECs) and db/db mouse aortas. Importantly, miR-92a inhibition by Ad-anti-miR-92a improved EDRs and reduced reactive oxygen species (ROS) production in db/db mouse aortas. HO-1 inhibition by SnMP or HO-1 knockdown by shHO-1 reversed the suppressive effect of miR-92a inhibition on ROS production induced by AGE treatment in C57BL/6 mouse aortas. In addition, SnMP reversed miR-92a inhibition-induced improvement of EDRs in AGE-treated C57BL/6 mouse aortas and in db/db mouse aortas. Expression of miR-92a is increased in diabetic aortic endothelium and inhibition of miR-92a exerts vasoprotective effect in diabetic mice through HO-1 upregulation in ECs. MiR-92a expression is elevated in diabetic ECs. MiR-92a overexpression impairs endothelial function and suppresses HO-1 expression in ECs. Inhibition of miR-92a attenuates oxidative stress and improves endothelial function through enhancing HO-1 expression and activity in db/db mouse aortas. Antioxid. Redox Signal. 28, 358-370.

  1. FlavorDB: a database of flavor molecules.

    Science.gov (United States)

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

    2018-01-04

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

  2. GiSAO.db: a database for ageing research

    Directory of Open Access Journals (Sweden)

    Grillari Johannes

    2011-05-01

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

  3. Procurement of Beams in Multiple D&B Bridge Projects

    Directory of Open Access Journals (Sweden)

    CT. Ramanathan

    2010-06-01

    Full Text Available Selected infrastructure development projects are being implemented by Design and Build (D&B pocurement system in Sabah (East Malaysia by the Public Works Department (PWD. In the first phase 45 bridge replacement projects were awarded in 5 packages. These simultaneous multiple Bridge projects are for the development of the backward areas and hence their timely completion is utmost important. Procurement and production of bridge beams have been the critical element of construction in these rural areas and no researches has been reported on various aspects of procurement of the bridge beams in multiple D&B projects. The aspects of procurement researched in this work include the determination of a common beam element for the ease of procurement and the optimization of the construction methodology, the finalization and purchasing plate dimensions to suite the manufacturer's production range, the delivery of materials, the planning and monitoring of fabrication, the preparation and assembly, and the erection and launching of beams. The beams are optimized using element optimization techniques. The most important problems in fabricating steel girders were in planning and scheduling of materials for the fabrication and the fabrication process. Findings in all the aspects of production of steel girders are highlighted through a case study of six long span bridges at various locations in Sabah. Solutions drawn from lessons learnt which minimize wastages, and aids in timely completion of beams in multiple bridge construction are discussed.

  4. MultitaskProtDB: a database of multitasking proteins.

    Science.gov (United States)

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

    2014-01-01

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

  5. Chemotherapy of second stage human African trypanosomiasis: comparison between the parenteral diamidine DB829 and its oral prodrug DB868 in vervet monkeys.

    Directory of Open Access Journals (Sweden)

    John K Thuita

    2015-02-01

    Full Text Available Human African trypanosomiasis (HAT, sleeping sickness ranks among the most neglected tropical diseases based on limited availability of drugs that are safe and efficacious, particularly against the second stage (central nervous system [CNS] of infection. In response to this largely unmet need for new treatments, the Consortium for Parasitic Drug Development developed novel parenteral diamidines and corresponding oral prodrugs that have shown cure of a murine model of second stage HAT. As a rationale for selection of one of these compounds for further development, the pharmacokinetics and efficacy of intramuscular (IM active diamidine 2,5-bis(5-amidino-2-pyridylfuran (DB829; CPD-0802 and oral prodrug2,5-bis[5-(N-methoxyamidino-2-pyridyl]furan (DB868 were compared in the vervet monkey model of second stage HAT. Treatment was initiated 28 days post-infection of monkeys with T. b. rhodesiense KETRI 2537. Results showed that IM DB829 at 5 mg/kg/day for 5 consecutive days, 5 mg/kg/day every other day for 5 doses, or 2.5 mg/kg/day for 5 consecutive days cured all monkeys (5/5. Oral DB868 was less successful, with no cures (0/2 at 3 mg/kg/day for 10 days and cure rates of 1/4 at 10 mg/kg/day for 10 days and 20 mg/kg/day for 10 days; in total, only 2/10 monkeys were cured with DB868 dose regimens. The geometric mean plasma Cmax of IM DB829 at 5 mg/kg following the last of 5 doses was 25-fold greater than that after 10 daily oral doses of DB868 at 20 mg/kg. These data suggest that the active diamidine DB829, administered IM, should be considered for further development as a potential new treatment for second stage HAT.

  6. Chemotherapy of Second Stage Human African Trypanosomiasis: Comparison between the Parenteral Diamidine DB829 and Its Oral Prodrug DB868 in Vervet Monkeys

    Science.gov (United States)

    Thuita, John K.; Wolf, Kristina K.; Murilla, Grace A.; Bridges, Arlene S.; Boykin, David W.; Mutuku, James N.; Liu, Qiang; Jones, Susan K.; Gem, Charles O.; Ching, Shelley; Tidwell, Richard R.; Wang, Michael Z.; Paine, Mary F.; Brun, Reto

    2015-01-01

    Human African trypanosomiasis (HAT, sleeping sickness) ranks among the most neglected tropical diseases based on limited availability of drugs that are safe and efficacious, particularly against the second stage (central nervous system [CNS]) of infection. In response to this largely unmet need for new treatments, the Consortium for Parasitic Drug Development developed novel parenteral diamidines and corresponding oral prodrugs that have shown cure of a murine model of second stage HAT. As a rationale for selection of one of these compounds for further development, the pharmacokinetics and efficacy of intramuscular (IM) active diamidine 2,5-bis(5-amidino-2-pyridyl)furan (DB829; CPD-0802) and oral prodrug2,5-bis[5-(N-methoxyamidino)-2-pyridyl]furan (DB868) were compared in the vervet monkey model of second stage HAT. Treatment was initiated 28 days post-infection of monkeys with T. b. rhodesiense KETRI 2537. Results showed that IM DB829 at 5 mg/kg/day for 5 consecutive days, 5 mg/kg/day every other day for 5 doses, or 2.5 mg/kg/day for 5 consecutive days cured all monkeys (5/5). Oral DB868 was less successful, with no cures (0/2) at 3 mg/kg/day for 10 days and cure rates of 1/4 at 10 mg/kg/day for 10 days and 20 mg/kg/day for 10 days; in total, only 2/10 monkeys were cured with DB868 dose regimens. The geometric mean plasma Cmax of IM DB829 at 5 mg/kg following the last of 5 doses was 25-fold greater than that after 10 daily oral doses of DB868 at 20 mg/kg. These data suggest that the active diamidine DB829, administered IM, should be considered for further development as a potential new treatment for second stage HAT. PMID:25654243

  7. Chemotherapy of second stage human African trypanosomiasis: comparison between the parenteral diamidine DB829 and its oral prodrug DB868 in vervet monkeys.

    Science.gov (United States)

    Thuita, John K; Wolf, Kristina K; Murilla, Grace A; Bridges, Arlene S; Boykin, David W; Mutuku, James N; Liu, Qiang; Jones, Susan K; Gem, Charles O; Ching, Shelley; Tidwell, Richard R; Wang, Michael Z; Paine, Mary F; Brun, Reto

    2015-02-01

    Human African trypanosomiasis (HAT, sleeping sickness) ranks among the most neglected tropical diseases based on limited availability of drugs that are safe and efficacious, particularly against the second stage (central nervous system [CNS]) of infection. In response to this largely unmet need for new treatments, the Consortium for Parasitic Drug Development developed novel parenteral diamidines and corresponding oral prodrugs that have shown cure of a murine model of second stage HAT. As a rationale for selection of one of these compounds for further development, the pharmacokinetics and efficacy of intramuscular (IM) active diamidine 2,5-bis(5-amidino-2-pyridyl)furan (DB829; CPD-0802) and oral prodrug2,5-bis[5-(N-methoxyamidino)-2-pyridyl]furan (DB868) were compared in the vervet monkey model of second stage HAT. Treatment was initiated 28 days post-infection of monkeys with T. b. rhodesiense KETRI 2537. Results showed that IM DB829 at 5 mg/kg/day for 5 consecutive days, 5 mg/kg/day every other day for 5 doses, or 2.5 mg/kg/day for 5 consecutive days cured all monkeys (5/5). Oral DB868 was less successful, with no cures (0/2) at 3 mg/kg/day for 10 days and cure rates of 1/4 at 10 mg/kg/day for 10 days and 20 mg/kg/day for 10 days; in total, only 2/10 monkeys were cured with DB868 dose regimens. The geometric mean plasma Cmax of IM DB829 at 5 mg/kg following the last of 5 doses was 25-fold greater than that after 10 daily oral doses of DB868 at 20 mg/kg. These data suggest that the active diamidine DB829, administered IM, should be considered for further development as a potential new treatment for second stage HAT.

  8. A Tutorial in Creating Web-Enabled Databases with Inmagic DB/TextWorks through ODBC.

    Science.gov (United States)

    Breeding, Marshall

    2000-01-01

    Explains how to create Web-enabled databases. Highlights include Inmagic's DB/Text WebPublisher product called DB/TextWorks; ODBC (Open Database Connectivity) drivers; Perl programming language; HTML coding; Structured Query Language (SQL); Common Gateway Interface (CGI) programming; and examples of HTML pages and Perl scripts. (LRW)

  9. Update History of This Database - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us MicrobeDB.jp Update History of This Database Date Update contents 2017/06/29 Archive V2 is r...ion Download License Update History of This Database Site Policy | Contact Us Update History of This Database - MicrobeDB.jp | LSDB Archive ...

  10. Update History of This Database - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us Dicty_cDB Update History of This Database Date Update contents 2015/01/09 The original websi...ase Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - Dicty_cDB | LSDB Archive ...

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

    Lifescience Database Archive (English)

    Full Text Available List Contact us MicrobeDB.jp Ontology Data detail Data name Ontology DOI 10.18908/lsdba.nbdc01181-004.V002 V...atabase Description Download License Update History of This Database Site Policy | Contact Us Ontology - MicrobeDB.jp | LSDB Archive ...

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

    Directory of Open Access Journals (Sweden)

    I Gede Winaya

    2016-01-01

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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

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

    Science.gov (United States)

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

    2018-03-01

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

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

    Directory of Open Access Journals (Sweden)

    Eunjin Sohn

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    L. R. Cataldo

    2016-01-01

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

  2. A PPARγ, NF-κB and AMPK-dependent mechanism may be involved in the beneficial effects of curcumin in the diabetic db/db mice liver.

    Science.gov (United States)

    Jiménez-Flores, Lizbeth M; López-Briones, Sergio; Macías-Cervantes, Maciste H; Ramírez-Emiliano, Joel; Pérez-Vázquez, Victoriano

    2014-06-18

    Turmeric (Curcuma longa) is a rhizomatous herbaceous perennial plant of the ginger family which has been used to treat biliary disorders, anorexia, cough, rheumatism, cancer, sinusitis, hepatic disorders, hyperglycemia, obesity, and diabetes in both Ayurvedic and Traditional Chinese Medicine. Suggested mechanisms of action include the modulation of signal transduction cascades and effects on gene expression, however they remain to be elucidated. In this study, the expression of some proteins responsible for transcription factors, inflammation, and metabolic control were evaluated by western blot in 15-week-old db/db mice livers treated with curcumin 0.75% mixed in their diet for 8 weeks. In addition, nitrosative stress was evaluated. Curcumin increased the expression of AMPK and PPARγ, and diminished NF-κB protein in db/db mice. However, it did not modify the expression of PGC-1α or SIRT1. Nitrosative stress present in db/db mice livers was determined by a unique nitrotyrosylated protein band (75 kDa) and was not reverted with curcumin. In conclusion, curcumin regulates the expression of AMPK, PPARγ, and NF-κB; suggesting a beneficial effect for treatment of T2DM complications. In order to observe best beneficial effects it is desirable to administer curcumin in the earlier states of T2DM.

  3. A PPARγ, NF-κB and AMPK-Dependent Mechanism May Be Involved in the Beneficial Effects of Curcumin in the Diabetic db/db Mice Liver

    Directory of Open Access Journals (Sweden)

    Lizbeth M. Jiménez-Flores

    2014-06-01

    Full Text Available Turmeric (Curcuma longa is a rhizomatous herbaceous perennial plant of the ginger family which has been used to treat biliary disorders, anorexia, cough, rheumatism, cancer, sinusitis, hepatic disorders, hyperglycemia, obesity, and diabetes in both Ayurvedic and Traditional Chinese Medicine. Suggested mechanisms of action include the modulation of signal transduction cascades and effects on gene expression, however they remain to be elucidated. In this study, the expression of some proteins responsible for transcription factors, inflammation, and metabolic control were evaluated by western blot in 15-week-old db/db mice livers treated with curcumin 0.75% mixed in their diet for 8 weeks. In addition, nitrosative stress was evaluated. Curcumin increased the expression of AMPK and PPARγ, and diminished NF-κB protein in db/db mice. However, it did not modify the expression of PGC-1α or SIRT1. Nitrosative stress present in db/db mice livers was determined by a unique nitrotyrosylated protein band (75 kDa and was not reverted with curcumin. In conclusion, curcumin regulates the expression of AMPK, PPARγ, and NF-κB; suggesting a beneficial effect for treatment of T2DM complications. In order to observe best beneficial effects it is desirable to administer curcumin in the earlier states of T2DM.

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

    CERN Document Server

    Sanders, Roger E

    2007-01-01

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

  5. IntegromeDB: an integrated system and biological search engine.

    Science.gov (United States)

    Baitaluk, Michael; Kozhenkov, Sergey; Dubinina, Yulia; Ponomarenko, Julia

    2012-01-19

    With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback.

  6. Doubling the number of pulsating DB white dwarfs

    International Nuclear Information System (INIS)

    Nitta, Atsuko; Kleinman, S J; Krzenski, J; Kepler, S O; Metcalfe, T S; Mukadam, Anjum S; Mullally, F; Nather, R E; Winget, D E; Sullivan, D; Thompson, Susan E

    2009-01-01

    We are searching for new pulsating DB white dwarf stars (DBVs) based on the newly found white dwarf stars from the spectra obtained by the Sloan Digital Sky Survey. DBVs pulsate at hotter temperature ranges than their better known cousins, DAVs or ZZ Ceti stars. Since the evolution of white dwarf stars is characterized by cooling, asteroseismological studies of DBVs give us opportunities to study white dwarf structure at a different evolutionary stage than the DAVs. The hottest DBVs are thought to have neutrino luminosities exceeding their photon luminosities (Winget et al. 2004), a quantity measurable through asteroseismology. Therefore, they can also be used to study neutrino physics in the stellar interior. At the time of the meeting, we reported on the nine new DBVs, doubling the number of previously known DBVs. Here we report the new nine pulsators' lightcurves and power spectra.

  7. Scientific Data Bases at Scale and SciDB

    CERN Multimedia

    CERN. Geneva

    2013-01-01

    Abstract: As a general rule, scientists have shunned relational data management systems (RDBMS), choosing instead to “roll their own” on top of file system technology.  We first discuss why file systems are a poor choice for science data storage, especially as data volumes become large and scalability becomes important.   Then, we continue with the reasons why RDBMSs work poorly on most science applications.  These include a data model “impedance mismatch” and missing features. We discuss array DBMSs, and why they are a much better choice for science applications, and use SciDB as an exemplar of this new class of DBMSs.   Most science applications require a mix of data management and complex analytics.  In most cases, the analytics entail a sequence of linear algebra computations.  We discuss the possible ways of integrating a DBMS with statistical calculations, and conclude with the mechanism being used by S...

  8. Evaluation of Effects of Chinese Prescription Kangen-karyu on Diabetes-Induced Alterations such as Oxidative Stress and Apoptosis in the Liver of Type 2 Diabetic db/db Mice

    Directory of Open Access Journals (Sweden)

    Chan Hum Park

    2012-01-01

    Full Text Available The present study was conducted to examine whether Kangen-karyu has an ameliorative effect on diabetes-induced alterations such as oxidative stress and apoptosis in the liver of type 2 diabetic db/db mice. Kangen-karyu (100 or 200 mg/kg body weight/day, p.o. was administered every day for 18 weeks to db/db mice and its effect was compared with vehicle-treated db/db and m/m mice. The administration of Kangen-karyu decreased the elevated serum glucose and leptin concentrations in db/db mice, and reduced the increased oxidative biomarkers including the generation of reactive oxygen species and lipid peroxidation in the liver. The db/db mice exhibited the upregulation of nicotinamide adenine dinucleotide phosphate oxidase subunits, NF-E2-related factor 2, heme oxygenase-1, nuclear factor-kappa B, cyclooxygenase-2, and inducible nitric oxide synthase levels in the liver; however, Kangen-karyu treatment significantly reduced those expressions. Moreover, the augmented expressions of apoptosis-related proteins, Bax, cytochrome c, c-Jun N-terminal kinase (JNK, phosphor-JNK, AP-1, and caspase-3, were downregulated by Kangen-karyu administration. Hematoxylin-eosin staining showed that the increased hepatocellular damage in the liver of db/db mice improved by Kangen-karyu administration. Our findings support the therapeutic evidence for Kangen-karyu ameliorating the development of diabetic hepatic complications via regulating oxidative stress and apoptosis.

  9. SoyDB: a knowledge database of soybean transcription factors

    Directory of Open Access Journals (Sweden)

    Valliyodan Babu

    2010-01-01

    Full Text Available Abstract Background Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors. Description The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database for all the transcription factors in the soybean genome. The database contains protein sequences, predicted tertiary structures, putative DNA binding sites, domains, homologous templates in the Protein Data Bank (PDB, protein family classifications, multiple sequence alignments, consensus protein sequence motifs, web logo of each family, and web links to the soybean transcription factor database PlantTFDB, known EST sequences, and other general protein databases including Swiss-Prot, Gene Ontology, KEGG, EMBL, TAIR, InterPro, SMART, PROSITE, NCBI, and Pfam. The database can be accessed via an interactive and convenient web server, which supports full-text search, PSI-BLAST sequence search, database browsing by protein family, and automatic classification of a new protein sequence into one of 64 annotated transcription factor families by hidden Markov models. Conclusions A comprehensive soybean transcription factor database was constructed and made publicly accessible at http://casp.rnet.missouri.edu/soydb/.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-08-07

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

  11. Impairment of endothelium-dependent ACh-induced relaxation in aorta of diabetic db/db mice--possible dysfunction of receptor and/or receptor-G protein coupling.

    Science.gov (United States)

    Miike, Tomohiro; Kunishiro, Kazuyoshi; Kanda, Mamoru; Azukizawa, Satoru; Kurahashi, Kazuyoshi; Shirahase, Hiroaki

    2008-06-01

    Diabetes is a risk factor of ischemic heart disease, cerebral ischemia, and atherosclerosis, in which endothelial dysfunction plays a role in the pathogenesis. We examined vascular responses in the aorta of pre-diabetic db/db mice with normoglycemia, hyperlipidemia, and hyperinsulinemia (6 weeks old), and diabetic db/db mice with hyperglycemia, hyperlipidemia, and hyperinsulinemia (11 weeks old) in comparison with age-matched non-diabetic db/+ mice. Prostaglandin F2alpha (PGF2alpha)-induced contraction was significantly enhanced in the aorta of diabetic but not pre-diabetic db/db mice compared to age-matched non-diabetic db/+ mice. Acetylcholine (ACh), adenosine-5'-diphosphate (ADP), NaF, a G protein activator and A-23187, a Ca-ionophore, caused endothelium-dependent and nitric oxide (NO)-mediated relaxation, and sodium nitroprusside (SNP), an NO donor, caused endothelium-independent relaxation in the pre-contracted aorta of db/db mice. Maximal endothelium-dependent ACh-induced relaxation was reduced in diabetic but not pre-diabetic db/db mice compared to age-matched db/+ mice, while maximal SNP-induced relaxation was not different between diabetic and non-diabetic mice. ACh-induced relaxation in diabetic db/db mice was not affected by ozagrel, a thromboxane A2 (TXA2) synthetase inhibitor, or acetylsalicylic acid (aspirin), a cyclooxygenase inhibitor, suggesting no involvement of endogenous TXA2 or prostanoids in the reduction of relaxation. Maximal endothelium-dependent ADP-, A-23187-, and NaF-induced relaxation was not reduced in diabetic db/db mice. EC50 values for ACh- and SNP-induced relaxation were increased in diabetic but not pre-diabetic db/db mice, suggesting decreases in sensitivity to NO in diabetic mice. Two-week treatment with KV-5070, a PPARgamma agonist, lowered plasma glucose, triglyceride (TG), and insulin but not cholesterol, and reversed the reduced ACh-induced relaxation. In conclusion, ACh-induced endothelium-dependent relaxation is impaired

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

    Directory of Open Access Journals (Sweden)

    Garris David R

    2006-02-01

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

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

    Science.gov (United States)

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

    2014-09-01

    Type-2 diabetes is associated with a chronic low-grade systemic inflammation accompanied by an increased production of adipokines/cytokines by obese adipose tissue. The search for new antidiabetic drugs with different mechanisms of action, such as insulin sensitizers, insulin secretagogues and α-glucosidase inhibitors, has directed the focus on the potential use of flavonoids in the management of type-2 diabetes. Thirty six diabetic male C57BL/6J db/db mice were fed a standard diet and randomly assigned into four experimental groups: non-treated control, (n = 8); acarbose (5 mg per kg bw, n = 8); helichrysum (1 g per kg bw, n = 10) and grapefruit (0.5 g per kg bw, n = 10) for 6 weeks. The mRNA expression in pancreas, liver and epididymal adipose tissue was determined by RT-PCR. DNA methylation was quantified in epididymal fat using pyrosequencing. Mice supplemented with helichrysum and grapefruit extracts showed a significant decrease in fasting glucose levels (p < 0.05). A possible mechanism of action could be the up-regulation of liver glucokinase (p < 0.05). The antihyperglycemic effect of both extracts was accompanied by decreased mRNA expression of some proinflammatory genes (monocyte chemotactic protein-1, tumor necrosis factor-α, cyclooxygenase-2, nuclear factor-kappaB) in the liver and epididymal adipose tissue. The CpG3 site of TNFα, located 5 bp downstream of the transcription start site, showed increased DNA methylation in the grapefruit group compared with the non-treated group (p < 0.01). In conclusion, helichrysum and grapefruit extracts improved hyperglycemia through the regulation of glucose metabolism in the liver and reduction of the expression of proinflammatory genes in the liver and visceral fat. The hypermethylation of TNFα in adipose tissue may contribute to reduce the inflammation associated with diabetes and obesity.

  14. Celastrol, an NF-κB inhibitor, improves insulin resistance and attenuates renal injury in db/db mice.

    Directory of Open Access Journals (Sweden)

    Jung Eun Kim

    Full Text Available The NF-κB pathway plays an important role in chronic inflammatory and autoimmune diseases. Recently, NF-κB has also been suggested as an important mechanism linking obesity, inflammation, and metabolic disorders. However, there is no current evidence regarding the mechanism of action of NF-κB inhibition in insulin resistance and diabetic nephropathy in type 2 diabetic animal models. We investigated the effects of the NF-κB inhibitor celastrol in db/db mice. The treatment with celastrol for 2 months significantly lowered fasting plasma glucose (FPG, HbA1C and homeostasis model assessment index (HOMA-IR levels. Celastrol also exhibited significant decreases in body weight, kidney/body weight and adiposity. Celastrol reduced insulin resistance and lipid abnormalities and led to higher plasma adiponectin levels. Celastrol treatment also significantly mitigated lipid accumulation and oxidative stress in organs including the kidney, liver and adipose tissue. The treated group also exhibited significantly lower creatinine levels and urinary albumin excretion was markedly reduced. Celastrol treatment significantly lowered mesangial expansion and suppressed type IV collagen, PAI-1 and TGFβ1 expressions in renal tissues. Celastrol also improved abnormal lipid metabolism, oxidative stress and proinflammatory cytokine activity in the kidney. In cultured podocytes, celastrol treatment abolished saturated fatty acid-induced proinflammatory cytokine synthesis. Taken together, celastrol treatment not only improved insulin resistance, glycemic control and oxidative stress, but also improved renal functional and structural changes through both metabolic and anti-inflammatory effects in the kidney. These results suggest that targeted therapy for NF-κB may be a useful new therapeutic approach for the management of type II diabetes and diabetic nephropathy.

  15. Stair climbing/descending exercise for a short time decreases blood glucose levels after a meal in people with type 2 diabetes.

    Science.gov (United States)

    Honda, Hiroto; Igaki, Makoto; Hatanaka, Yuki; Komatsu, Motoaki; Tanaka, Shin-Ichiro; Miki, Tetsuo; Suzuki, Taiga; Takaishi, Tetsuo; Hayashi, Tatsuya

    2016-01-01

    We examined whether stair climbing-descending exercise (ST-EX), a convenient method to increase physical activity in daily life, for a short period would acutely improve the postprandial blood glucose (BG) response in people with type 2 diabetes (T2D). 16 people with T2D (age 65.4±1.1 years) participated in 2 separate sessions. After an overnight fast, each participant consumed a test meal and then kept resting for 180 min, except when performing each 3 min bout of ST-EX at 60 and 120 min after the meal (ST-EX session), or kept resting for 180 min (REST session). ST-EX comprised 6 continuous repetitions of climbing to the second floor (21 steps) at a rate of 80-110 steps/min followed by walking down slowly to the first floor at a free step rate. The BG at 60 min after the meal during the ST-EX session (immediately before the first ST-EX) did not differ from that during the REST session, but analysis of variance revealed a significant interaction between time and treatment (p<0.01). The BG at 150 min after the meal (30 min after the second ST-EX) was significantly lower than that during the REST session (p<0.01). The area under the curve was also 18% lower during the ST-EX session than during the REST session (p<0.05). The heart rate and blood lactate levels indicated that the actual intensity of ST-EX was 'hard'. In contrast, the rating of perceived exertion (RPE) indicated that the overall intensity of ST-EX was 'moderate' because of decreased RPE scores during descent. The present findings suggest that performing 3 min ST-EX 60 and 120 min after a meal may be a useful strategy to accelerate the decrease in postprandial BG levels in people with T2D.

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

    Science.gov (United States)

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

    2012-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Andrew MacDonald

    2016-03-01

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

  18. DB2 9 for zOS Database Administration Certification Study Guide

    CERN Document Server

    Lawson, Susan

    2008-01-01

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

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

    CERN Document Server

    O'Higgins, Niall

    2011-01-01

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

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

    Science.gov (United States)

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

    2010-01-01

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

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

    International Nuclear Information System (INIS)

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

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-02-12

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

  3. GenMapDB: a database of mapped human BAC clones

    OpenAIRE

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

    2001-01-01

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

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

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

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

    African Journals Online (AJOL)

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

  7. AutDB: a platform to decode the genetic architecture of autism.

    Science.gov (United States)

    Pereanu, Wayne; Larsen, Eric C; Das, Ishita; Estévez, Marcel A; Sarkar, Anjali A; Spring-Pearson, Senanu; Kollu, Ravi; Basu, Saumyendra N; Banerjee-Basu, Sharmila

    2018-01-04

    AutDB is a deeply annotated resource for exploring the impact of genetic variations associated with autism spectrum disorders (ASD). First released in 2007, AutDB has evolved into a multi-modular resource of diverse types of genetic and functional evidence related to ASD. Current modules include: Human Gene, which annotates all ASD-linked genes and their variants; Animal Model, which catalogs behavioral, anatomical and physiological data from rodent models of ASD; Protein Interaction (PIN), which builds interactomes from direct relationships of protein products of ASD genes; and Copy Number Variant (CNV), which catalogs deletions and duplications of chromosomal loci identified in ASD. A multilevel data-integration strategy is utilized to connect the ASD genes to the components of the other modules. All information in this resource is manually curated by expert scientists from primary scientific publications and is referenced to source articles. AutDB is actively maintained with a rigorous quarterly data release schedule. As of June 2017, AutDB contains detailed annotations for 910 genes, 2197 CNV loci, 1060 rodent models and 38 296 PINs. With its widespread use by the research community, AutDB serves as a reference resource for analysis of large datasets, accelerating ASD research and potentially leading to targeted drug treatments. AutDB is available at http://autism.mindspec.org/autdb/Welcome.do. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

    Science.gov (United States)

    Breuer, Karin; Foroushani, Amir K.; Laird, Matthew R.; Chen, Carol; Sribnaia, Anastasia; Lo, Raymond; Winsor, Geoffrey L.; Hancock, Robert E. W.; Brinkman, Fiona S. L.; Lynn, David J.

    2013-01-01

    InnateDB (http://www.innatedb.com) is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. In this article, we provide details of recent updates and improvements to the database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. More recently, InnateDB has also initiated the curation of allergy- and asthma-related interactions. Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface, enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools. Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism. PMID:23180781

  9. InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation.

    Science.gov (United States)

    Breuer, Karin; Foroushani, Amir K; Laird, Matthew R; Chen, Carol; Sribnaia, Anastasia; Lo, Raymond; Winsor, Geoffrey L; Hancock, Robert E W; Brinkman, Fiona S L; Lynn, David J

    2013-01-01

    InnateDB (http://www.innatedb.com) is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. In this article, we provide details of recent updates and improvements to the database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. More recently, InnateDB has also initiated the curation of allergy- and asthma-related interactions. Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface, enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools. Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism.

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

    Directory of Open Access Journals (Sweden)

    Longgang Xiang

    2016-07-01

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

  11. A 60-dB linear VGA with novel exponential gain approximation

    International Nuclear Information System (INIS)

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

    2009-01-01

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

  12. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.

    Science.gov (United States)

    Llorens, Carlos; Futami, Ricardo; Covelli, Laura; Domínguez-Escribá, Laura; Viu, Jose M; Tamarit, Daniel; Aguilar-Rodríguez, Jose; Vicente-Ripolles, Miguel; Fuster, Gonzalo; Bernet, Guillermo P; Maumus, Florian; Munoz-Pomer, Alfonso; Sempere, Jose M; Latorre, Amparo; Moya, Andres

    2011-01-01

    This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.

  13. PhenoDB: an integrated client/server database for linkage and population genetics.

    Science.gov (United States)

    Cheung, K H; Nadkarni, P; Silverstein, S; Kidd, J R; Pakstis, A J; Miller, P; Kidd, K K

    1996-08-01

    In this paper we describe PhenoDB, an Internet-accessible client/server database application for population and linkage genetics. PhenoDB stores genetic marker data on pedigrees and populations. A database for population and linkage genetics requires two core functions: data management tasks, such as interactive validation during data entry and editing, and data analysis tasks, such as generating summary population statistics and performing linkage analyses. In PhenoDB we attempt to make these tasks as easy as possible. The client/server architecture allows efficient management and manipulation of large datasets via an easy-to-use graphical interface. PhenoDB data (73 populations, 34 pedigrees, approximately 4200 individuals, and close to 80,000 typings) are stored in a generic format that can be readily exported to (or imported from) the file formats required by various existing analysis programs such as LIPED and Lathrop and Lalouel's Multipoint Linkage. PhenoDB allows performance of complex ad-hoc queries and can generate reports for use in project management. Finally, PhenoDB can produce statistical summaries such as allele frequencies, phenotype frequencies, and Chi-square tests of Hardy-Weinberg ratios of population/pedigree data.

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

    Directory of Open Access Journals (Sweden)

    Jing Chen

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

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

    Directory of Open Access Journals (Sweden)

    Kwang-Hyoung Lee

    2014-05-01

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

  16. Red raspberry decreases heart biomarkers of cardiac remodeling associated with oxidative and inflammatory stress in obese diabetic db/db mice.

    Science.gov (United States)

    Noratto, Giuliana; Chew, Boon P; Ivanov, Ivan

    2016-12-07

    Early diagnosis of risks of heart disease can be critical to fight cardiovascular diseases (CVD) associated with obesity and diabetes and for the implementation of nutritional interventions. The objective of this study was to investigate the cardioprotective effects of red raspberry consumption in the obese diabetic (db/db) mice using proteomic analysis as a tool. Hearts harvested from db/db mice fed an isocaloric diet (AIN-93G, control group) or AIN-93G supplemented with freeze-dried raspberry (raspberry group) for eight weeks were analyzed for changes in protein expression. Bioinformatics and pathway analysis of proteomic data detected in >50% samples were scrutinized with Database for Annotation, Visualization and Integrated Discovery (DAVID). Histologic analysis, adipokines and lipid quantification in heart tissues were assessed as end points for disease biomarkers. Results from proteomic data identified five proteins unique to the control group involved in cardiac remodeling and one involved in stress response. Twenty-five proteins expressed in both groups were differentially downregulated in the raspberry group (p raspberry and control groups were detected in heart lipid composition, adipokines, and morphology within the study timeframe. In conclusion, raspberry consumption may be effective in decreasing the levels of oxidative and inflammatory stress that promote morphological changes in the heart at an older age, thus preventing or delaying heart diseases.

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

    Directory of Open Access Journals (Sweden)

    An Chen

    2015-03-01

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

  18. A Response Surface Methodology Approach to Investigate the Effect of Sulfur Dioxide, pH, and Ethanol on DbCD and DbVPR Gene Expression and on the Volatile Phenol Production in Dekkera/Brettanomyces bruxellensis CBS2499

    Directory of Open Access Journals (Sweden)

    Federica Valdetara

    2017-09-01

    Full Text Available Dekkera/Brettanomyces bruxellensis, the main spoilage yeast in barrel-aged wine, metabolize hydroxycinnamic acids into off-flavors, namely ethylphenols. Recently, both the enzymes involved in this transformation, the cinnamate decarboxylase (DbCD and the vinylphenol reductase (DbVPR, have been identified. To counteract microbial proliferation in wine, sulfur dioxide (SO2 is used commonly to stabilize the final product, but limiting its use is advised to preserve human health and boost sustainability in winemaking. In the present study, the influence of SO2 was investigated in relation with pH and ethanol factors on the expression of DbCD and DbVPR genes and volatile phenol production in D. bruxellensis CBS2499 strain under different model wines throughout a response surface methodology (RSM. In order to ensure an exact quantification of DbCD and DbVPR expression, an appropriate housekeeping gene was sought among DbPDC, DbALD, DbEF, DbACT, and DbTUB genes by GeNorm and Normfinder algorithms. The latter gene showed the highest expression stability and it was chosen as the reference housekeeping gene in qPCR assays. Even though SO2 could not be commented as main factor because of its statistical irrelevance on the response of DbCD gene, linear interactions with pH and ethanol concurred to define a significant effect (p < 0.05 on its expression. The DbCD gene was generally downregulated respect to a permissive growth condition (0 mg/L mol. SO2, pH 4.5 and 5% v/v ethanol; the combination of the factor levels that maximizes its expression (0.83-fold change was calculated at 0.25 mg/L mol. SO2, pH 4.5 and 12.5% (v/v ethanol. On the contrary, DbVPR expression was not influenced by main factors or by their interactions; however, its expression is maximized (1.80-fold change at the same conditions calculated for DbCD gene. While no linear interaction between factors influenced the off-flavor synthesis, ethanol and pH produced a significant effect as

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

    OpenAIRE

    An Chen; Filip Uzelac

    2015-01-01

    This paper compares two different types of private retirement plans from the perspective of a representative beneficiary: a defined benefit (DB) and a defined contribution (DC) plan. While salary risk is the main common risk factor in DB and DC pension plans, one of the key differences is that DB plans carry portability risks, whereas DC plans bear asset price risk. We model these tradeoffs explicitly in this paper and compare these two plans in a utility-based framework. Our numerical analys...

  20. An Intact Anterior Cruciate Ligament at the Time of Posterior Cruciate Ligament-Retaining Total Knee Arthroplasty Was Associated With Reduced Patient Satisfaction and Inferior Pain and Stair Function.

    Science.gov (United States)

    Jacobs, Cale A; Christensen, Christian P; Karthikeyan, Tharun

    2016-08-01

    Patients with an intact anterior cruciate ligament (ACL) at the time of ACL-sacrificing total knee arthroplasty (TKA) have been suggested to have inferior outcomes compared with those with a dysfunctional ACL. However, to date, no published clinical studies have evaluated the potential link between the condition of the ACL at the time of posterior cruciate ligament-retaining TKA and postoperative pain, function, and satisfaction. As such, the purpose of this study was to compare subjective function, movement-elicited pain, pain at rest, and patient satisfaction between those with an intact or dysfunctional ACL. We identified 562 posterior cruciate ligament-retaining TKAs with complete intraoperative and postoperative data. Patients were categorized based on the condition of the ACL at the time of TKA as either being intact or dysfunctional (absent or lax). Knee Society Function Scores, movement-elicited pain, pain at rest, and patient satisfaction were then compared between groups. At mean follow-up of 5.1 years, a significantly lower proportion of patients in the intact group were satisfied with their operation (intact: 391/453 [86.3%] vs dysfunctional: 102/109 [93.6%], P = .0496). Inspection of the individual activities revealed that the groups did not differ in walking ability or pain when walking; however, the intact group reported significantly reduced ability to navigate stairs with greater pain during that activity. The lack of difference in pain at rest between groups suggests that pain and functional impairments during more demanding activities such as navigating stairs may be associated with the lost function of the ACL rather than by altered central pain processing. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. CartoDB: Una base de datos geoespacial para el desarrollo fácil de aplicaciones web

    OpenAIRE

    Torre Alonso, Javier de la; Álvarez Leiva, Sergio; Santana, Javier

    2012-01-01

    CartoDB es una base de datos geoespacial Open Source. Internamente funciona con PostGIS, Node.js y Mapnik. CartoDB proporciona una interfaz para importar y visualizar datos geoespaciales y una serie de APIs para acceder a los datos mediante sentencias SQL y Tiles. CartoDB puede ser utilizado para múltiples tipos de aplicaciones y visualizaciones online, desde aplicaciones móviles, visualizaciones online, portales geoespaciales y prácticamente cualquier tipo de aplicación geoespacial. CartoDB ...

  2. MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments.

    Science.gov (United States)

    Oliveira, Francislon S; Brestelli, John; Cade, Shon; Zheng, Jie; Iodice, John; Fischer, Steve; Aurrecoechea, Cristina; Kissinger, Jessica C; Brunk, Brian P; Stoeckert, Christian J; Fernandes, Gabriel R; Roos, David S; Beiting, Daniel P

    2018-01-04

    MicrobiomeDB (http://microbiomeDB.org) is a data discovery and analysis platform that empowers researchers to fully leverage experimental variables to interrogate microbiome datasets. MicrobiomeDB was developed in collaboration with the Eukaryotic Pathogens Bioinformatics Resource Center (http://EuPathDB.org) and leverages the infrastructure and user interface of EuPathDB, which allows users to construct in silico experiments using an intuitive graphical 'strategy' approach. The current release of the database integrates microbial census data with sample details for nearly 14 000 samples originating from human, animal and environmental sources, including over 9000 samples from healthy human subjects in the Human Microbiome Project (http://portal.ihmpdcc.org/). Query results can be statistically analyzed and graphically visualized via interactive web applications launched directly in the browser, providing insight into microbial community diversity and allowing users to identify taxa associated with any experimental covariate. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2016-01-18

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

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

    Directory of Open Access Journals (Sweden)

    Ji-Hyun Lee

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

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

    Directory of Open Access Journals (Sweden)

    Luciano Ramalho

    2011-04-01

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

  7. HippDB: a database of readily targeted helical protein–protein interactions

    Science.gov (United States)

    Bergey, Christina M.; Watkins, Andrew M.; Arora, Paramjit S.

    2013-01-01

    Summary: HippDB catalogs every protein–protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface. The Web site accepts queries on variables such as helix length and sequence, and it provides computational alanine scanning and change in solvent-accessible surface area values for every interfacial residue. HippDB is intended to serve as a starting point for structure-based small molecule and peptidomimetic drug development. Availability and implementation: HippDB is freely available on the web at http://www.nyu.edu/projects/arora/hippdb. The Web site is implemented in PHP, MySQL and Apache. Source code freely available for download at http://code.google.com/p/helidb, implemented in Perl and supported on Linux. Contact: arora@nyu.edu PMID:23958730

  8. HippDB: a database of readily targeted helical protein-protein interactions.

    Science.gov (United States)

    Bergey, Christina M; Watkins, Andrew M; Arora, Paramjit S

    2013-11-01

    HippDB catalogs every protein-protein interaction whose structure is available in the Protein Data Bank and which exhibits one or more helices at the interface. The Web site accepts queries on variables such as helix length and sequence, and it provides computational alanine scanning and change in solvent-accessible surface area values for every interfacial residue. HippDB is intended to serve as a starting point for structure-based small molecule and peptidomimetic drug development. HippDB is freely available on the web at http://www.nyu.edu/projects/arora/hippdb. The Web site is implemented in PHP, MySQL and Apache. Source code freely available for download at http://code.google.com/p/helidb, implemented in Perl and supported on Linux. arora@nyu.edu.

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

    Science.gov (United States)

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

    2014-11-01

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

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

    Science.gov (United States)

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

    2018-03-12

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

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

    CERN Document Server

    Dimitrov, Gancho; The ATLAS collaboration

    2017-01-01

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

  12. CerealsDB 3.0: expansion of resources and data integration.

    Science.gov (United States)

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

    2016-06-24

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

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

    Science.gov (United States)

    Smith, Randall

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

  14. MorusDB: a resource for mulberry genomics and genome biology.

    Science.gov (United States)

    Li, Tian; Qi, Xiwu; Zeng, Qiwei; Xiang, Zhonghuai; He, Ningjia

    2014-01-01

    Mulberry is an important cultivated plant that has received the attention of biologists interested in sericulture and plant-insect interaction. Morus notabilis, a wild mulberry species with a minimal chromosome number is an ideal material for whole-genome sequencing and assembly. The genome and transcriptome of M. notabilis were sequenced and analyzed. In this article, a web-based and open-access database, the Morus Genome Database (MorusDB), was developed to enable easy-to-access and data mining. The MorusDB provides an integrated data source and an easy accession of mulberry large-scale genomic sequencing and assembly, predicted genes and functional annotations, expressed sequence tags (ESTs), transposable elements (TEs), Gene Ontology (GO) terms, horizontal gene transfers between mulberry and silkworm and ortholog and paralog groups. Transcriptome sequencing data for M. notabilis root, leaf, bark, winter bud and male flower can also be searched and downloaded. Furthermore, MorusDB provides an analytical workbench with some built-in tools and pipelines, such as BLAST, Search GO, Mulberry GO and Mulberry GBrowse, to facilitate genomic studies and comparative genomics. The MorusDB provides important genomic resources for scientists working with mulberry and other Moraceae species, which include many important fruit crops. Designed as a basic platform and accompanied by the SilkDB, MorusDB strives to be a comprehensive platform for the silkworm-mulberry interaction studies. Database URL: http://morus.swu.edu.cn/morusdb. © The Author(s) 2014. Published by Oxford University Press.

  15. Hypolipidemic and Antidiabetic Effects of Functional Rice Cookies in High-Fat Diet-Fed ICR Mice and db/db Mice.

    Science.gov (United States)

    Hong, Sun Hee; Woo, Minji; Kim, Mijeong; Song, Yeong Ok

    2018-02-23

    We have previously reported the lipid-lowering effects of a Korean rice cookie called dasik (RCD) in comparison with a western style cookie. In this study, Schisandra chinensis (Turcz.) Baill. (Chinese magnolia vine) fruit-supplemented RCD (SRCD) was added to a diet, and the hypolipidemic and antidiabetic effects of different diets were examined by using the ICR and db/db mouse models, respectively. ICR mice were fed the AIN-76 diet, or high-fat diet (HFD), or the RCD- or SRCD-supplemented HFD (10%, w/w) for 9 weeks (n = 7 per group). Compared with the RCD group, plasma and hepatic triglyceride and cholesterol concentrations were decreased in the SRCD group. Hepatic expressions for fatty acid and cholesterol synthesis were downregulated, whereas those for beta-oxidation and cholesterol export were upregulated (P RCD with respect to the suppression of lipid synthesis, oxidative stress, and inflammation and the improvement of glucose metabolism.

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

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

    CERN Document Server

    Sanders, Roger E

    2008-01-01

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

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

    Science.gov (United States)

    Wrenn, Gregory A.

    2005-01-01

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

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

    Lifescience Database Archive (English)

    Full Text Available List Contact us MicrobeDB.jp GOLD Data detail Data name GOLD DOI 10.18908/lsdba.nbdc01181-008.V002 Version V...henotypes of genome-sequenced microbes in JGI GOLD by using MPO. Data file File name: gold.tar.gz File URL: ... Simple search URL - Data acquisition method Metadata of genome-sequenced microbes were obtained from JGI GOLD... Download License Update History of This Database Site Policy | Contact Us GOLD - MicrobeDB.jp | LSDB Archive ...

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

    International Nuclear Information System (INIS)

    Over, H.H.

    2009-01-01

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

  1. Využití MongoDB s Node.js

    OpenAIRE

    Hejtmánková, Kateřina

    2015-01-01

    The aim of my thesis is to provide a collection of examples about document oriented MongoDB database using Node.js platform, specifically using the Mongoose program, for object-document mapping (ODM). The aim is met by analysis of Mongoose and Async module, which provides functions for more comprehensive asynchronous querying, needed for working with input/output to the MongoDB database in Node.js. The main merit of this thesis is (in the general sense) a demonstration of how to create a admi...

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

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Mi... NCBI related data (i.e., BioProject, BioSample, PubMed, and Assembly) which are important to integrate data in Mi...ctories (see the following table). Data file File name: ncbi.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/mi... are important to integrate data in MicrobeDB.jp version 2 were obtained by parsi...ports in NCBI Assembly. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us NCBI - MicrobeDB.jp | LSDB Archive ...

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

    Science.gov (United States)

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

    2008-10-01

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

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

    Science.gov (United States)

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

    2010-08-24

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

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

    Directory of Open Access Journals (Sweden)

    Hoo Ruby LC

    2010-08-01

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

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

    Directory of Open Access Journals (Sweden)

    Shiota Asuka

    2012-11-01

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

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

    International Nuclear Information System (INIS)

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

    1998-01-01

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

  8. ToxRefDB 2.0: Improvements in Capturing Qualitative and Quantitative Data from in vivo Toxicity Studies (SOT)

    Science.gov (United States)

    The Toxicity Reference Database (ToxRefDB) is a publicly accessible resource that contains 40+ years of in vivo dose-response toxicological studies. ToxRefDB provides curated in vivo toxicity data for systematic evaluation of a continuously expanding catalog of chemicals, and co...

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

    Lifescience Database Archive (English)

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

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

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...e following table). Data file File name: sra.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/L...t This Database Database Description Download License Update History of This Database Site Policy | Contact Us SRA - MicrobeDB.jp | LSDB Archive ...

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

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...table). Data file File name: brc.tar.gz File URL: ftp://ftp.biosciencedbc.jp/archive/microbedb/LATEST/brc.ta...rains in JCM. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us BRC - MicrobeDB.jp | LSDB Archive ...

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

    Directory of Open Access Journals (Sweden)

    Is Helianti

    2016-07-01

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

  13. DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.

    Science.gov (United States)

    Sagendorf, Jared M; Berman, Helen M; Rohs, Remo

    2017-07-03

    Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA-protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA-protein complexes. The extracted features are organized in structured data files, which are easily parsed with any programming language or viewed in a browser. We processed a large number of DNA-protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store this data. Users can search the database by combining features of the DNA, protein or DNA-protein interactions at the interface. Additionally, users can upload their own structures for processing privately and securely. DNAproDB provides several interactive and customizable tools for creating visualizations of the DNA-protein interface at different levels of abstraction that can be exported as high quality figures. All functionality is documented and freely accessible at http://dnaprodb.usc.edu. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. The Development of the TPR-DB as Grounded Theory Method

    DEFF Research Database (Denmark)

    Carl, Michael; Schaeffer, Moritz

    2018-01-01

    Initial versions of the translation process research database (TPR-DB), were released around 2011 in an attempt to integrate translation process data from several until then individually collected and scattered translation research projects. While the earlier individual studies had a clear focus ...... and used in qualitative research in social science ad many other research areas. We analyze the TPR-DB development as a Grounded Theory Method....... on quantitative assessment of well-defined research questions on cognitive processes in human translation production, the integration of the data into the TPR-DB allowed for broader qualitative and exploratory research which has led to new codes, categories and research themes. In a constant effort to develop...... and refine the emerging concepts and categories and to validate the developing theories, the TPR-DB has been extended with further translation studies in different languages and translation modes. In this respect, it shares many features with Grounded Theory Method. This method was discovered in 1967...

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

    Directory of Open Access Journals (Sweden)

    Hanspers Kristina

    2010-01-01

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

  16. Integrating XQuery and P2P in MonetDB/XQuery*

    NARCIS (Netherlands)

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

    2007-01-01

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

  17. AmbientDB : relational query processing in a P2P network

    NARCIS (Netherlands)

    P.A. Boncz (Peter); C. Treijtel

    2003-01-01

    textabstractA new generation of applications running on a network of nodes, that share data on an ad-hoc basis, will benefit from data management services including powerful querying facilities. In this paper, we introduce the goals, assumptions and architecture of AmbientDB, a new peer-to-peer

  18. AmbientDB: relational query processing in a P2P network

    NARCIS (Netherlands)

    P.A. Boncz (Peter); C. Treijtel

    2003-01-01

    textabstractA new generation of applications running on a network of nodes, that share data on an ad-hoc basis, will benefit from data management services including powerful querying facilities. In this paper, we introduce the goals, assumptions and architecture of AmbientDB, a new peer-to-peer

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

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Mi... data descriptions are about the downloadable data in this page. They might not correspond to the contents o...ense Update History of This Database Site Policy | Contact Us Download - MicrobeDB.jp | LSDB Archive ...

  20. Fast faceted search in XML: using XQuery and ondexes in eXist-db

    NARCIS (Netherlands)

    Schuth, A.; Marx, M.

    2011-01-01

    We present and compare three implementations of faceted search in eXist-db, an XML database. The bit-vector based implementation outperforms the other two implementations in that performance is near constant when the size of the database grows. We investigate this method in detail to pinpoint the

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

    Science.gov (United States)

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

    2015-04-01

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

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

    Science.gov (United States)

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

    2016-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Ogurtsov Aleksey Y

    2008-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Lucchetti-Miganeh Céline

    2010-03-01

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

  5. HIVsirDB: a database of HIV inhibiting siRNAs.

    Directory of Open Access Journals (Sweden)

    Atul Tyagi

    Full Text Available Human immunodeficiency virus (HIV is responsible for millions of deaths every year. The current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. RNA interference (RNAi is a potent candidate for the future treatment of HIV, uses short interfering RNA (siRNA/shRNA for silencing HIV genes. In this study, attempts have been made to create a database HIVsirDB of siRNAs responsible for silencing HIV genes.HIVsirDB is a manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. Information was collected and compiled from literature and public resources. This database contains around 750 siRNAs that includes 75 partially complementary siRNAs differing by one or more bases with the target sites and over 100 escape mutant sequences. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. In order to facilitate user, many tools have been integrated in this database that includes; i siRNAmap for mapping siRNAs on target sequence, ii HIVsirblast for BLAST search against database, iii siRNAalign for aligning siRNAs.HIVsirDB is a freely accessible database of siRNAs which can silence or degrade HIV genes. It covers 26 types of HIV strains and 28 cell types. This database will be very useful for developing models for predicting efficacy of HIV inhibiting siRNAs. In summary this is a useful resource for researchers working in the field of siRNA based HIV therapy. HIVsirDB database is accessible at http://crdd.osdd.net/raghava/hivsir/.

  6. HIVsirDB: a database of HIV inhibiting siRNAs.

    Science.gov (United States)

    Tyagi, Atul; Ahmed, Firoz; Thakur, Nishant; Sharma, Arun; Raghava, Gajendra P S; Kumar, Manoj

    2011-01-01

    Human immunodeficiency virus (HIV) is responsible for millions of deaths every year. The current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. RNA interference (RNAi) is a potent candidate for the future treatment of HIV, uses short interfering RNA (siRNA/shRNA) for silencing HIV genes. In this study, attempts have been made to create a database HIVsirDB of siRNAs responsible for silencing HIV genes. HIVsirDB is a manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. Information was collected and compiled from literature and public resources. This database contains around 750 siRNAs that includes 75 partially complementary siRNAs differing by one or more bases with the target sites and over 100 escape mutant sequences. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. In order to facilitate user, many tools have been integrated in this database that includes; i) siRNAmap for mapping siRNAs on target sequence, ii) HIVsirblast for BLAST search against database, iii) siRNAalign for aligning siRNAs. HIVsirDB is a freely accessible database of siRNAs which can silence or degrade HIV genes. It covers 26 types of HIV strains and 28 cell types. This database will be very useful for developing models for predicting efficacy of HIV inhibiting siRNAs. In summary this is a useful resource for researchers working in the field of siRNA based HIV therapy. HIVsirDB database is accessible at http://crdd.osdd.net/raghava/hivsir/.

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

    Directory of Open Access Journals (Sweden)

    Amit Kumar

    2018-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Jose F. Garcia-Mazcorro

    2018-01-01

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

  9. MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome

    Science.gov (United States)

    Liu, Hui; Wang, Huaizhi; Wei, Zhen; Zhang, Songyao; Hua, Gang; Zhang, Shao-Wu; Zhang, Lin; Gao, Shou-Jiang

    2018-01-01

    Abstract Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. A knowledge base with the systematic collection and curation of context specific transcriptome-wide methylations is critical for elucidating their biological functions as well as for developing bioinformatics tools. Since its inception in 2014, the Met-DB (Liu, H., Flores, M.A., Meng, J., Zhang, L., Zhao, X., Rao, M.K., Chen, Y. and Huang, Y. (2015) MeT-DB: a database of transcriptome methylation in mammalian cells. Nucleic Acids Res., 43, D197–D203), has become an important resource for methyltranscriptome, especially in the N6-methyl-adenosine (m6A) research community. Here, we report Met-DB v2.0, the significantly improved second version of Met-DB, which is entirely redesigned to focus more on elucidating context-specific m6A functions. Met-DB v2.0 has a major increase in context-specific m6A peaks and single-base sites predicted from 185 samples for 7 species from 26 independent studies. Moreover, it is also integrated with a new database for targets of m6A readers, erasers and writers and expanded with more collections of functional data. The redesigned Met-DB v2.0 web interface and genome browser provide more friendly, powerful, and informative ways to query and visualize the data. More importantly, MeT-DB v2.0 offers for the first time a series of tools specifically designed for understanding m6A functions. Met-DB V2.0 will be a valuable resource for m6A methyltranscriptome research. The Met-DB V2.0 database is available at http://compgenomics.utsa.edu/MeTDB/ and http://www.xjtlu.edu.cn/metdb2. PMID:29126312

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

    Science.gov (United States)

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

    2008-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Qichang Xing

    2018-01-01

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

  12. High-throughput screening for GPR119 modulators identifies a novel compound with anti-diabetic efficacy in db/db mice.

    Directory of Open Access Journals (Sweden)

    Meng Zhang

    Full Text Available G protein-coupled receptor 119 (GPR119 is highly expressed in pancreatic β cells and enteroendocrine cells. It is involved in glucose-stimulated insulin secretion and glucagon-like peptide-1 (GLP-1 release, thereby representing a promising target for the treatment of type 2 diabetes. Although a number of GPR119 agonists were developed, no positive allosteric modulator (PAM to this receptor has been reported. Here we describe a high-throughput assay for screening GPR119 PAMs and agonists simultaneously. Following screening of a small molecule compound library containing 312,000 synthetic and natural product-derived samples, one potent GPR119 agonist with novel chemical structure, MW1219, was identified. Exposure of MIN6 and GLUTag cells to MW1219 enhanced glucose-stimulated insulin secretion and GLP-1 release; once-daily oral dosing of MW1219 for 6 weeks in diabetic db/db mice reduced hemoglobin A1c (HbA1c and improved plasma glucose, insulin and GLP-1 levels; it also increased glucose tolerance. The results demonstrate that MW1219 is capable of effectively controlling blood glucose level and may have the potential to be developed as a new class of anti-diabetic agents.

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

    Directory of Open Access Journals (Sweden)

    Na Hu

    2013-01-01

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

  14. Delayed Wound Healing in Diabetic (db/db) Mice with Pseudomonas aeruginosa Biofilm Challenge – A Model for the Study of Chronic Wounds

    Science.gov (United States)

    Zhao, Ge; Hochwalt, Phillip C.; Usui, Marcia L.; Underwood, Robert A.; Singh, Pradeep K.; James, Garth A.; Stewart, Philip S.; Fleckman, Philip; Olerud, John E.

    2010-01-01

    Chronic wounds are a major clinical problem that leads to considerable morbidity and mortality. We hypothesized that an important factor in the failure of chronic wounds to heal was the presence of microbial biofilm resistant to antibiotics and protected from host defenses. A major difficulty in studying chronic wounds is the absence of suitable animal models. The goal of this study was to create a reproducible chronic wound model in diabetic mice by application of bacterial biofilm. Six millimeter punch biopsy wounds were created on the dorsal surface of diabetic (db/db) mice, subsequently challenged with Pseudomonas aeruginosa (PAO1) biofilms two days post-wounding, and covered with semi-occlusive dressings for two weeks. Most of the control wounds were epithelialized by 28 days post-wounding. In contrast, none of biofilm challenged wounds were closed. Histological analysis showed extensive inflammatory cell infiltration, tissue necrosis and epidermal hyperplasia adjacent to challenged wounds- all indicators of an inflammatory non-healing wound. Quantitative cultures and transmission electron microscopy demonstrated that the majority of bacteria were in the scab above the wound bed rather than in the wound tissue. The model was reproducible, allowed localized cutaneous wound infections without high mortality and demonstrated delayed wound healing following biofilm challenge. This model may provide an approach to study the role of microbial biofilms in chronic wounds as well as the effect of specific biofilm therapy on wound healing. PMID:20731798

  15. Sustained release of human growth hormone (hGH) from collagen film and evaluation of effect on wound healing in db/db mice.

    Science.gov (United States)

    Maeda, M; Kadota, K; Kajihara, M; Sano, A; Fujioka, K

    2001-12-13

    Collagen films containing human growth hormone (hGH) were prepared and the release of hGH from these films and their effect on healing of full-thickness wounds in db/db mice were evaluated. The release profiles of hGH from the collagen films varied with composition and preparation conditions. The film prepared by air-drying of the mixture of hGH and collagen solution released hGH continuously over 3 days both in vitro and in vivo. By application of collagen film containing 3 mg of hGH twice at an interval of 6 days to wounds, area of wounds on day 21 was significantly reduced compared with that of non-treated wounds. Application of hGH alone at the same dose had no significant effect on wound healing. The maximum serum hGH concentration after single administration of the hGH collagen film was lower than that with hGH alone, and hGH persisted in serum over 3 days. These results suggest that hGH collagen film may be a useful topical formulation for the treatment of wounds.

  16. Writing and querying MapReduce views in CouchDB

    CERN Document Server

    Holt, Bradley

    2011-01-01

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

  17. SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss

    Science.gov (United States)

    Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

    2011-01-01

    SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/ PMID:22120661

  18. TaDb: A time-aware diffusion-based recommender algorithm

    Science.gov (United States)

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

    2015-02-01

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

  19. Programming Amazon Web Services S3, EC2, SQS, FPS, and SimpleDB

    CERN Document Server

    Murty, James

    2009-01-01

    With this book, you'll learn how companies can take advantage of Amazon Web Services (AWS) to rent" computing power, data storage and bandwidth on Amazon's vast network infrastructure. Programming Amazon Web Services gives developers the background and technical detail they need for using Amazon's subscription-based Simple Storage Service (S3), Elastic Compute Cloud (EC2), Simple Queue Service (SQS), Flexible Payments Service (FPS), and SimpleDB to build web-scale business applications. "

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

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...V002 Version V2 10.18908/lsdba.nbdc01181-005.V002 Update History V1 10.18908/lsdba.nbdc01181-005.V001 - Desc...tabase Description Download License Update History of This Database Site Policy | Contact Us Refsequence - MicrobeDB.jp | LSDB Archive ...

  1. Distribution of strontium in DB18K6 and DTBDB18K6 systems

    International Nuclear Information System (INIS)

    Usarov, Z.O.; Khujaev, S.

    2007-01-01

    Distributions of strontium in DB18K6 and DTBDB18K6 crown-ethers in chloroform were investigated for extraction of strontium from water solutions of nitric acid. Nitrate solutions with various pH were considered. In both crown-ethers the most extraction of strontium was observed for the moderate pH values. Equilibrium of extraction process is reached for comparatively short time and is occurred to be 20 min (authors)

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

    Science.gov (United States)

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

    2018-01-01

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

  3. MatDB Online analysis of HTR materials data from European R and D

    International Nuclear Information System (INIS)

    Over, H.H.; Hähner, P.

    2012-01-01

    Recent high temperature reactor (HTR) concepts for nuclear co-generation foresee hot gas temperatures up to 850 °C. While suitable materials for the high temperature exposed components well-known from conventional technologies are taken into consideration, extended material qualification tests must still be performed for reactor design and licensing to guarantee safe and economic operation. For this purpose data management tools are required. For administration of materials data coming from European R and D projects the Joint Research Centre – Institute for Energy (JRC-IE) offers the web-enabled MAterials DataBase (MatDB Online) free of charge to the European research community. It represents a comprehensive tool for storing, retrieving and evaluating materials test data together with related documentation in a linked document management database (DoMa). MatDB Online hosts materials data from the former German high temperature reactor programme and was, respectively is involved in several GENeration IV (GEN IV) reactor systems related European R and D projects such as HTR-M/M1 (high temperature reactor materials) and RAPHAEL (reactor for process heat, hydrogen and electricity generation) and the cross-cutting project GETMAT (GEN IV and transmutation materials). The paper gives an overview of MatDB Online and DoMa as a central storage system for European R and D materials data and documents, describes the HTR materials and the data content within MatDB Online, and gives evaluation examples of HTR materials data. Noting the data transfer obligations within GIF (GEN IV International Forum), the paper concludes with recommendations for further materials testing.

  4. ExpressionDB: An open source platform for distributing genome-scale datasets.

    Directory of Open Access Journals (Sweden)

    Laura D Hughes

    Full Text Available RNA-sequencing (RNA-seq and microarrays are methods for measuring gene expression across the entire transcriptome. Recent advances have made these techniques practical and affordable for essentially any laboratory with experience in molecular biology. A variety of computational methods have been developed to decrease the amount of bioinformatics expertise necessary to analyze these data. Nevertheless, many barriers persist which discourage new labs from using functional genomics approaches. Since high-quality gene expression studies have enduring value as resources to the entire research community, it is of particular importance that small labs have the capacity to share their analyzed datasets with the research community. Here we introduce ExpressionDB, an open source platform for visualizing RNA-seq and microarray data accommodating virtually any number of different samples. ExpressionDB is based on Shiny, a customizable web application which allows data sharing locally and online with customizable code written in R. ExpressionDB allows intuitive searches based on gene symbols, descriptions, or gene ontology terms, and it includes tools for dynamically filtering results based on expression level, fold change, and false-discovery rates. Built-in visualization tools include heatmaps, volcano plots, and principal component analysis, ensuring streamlined and consistent visualization to all users. All of the scripts for building an ExpressionDB with user-supplied data are freely available on GitHub, and the Creative Commons license allows fully open customization by end-users. We estimate that a demo database can be created in under one hour with minimal programming experience, and that a new database with user-supplied expression data can be completed and online in less than one day.

  5. CerealsDB 2.0: an integrated resource for plant breeders and scientists

    Directory of Open Access Journals (Sweden)

    Wilkinson Paul A

    2012-09-01

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

  6. iPPI-DB: an online database of modulators of protein-protein interactions.

    Science.gov (United States)

    Labbé, Céline M; Kuenemann, Mélaine A; Zarzycka, Barbara; Vriend, Gert; Nicolaes, Gerry A F; Lagorce, David; Miteva, Maria A; Villoutreix, Bruno O; Sperandio, Olivier

    2016-01-04

    In order to boost the identification of low-molecular-weight drugs on protein-protein interactions (PPI), it is essential to properly collect and annotate experimental data about successful examples. This provides the scientific community with the necessary information to derive trends about privileged physicochemical properties and chemotypes that maximize the likelihood of promoting a given chemical probe to the most advanced stages of development. To this end we have developed iPPI-DB (freely accessible at http://www.ippidb.cdithem.fr), a database that contains the structure, some physicochemical characteristics, the pharmacological data and the profile of the PPI targets of several hundreds modulators of protein-protein interactions. iPPI-DB is accessible through a web application and can be queried according to two general approaches: using physicochemical/pharmacological criteria; or by chemical similarity to a user-defined structure input. In both cases the results are displayed as a sortable and exportable datasheet with links to external databases such as Uniprot, PubMed. Furthermore each compound in the table has a link to an individual ID card that contains its physicochemical and pharmacological profile derived from iPPI-DB data. This includes information about its binding data, ligand and lipophilic efficiencies, location in the PPI chemical space, and importantly similarity with known drugs, and links to external databases like PubChem, and ChEMBL. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. iPPI-DB: an online database of modulators of protein–protein interactions

    Science.gov (United States)

    Labbé, Céline M.; Kuenemann, Mélaine A.; Zarzycka, Barbara; Vriend, Gert; Nicolaes, Gerry A.F.; Lagorce, David; Miteva, Maria A.; Villoutreix, Bruno O.; Sperandio, Olivier

    2016-01-01

    In order to boost the identification of low-molecular-weight drugs on protein–protein interactions (PPI), it is essential to properly collect and annotate experimental data about successful examples. This provides the scientific community with the necessary information to derive trends about privileged physicochemical properties and chemotypes that maximize the likelihood of promoting a given chemical probe to the most advanced stages of development. To this end we have developed iPPI-DB (freely accessible at http://www.ippidb.cdithem.fr), a database that contains the structure, some physicochemical characteristics, the pharmacological data and the profile of the PPI targets of several hundreds modulators of protein–protein interactions. iPPI-DB is accessible through a web application and can be queried according to two general approaches: using physicochemical/pharmacological criteria; or by chemical similarity to a user-defined structure input. In both cases the results are displayed as a sortable and exportable datasheet with links to external databases such as Uniprot, PubMed. Furthermore each compound in the table has a link to an individual ID card that contains its physicochemical and pharmacological profile derived from iPPI-DB data. This includes information about its binding data, ligand and lipophilic efficiencies, location in the PPI chemical space, and importantly similarity with known drugs, and links to external databases like PubChem, and ChEMBL. PMID:26432833

  8. A basic study on the international cooperation using international nuclear DB

    International Nuclear Information System (INIS)

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

    2001-12-01

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

  9. The rice proteogenomics database OryzaPG-DB: development, expansion and new features

    Directory of Open Access Journals (Sweden)

    Mohamed eHelmy

    2012-04-01

    Full Text Available Proteogenomics is the utilization of large-scale proteome data in genome annotation refinement. Our recently developed rice proteogenomics database (OryzaPG-DB is the first sustainable resource for rice shotgun-based proteogenomics, providing information on peptides identified in rice protein digested peptides measured by means of liquid chromatography-tandem mass spectrometry (LC-MS/MS, and mapping of the peptides to their genomic origins and the genomic novelty of each peptide. The sequences of the peptides, proteins, cDNAs and genes, and the gene annotations are available for download in FASTA and GFF3 formats, respectively. Further, an annotated visualization of the gene models, corresponding peptides and genomic novelty is available for each gene, and MS/MS spectra are available for each peptide. In this article, we discuss the utilization of OryzaPG-DB and report on its development, recent content expansions and newly added features in the current version (OryzaPG-DB v1.1.

  10. The DB gap and a new class of pulsating white dwarfs

    Directory of Open Access Journals (Sweden)

    Shibahashi H.

    2013-03-01

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

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

    CERN Document Server

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

    2003-01-01

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

  12. RAId_DbS: Peptide Identification using Database Searches with Realistic Statistics

    Directory of Open Access Journals (Sweden)

    Ogurtsov Aleksey Y

    2007-10-01

    Full Text Available Abstract Background The key to mass-spectrometry-based proteomics is peptide identification. A major challenge in peptide identification is to obtain realistic E-values when assigning statistical significance to candidate peptides. Results Using a simple scoring scheme, we propose a database search method with theoretically characterized statistics. Taking into account possible skewness in the random variable distribution and the effect of finite sampling, we provide a theoretical derivation for the tail of the score distribution. For every experimental spectrum examined, we collect the scores of peptides in the database, and find good agreement between the collected score statistics and our theoretical distribution. Using Student's t-tests, we quantify the degree of agreement between the theoretical distribution and the score statistics collected. The T-tests may be used to measure the reliability of reported statistics. When combined with reported P-value for a peptide hit using a score distribution model, this new measure prevents exaggerated statistics. Another feature of RAId_DbS is its capability of detecting multiple co-eluted peptides. The peptide identification performance and statistical accuracy of RAId_DbS are assessed and compared with several other search tools. The executables and data related to RAId_DbS are freely available upon request.

  13. Establishment and Analysis of Nuclear Structure Data DB for Nuclear Safety Regulation Technique Applications

    International Nuclear Information System (INIS)

    Lee, Young Ouk; Yoo, Jae Kwon; Gil, Choong; Cho, Young Sik; Kim, Hyung Il; Kim, Jong Woon; Kwon, Duk Hee; Lee, Jong Hwa

    2013-10-01

    The contents of the project consisting of four research fields carried out are: Ο Installation of DB with nuclear structure/decay datasets - Setup a computer system for production of nuclear structure/decay data in ENSDF format - Production of nuclear structure/decay data in ENSDF format( 211 , 215 Po, 136 Cs) and setup a data converting system from ENSDF format to ENDF-6 format. Ο Computer simulation of nuclear decay and burnup using the ENSDF DB - Calculation of decay heats of the several radioactive nuclides with Geant4 - Burnup calculation with full decay chain using Monte Carlo method Ο Comparison and analysis of nuclear structure/decay and fission product yields data. - Acquisitions and Analyses of decay and fission yields data in ENDF-6 format - Research for theoretical evaluation method of fission product yields data. Ο Analysis of SCALE(ORIGEN-s, -ARP) libraries - Analysis of ORIGEN library structure of nuclear decay/yields data. - Methodological studies to improve nuclear decay/yield ORIGEN libraries by use of nuclear structure/yield data in ENDF-6 format. The results of this project will be a basis to establish the nuclear decay and fission yield data DB in Korea. Additionally, new decay and yield data can be immediately served for the users to utilize those data for nuclear research and/or development

  14. Chemical studies of Rf and Db in liquid-phases using automated rapid chemical separation apparatuses at JAEA

    International Nuclear Information System (INIS)

    Tsukada, Kazuaki; Toyoshima, Atsushi; Asai, Masato; Ishii, Yasuo; Sato, Tetsuya K.; Nagame, Yuichi; Schädel, M.; Kasamatsu, Y.; Li, Z.J.; Haba, H.

    2013-01-01

    We present chemical studies of element 104, rutherfordium (Rf), and element 105, dubnium (Db), in liquid-phases at JAEA. The experiments based on an atom-at-a-time scale have been performed using an automated rapid ion-exchange separation apparatuses, AIDA and AIDA-II. We have found interesting information for the complex formations of Rf with chloride, nitrate, sulfate, and fluoride ions and Db with fluoride ions in aqueous solutions. (author)

  15. Fully etched apodized grating coupler on the SOI platform with -0.58 dB coupling efficiency.

    Science.gov (United States)

    Ding, Yunhong; Peucheret, Christophe; Ou, Haiyan; Yvind, Kresten

    2014-09-15

    We design and fabricate an ultrahigh coupling efficiency (CE) fully etched apodized grating coupler on the silicon-on-insulator (SOI) platform using subwavelength photonic crystals and bonded aluminum mirror. Fabrication error sensitivity and coupling angle dependence are experimentally investigated. A record ultrahigh CE of -0.58 dB with a 3 dB bandwidth of 71 nm and low back reflection are demonstrated.

  16. Safety, pharmacokinetic, and efficacy studies of oral DB868 in a first stage vervet monkey model of human African trypanosomiasis.

    Directory of Open Access Journals (Sweden)

    John K Thuita

    Full Text Available There are no oral drugs for human African trypanosomiasis (HAT, sleeping sickness. A successful oral drug would have the potential to reduce or eliminate the need for patient hospitalization, thus reducing healthcare costs of HAT. The development of oral medications is a key objective of the Consortium for Parasitic Drug Development (CPDD. In this study, we investigated the safety, pharmacokinetics, and efficacy of a new orally administered CPDD diamidine prodrug, 2,5-bis[5-(N-methoxyamidino-2-pyridyl]furan (DB868; CPD-007-10, in the vervet monkey model of first stage HAT. DB868 was well tolerated at a dose up to 30 mg/kg/day for 10 days, a cumulative dose of 300 mg/kg. Mean plasma levels of biomarkers indicative of liver injury (alanine aminotransferase, aspartate aminotransferase were not significantly altered by drug administration. In addition, no kidney-mediated alterations in creatinine and urea concentrations were detected. Pharmacokinetic analysis of plasma confirmed that DB868 was orally available and was converted to the active compound DB829 in both uninfected and infected monkeys. Treatment of infected monkeys with DB868 began 7 days post-infection. In the infected monkeys, DB829 attained a median C(max (dosing regimen that was 12-fold (3 mg/kg/day for 7 days, 15-fold (10 mg/kg/day for 7 days, and 31-fold (20 mg/kg/day for 5 days greater than the IC50 (14 nmol/L against T. b. rhodesiense STIB900. DB868 cured all infected monkeys, even at the lowest dose tested. In conclusion, oral DB868 cured monkeys with first stage HAT at a cumulative dose 14-fold lower than the maximum tolerated dose and should be considered a lead preclinical candidate in efforts to develop a safe, short course (5-7 days, oral regimen for first stage HAT.

  17. Safety, Pharmacokinetic, and Efficacy Studies of Oral DB868 in a First Stage Vervet Monkey Model of Human African Trypanosomiasis

    Science.gov (United States)

    Thuita, John K.; Wolf, Kristina K.; Murilla, Grace A.; Liu, Qiang; Mutuku, James N.; Chen, Yao; Bridges, Arlene S.; Mdachi, Raymond E.; Ismail, Mohamed A.; Ching, Shelley; Boykin, David W.; Hall, James Edwin; Tidwell, Richard R.; Paine, Mary F.; Brun, Reto; Wang, Michael Zhuo

    2013-01-01

    There are no oral drugs for human African trypanosomiasis (HAT, sleeping sickness). A successful oral drug would have the potential to reduce or eliminate the need for patient hospitalization, thus reducing healthcare costs of HAT. The development of oral medications is a key objective of the Consortium for Parasitic Drug Development (CPDD). In this study, we investigated the safety, pharmacokinetics, and efficacy of a new orally administered CPDD diamidine prodrug, 2,5-bis[5-(N-methoxyamidino)-2-pyridyl]furan (DB868; CPD-007-10), in the vervet monkey model of first stage HAT. DB868 was well tolerated at a dose up to 30 mg/kg/day for 10 days, a cumulative dose of 300 mg/kg. Mean plasma levels of biomarkers indicative of liver injury (alanine aminotransferase, aspartate aminotransferase) were not significantly altered by drug administration. In addition, no kidney-mediated alterations in creatinine and urea concentrations were detected. Pharmacokinetic analysis of plasma confirmed that DB868 was orally available and was converted to the active compound DB829 in both uninfected and infected monkeys. Treatment of infected monkeys with DB868 began 7 days post-infection. In the infected monkeys, DB829 attained a median Cmax (dosing regimen) that was 12-fold (3 mg/kg/day for 7 days), 15-fold (10 mg/kg/day for 7 days), and 31-fold (20 mg/kg/day for 5 days) greater than the IC50 (14 nmol/L) against T. b. rhodesiense STIB900. DB868 cured all infected monkeys, even at the lowest dose tested. In conclusion, oral DB868 cured monkeys with first stage HAT at a cumulative dose 14-fold lower than the maximum tolerated dose and should be considered a lead preclinical candidate in efforts to develop a safe, short course (5–7 days), oral regimen for first stage HAT. PMID:23755309

  18. Image files of PCR data plotted on the FACS profiles - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Plabrain DB Image files of PCR data plotted on the FACS profiles Data detail Data name Image files of PCR data plotte...s FACS-based single-cell PCR data was plotted on the FACS profile, in which cells are sorted by DNA content ...d License Update History of This Database Site Policy | Contact Us Image files of PCR data plotted on the FACS profiles - Plabrain DB | LSDB Archive ...

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Kuczmarski Thomas A

    2006-10-01

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

  1. Overactivity of Liver-Related Neurons in the Paraventricular Nucleus of the Hypothalamus: Electrophysiological Findings indb/dbMice.

    Science.gov (United States)

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

    2017-11-15

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

  2. The SGLT2 inhibitor empagliflozin improves insulin sensitivity in db/db mice both as monotherapy and in combination with linagliptin.

    Science.gov (United States)

    Kern, Matthias; Klöting, Nora; Mark, Michael; Mayoux, Eric; Klein, Thomas; Blüher, Matthias

    2016-02-01

    Combining different drug classes to improve glycemic control is one treatment strategy for type 2 diabetes. The effects on insulin sensitivity of long-term treatment with the sodium glucose co-transporter 2 (SGLT2) inhibitor empagliflozin alone or co-administered with the dipeptidyl peptidase-4 inhibitor linagliptin (both approved antidiabetes drugs) were investigated in mice using euglycemic-hyperinsulinemic clamps. db/db mice (n=15/group) were treated for 8weeks with 10mg/kg/day empagliflozin monotherapy, 10mg/kg/day empagliflozin plus 3mg/kg/day linagliptin combination therapy, or 3mg/kg/day linagliptin monotherapy. At the end of the study, euglycemic-hyperinsulinemic clamp studies were performed 4days after the last dose of treatment. HbA1c and 2-hour fasting glucose concentrations were improved with empagliflozin monotherapy and combination therapy compared with vehicle and linagliptin monotherapy. During the clamp, glucose disposal rates increased and hepatic glucose production decreased with empagliflozin monotherapy and combination therapy compared with vehicle and linagliptin monotherapy. Glucose uptake in liver and kidney was higher with empagliflozin monotherapy and combination therapy compared with vehicle; glucose uptake into both muscle and adipose tissue was only affected by linagliptin treatment. Empagliflozin and combination therapy altered the expression of genes involved in the inflammatory response, fatty acid synthesis and oxidation. These findings suggest that the insulin-sensitizing effects of SGLT2 inhibition contribute to improvements in glycemic control in insulin-resistant states. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Standardized Mori ramulus extract improves insulin secretion and insulin sensitivity in C57BLKS/J db/db mice and INS-1 cells.

    Science.gov (United States)

    Park, Soo-Yeon; Jin, Bora; Shin, Jae-Ho; Adisakwattana, Sirichai; Kwon, Oran

    2017-08-01

    Abnormalities in the hyperbolic relationship between insulin sensitivity and insulin secretion may cause oxidative stress and non-enzymatic glycation, resulting in an increased risk of type 2 diabetes. Here, we performed a 14-week study to investigate the effects of ethanolic extract of Mori ramulus (MRE; 0, 800, and 1600mg/kg body weight) and its signature component oxyresveratrol (OXY; 800mg/kg body weight) on β-cell dysfunction and insulin resistance in C57BLKS/J db/db mice fed with a high-fat diet. Compared with the diabetic control group, the high-dose MRE group showed a significant decrease in fasting blood glucose (p=0.0024); a significant increase in insulin secretion as measured by insulin (p=0.0012) and C-peptide (p=0.0103) levels in plasma and insulin content (p=0.0440) and homeobox factor-1 protein expression (p=0.0148) in the pancreas; and a significant increase in insulin sensitivity as measured by insulin receptor mRNA expression in the liver (p=0.0179) and adipose tissue (p=0.0491). In addition, improvements in the reactive oxygen species level and inflammatory pancreatic and hepatic tissue damage were also observed in the MRE group as assessed by histological findings. A similar but weaker effect was found in the OXY group. Furthermore, we observed a potentiating effect of MRE and OXY on insulin secretion in INS-1 cells in the presence of 27mM glucose, together with an anti-glycation effect as indicated by methylglyoxal-trapping capacity and inhibition of advanced glycation end-product formation. Taken together, these data suggest that MRE could ameliorate β-cell dysfunction and insulin resistance by reducing oxidative damage and advanced glycation end-product (Wagenknecht et al., 2003) formation and that these effects are due, at least in part, to OXY. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  4. MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants

    Directory of Open Access Journals (Sweden)

    Arthur Zwaenepoel

    2018-03-01

    Full Text Available Recent times have seen an enormous growth of “omics” data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms. Besides the identification of missing genes in pathways, these methods also typically enable the discovery of biological regulators (i.e., transcription factors or signaling genes. A previously built guilt-by-association method is MORPH, which was proven to be an efficient algorithm that performs particularly well in identifying and prioritizing missing genes in plant metabolic pathways. Here, we present MorphDB, a resource where MORPH-based candidate genes for large-scale functional annotations (Gene Ontology, MapMan bins are integrated across multiple plant species. Besides a gene centric query utility, we present a comparative network approach that enables researchers to efficiently browse MORPH predictions across functional gene sets and species, facilitating efficient gene discovery and candidate gene prioritization. MorphDB is available at http://bioinformatics.psb.ugent.be/webtools/morphdb/morphDB/index/. We also provide a toolkit, named “MORPH bulk” (https://github.com/arzwa/morph-bulk, for running MORPH in bulk mode on novel data sets, enabling researchers to apply MORPH to their own species of interest.

  5. PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides

    Directory of Open Access Journals (Sweden)

    Sarkar Anita

    2012-11-01

    Full Text Available Abstract Background Polysaccharides are ubiquitously present in the living world. Their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. The knowledge of polysaccharide three-dimensional (3D structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and vaccine development as well as material science applications or production of bio-ethanol. Description PolySac3DB is an annotated database that contains the 3D structural information of 157 polysaccharide entries that have been collected from an extensive screening of scientific literature. They have been systematically organized using standard names in the field of carbohydrate research into 18 categories representing polysaccharide families. Structure-related information includes the saccharides making up the repeat unit(s and their glycosidic linkages, the expanded 3D representation of the repeat unit, unit cell dimensions and space group, helix type, diffraction diagram(s (when applicable, experimental and/or simulation methods used for structure description, link to the abstract of the publication, reference and the atomic coordinate files for visualization and download. The database is accompanied by a user-friendly graphical user interface (GUI. It features interactive displays of polysaccharide structures and customized search options for beginners and experts, respectively. The site also serves as an information portal for polysaccharide structure determination techniques. The web-interface also references external links where other carbohydrate-related resources are available. Conclusion PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available

  6. Packet Capture Solutions: PcapDB Benchmark for High-Bandwidth Capture, Storage, and Searching

    Energy Technology Data Exchange (ETDEWEB)

    Steinfadt, Shannon Irene [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ferrell, Paul Steven [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-03-21

    PcapDB stands alone when looking at the overall field of competitors, from the cost-effective COTS hardware, to the efficient utilization of disk space that enables a longer packet history. A scalable, 100GbE-enabled system that indexes every packet and indexes flow data without complicated load-balancing requirements. The Transport Layer search and indexing approach led to patent-pending flow indexing technology, providing a specialized database system specifically optimized around providing fast flow searches. While there are a plethora of options in network packet capture, there are very few that are able to effectively manage capture rates of more than 10 Gb/s, distributed capture and querying, and a responsive user interface. By far, the primary competitor in the market place is Endace and DeepSee; in addition to meeting the technical requirements we set out in this document, they provide technical support and a fully 'appliance like' system. In terms of cost, however, our experience has been that the yearly maintenance charges alone outstrip the entire hardware cost of solutions like PcapDB. Investment in cyber security research and development is a large part of what has enabled us to build the base of knowlegable workers needed to defend government resources in the rapidly evolving cyber security landscape. We believe projects like Bro, WireCap, and Farm do more than just fill temporary gaps in our capabilities. They give allow us to build the firm foundation needed to tackle the next generation of cyber challenges. PcapDB was built with loftier ambitions than simply solving the packet capture of a single lab site, but instead to provide a robust, scaleable packet capture solution to the DOE complex and beyond.

  7. OpenFluDB, a database for human and animal influenza virus.

    Science.gov (United States)

    Liechti, Robin; Gleizes, Anne; Kuznetsov, Dmitry; Bougueleret, Lydie; Le Mercier, Philippe; Bairoch, Amos; Xenarios, Ioannis

    2010-07-06

    Although research on influenza lasted for more than 100 years, it is still one of the most prominent diseases causing half a million human deaths every year. With the recent observation of new highly pathogenic H5N1 and H7N7 strains, and the appearance of the influenza pandemic caused by the H1N1 swine-like lineage, a collaborative effort to share observations on the evolution of this virus in both animals and humans has been established. The OpenFlu database (OpenFluDB) is a part of this collaborative effort. It contains genomic and protein sequences, as well as epidemiological data from more than 27,000 isolates. The isolate annotations include virus type, host, geographical location and experimentally tested antiviral resistance. Putative enhanced pathogenicity as well as human adaptation propensity are computed from protein sequences. Each virus isolate can be associated with the laboratories that collected, sequenced and submitted it. Several analysis tools including multiple sequence alignment, phylogenetic analysis and sequence similarity maps enable rapid and efficient mining. The contents of OpenFluDB are supplied by direct user submission, as well as by a daily automatic procedure importing data from public repositories. Additionally, a simple mechanism facilitates the export of OpenFluDB records to GenBank. This resource has been successfully used to rapidly and widely distribute the sequences collected during the recent human swine flu outbreak and also as an exchange platform during the vaccine selection procedure. Database URL: http://openflu.vital-it.ch.

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

    Science.gov (United States)

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

    2018-01-01

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

  9. Acoustic effects of the ATOC signal (75 Hz, 195 dB) on dolphins and whales

    Energy Technology Data Exchange (ETDEWEB)

    Au, W.W.; Nachtigall, P.E.; Pawloski, J.L. [Marine Mammal Research Program, Hawaii Institute of Marine Biology, University of Hawaii, P.O. Box 1106, Kailua, Hawaii 96734 (United States)

    1997-05-01

    The Acoustic Thermometry of Ocean Climate (ATOC) program of Scripps Institution of Oceanography and the Applied Physics Laboratory, University of Washington, will broadcast a low-frequency 75-Hz phase modulated acoustic signal over ocean basins in order to study ocean temperatures on a global scale and examine the effects of global warming. One of the major concerns is the possible effect of the ATOC signal on marine life, especially on dolphins and whales. In order to address this issue, the hearing sensitivity of a false killer whale ({ital Pseudorca crassidens}) and a Risso{close_quote}s dolphin ({ital Grampus griseus}) to the ATOC sound was measured behaviorally. A staircase procedure with the signal levels being changed in 1-dB steps was used to measure the animals{close_quote} threshold to the actual ATOC coded signal. The results indicate that small odontocetes such as the {ital Pseudorca} and {ital Grampus} swimming directly above the ATOC source will not hear the signal unless they dive to a depth of approximately 400 m. A sound propagation analysis suggests that the sound-pressure level at ranges greater than 0.5 km will be less than 130 dB for depths down to about 500 m. Several species of baleen whales produce sounds much greater than 170{endash}180 dB. With the ATOC source on the axis of the deep sound channel (greater than 800 m), the ATOC signal will probably have minimal physical and physiological effects on cetaceans. {copyright} {ital 1997 Acoustical Society of America.}

  10. A survey of pulsating DA and DB white dwarfs Observations with the Whole Earth Telescope

    Science.gov (United States)

    Provencal, J. L.; Montgomery, M.; Shipman, H.

    2017-09-01

    White dwarfs represent the end point of stellar evolution for the majority of stars. As such, they are excellent astrophysical laboratories. They are structurally simple, with electron degenerate cores surrounded by thin surface layers of helium and/or hydrogen. The g-mode pulsations provide a window into their internal structure. The Whole Earth Telescope has been conducting a long-term survey of pulsating white dwarfs with the goal of providing an empirical map of convection parameters across the DA and DB instability strips. We present an overview of white dwarf asteroseismology, and discuss the current status of our survey.

  11. DbAccess: Interactive Statistics and Graphics for Plasma Physics Databases

    International Nuclear Information System (INIS)

    Davis, W.; Mastrovito, D.

    2003-01-01

    DbAccess is an X-windows application, written in IDL(reg s ign), meeting many specialized statistical and graphical needs of NSTX [National Spherical Torus Experiment] plasma physicists, such as regression statistics and the analysis of variance. Flexible ''views'' and ''joins,'' which include options for complex SQL expressions, facilitate mixing data from different database tables. General Atomics Plot Objects add extensive graphical and interactive capabilities. An example is included for plasma confinement-time scaling analysis using a multiple linear regression least-squares power fit

  12. T3DB: an integrated database for bacterial type III secretion system

    OpenAIRE

    Wang, Yejun; Huang, He; Sun, Ming’an; Zhang, Qing; Guo, Dianjing

    2012-01-01

    Abstract Background Type III Secretion System (T3SS), which plays important roles in pathogenesis or symbiosis, is widely expressed in a variety of gram negative bacteria. However, lack of unique nomenclature for T3SS genes has hindered T3SS related research. It is necessary to set up a knowledgebase integrating T3SS-related research data to facilitate the communication between different research groups interested in different bacteria. Description A T3SS-related Database (T3DB) was developed...

  13. Protocolo Anamnesis Auditiva para trabajadores expuestos a ruido mayor de 85 dB

    OpenAIRE

    Peñuela Díaz, Ivonne Andrea

    2008-01-01

    Esta obra permite ver la anamnesis como herramienta fundamental y oportuna en el seguimiento a los trabajadores expuestos a ruido mayor de 85dB. A lo largo del texto se realiza una explicación concisa de los temas, mediante recursos didácticos, como guías, cuestionarios, procedimientos, tablas y protocolos, necesarios para el estudio de las leyes y patologías relacionadas con el ruido. Se precisa el papel del fonoaudiólogo en la toma de los datos y de la investigación, en los factores que ...

  14. Component reliability analysis for development of component reliability DB of Korean standard NPPs

    International Nuclear Information System (INIS)

    Choi, S. Y.; Han, S. H.; Kim, S. H.

    2002-01-01

    The reliability data of Korean NPP that reflects the plant specific characteristics is necessary for PSA and Risk Informed Application. We have performed a project to develop the component reliability DB and calculate the component reliability such as failure rate and unavailability. We have collected the component operation data and failure/repair data of Korean standard NPPs. We have analyzed failure data by developing a data analysis method which incorporates the domestic data situation. And then we have compared the reliability results with the generic data for the foreign NPPs

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

    Lifescience Database Archive (English)

    Full Text Available List Contact us MicrobeDB.jp License License to Use This Database Last updated : 2017/06/29 You may use this database...the license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons Attribut...ion-Share Alike 4.0 International . If you use data from this database, please be sure attribute this database... Creative Commons Attribution-Share Alike 4.0 International is found here . With regard to this database, yo

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

    Lifescience Database Archive (English)

    Full Text Available List Contact us dbQSNP License License to Use This Database Last updated : 2017/02/16 You may use this database...cense terms regarding the use of this database and the requirements you must follow in using this database. The license for this data...are Alike 4.0 International . If you use data from this database, please be sure attribute this database as ... ... . The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here . With regard to this database..., you are licensed to: freely access part or whole of this database, and acquire data; fre

  17. License - D-HaploDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us D-HaploDB License License to Use This Database Last updated : 2011/08/25 You may use this database... license terms regarding the use of this database and the requirements you must follow in using this database...-Share Alike 2.1 Japan. If you use data from this database, please be sure attribute this database as follow...ry of the Creative Commons Attribution-Share Alike 2.1 Japan is found here . With regard to this database..., you are licensed to: freely access part or whole of this database, and acquire dat

  18. License - DB-SPIRE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us DB-SPIRE License License to Use This Database Last updated : 2017/02/16 You may use this database...license terms regarding the use of this database and the requirements you must follow in using this database...Share Alike 4.0 International . If you use data from this database, please be sure attribute this database a...eative Commons Attribution-Share Alike 4.0 International is found here . With regard to this database, you a...re licensed to: freely access part or whole of this database, and acquire data; freely redistribute part or

  19. EST sequences and their annotation (amino acid sequence and results of homology search) - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available esource Project ( http://www.nbrp.jp/ ). The link to the National BioResource Pro...List Contact us Dicty_cDB EST sequences and their annotation (amino acid sequence and results of homology se...arch) Data detail Data name EST sequences and their annotation (amino acid sequence and results of homology ...search) DOI 10.18908/lsdba.nbdc00419-001 Description of data contents Sequences of cDNA clones of Dictyostelium discoideum and the...s (with target DBs: dicty EST-DB, DNA-DB and protein-DB)). Links to the Atlas database ( http://dictycdb.bio

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

    International Nuclear Information System (INIS)

    Ginzinger, Simon W.; Coles, Murray

    2009-01-01

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

  1. Establishment and Evaluation of Decommissioning Plant Inventory DB and Waste Quantity

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Jae Yong; Moon, Sang-Rae; Yun, Taesik; Kim, Hee-Geun [KHNP CRI, Daejeon (Korea, Republic of); Sung, Nak-Hoon; Jung, Seung Hyuk [KONES Corp., Seoul (Korea, Republic of)

    2016-10-15

    Korea Hydro and Nuclear Power (KHNP) made a decision for permanent shutdown of Kori-1 and has progressed the strategy determination and R and D for the decommissioning of Kori-1. Decommissioning waste, Structure, System and Components (SSCs) is one of the most important elements. Decommissioning waste quantity is calculated based on Plant Inventory Database (PI DB) with activation and contamination data. Due to the largest portion of waste management and disposal in decommissioning, it is necessary to exactly evaluate waste quantity (applying the regulation, guideline and site-specific characterization) for economic feasibility. In this paper, construction of PI DB and evaluation of waste quantity for Optimized Pressurized Reactor (OPR-1000) are mainly described. Decommissioning waste quantities evaluated are going to be applied to calculation of the project cost. In fact, Ministry of Trade, Industry and Energy (MOTIE) in Korea expected the decommissioning waste quantity in a range of 14,500-18,850 drums, and predicted appropriate liability for decommissioning fund by using waste quantity. The result of this study is also computed by the range of 14,500-18,850 drums. Since there is no site-specific data for the NPP site, this evaluation is the preliminary analysis.

  2. Performance Prediction of a MongoDB-Based Traceability System in Smart Factory Supply Chains

    Science.gov (United States)

    Kang, Yong-Shin; Park, Il-Ha; Youm, Sekyoung

    2016-01-01

    In the future, with the advent of the smart factory era, manufacturing and logistics processes will become more complex, and the complexity and criticality of traceability will further increase. This research aims at developing a performance assessment method to verify scalability when implementing traceability systems based on key technologies for smart factories, such as Internet of Things (IoT) and BigData. To this end, based on existing research, we analyzed traceability requirements and an event schema for storing traceability data in MongoDB, a document-based Not Only SQL (NoSQL) database. Next, we analyzed the algorithm of the most representative traceability query and defined a query-level performance model, which is composed of response times for the components of the traceability query algorithm. Next, this performance model was solidified as a linear regression model because the response times increase linearly by a benchmark test. Finally, for a case analysis, we applied the performance model to a virtual automobile parts logistics. As a result of the case study, we verified the scalability of a MongoDB-based traceability system and predicted the point when data node servers should be expanded in this case. The traceability system performance assessment method proposed in this research can be used as a decision-making tool for hardware capacity planning during the initial stage of construction of traceability systems and during their operational phase. PMID:27983654

  3. GreenPhylDB v2.0: comparative and functional genomics in plants.

    Science.gov (United States)

    Rouard, Mathieu; Guignon, Valentin; Aluome, Christelle; Laporte, Marie-Angélique; Droc, Gaëtan; Walde, Christian; Zmasek, Christian M; Périn, Christophe; Conte, Matthieu G

    2011-01-01

    GreenPhylDB is a database designed for comparative and functional genomics based on complete genomes. Version 2 now contains sixteen full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families. For each gene cluster or gene family, easy access to gene composition, protein domains, publications, external links and orthologous gene predictions is provided. Web interfaces have been further developed to improve the navigation through information related to gene families. New analysis tools are also available, such as a gene family ontology browser that facilitates exploration. GreenPhylDB is a component of the South Green Bioinformatics Platform (http://southgreen.cirad.fr/) and is accessible at http://greenphyl.cirad.fr. It enables comparative genomics in a broad taxonomy context to enhance the understanding of evolutionary processes and thus tends to speed up gene discovery.

  4. Performance Prediction of a MongoDB-Based Traceability System in Smart Factory Supply Chains

    Directory of Open Access Journals (Sweden)

    Yong-Shin Kang

    2016-12-01

    Full Text Available In the future, with the advent of the smart factory era, manufacturing and logistics processes will become more complex, and the complexity and criticality of traceability will further increase. This research aims at developing a performance assessment method to verify scalability when implementing traceability systems based on key technologies for smart factories, such as Internet of Things (IoT and BigData. To this end, based on existing research, we analyzed traceability requirements and an event schema for storing traceability data in MongoDB, a document-based Not Only SQL (NoSQL database. Next, we analyzed the algorithm of the most representative traceability query and defined a query-level performance model, which is composed of response times for the components of the traceability query algorithm. Next, this performance model was solidified as a linear regression model because the response times increase linearly by a benchmark test. Finally, for a case analysis, we applied the performance model to a virtual automobile parts logistics. As a result of the case study, we verified the scalability of a MongoDB-based traceability system and predicted the point when data node servers should be expanded in this case. The traceability system performance assessment method proposed in this research can be used as a decision-making tool for hardware capacity planning during the initial stage of construction of traceability systems and during their operational phase.

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

    Science.gov (United States)

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

    2012-01-01

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

  6. Performance Prediction of a MongoDB-Based Traceability System in Smart Factory Supply Chains.

    Science.gov (United States)

    Kang, Yong-Shin; Park, Il-Ha; Youm, Sekyoung

    2016-12-14

    In the future, with the advent of the smart factory era, manufacturing and logistics processes will become more complex, and the complexity and criticality of traceability will further increase. This research aims at developing a performance assessment method to verify scalability when implementing traceability systems based on key technologies for smart factories, such as Internet of Things (IoT) and BigData. To this end, based on existing research, we analyzed traceability requirements and an event schema for storing traceability data in MongoDB, a document-based Not Only SQL (NoSQL) database. Next, we analyzed the algorithm of the most representative traceability query and defined a query-level performance model, which is composed of response times for the components of the traceability query algorithm. Next, this performance model was solidified as a linear regression model because the response times increase linearly by a benchmark test. Finally, for a case analysis, we applied the performance model to a virtual automobile parts logistics. As a result of the case study, we verified the scalability of a MongoDB-based traceability system and predicted the point when data node servers should be expanded in this case. The traceability system performance assessment method proposed in this research can be used as a decision-making tool for hardware capacity planning during the initial stage of construction of traceability systems and during their operational phase.

  7. Design and development of 3 dB patch compensated tandem hybrid coupler.

    Science.gov (United States)

    Yadav, Rana Pratap; Kumar, Sunil; Kulkarani, S V

    2013-01-01

    Design and development procedure of the strip line based 3 dB patch compensated tandem hybrid coupler at 91.2 ± 15 MHz and 2.5 kW is presented. The coupled strip-line structure is designed and electromagnetic analysis software is used for accurate modelling and optimization of parameters. Coupled strip lines are well known for poor impedance matching and poor isolation due to discontinuities, fabrication tolerance constraints, and theoretical approximations in design. These effects are realized and compensated or taken into consideration. The conventional methods of compensation like open stubs or lumped capacitors are useful in the low rf power applications only. In the present paper, patch compensation technique is explored, explained, applied, and incorporated in the development of a 3 dB tandem hybrid coupler. This newly explored patch compensation technique is found substantially effective in improving the overall performance in terms of return loss and isolation. A prototype tandem coupler rated for 2.5 kW at 91.2 ± 15 MHz, has been developed, fabricated, tested, and the effect of patch compensation technique is found to be quite effective.

  8. Mechanism-informed read-across assessment of skin sensitizers based on SkinSensDB.

    Science.gov (United States)

    Tung, Chun-Wei; Wang, Chia-Chi; Wang, Shan-Shan

    2018-02-24

    Integrative testing strategies using adverse outcome pathway (AOP)-based alternative assays for assessing skin sensitizers show the potential for replacing animal testing. However, the application of alternative assays for a large number of chemicals is still time-consuming and expensive. In order to facilitate the assessment of skin sensitizers based on integrative testing strategies, a mechanism-informed read-across assessment method was proposed and evaluated using data from SkinSensDB. First, the prediction performance of two integrated testing strategy models was evaluated giving the highest area under the receiver operating characteristic curve (AUC) values of 0.928 and 0.837 for predicting human and LLNA data, respectively. The proposed read-across prediction method achieves AUC values of 0.957 and 0.802 for predicting human and LLNA data, respectively, with interpretable activation statuses of AOP events. As data grows, a better prediction performance is expected. A user-friendly tool has been constructed and integrated into SkinSensDB that is publicly accessible at http://cwtung.kmu.edu.tw/skinsensdb. Copyright © 2018 Elsevier Inc. All rights reserved.

  9. OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes

    Directory of Open Access Journals (Sweden)

    Kashish Chetal

    2015-01-01

    Full Text Available Background. In prokaryotic organisms, a substantial fraction of adjacent genes are organized into operons—codirectionally organized genes in prokaryotic genomes with the presence of a common promoter and terminator. Although several available operon databases provide information with varying levels of reliability, very few resources provide experimentally supported results. Therefore, we believe that the biological community could benefit from having a new operon prediction database with operons predicted using next-generation RNA-seq datasets. Description. We present operomeDB, a database which provides an ensemble of all the predicted operons for bacterial genomes using available RNA-sequencing datasets across a wide range of experimental conditions. Although several studies have recently confirmed that prokaryotic operon structure is dynamic with significant alterations across environmental and experimental conditions, there are no comprehensive databases for studying such variations across prokaryotic transcriptomes. Currently our database contains nine bacterial organisms and 168 transcriptomes for which we predicted operons. User interface is simple and easy to use, in terms of visualization, downloading, and querying of data. In addition, because of its ability to load custom datasets, users can also compare their datasets with publicly available transcriptomic data of an organism. Conclusion. OperomeDB as a database should not only aid experimental groups working on transcriptome analysis of specific organisms but also enable studies related to computational and comparative operomics.

  10. PcapDB: Search Optimized Packet Capture, Version 0.1.0.0

    Energy Technology Data Exchange (ETDEWEB)

    2016-11-04

    PcapDB is a packet capture system designed to optimize the captured data for fast search in the typical (network incident response) use case. The technology involved in this software has been submitted via the IDEAS system and has been filed as a provisional patent. It includes the following primary components: capture: The capture component utilizes existing capture libraries to retrieve packets from network interfaces. Once retrieved the packets are passed to additional threads for sorting into flows and indexing. The sorted flows and indexes are passed to other threads so that they can be written to disk. These components are written in the C programming language. search: The search components provide a means to find relevant flows and the associated packets. A search query is parsed and represented as a search tree. Various search commands, written in C, are then used resolve this tree into a set of search results. The tree generation and search execution management components are written in python. interface: The PcapDB web interface is written in Python on the Django framework. It provides a series of pages, API's, and asynchronous tasks that allow the user to manage the capture system, perform searches, and retrieve results. Web page components are written in HTML,CSS and Javascript.

  11. MycoDB, a global database of plant response to mycorrhizal fungi

    Science.gov (United States)

    Chaudhary, V. Bala; Rúa, Megan A.; Antoninka, Anita; Bever, James D.; Cannon, Jeffery; Craig, Ashley; Duchicela, Jessica; Frame, Alicia; Gardes, Monique; Gehring, Catherine; Ha, Michelle; Hart, Miranda; Hopkins, Jacob; Ji, Baoming; Johnson, Nancy Collins; Kaonongbua, Wittaya; Karst, Justine; Koide, Roger T.; Lamit, Louis J.; Meadow, James; Milligan, Brook G.; Moore, John C.; Pendergast, Thomas H., IV; Piculell, Bridget; Ramsby, Blake; Simard, Suzanne; Shrestha, Shubha; Umbanhowar, James; Viechtbauer, Wolfgang; Walters, Lawrence; Wilson, Gail W. T.; Zee, Peter C.; Hoeksema, Jason D.

    2016-05-01

    Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis metrics and 24 additional explanatory variables that describe the biotic and abiotic context of each study. We also include phylogenetic trees for all plants and fungi in the database. To our knowledge, MycoDB is the largest ecological meta-analysis database. We aim to share these data to highlight significant gaps in mycorrhizal research and encourage synthesis to explore the ecological and evolutionary generalities that govern mycorrhizal functioning in ecosystems.

  12. MUFOLD-DB: a processed protein structure database for protein structure prediction and analysis.

    Science.gov (United States)

    He, Zhiquan; Zhang, Chao; Xu, Yang; Zeng, Shuai; Zhang, Jingfen; Xu, Dong

    2014-01-01

    Protein structure data in Protein Data Bank (PDB) are widely used in studies of protein function and evolution and in protein structure prediction. However, there are two main barriers in large-scale usage of PDB data: 1) PDB data are highly redundant in terms of sequence and structure similarity; and 2) many PDB files have issues due to inconsistency of data and standards as well as missing residues, so that automated retrieval and analysis are often difficult. To address these issues, we have created MUFOLD-DB http://mufold.org/mufolddb.php, a web-based database, to collect and process the weekly PDB files thereby providing users with non-redundant, cleaned and partially-predicted structure data. For each of the non-redundant sequences, we annotate the SCOP domain classification and predict structures of missing regions by loop modelling. In addition, evolutional information, secondary structure, disorder region, and processed three-dimensional structure are computed and visualized to help users better understand the protein. MUFOLD-DB integrates processed PDB sequence and structure data and multiple computational results, provides a friendly interface for users to retrieve, browse and download these data, and offers several useful functionalities to facilitate users' data operation.

  13. H2DB: a heritability database across multiple species by annotating trait-associated genomic loci.

    Science.gov (United States)

    Kaminuma, Eli; Fujisawa, Takatomo; Tanizawa, Yasuhiro; Sakamoto, Naoko; Kurata, Nori; Shimizu, Tokurou; Nakamura, Yasukazu

    2013-01-01

    H2DB (http://tga.nig.ac.jp/h2db/), an annotation database of genetic heritability estimates for humans and other species, has been developed as a knowledge database to connect trait-associated genomic loci. Heritability estimates have been investigated for individual species, particularly in human twin studies and plant/animal breeding studies. However, there appears to be no comprehensive heritability database for both humans and other species. Here, we introduce an annotation database for genetic heritabilities of various species that was annotated by manually curating online public resources in PUBMED abstracts and journal contents. The proposed heritability database contains attribute information for trait descriptions, experimental conditions, trait-associated genomic loci and broad- and narrow-sense heritability specifications. Annotated trait-associated genomic loci, for which most are single-nucleotide polymorphisms derived from genome-wide association studies, may be valuable resources for experimental scientists. In addition, we assigned phenotype ontologies to the annotated traits for the purposes of discussing heritability distributions based on phenotypic classifications.

  14. 0dB Eb/N(0) burst mode SCPC modem with high coding gain FEC

    Science.gov (United States)

    Namiki, Junji; Ohtani, Susumu; Yasuda, Yutaka

    A digital SCPC modem for 0dB Eb/N(0) burst signal is described in this paper. When demodulation process is followed by a powerful error correction function, carrier phase and clock timing control systems should maintain control in a higher bit error rate (BER) environment so as to obtain a sufficient error correction performance. This paper presents new digital demodulator structure satisfying above mentioned requirements by using digital signal processors. A proposed demodulator has a new adaptive PLL called 'Beatless Pull-In PLL', and a highly reliable 'carrier detector' to detect carrier portion of preamble. A proposed demodulator has been manufactured, and a misacquisition probability was experimentally verified to be less than .0025 at C/N = 3 dB (Eb/N(0) = 0db).

  15. DB4US: A Decision Support System for Laboratory Information Management.

    Science.gov (United States)

    Carmona-Cejudo, José M; Hortas, Maria Luisa; Baena-García, Manuel; Lana-Linati, Jorge; González, Carlos; Redondo, Maximino; Morales-Bueno, Rafael

    2012-11-14

    Until recently, laboratory automation has focused primarily on improving hardware. Future advances are concentrated on intelligent software since laboratories performing clinical diagnostic testing require improved information systems to address their data processing needs. In this paper, we propose DB4US, an application that automates information related to laboratory quality indicators information. Currently, there is a lack of ready-to-use management quality measures. This application addresses this deficiency through the extraction, consolidation, statistical analysis, and visualization of data related to the use of demographics, reagents, and turn-around times. The design and implementation issues, as well as the technologies used for the implementation of this system, are discussed in this paper. To develop a general methodology that integrates the computation of ready-to-use management quality measures and a dashboard to easily analyze the overall performance of a laboratory, as well as automatically detect anomalies or errors. The novelty of our approach lies in the application of integrated web-based dashboards as an information management system in hospital laboratories. We propose a new methodology for laboratory information management based on the extraction, consolidation, statistical analysis, and visualization of data related to demographics, reagents, and turn-around times, offering a dashboard-like user web interface to the laboratory manager. The methodology comprises a unified data warehouse that stores and consolidates multidimensional data from different data sources. The methodology is illustrated through the implementation and validation of DB4US, a novel web application based on this methodology that constructs an interface to obtain ready-to-use indicators, and offers the possibility to drill down from high-level metrics to more detailed summaries. The offered indicators are calculated beforehand so that they are ready to use when the user

  16. Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.

    Science.gov (United States)

    Narsai, Reena; Devenish, James; Castleden, Ian; Narsai, Kabir; Xu, Lin; Shou, Huixia; Whelan, James

    2013-12-01

    Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au). © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

  17. New Role for DCR-1/Dicer in Caenorhabditis elegans Innate Immunity against the Highly Virulent Bacterium Bacillus thuringiensis DB27

    Science.gov (United States)

    Iatsenko, Igor; Sinha, Amit; Rödelsperger, Christian

    2013-01-01

    Bacillus thuringiensis produces toxins that target invertebrates, including Caenorhabditis elegans. Virulence of Bacillus strains is often highly specific, such that B. thuringiensis strain DB27 is highly pathogenic to C. elegans but shows no virulence for another model nematode, Pristionchus pacificus. To uncover the underlying mechanisms of the differential responses of the two nematodes to B. thuringiensis DB27 and to reveal the C. elegans defense mechanisms against this pathogen, we conducted a genetic screen for C. elegans mutants resistant to B. thuringiensis DB27. Here, we describe a B. thuringiensis DB27-resistant C. elegans mutant that is identical to nasp-1, which encodes the C. elegans homolog of the nuclear-autoantigenic-sperm protein. Gene expression analysis indicated a substantial overlap between the genes downregulated in the nasp-1 mutant and targets of C. elegans dcr-1/Dicer, suggesting that dcr-1 is repressed in nasp-1 mutants, which was confirmed by quantitative PCR. Consistent with this, the nasp-1 mutant exhibits RNA interference (RNAi) deficiency and reduced longevity similar to those of a dcr-1 mutant. Building on these surprising findings, we further explored a potential role for dcr-1 in C. elegans innate immunity. We show that dcr-1 mutant alleles deficient in microRNA (miRNA) processing, but not those deficient only in RNAi, are resistant to B. thuringiensis DB27. Furthermore, dcr-1 overexpression rescues the nasp-1 mutant's resistance, suggesting that repression of dcr-1 determines the nasp-1 mutant's resistance. Additionally, we identified the collagen-encoding gene col-92 as one of the downstream effectors of nasp-1 that play an important role in resistance to DB27. Taken together, these results uncover a previously unknown role for DCR-1/Dicer in C. elegans antibacterial immunity that is largely associated with miRNA processing. PMID:23918784

  18. 20 dB net-gain polarization-insensitive fiber optical parametric amplifier with >2 THz bandwidth.

    Science.gov (United States)

    Stephens, M F C; Gordienko, V; Doran, N J

    2017-05-01

    A black-box polarization insensitive fiber optical parametric amplifier (PI-FOPA) is characterized for the first time using a commercial 127 Gb/s polarization-division multiplexed PDM-QPSK transponder within a multiplex of twenty-two equivalent DWDM signals across a 2.3 THz bandwidth portion of the C-band. The PI-FOPA employs a recently demonstrated diversity loop arrangement comprising two lengths of highly nonlinear fiber (HNLF) with the parametric pump being removed after the first HNLF in both directions about the loop. This arrangement is named the Half-Pass Loop FOPA or HPL-FOPA. In total, a record equivalent 2.3 Tb/s of data is amplified within the HPL-FOPA for three different pump power regimes producing net-gains of 10 dB, 15 dB and 20 dB (averaged over all signals). For the latter two regimes, the gain bandwidth is observed to extend considerably beyond the C-band, illustrating the potential for this design to amplify signals over bandwidths commensurate with the EDFA and beyond. Under the 15 dB gain condition, the average OSNR penalty to achieve 10-3 bit error rate for all twenty three signals was found to be 0.5 ± 0.3 dB. Worst case penalty was 0.8 ± 0.3 dB, verifying the use of the architecture for polarization insensitive operation. The growth of four-wave mixing signal-signal crosstalk is additionally characterized and found to be gain independent for a fixed output power per signal. A simple effective length model is developed which predicts this behavior and suggests a new configuration for significantly reduced crosstalk.

  19. Practical defeasible reasoning for description logics (STAIRS)

    CSIR Research Space (South Africa)

    Moodley, K

    2014-08-01

    Full Text Available (26):6696–6702, 1993. [18] R Verani, J Olson, and J. L. Moake. Intrathoracic extramedullary hematopoiesis: report of a case in a patient with sickle-cell disease-beta-thalassemia. American journal of clinical pathology, 73(1):133–137, 1980. ...

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

    Lifescience Database Archive (English)

    Full Text Available Policy | Contact Us QTL list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

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

    Lifescience Database Archive (English)

    Full Text Available Database Site Policy | Contact Us Marker list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  2. Substrate integrated waveguide (SIW 3 dB coupler for K-Band applications

    Directory of Open Access Journals (Sweden)

    Khalid Nurehansafwanah

    2017-01-01

    Full Text Available This paper presented a designed coupler by using Rogers RO4003C with thickness (h 0.508 mm and relative permittivity (εr 3.55. The four port network coupler operates in K-band (18-27 GHz and design by using substrate integrated waveguide (SIW method. The reflection coefficient and isolation coefficient of propose Substrate Integrated Waveguide (SIW coupler is below than -10 dB. Meanwhile the coupler requirements are phase shift 90° between coupled port and output. SIW are high performance broadband interconnects with excellent immunity to electromagnetic interference and suitable for use in microwave and communication electronics, as well as increase bandwidth systems. The designs of coupler are investigated using CST Microwave Studio simulation tool. This proposed couplers are varied from parameters that cover the frequency range (21 -24 GHz and better performance of scattering (S-parameter.

  3. MapsiDB: an integrated web database for type I polyketide synthases.

    Science.gov (United States)

    Tae, Hongseok; Sohng, Jae Kyung; Park, Kiejung

    2009-10-01

    Polyketides have diverse biological activities, including pharmacological functions such as antibiotic, antitumor and agrochemical properties. They are biosynthesized from short carboxylic acid precursors by polyketide synthases (PKSs). As natural polyketide products include many clinically important drugs and the volume of data on polyketides is rapidly increasing, the development of a database system to manage polyketide data is essential. MapsiDB is an integrated web database formulated to contain data on type I polyketides and their PKSs, including domain and module composition and related genome information. Data on polyketides were collected from journals and online resources and processed with analysis programs. Web interfaces were utilized to construct and to access this database, allowing polyketide researchers to add their data to this database and to use it easily.

  4. 1DB, a one-dimensional diffusion code for nuclear reactor analysis

    International Nuclear Information System (INIS)

    Little, W.W. Jr.

    1991-09-01

    1DB is a multipurpose, one-dimensional (plane, cylinder, sphere) diffusion theory code for use in reactor analysis. The code is designed to do the following: To compute k eff and perform criticality searches on time absorption, reactor composition, reactor dimensions, and buckling by means of either a flux or an adjoint model; to compute collapsed microscopic and macroscopic cross sections averaged over the spectrum in any specified zone; to compute resonance-shielded cross sections using data in the shielding factor formnd to compute isotopic burnup using decay chains specified by the user. All programming is in FORTRAN. Because variable dimensioning is employed, no simple restrictions on problem complexity can be stated. The number of spatial mesh points, energy groups, upscattering terms, etc. is limited only by the available memory. The source file contains about 3000 cards. 4 refs

  5. Observation of the time dependence of B0d-B0d mixing

    Science.gov (United States)

    Buskulic, D.; de Bonis, I.; Decamp, D.; Ghez, P.; Goy, C.; Lees, J.-P.; Minard, M.-N.; Pietrzyk, B.; Ariztizabal, F.; Comas, P.; Crespo, J. M.; Delfino, M.; Efthymiopoulos, I.; Fernandez, E.; Fernandez-Bosman, M.; Gaitan, V.; Garrido, Ll.; Mattison, T.; Pacheco, A.; Padilla, C.; Pascual, A.; Creanza, D.; de Palma, M.; Farilla, A.; Iaselli, G.; Maggi, G.; Natali, S.; Nuzzo, S.; Quattromini, M.; Ranieri, A.; Raso, G.; Romano, F.; Ruggieri, F.; Selvaggi, G.; Silvestris, L.; Tempesta, P.; Zito, G.; Chai, Y.; Hu, H.; Huang, D.; Huang, X.; Lin, J.; Wang, T.; Xie, Y.; Xu, D.; Xu, R.; Zhang, J.; Zhang, L.; Zhao, W.; Blucher, E.; Bonvicini, G.; Boudreau, J.; Casper, D.; Drevermann, H.; Forty, R. W.; Ganis, G.; Gay, C.; Hagelberg, R.; Harvey, J.; Hilgart, J.; Jacobsen, R.; Jost, B.; Knobloch, J.; Lehraus, I.; Lohse, T.; Maggi, M.; Markou, C.; Martinez, M.; Mato, P.; Meinhard, H.; Minten, A.; Miotto, A.; Miquel, R.; Moser, H.-G.; Palazzi, P.; Pater, J. R.; Perlas, J. A.; Pusztaszeri, J.-F.; Ranjard, F.; Redlinger, G.; Rolandi, L.; Rothberg, J.; Ruan, T.; Saich, M.; Schlatter, D.; Schmelling, M.; Sefkow, F.; Tejessy, W.; Tomalin, I. R.; Veenhof, R.; Wachsmuth, H.; Wasserbaech, S.; Wiedenmann, W.; Wildish, T.; Witzeling, W.; Wotschack, J.; Ajaltouni, Z.; Badaud, F.; Bardadin-Otwinowska, M.; El Fellous, R.; Falvard, A.; Gay, P.; Guicheney, C.; Henrard, P.; Jousset, J.; Michel, B.; Montret, J.-C.; Pallin, D.; Perret, P.; Podlyski, F.; Proriol, J.; Prulhière, F.; Saadi, F.; Fearnley, T.; Hansen, J. B.; Hansen, J. D.; Hansen, J. R.; Hansen, P. H.; Møllerud, R.; Nilsson, B. S.; Kyriakis, A.; Simopoulou, E.; Siotis, I.; Vayaki, A.; Zachariadou, K.; Badier, J.; Blondel, A.; Bonneaud, G.; Brient, J. C.; Fouque, G.; Orteu, S.; Rougé, A.; Rumpf, M.; Tanaka, R.; Verderi, M.; Videau, H.; Candlin, D. J.; Parsons, M. I.; Veitch, E.; Focardi, E.; Moneta, L.; Parrini, G.; Corden, M.; Georgiopoulos, C.; Ikeda, M.; Levinthal, D.; Antonelli, A.; Baldini, R.; Bencivenni, G.; Bologna, G.; Bossi, F.; Campana, P.; Capon, G.; Cerutti, F.; Chiarella, V.; D'Ettorre-Piazzoli, B.; Felici, G.; Laurelli, P.; Mannocchi, G.; Murtas, F.; Murtas, G. P.; Passalacqua, L.; Pepe-Altarelli, M.; Picchi, P.; Colrain, P.; Ten Have, I.; Lynch, J. G.; Maitland, W.; Morton, W. T.; Raine, C.; Reeves, P.; Scarr, J. M.; Smith, K.; Smith, M. G.; Thompson, A. S.; Turnbull, R. M.; Brandl, B.; Braun, O.; Geweniger, C.; Hanke, P.; Hepp, V.; Kluge, E. E.; Maumary, Y.; Putzer, A.; Rensch, B.; Stahl, A.; Tittel, K.; Wunsch, M.; Beuselinck, R.; Binnie, D. M.; Cameron, W.; Cattaneo, M.; Colling, D. J.; Dornan, P. J.; Greene, A. M.; Hassard, J. F.; Lieske, N. M.; Moutoussi, A.; Nash, J.; Patton, S.; Payne, D. G.; Phillips, M. J.; San Martin, G.; Sedgbeer, J. K.; Wright, A. G.; Girtler, P.; Kuhn, D.; Rudolph, G.; Vogl, R.; Bowdery, C. K.; Brodbeck, T. J.; Finch, A. J.; Foster, F.; Hughes, G.; Jackson, D.; Keemer, N. R.; Nuttall, M.; Patel, A.; Sloan, T.; Snow, S. W.; Whelan, E. P.; Kleinknecht, K.; Raab, J.; Renk, B.; Sander, H.-G.; Schmidt, H.; Steeg, F.; Walther, S. M.; Wanke, R.; Wolf, B.; Bencheikh, A. M.; Benchouk, C.; Bonissent, A.; Carr, J.; Coyle, P.; Drinkard, J.; Etienne, F.; Nicod, D.; Papalexiou, S.; Payre, P.; Roos, L.; Rousseau, D.; Schwemling, P.; Talby, M.; Adlung, S.; Assmann, R.; Bauer, C.; Blum, W.; Brown, D.; Cattaneo, P.; Dehning, B.; Dietl, H.; Dydak, F.; Frank, M.; Halley, A. W.; Jakobs, K.; Lauber, J.; Lütjens, G.; Lutz, G.; Männer, W.; Richter, R.; Schröder, J.; Schwarz, A. S.; Settles, R.; Seywerd, H.; Stierlin, U.; Stiegler, U.; Denis, R. St.; Wolf, G.; Alemany, R.; Boucrot, J.; Callot, O.; Cordier, A.; Davier, M.; Duflot, L.; Grivaz, J.-F.; Heusse, Ph.; Jaffe, D. E.; Janot, P.; Kim, D. W.; Le Diberder, F.; Lefrançois, J.; Lutz, A.-M.; Schune, M.-H.; Veillet, J.-J.; Videau, I.; Zhang, Z.; Abbaneo, D.; Bagliesi, G.; Batignani, G.; Bottigli, U.; Bozzi, C.; Calderini, G.; Carpinelli, M.; Ciocci, M. A.; Ciulli, V.; dell'Orso, R.; Ferrante, I.; Fidecaro, F.; Foà, L.; Forti, F.; Giassi, A.; Giorgi, M. A.; Gregorio, A.; Ligabue, F.; Lusiani, A.; Mannelli, E. B.; Marrocchesi, P. S.; Messineo, A.; Palla, F.; Rizzo, G.; Sanguinetti, G.; Spagnolo, P.; Steinberger, J.; Tenchini, R.; Tonelli, G.; Triggiani, G.; Valassi, A.; Vannini, C.; Venturi, A.; Verdini, P. G.; Walsh, J.; Betteridge, A. P.; Gao, Y.; Green, M. G.; March, P. V.; Mir, Ll. M.; Medcalf, T.; Quazi, I. S.; Strong, J. A.; West, L. R.; Botterill, D. R.; Clifft, R. W.; Edgecock, T. R.; Haywood, S.; Norton, P. R.; Thompson, J. C.; Bloch-Devaux, B.; Colas, P.; Duarte, H.; Emery, S.; Kozanecki, W.; Lançon, E.; Lemaire, M. C.; Locci, E.; Marx, B.; Perez, P.; Rander, J.; Renardy, J.-F.; Rosowsky, A.; Roussarie, A.; Schuller, J.-P.; Schwindling, J.; Si Mohand, D.; Vallage, B.; Johnson, R. P.; Litke, A. M.; Taylor, G.; Wear, J.; Ashman, J. G.; Babbage, W.; Booth, C. N.; Buttar, C.; Cartwright, S.; Combley, F.; Dawson, I.; Thompson, L. F.; Barberio, E.; Böhrer, A.; Brandt, S.; Cowan, G.; Grupen, C.; Lutters, G.; Rivera, F.; Schäfer, U.; Smolik, L.; Bosisio, L.; della Marina, R.; Giannini, G.; Gobbo, B.; Ragusa, F.; Bellantoni, L.; Chen, W.; Conway, J. S.; Feng, Z.; Ferguson, D. P. S.; Gao, Y. S.; Grahl, J.; Harton, J. L.; Hayes, O. J.; Nachtman, J. M.; Pan, Y. B.; Saadi, Y.; Schmitt, M.; Scott, I.; Sharma, V.; Shi, Z. H.; Turk, J. D.; Walsh, A. M.; Weber, F. V.; Sau, Lan, Wu; Zheng, M.; Zobernig, G.

    1993-09-01

    The time dependence of B0d-B0d oscillations has been observed using events with a d*, decaying into a D0π+, and a lepton in opposite hemispheres. The time dependence of the oscillations is derived from the displacement of the D0 vertex and the D*-lepton charge correlation. From a fit for the oscillation frequency the mass difference of the B0d states is measured: Δm = [3.44+0.65-0.70(stat.)+0.26-0.20(syst.)] × 10-4 eV/c2. Supported by the US Department of Energy, contract DE-AC02-76ER00881.

  6. A high sensitive 66 dB linear dynamic range receiver for 3-D laser radar

    Science.gov (United States)

    Ma, Rui; Zheng, Hao; Zhu, Zhangming

    2017-08-01

    This study presents a CMOS receiver chip realized in 0.18 μm standard CMOS technology and intended for high precision 3-D laser radar. The chip includes an adjustable gain transimpedance pre-amplifier, a post-amplifier and two timing comparators. An additional feedback is employed in the regulated cascode transimpedance amplifier to decrease the input impedance, and a variable gain transimpedance amplifier controlled by digital switches and analog multiplexer is utilized to realize four gain modes, extending the input dynamic range. The measurement shows that the highest transimpedance of the channel is 50 k {{Ω }}, the uncompensated walk error is 1.44 ns in a wide linear dynamic range of 66 dB (1:2000), and the input referred noise current is 2.3 pA/\\sqrt{{Hz}} (rms), resulting in a very low detectable input current of 1 μA with SNR = 5.

  7. VizieR Online Data Catalog: 2014-2017 photometry for ASASSN-13db (Sicilia-Aguilar+, 2017)

    Science.gov (United States)

    Sicilia-Aguilar, A.; Oprandi, A.; Froebrich, D.; Fang, M.; Prieto, J. L.; Stanek, K.; Scholz, A.; Kochanek, C. S.; Henning, T.; Gredel, R.; Holoien, T. S. W.; Rabus, M.; Shappee, B. J.; Billington, S. J.; Campbell-White, J.; Zegmott, T. J.

    2017-08-01

    Table 1 contains the full photometry from the All Sky Automated Survey for Supernovae (ASAS-SN) for the variable star ASASSN-13db. Detections with their errors and 5-sigma upper limits are given. Upper limits are marked by the "<" sign and have the error column set to 99.99. (1 data file).

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

    Science.gov (United States)

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

    2017-01-04

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

  9. PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features.

    Science.gov (United States)

    Hamosh, Ada; Sobreira, Nara; Hoover-Fong, Julie; Sutton, V Reid; Boehm, Corinne; Schiettecatte, François; Valle, David

    2013-04-01

    To interpret whole exome/genome sequence data for clinical and research purposes, comprehensive phenotypic information, knowledge of pedigree structure, and results of previous clinical testing are essential. With these requirements in mind and to meet the needs of the Centers for Mendelian Genomics project, we have developed PhenoDB (http://phenodb.net), a secure, Web-based portal for entry, storage, and analysis of phenotypic and other clinical information. The phenotypic features are organized hierarchically according to the major headings and subheadings of the Online Mendelian Inheritance in Man (OMIM®) clinical synopses, with further subdivisions according to structure and function. Every string allows for a free-text entry. All of the approximately 2,900 features use the preferred term from Elements of Morphology and are fully searchable and mapped to the Human Phenotype Ontology and Elements of Morphology. The PhenoDB allows for ascertainment of relevant information from a case in a family or cohort, which is then searchable by family, OMIM number, phenotypic feature, mode of inheritance, genes screened, and so on. The database can also be used to format phenotypic data for submission to dbGaP for appropriately consented individuals. PhenoDB was built using Django, an open source Web development tool, and is freely available through the Johns Hopkins McKusick-Nathans Institute of Genetic Medicine (http://phenodb.net). © 2013 Wiley Periodicals, Inc.

  10. Verification of the Chromosome Region 9q21 Association with Pelvic Organ Prolapse Using RegulomeDB Annotations

    Directory of Open Access Journals (Sweden)

    Maryam B. Khadzhieva

    2015-01-01

    Full Text Available Pelvic organ prolapse (POP is a common highly disabling disorder with a large hereditary component. It is characterized by a loss of pelvic floor support that leads to the herniation of the uterus in or outside the vagina. Genome-wide linkage studies have shown an evidence of POP association with the region 9q21 and six other loci in European pedigrees. The aim of our study was to test the above associations in a case-control study in Russian population. Twelve SNPs including SNPs cited in the above studies and those selected using the RegulomeDB annotations for the region 9q21 were genotyped in 210 patients with POP (stages III-IV and 292 controls with no even minimal POP. Genotyping was performed using the polymerase chain reaction with confronting two-pair primers (PCR–CTPP. Association analyses were conducted for individual SNPs, 9q21 haplotypes, and SNP-SNP interactions. SNP rs12237222 with the highest RegulomeDB score 1a appeared to be the key SNP in haplotypes associated with POP. Other RegulomeDB Category 1 SNPs, rs12551710 and rs2236479 (scores 1d and 1f, resp., exhibited epistatic effects. In this study, we verified the region 9q21 association with POP in Russians, using RegulomeDB annotations.

  11. Daily MODIS 500 m Reflectance Anisotropy Direct Broadcast (DB) Products for Monitoring Vegetation Phenology Dynamics

    Science.gov (United States)

    Shuai, Yanmin; Schaaf, Crystal; Zhang, Xiaoyang; Strahler, Alan; Roy, David; Morisette, Jeffrey; Wang, Zhuosen; Nightingale, Joanne; Nickeson, Jaime; Richardson, Andrew D.; hide

    2013-01-01

    Land surface vegetation phenology is an efficient bio-indicator for monitoring ecosystem variation in response to changes in climatic factors. The primary objective of the current article is to examine the utility of the daily MODIS 500 m reflectance anisotropy direct broadcast (DB) product for monitoring the evolution of vegetation phenological trends over selected crop, orchard, and forest regions. Although numerous model-fitted satellite data have been widely used to assess the spatio-temporal distribution of land surface phenological patterns to understand phenological process and phenomena, current efforts to investigate the details of phenological trends, especially for natural phenological variations that occur on short time scales, are less well served by remote sensing challenges and lack of anisotropy correction in satellite data sources. The daily MODIS 500 m reflectance anisotropy product is employed to retrieve daily vegetation indices (VI) of a 1 year period for an almond orchard in California and for a winter wheat field in northeast China, as well as a 2 year period for a deciduous forest region in New Hampshire, USA. Compared with the ground records from these regions, the VI trajectories derived from the cloud-free and atmospherically corrected MODIS Nadir BRDF (bidirectional reflectance distribution function) adjusted reflectance (NBAR) capture not only the detailed footprint and principal attributes of the phenological events (such as flowering and blooming) but also the substantial inter-annual variability. This study demonstrates the utility of the daily 500 m MODIS reflectance anisotropy DB product to provide daily VI for monitoring and detecting changes of the natural vegetation phenology as exemplified by study regions comprising winter wheat, almond trees, and deciduous forest.

  12. MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones.

    Science.gov (United States)

    El Kennani, Sara; Adrait, Annie; Shaytan, Alexey K; Khochbin, Saadi; Bruley, Christophe; Panchenko, Anna R; Landsman, David; Pflieger, Delphine; Govin, Jérôme

    2017-01-01

    Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants. We propose two proteomics-oriented manually curated databases for mouse and human histone variants. We manually curated >1700 gene, transcript and protein entries to produce a non-redundant list of 83 mouse and 85 human histones. These entries were annotated in accordance with the current nomenclature and unified with the "HistoneDB2.0 with Variants" database. This resource is provided in a format that can be directly read by programs used for mass spectrometry data interpretation. In addition, it was used to interpret mass spectrometry data acquired on histones extracted from mouse testis. Several histone variants, which had so far only been inferred by homology or detected at the RNA level, were detected by mass spectrometry, confirming the existence of their protein form. Mouse and human histone entries were collected from different databases and subsequently curated to produce a non-redundant protein-centric resource, MS_HistoneDB. It is dedicated to the proteomic study of histones in mouse and human and will hopefully facilitate the identification and functional study of histone variants.

  13. Research on noise and vibration reduction at DB to improve the environmental friendliness of railway traffic

    Science.gov (United States)

    Schulte-Werning, B.; Beier, M.; Degen, K. G.; Stiebel, D.

    2006-06-01

    One of the most prominent keywords relating to the environmental friendliness of railway traffic is noise reduction. Thus, the research and development programme "Low Noise Railway" of Deutsche Bahn (DB) is under way to treat the noise of the vehicles and infrastructure. The noise reduction of the trains and the rail/wheel system are being tackled within several projects. The direct noise experienced by railway-lineside residents due to train movements on the track can be reduced by minimising the sound radiation directly at the source. This is the first-choice solution, as it proves to be the most effective countermeasure regarding a cost-benefit relation. The limit values for the noise emission as specified in the technical specification for interoperability are an essential criterion to be confirmed during the procurement process of railway vehicles. A recently developed acoustical quality management scheme establishes systematic noise management to complete the vehicle procurement process in the phases of concept, design, construction and manufacturing. In freight traffic quiet railway wheels for block brake operation will play an important role in the future to meet the goal of a low-noise railway system. A first attempt to realise successfully the low-noise potential of such optimised wheels was performed, even if with mixed results. To show ways of reducing the noise of the cooling ventilation in locomotives, DB is a partner in a development project led by Siemens. A notable 8 dB(A) noise reduction was measured. Concerning bridge noise, a project was started based on an effective and cost-efficient combination of experiments and simulations in order to develop specifications for the construction of generic low-noise bridges.

  14. LenVarDB: database of length-variant protein domains.

    Science.gov (United States)

    Mutt, Eshita; Mathew, Oommen K; Sowdhamini, Ramanathan

    2014-01-01

    Protein domains are functionally and structurally independent modules, which add to the functional variety of proteins. This array of functional diversity has been enabled by evolutionary changes, such as amino acid substitutions or insertions or deletions, occurring in these protein domains. Length variations (indels) can introduce changes at structural, functional and interaction levels. LenVarDB (freely available at http://caps.ncbs.res.in/lenvardb/) traces these length variations, starting from structure-based sequence alignments in our Protein Alignments organized as Structural Superfamilies (PASS2) database, across 731 structural classification of proteins (SCOP)-based protein domain superfamilies connected to 2 730 625 sequence homologues. Alignment of sequence homologues corresponding to a structural domain is available, starting from a structure-based sequence alignment of the superfamily. Orientation of the length-variant (indel) regions in protein domains can be visualized by mapping them on the structure and on the alignment. Knowledge about location of length variations within protein domains and their visual representation will be useful in predicting changes within structurally or functionally relevant sites, which may ultimately regulate protein function. Non-technical summary: Evolutionary changes bring about natural changes to proteins that may be found in many organisms. Such changes could be reflected as amino acid substitutions or insertions-deletions (indels) in protein sequences. LenVarDB is a database that provides an early overview of observed length variations that were set among 731 protein families and after examining >2 million sequences. Indels are followed up to observe if they are close to the active site such that they can affect the activity of proteins. Inclusion of such information can aid the design of bioengineering experiments.

  15. KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba.

    Directory of Open Access Journals (Sweden)

    Gabriele Sales

    Full Text Available Antarctic krill (Euphausia superba is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tonnes. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem. One looming threat due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2 is ocean acidification (lowering of sea water pH by CO2 dissolving into the oceans. The genetics of Antarctic krill has long been of scientific interest for both for the analysis of population structure and analysis of functional genetics. However, the genetic resources available for the species are relatively modest. We have developed the most advanced genetic database on Euphausia superba, KrillDB, which includes comprehensive data sets of former and present transcriptome projects. In particular, we have built a de novo transcriptome assembly using more than 360 million Illumina sequence reads generated from larval krill including individuals subjected to different CO2 levels. The database gives access to: 1 the full list of assembled genes and transcripts; 2 their level of similarity to transcripts and proteins from other species; 3 the predicted protein domains contained within each transcript; 4 their predicted GO terms; 5 the level of expression of each transcript in the different larval stages and CO2 treatments. All references to external entities (sequences, domains, GO terms are equipped with a link to the appropriate source database. Moreover, the software implements a full-text search engine that makes it possible to submit free-form queries. KrillDB represents the first large-scale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future approaches devoted to physiological and molecular study of this key species in the Southern Ocean food web.

  16. KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba).

    Science.gov (United States)

    Sales, Gabriele; Deagle, Bruce E; Calura, Enrica; Martini, Paolo; Biscontin, Alberto; De Pittà, Cristiano; Kawaguchi, So; Romualdi, Chiara; Meyer, Bettina; Costa, Rodolfo; Jarman, Simon

    2017-01-01

    Antarctic krill (Euphausia superba) is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tonnes. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem. One looming threat due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2) is ocean acidification (lowering of sea water pH by CO2 dissolving into the oceans). The genetics of Antarctic krill has long been of scientific interest for both for the analysis of population structure and analysis of functional genetics. However, the genetic resources available for the species are relatively modest. We have developed the most advanced genetic database on Euphausia superba, KrillDB, which includes comprehensive data sets of former and present transcriptome projects. In particular, we have built a de novo transcriptome assembly using more than 360 million Illumina sequence reads generated from larval krill including individuals subjected to different CO2 levels. The database gives access to: 1) the full list of assembled genes and transcripts; 2) their level of similarity to transcripts and proteins from other species; 3) the predicted protein domains contained within each transcript; 4) their predicted GO terms; 5) the level of expression of each transcript in the different larval stages and CO2 treatments. All references to external entities (sequences, domains, GO terms) are equipped with a link to the appropriate source database. Moreover, the software implements a full-text search engine that makes it possible to submit free-form queries. KrillDB represents the first large-scale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future approaches devoted to physiological and molecular study of this key species in the Southern Ocean food web.

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

    Directory of Open Access Journals (Sweden)

    Jia-Sheng Wu

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

  18. Update History of This Database - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available L of The original website information 2014/10/10 PGDBj Registered plant list, Marker list, QTL list, Plant D...B link & Genome analysis methods English archive site is opened. 2012/08/08 PGDBj Regis...ate History of This Database - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  19. Altered metabolic incorporation of fucose and leucine into PNS myelin of 25-week-old diabetic (C57BL/Ks [db/db]) mice: effects of untreated diabetes on nerve metabolism

    International Nuclear Information System (INIS)

    Chez, M.G.; Peterson, R.G.

    1983-01-01

    Sciatic nerves of 25-week-old genetically diabetic (C57BL/Ks [db/db]) mice and their litter-mate controls were removed, and their metabolic incorporation of [ 3 H]fucose and [ 14 C]leucine into myelin was studied in vitro. Untreated diabetic animals showed significant increases (p less than 0.05) in the fucose/leucine incorporation into myelin when compared to values found for their litter-mates. These results correlated well with previous experiments performed on alloxan or streptozotocin-diabetic rats and thus show the in vitro incubation procedure to be a good indicator of altered metabolic conditions in peripheral nerves due to diabetes mellitus. The resulting ratio increases seen in diabetic animals is at variance with the decrease in ratios found in animals undergoing typical Wallerian degeneration. These results suggest that different metabolic processes operate in untreated diabetics than in normals or in those undergoing other degenerative nerve processes

  20. EuroPineDB: a high-coverage web database for maritime pine transcriptome

    Directory of Open Access Journals (Sweden)

    Cantón Francisco R

    2011-07-01

    Full Text Available Abstract Background Pinus pinaster is an economically and ecologically important species that is becoming a woody gymnosperm model. Its enormous genome size makes whole-genome sequencing approaches are hard to apply. Therefore, the expressed portion of the genome has to be characterised and the results and annotations have to be stored in dedicated databases. Description EuroPineDB is the largest sequence collection available for a single pine species, Pinus pinaster (maritime pine, since it comprises 951 641 raw sequence reads obtained from non-normalised cDNA libraries and high-throughput sequencing from adult (xylem, phloem, roots, stem, needles, cones, strobili and embryonic (germinated embryos, buds, callus maritime pine tissues. Using open-source tools, sequences were optimally pre-processed, assembled, and extensively annotated (GO, EC and KEGG terms, descriptions, SNPs, SSRs, ORFs and InterPro codes. As a result, a 10.5× P. pinaster genome was covered and assembled in 55 322 UniGenes. A total of 32 919 (59.5% of P. pinaster UniGenes were annotated with at least one description, revealing at least 18 466 different genes. The complete database, which is designed to be scalable, maintainable, and expandable, is freely available at: http://www.scbi.uma.es/pindb/. It can be retrieved by gene libraries, pine species, annotations, UniGenes and microarrays (i.e., the sequences are distributed in two-colour microarrays; this is the only conifer database that provides this information and will be periodically updated. Small assemblies can be viewed using a dedicated visualisation tool that connects them with SNPs. Any sequence or annotation set shown on-screen can be downloaded. Retrieval mechanisms for sequences and gene annotations are provided. Conclusions The EuroPineDB with its integrated information can be used to reveal new knowledge, offers an easy-to-use collection of information to directly support experimental work (including

  1. A 14-bit 100-MS/s 85.2-dB SFDR pipelined ADC without calibration

    Science.gov (United States)

    Nan, Zhao; Hua, Luo; Qi, Wei; Huazhong, Yang

    2014-07-01

    This paper describes a 14-bit 100-MS/s calibration-free pipelined analog-to-digital converter (ADC). Choices for stage resolution as well as circuit topology are carefully considered to obtain high linearity without any calibration algorithm. An adjusted timing diagram with an additional clock phase is proposed to give residue voltage more settling time and minimize its distortion. The ADC employs an LVDS clock input buffer with low-jitter consideration to ensure good performance at high sampling rate. Implemented in a 0.18-μm CMOS technology, the ADC prototype achieves a spurious free dynamic range (SFDR) of 85.2 dB and signal-to-noise-and-distortion ratio (SNDR) of 63.4 dB with a 19.1-MHz input signal, while consuming 412-mW power at 2.0-V supply and occupying an area of 2.9 × 3.7mm2.

  2. Evaluating the Impact of Data Placement to Spark and SciDB with an Earth Science Use Case

    Science.gov (United States)

    Doan, Khoa; Oloso, Amidu; Kuo, Kwo-Sen; Clune, Thomas; Yu, Hongfeng; Nelson, Brian; Zhang, Jian

    2016-01-01

    We investigate the impact of data placement for two Big Data technologies, Spark and SciDB, with a use case from Earth Science where data arrays are multidimensional. Simultaneously, this investigation provides an opportunity to evaluate the performance of the technologies involved. Two datastores, HDFS and Cassandra, are used with Spark for our comparison. It is found that Spark with Cassandra performs better than with HDFS, but SciDB performs better yet than Spark with either datastore. The investigation also underscores the value of having data aligned for the most common analysis scenarios in advance on a shared nothing architecture. Otherwise, repartitioning needs to be carried out on the fly, degrading overall performance.

  3. An 11 mW 79 dB DR ΔΣ modulator for ADSL applications

    Science.gov (United States)

    Yingjia, Zhu; Liyuan, Liu; Dongmei, Li

    2009-10-01

    This paper shows the design of a second-order multi-bit ΔΣ modulator with hybrid structure for ADSL applications. A modified two phase non-overlapping clock generator is designed to let PH2 borrow 12% of the time from PH1, which relaxes the speed of OTAs, comparators and the DEM block. The clock feed through problem of the passive adder is solved by revising the timing of the comparators and the adder. The chip is designed and fabricated in UMC 0.18 μm CMOS technology. Measurement results show that with an oversampling ratio of 32 and a clock rate of 80 MHz, the modulator can achieve 79 dB dynamic range, 71.3 dB SNDR, 11 mW power consumption from a 1.8 V power supply. The FOM is 1.47 pJ/step.

  4. An 11 mW 79 dB DR {Delta}{Sigma} modulator for ADSL applications

    Energy Technology Data Exchange (ETDEWEB)

    Zhu Yingjia; Li Dongmei [Department of Electronic Engineering, Tsinghua University, Beijing 100084 (China); Liu Liyuan, E-mail: syj03@mails.tsinghua.edu.c [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China)

    2009-10-15

    This paper shows the design of a second-order multi-bit {Delta}{Sigma} modulator with hybrid structure for ADSL applications. A modified two phase non-overlapping clock generator is designed to let PH2 borrow 12% of the time from PH1, which relaxes the speed of OTAs, comparators and the DEM block. The clock feed through problem of the passive adder is solved by revising the timing of the comparators and the adder. The chip is designed and fabricated in UMC 0.18 {mu}m CMOS technology. Measurement results show that with an oversampling ratio of 32 and a clock rate of 80 MHz, the modulator can achieve 79 dB dynamic range, 71.3 dB SNDR, 11 mW power consumption from a 1.8 V power supply. The FOM is 1.47 pJ/step.

  5. iMonDB: Mass Spectrometry Quality Control through Instrument Monitoring.

    Science.gov (United States)

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

    2015-05-01

    Over the past few years, awareness has risen that for mass-spectrometry-based proteomics methods to mature into everyday analytical and clinical practices, extensive quality assessment is mandatory. A currently overlooked source of qualitative information originates from the mass spectrometer itself. Apart from the actual mass spectral data, raw-data objects also contain parameter settings and sensory information about the mass instrument. This information gives a detailed account of the operation of the instrument, which eventually can be related to observations in mass spectral data. The advantage of instrument information at the lowest level is the high sensitivity to detect emerging defects in a timely fashion. To this end, we introduce the Instrument MONitoring DataBase (iMonDB), which allows us to automatically extract, store, and manage the instrument parameters from raw-data objects into a highly efficient database structure. This enables us to monitor the instrument parameters over a considerable time period. Time course information about the instrument performance is necessary to define the normal range of operation and to detect anomalies that may correlate with instrument failure. The proposed tools foster an additional handle on quality control and are released as open source under the permissive Apache 2.0 license. The tools can be downloaded from https://bitbucket.org/proteinspector/imondb.

  6. A study on properties-performances of coated particle fuel and on-line DB establishment

    International Nuclear Information System (INIS)

    Kim, Yong Soo; Lee, Hyo Cheol; Jang, Jeong Nam; Kwon, Seok Hwan

    2007-03-01

    Recently national project for HTGR for hydrogen production has been kicked off. However, For the successful development of the high temperature gas cooled reactor high temperature and burn-up dependent properties of the reactor materials are essentially and crucially required. Therefore, it was proposed to build up the materials properties and fuel performance data base. In this study, a phase - 1 properties and performance DB for coated particle fuel was developed. This database report consists two sections: materials properties and fuel performance. The materials properties has three parts: kernel materials, carbide coating materials, and fuel elements and graphite matrix. UO2 and UCO belong to kernel materials while PyC, SiC, and ZrC comprises the coating materials section. Thermal, mechanical and physical properties data of these materials were collected, reviewed, and summarized. Additionally, the property change induced by manufacture process and irradiation were reviewed. Fuel performance data were also collected, reviewed, and analyzed based on the key phenomena and failure mechanism, These performance data are divided into two: normal and accident. All of these data will be accessible in the pc based stand-alone system. These results will be directly used for HTGR fuel design and fabrication and preliminary fuel performance analysis under irradiation

  7. RetroTransformDB: A Dataset of Generic Transforms for Retrosynthetic Analysis

    Directory of Open Access Journals (Sweden)

    Svetlana Avramova

    2018-04-01

    Full Text Available Presently, software tools for retrosynthetic analysis are widely used by organic, medicinal, and computational chemists. Rule-based systems extensively use collections of retro-reactions (transforms. While there are many public datasets with reactions in synthetic direction (usually non-generic reactions, there are no publicly-available databases with generic reactions in computer-readable format which can be used for the purposes of retrosynthetic analysis. Here we present RetroTransformDB—a dataset of transforms, compiled and coded in SMIRKS line notation by us. The collection is comprised of more than 100 records, with each one including the reaction name, SMIRKS linear notation, the functional group to be obtained, and the transform type classification. All SMIRKS transforms were tested syntactically, semantically, and from a chemical point of view in different software platforms. The overall dataset design and the retrosynthetic fitness were analyzed and curated by organic chemistry experts. The RetroTransformDB dataset may be used by open-source and commercial software packages, as well as chemoinformatics tools.

  8. jSPyDB, an open source database-independent tool for data management

    International Nuclear Information System (INIS)

    Pierro, Giuseppe Antonio; Cavallari, Francesca; Di Guida, Salvatore; Innocente, Vincenzo

    2011-01-01

    Nowadays, the number of commercial tools available for accessing Databases, built on Java or .Net, is increasing. However, many of these applications have several drawbacks: usually they are not open-source, they provide interfaces only with a specific kind of database, they are platform-dependent and very CPU and memory consuming. jSPyDB is a free web-based tool written using Python and Javascript. It relies on jQuery and python libraries, and is intended to provide a simple handler to different database technologies inside a local web browser. Such a tool, exploiting fast access libraries such as SQLAlchemy, is easy to install, and to configure. The design of this tool envisages three layers. The front-end client side in the local web browser communicates with a backend server. Only the server is able to connect to the different databases for the purposes of performing data definition and manipulation. The server makes the data available to the client, so that the user can display and handle them safely. Moreover, thanks to jQuery libraries, this tool supports export of data in different formats, such as XML and JSON. Finally, by using a set of pre-defined functions, users are allowed to create their customized views for a better data visualization. In this way, we optimize the performance of database servers by avoiding short connections and concurrent sessions. In addition, security is enforced since we do not provide users the possibility to directly execute any SQL statement.

  9. Deep Insight into the Phosphatomes of Parasitic Protozoa and a Web Resource ProtozPhosDB.

    Science.gov (United States)

    Anwar, Tamanna; Gourinath, Samudrala

    2016-01-01

    Phosphorylation dynamically regulates the function of proteins by maintaining a balance between protein kinase and phosphatase activity. A comprehensive understanding of the role phosphatases in cellular signaling is lacking in case of protozoans of medical and veterinary importance worldwide. The drugs used to treat protozoal diseases have many undesired effects and the development of resistance, highlights the need for new effective and safer antiprotozoal agents. In the present study we have analyzed phosphatomes of 15 protozoans of medical significance. We identified ~2000 phosphatases, out of which 21% are uncharacterized proteins. A significant positive correlation between phosphatome and proteome size was observed except for E. histolytica, having highest density of phosphatases irrespective of its proteome size. A difference in the number of phosphatases among different genera shows the variation in the signaling pathways they are involved in. The phosphatome of parasites is dominated by ser/thr phosphatases contrary to the vertebrate host dominated by tyrosine phosphatases. Phosphatases were widely distributed throughout the cell suggesting physiological adaptation of the parasite to regulate its host. 20% to 45% phosphatome of different protozoa consists of ectophosphatases, i.e. crucial for the survival of parasites. A database and a webserver "ProtozPhosDB" can be used to explore the phosphatomes of protozoans of medical significance.

  10. Cascadia, an ultracompact seismic instrument with over 200dB of dynamic range

    Science.gov (United States)

    Parker, Tim; Devanney, Peter; Bainbridge, Geoff; Townsend, Bruce

    2017-04-01

    Integration of geophysical instrumentation is clearly a way to lower overall station cost, make installations less complex, reduce installation time, increase station utility and value to a wider group of researchers, data miners and monitoring groups. Initiatives to expand early earthquake warning networks and observatories can use these savings for increasing station density. Integration of mature instrument systems such as broadband sensors and accelerometers used in strong motion studies has to be done with care to preserve the low noise and low frequency performance while providing over 200dB of dynamic range. Understanding the instrument complexities and deployment challenges allows the engineering teams to optimize the packaging to make installation and servicing cost effective, simple, routine and ultimately more reliable. We discuss early results from testing both in the lab and in the field of a newly released instrument called the Cascadia that integrates a broadband seismometer with a class A (USGS rating) accelerometer in a small stainless steel sonde suited for dense arrays in either ad hoc direct bury field deployments or in observatory quality shallow boreholes.

  11. jSPyDB, an open source database-independent tool for data management

    CERN Document Server

    Pierro, Giuseppe Antonio

    2010-01-01

    Nowadays, the number of commercial tools available for accessing Databases, built on Java or .Net, is increasing. However, many of these applications have several drawbacks: usually they are not open-source, they provide interfaces only with a specific kind of database, they are platform-dependent and very CPU and memory consuming. jSPyDB is a free web based tool written using Python and Javascript. It relies on jQuery and python libraries, and is intended to provide a simple handler to different Database technologies inside a local web browser. Such a tool, exploiting fast access libraries such as SQLAlchemy, is easy to install, and to configure. The design of this tool envisages three layers. The front-end client side in the local web browser communicates with a backend server. Only the server is able to connect to the different databases for the purposes of performing data definition and manipulation. The server makes the data available to the client, so that the user can display and handle them safely. ...

  12. ChromaStarDB: SQL Database-driven Spectrum Synthesis and More

    Science.gov (United States)

    Short, C. Ian

    2017-09-01

    We present an alternate deployment of the GrayStarServer (now ChromaStarServer (CSS)) pedagogical stellar atmosphere and spectrum synthesis WWW application, namely ChromaStarDB (CSDB), in which the atomic line list used for spectrum synthesis is implemented as an SQL database table rather than as a more conventional byte-data file. This allows for very flexible selection criteria to determine which transitions are extracted from the line list for inclusion in the synthesis, and enables novel pedagogical and research experiments in spectrum synthesis. This line selection flexibility is reflected in the CSDB UI. The database extraction is very fast and would be appropriate for the larger line lists of research-grade modeling codes. We also take the opportunity to present major additions to the ChromaStar and CSS codes that are also reflected in CSDB: (1) TiO band opacity in the JOLA approximation, (2) Metal b - f and Rayleigh scattering opacity, (3) 2D implementation of the flux integral, (4) Improvement of the {n}{{e}} convergence, (5) Expansion of the exo-planet modeling parameters, (6) A red giant template model for the initial guess at the structure, and (7) General improvements to the UI. The applications may be found at the home page of the OpenStar project: http://www.ap.smu.ca/OpenStars/.

  13. Deep Insight into the Phosphatomes of Parasitic Protozoa and a Web Resource ProtozPhosDB.

    Directory of Open Access Journals (Sweden)

    Tamanna Anwar

    Full Text Available Phosphorylation dynamically regulates the function of proteins by maintaining a balance between protein kinase and phosphatase activity. A comprehensive understanding of the role phosphatases in cellular signaling is lacking in case of protozoans of medical and veterinary importance worldwide. The drugs used to treat protozoal diseases have many undesired effects and the development of resistance, highlights the need for new effective and safer antiprotozoal agents. In the present study we have analyzed phosphatomes of 15 protozoans of medical significance. We identified ~2000 phosphatases, out of which 21% are uncharacterized proteins. A significant positive correlation between phosphatome and proteome size was observed except for E. histolytica, having highest density of phosphatases irrespective of its proteome size. A difference in the number of phosphatases among different genera shows the variation in the signaling pathways they are involved in. The phosphatome of parasites is dominated by ser/thr phosphatases contrary to the vertebrate host dominated by tyrosine phosphatases. Phosphatases were widely distributed throughout the cell suggesting physiological adaptation of the parasite to regulate its host. 20% to 45% phosphatome of different protozoa consists of ectophosphatases, i.e. crucial for the survival of parasites. A database and a webserver "ProtozPhosDB" can be used to explore the phosphatomes of protozoans of medical significance.

  14. A database for reproducible manipulation research: CapriDB – Capture, Print, Innovate

    Directory of Open Access Journals (Sweden)

    Florian T. Pokorny

    2017-04-01

    Full Text Available We present a novel approach and database which combines the inexpensive generation of 3D object models via monocular or RGB-D camera images with 3D printing and a state of the art object tracking algorithm. Unlike recent efforts towards the creation of 3D object databases for robotics, our approach does not require expensive and controlled 3D scanning setups and aims to enable anyone with a camera to scan, print and track complex objects for manipulation research. The proposed approach results in detailed textured mesh models whose 3D printed replicas provide close approximations of the originals. A key motivation for utilizing 3D printed objects is the ability to precisely control and vary object properties such as the size, material properties and mass distribution in the 3D printing process to obtain reproducible conditions for robotic manipulation research. We present CapriDB – an extensible database resulting from this approach containing initially 40 textured and 3D printable mesh models together with tracking features to facilitate the adoption of the proposed approach.

  15. CERN Computing Colloquium | Scientific Databases at Scale and SciDB | 27 May

    CERN Multimedia

    2013-01-01

    by Dr. Michael Stonebraker (MIT - Massachusetts Institute of Technology - Cambridge MA, USA) Monday 27 May 2013 from 2 p.m. to 4 p.m. at CERN ( 222-R-001 - Filtration Plant ) Abstract: As a general rule, scientists have shunned relational data management systems (RDBMS), choosing instead to “roll their own” on top of file system technology.  We first discuss why file systems are a poor choice for science data storage, especially as data volumes become large and scalability becomes important. Then, we continue with the reasons why RDBMSs work poorly on most science applications.  These include a data model “impedance mismatch” and missing features. We discuss array DBMSs, and why they are a much better choice for science applications, and use SciDB as an exemplar of this new class of DBMSs. Most science applications require a mix of data management and complex analytics.  In most cases, the analytics entail a sequence of linear a...

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

    OpenAIRE

    Toossi, Mohammad Taghi Bahreyni; Mohebbi, Shokoufeh; Samani, Roghayeh Kamran; Soleymanifard, Shokouhozaman

    2014-01-01

    Radiation damages initiated by radiation-induced bystander effect (RIBE) are not limited to the first or immediate neighbors of the irradiated cells, but the effects have been observed in the cells far from the irradiation site. It has been postulated that bystander cells, by producing bystander factors, are actively involved in the propagation of bystander effect in the regions beyond the initial irradiated site. Current study was planned to test the hypothesis. MRC5 and QU-DB cell lines wer...

  17. OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci

    OpenAIRE

    Su, Wen-Hui; Chao, Chuan-Chuan; Yeh, Shiou-Hwei; Chen, Ding-Shinn; Chen, Pei-Jer; Jou, Yuh-Shan

    2006-01-01

    The OncoDB.HCC () is based on physical maps of rodent and human genomes containing quantitative trait loci of rodent HCC models and various human HCC somatic aberrations including chromosomal data from loss of heterozygosity and comparative genome hybridization analyses, altered expression of genes from microarray and proteomic studies, and finally experimental data of published HCC genes. Comprehensive integration of HCC genomic aberration data avoids potential pitfalls of data inconsistency...

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

    Science.gov (United States)

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

    2017-01-04

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

  19. SensorDB: a virtual laboratory for the integration, visualization and analysis of varied biological sensor data.

    Science.gov (United States)

    Salehi, Ali; Jimenez-Berni, Jose; Deery, David M; Palmer, Doug; Holland, Edward; Rozas-Larraondo, Pablo; Chapman, Scott C; Georgakopoulos, Dimitrios; Furbank, Robert T

    2015-01-01

    To our knowledge, there is no software or database solution that supports large volumes of biological time series sensor data efficiently and enables data visualization and analysis in real time. Existing solutions for managing data typically use unstructured file systems or relational databases. These systems are not designed to provide instantaneous response to user queries. Furthermore, they do not support rapid data analysis and visualization to enable interactive experiments. In large scale experiments, this behaviour slows research discovery, discourages the widespread sharing and reuse of data that could otherwise inform critical decisions in a timely manner and encourage effective collaboration between groups. In this paper we present SensorDB, a web based virtual laboratory that can manage large volumes of biological time series sensor data while supporting rapid data queries and real-time user interaction. SensorDB is sensor agnostic and uses web-based, state-of-the-art cloud and storage technologies to efficiently gather, analyse and visualize data. Collaboration and data sharing between different agencies and groups is thereby facilitated. SensorDB is available online at http://sensordb.csiro.au.

  20. G6PD-MutDB: a mutation and phenotype database of glucose-6-phosphate (G6PD) deficiency.

    Science.gov (United States)

    Zhao, Xin; Li, Zuofeng; Zhang, Xiaoyan

    2010-12-01

    Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common hereditary enzymatic disorder of red blood cells in humans due to mutations in the G6PD gene. The G6PD enzyme catalyzes the first step in the pentose phosphate pathway to protect cells against oxidative stress. Mutations in the G6PD gene will cause functional variants with various biochemical and clinical phenotypes. So far, about 160 mutations along with more than 400 biochemical variants have been described. G6PD-MutDB is a disease-specific resource of G6PD deficiency, collecting and integrating G6PD mutations with biochemical and clinical phenotypes. Data of G6PD deficiency is manually extracted from published papers, focusing primarily on variants with identified mutation and well-described quantitative phenotypes. G6PD-MutDB implements an approach, CNSHA predictor, to help identify a potential chronic non-spherocytic hemolytic anemia (CNSHA) phenotype of an unknown mutation. G6PD-MutDB is believed to facilitate analysis of relationship between molecular mutation and functional phenotype of G6PD deficiency owing to convenient data resource and useful tools. This database is available from http://202.120.189.88/mutdb.

  1. Open and scalable analytics of large Earth observation datasets: From scenes to multidimensional arrays using SciDB and GDAL

    Science.gov (United States)

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

    2018-04-01

    Earth observation (EO) datasets are commonly provided as collection of scenes, where individual scenes represent a temporal snapshot and cover a particular region on the Earth's surface. Using these data in complex spatiotemporal modeling becomes difficult as soon as data volumes exceed a certain capacity or analyses include many scenes, which may spatially overlap and may have been recorded at different dates. In order to facilitate analytics on large EO datasets, we combine and extend the geospatial data abstraction library (GDAL) and the array-based data management and analytics system SciDB. We present an approach to automatically convert collections of scenes to multidimensional arrays and use SciDB to scale computationally intensive analytics. We evaluate the approach in three study cases on national scale land use change monitoring with Landsat imagery, global empirical orthogonal function analysis of daily precipitation, and combining historical climate model projections with satellite-based observations. Results indicate that the approach can be used to represent various EO datasets and that analyses in SciDB scale well with available computational resources. To simplify analyses of higher-dimensional datasets as from climate model output, however, a generalization of the GDAL data model might be needed. All parts of this work have been implemented as open-source software and we discuss how this may facilitate open and reproducible EO analyses.

  2. A critical analysis of the ultraviolet temperature scale of the helium-dominated DB and DBV white dwarfs

    Science.gov (United States)

    Thejll, Peter; Vennes, Stephane; Shipman, Harry L.

    1991-01-01

    The temperatures of the hottest of the DB and of some of the variable DBV white dwarfs have been reanalyzed, using a new helium-rich model atmosphere grid and archival IUE data. The grid covers variations in the effective temperature, surface gravity, and trace hydrogen abundance. Significantly lower temperatures than those found by earlier investigations are found. This has influence on the issue of which mixing-length theory is the best one for treatment of convection in DB white dwarfs. The prototype of the DBV stars, GD 358, is given particular attention in view of the recently reported HE II 1640-A line. The sensitivity of the new results to input physics is analyzed. It is found that uncertainties in Stark broadening parameters, convective efficiency, and equation of state and the assumptions of a fixed gravity (log g = 8) and a negligible abundance of hydrogen can at most give an error in the effective temperature of 400 K for a typical DB star. The uncertainty on the absolute calibration of the IUE cameras and the effect of small interstellar reddening dominate the error analysis.

  3. ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data.

    Science.gov (United States)

    Rosenfeld, Aaron M; Meng, Wenzhao; Luning Prak, Eline T; Hershberg, Uri

    2017-01-15

    As high-throughput sequencing of B cells becomes more common, the need for tools to analyze the large quantity of data also increases. This article introduces ImmuneDB, a system for analyzing vast amounts of heavy chain variable region sequences and exploring the resulting data. It can take as input raw FASTA/FASTQ data, identify genes, determine clones, construct lineages, as well as provide information such as selection pressure and mutation analysis. It uses an industry leading database, MySQL, to provide fast analysis and avoid the complexities of using error prone flat-files. ImmuneDB is freely available at http://immunedb.comA demo of the ImmuneDB web interface is available at: http://immunedb.com/demo CONTACT: Uh25@drexel.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  4. TcruziDB, an Integrated Database, and the WWW Information Server for the Trypanosoma cruzi Genome Project

    Directory of Open Access Journals (Sweden)

    Degrave Wim

    1997-01-01

    Full Text Available Data analysis, presentation and distribution is of utmost importance to a genome project. A public domain software, ACeDB, has been chosen as the common basis for parasite genome databases, and a first release of TcruziDB, the Trypanosoma cruzi genome database, is available by ftp from ftp://iris.dbbm.fiocruz.br/pub/genomedb/TcruziDB as well as versions of the software for different operating systems (ftp://iris.dbbm.fiocruz.br/pub/unixsoft/. Moreover, data originated from the project are available from the WWW server at http://www.dbbm.fiocruz.br. It contains biological and parasitological data on CL Brener, its karyotype, all available T. cruzi sequences from Genbank, data on the EST-sequencing project and on available libraries, a T. cruzi codon table and a listing of activities and participating groups in the genome project, as well as meeting reports. T. cruzi discussion lists (tcruzi-l@iris.dbbm.fiocruz.br and tcgenics@iris.dbbm.fiocruz.br are being maintained for communication and to promote collaboration in the genome project

  5. Novel lncRNA Erbb4-IR Promotes Diabetic Kidney Injury indb/dbMice by Targeting miR-29b.

    Science.gov (United States)

    Sun, Si F; Tang, Patrick M K; Feng, Min; Xiao, Jun; Huang, Xiao R; Li, Ping; Ma, Ronald C W; Lan, Hui Y

    2018-04-01

    Transforming growth factor-β/Smad signaling plays an important role in diabetic nephropathy. The current study identified a novel Smad3-dependent long noncoding RNA (lncRNA) Erbb4-IR in the development of type 2 diabetic nephropathy (T2DN) in db/db mice. We found that Erbb4-IR was highly expressed in T2DN of db/db mice and specifically induced by advanced glycosylation end products (AGEs) via a Smad3-dependent mechanism. The functional role of Erbb4-IR in T2DN was revealed by kidney-specific silencing of Erbb4-IR to protect against the development of T2DN, such as elevated microalbuminuria, serum creatinine, and progressive renal fibrosis in db/db mice, and to block AGE-induced collagen I and IV expression in mouse mesangial cells (mMCs) and mouse tubular epithelial cells (mTECs). Mechanistically, we identified that the Erbb4-IR-microRNA (miR)-29b axis was a key mechanism of T2DN because Erbb4-IR was able to bind the 3' untranslated region of miR-29b genomic sequence to suppress miR-29b expression at transcriptional level. In contrast, silencing of renal Erbb4-IR increased miR-29b and therefore protected the kidney from progressive renal injury in db/db mice and prevented mTECs and mMCs from AGE-induced loss of miR-29b and fibrotic response in vitro. Collectively, we identify that Erbb4-IR is a Smad3-dependent lncRNA that promotes renal fibrosis in T2DN by suppressing miR-29b. Targeting Erbb4-IR may represent a novel therapy for T2DN. © 2017 by the American Diabetes Association.

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

    Lifescience Database Archive (English)

    Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Regis...tered plant list Data detail Data name Registered plant list DOI 10.18908/lsdba.nbdc01194-01-001 Descri...base Site Policy | Contact Us Registered plant list - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

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

    Lifescience Database Archive (English)

    Full Text Available arch and download 1 README README_e.html - 2 Registered plant list pgdbj_dna_marker_linkage_map_plant_specie... of This Database Site Policy | Contact Us Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

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

    Lifescience Database Archive (English)

    Full Text Available f you use data from this database, please be sure attribute this database as follows: ... PGDBj Registered plan... Policy | Contact Us License - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods

  9. Statistical Design of Experiment (DoE) based development and optimization of DB213 in situ thermosensitive gel for intranasal delivery.

    Science.gov (United States)

    Wang, Qianwen; Wong, Chun-Ho; Chan, H Y Edwin; Lee, Wai-Yip; Zuo, Zhong

    2018-03-25

    DB213 is an HIV-1 replication inhibitor targeting the Central Nervous System for the treatment of HIV-associated neurocognitive disorders. Current study aims to develop an in situ thermosensitive gelling system for intranasal delivery of DB213 facilitated by Statistical Design of Experiment (DoE) to conduct a more efficient experimentation by extracting the maximum amount of information from limited experiments. In our current study, information was extracted from twenty-five experimental designs from MODDE ® Software and a mathematical model was successfully developed to predict formulations to achieve desired performance as well as to analyze relationships between the amount of Pluronic F-127, Pluronic F-68, Chitosan, DB213 and the performances of in situ thermosensitive gels. Based on DoE, in situ thermosensitive gels of 1% DB213 (F1) and 5% DB213 (F2) were developed for further in vivo bioavailability and brain uptake evaluations in Sprague-Dawley rats and C57BL/6 mice, respectively. In comparison to DB213 water solution, intranasal administrations of F1 at 1 mg/kg in rats and F2 at 25 mg/kg in mice demonstrated relative bioavailabilities of 145% and 165% with significant increase in brain uptake. Copyright © 2018 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Andrzej Czamara

    2015-01-01

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

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

    KAUST Repository

    Schmeier, Sebastian

    2016-10-17

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

  12. AnClim and ProClimDB software for data quality control and homogenization of time series

    Science.gov (United States)

    Stepanek, Petr

    2015-04-01

    During the last decade, a software package consisting of AnClim, ProClimDB and LoadData for processing (mainly climatological) data has been created. This software offers a complex solution for processing of climatological time series, starting from loading the data from a central database (e.g. Oracle, software LoadData), through data duality control and homogenization to time series analysis, extreme value evaluations and RCM outputs verification and correction (ProClimDB and AnClim software). The detection of inhomogeneities is carried out on a monthly scale through the application of AnClim, or newly by R functions called from ProClimDB, while quality control, the preparation of reference series and the correction of found breaks is carried out by the ProClimDB software. The software combines many statistical tests, types of reference series and time scales (monthly, seasonal and annual, daily and sub-daily ones). These can be used to create an "ensemble" of solutions, which may be more reliable than any single method. AnClim software is suitable for educational purposes: e.g. for students getting acquainted with methods used in climatology. Built-in graphical tools and comparison of various statistical tests help in better understanding of a given method. ProClimDB is, on the contrary, tool aimed for processing of large climatological datasets. Recently, functions from R may be used within the software making it more efficient in data processing and capable of easy inclusion of new methods (when available under R). An example of usage is easy comparison of methods for correction of inhomogeneities in daily data (HOM of Paul Della-Marta, SPLIDHOM method of Olivier Mestre, DAP - own method, QM of Xiaolan Wang and others). The software is available together with further information on www.climahom.eu . Acknowledgement: this work was partially funded by the project "Building up a multidisciplinary scientific team focused on drought" No. CZ.1.07/2.3.00/20.0248.

  13. StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics.

    Science.gov (United States)

    Ramirez-Gonzalez, Ricardo H; Leggett, Richard M; Waite, Darren; Thanki, Anil; Drou, Nizar; Caccamo, Mario; Davey, Robert

    2013-01-01

    Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts of time. Additionally, techniques such as multiplex sequencing allow one run to contain hundreds of different samples. With such data comes a significant challenge to understand its quality and to understand how the quality and yield are changing across instruments and over time. As well as the desire to understand historical data, sequencing centres often have a duty to provide clear summaries of individual run performance to collaborators or customers. We present StatsDB, an open-source software package for storage and analysis of next generation sequencing run metrics. The system has been designed for incorporation into a primary analysis pipeline, either at the programmatic level or via integration into existing user interfaces. Statistics are stored in an SQL database and APIs provide the ability to store and access the data while abstracting the underlying database design. This abstraction allows simpler, wider querying across multiple fields than is possible by the manual steps and calculation required to dissect individual reports, e.g. "provide metrics about nucleotide bias in libraries using adaptor barcode X, across all runs on sequencer A, within the last month". The software is supplied with modules for storage of statistics from FastQC, a commonly used tool for analysis of sequence reads, but the open nature of the database schema means it can be easily adapted to other tools. Currently at The Genome Analysis Centre (TGAC), reports are accessed through our LIMS system or through a standalone GUI tool, but the API and supplied examples make it easy to develop custom reports and to interface with other packages.

  14. Pharmacology of DB844, an orally active aza analogue of pafuramidine, in a monkey model of second stage human African trypanosomiasis.

    Directory of Open Access Journals (Sweden)

    John K Thuita

    Full Text Available Novel drugs to treat human African trypanosomiasis (HAT are still urgently needed despite the recent addition of nifurtimox-eflornithine combination therapy (NECT to WHO Model Lists of Essential Medicines against second stage HAT, where parasites have invaded the central nervous system (CNS. The pharmacology of a potential orally available lead compound, N-methoxy-6-{5-[4-(N-methoxyamidino phenyl]-furan-2-yl}-nicotinamidine (DB844, was evaluated in a vervet monkey model of second stage HAT, following promising results in mice. DB844 was administered orally to vervet monkeys, beginning 28 days post infection (DPI with Trypanosoma brucei rhodesiense KETRI 2537. DB844 was absorbed and converted to the active metabolite 6-[5-(4-phenylamidinophenyl-furanyl-2-yl]-nicotinamide (DB820, exhibiting plasma C(max values of 430 and 190 nM for DB844 and DB820, respectively, after the 14th dose at 6 mg/kg qd. A 100-fold reduction in blood trypanosome counts was observed within 24 h of the third dose and, at the end of treatment evaluation performed four days post the last drug dose, trypanosomes were not detected in the blood or cerebrospinal fluid of any monkey. However, some animals relapsed during the 300 days of post treatment monitoring, resulting in a cure rate of 3/8 (37.5% and 3/7 (42.9% for the 5 mg/kg×10 days and the 6 mg/kg×14 days dose regimens respectively. These DB844 efficacy data were an improvement compared with pentamidine and pafuramidine both of which were previously shown to be non-curative in this model of CNS stage HAT. These data show that synthesis of novel diamidines with improved activity against CNS-stage HAT was possible.

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

    Science.gov (United States)

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

    2017-04-04

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

  16. Pharmacology of DB844, an Orally Active aza Analogue of Pafuramidine, in a Monkey Model of Second Stage Human African Trypanosomiasis

    Science.gov (United States)

    Thuita, John K.; Wang, Michael Z.; Kagira, John M.; Denton, Cathrine L.; Paine, Mary F.; Mdachi, Raymond E.; Murilla, Grace A.; Ching, Shelley; Boykin, David W.; Tidwell, Richard R.; Hall, James E.; Brun, Reto

    2012-01-01

    Novel drugs to treat human African trypanosomiasis (HAT) are still urgently needed despite the recent addition of nifurtimox-eflornithine combination therapy (NECT) to WHO Model Lists of Essential Medicines against second stage HAT, where parasites have invaded the central nervous system (CNS). The pharmacology of a potential orally available lead compound, N-methoxy-6-{5-[4-(N-methoxyamidino) phenyl]-furan-2-yl}-nicotinamidine (DB844), was evaluated in a vervet monkey model of second stage HAT, following promising results in mice. DB844 was administered orally to vervet monkeys, beginning 28 days post infection (DPI) with Trypanosoma brucei rhodesiense KETRI 2537. DB844 was absorbed and converted to the active metabolite 6-[5-(4-phenylamidinophenyl)-furanyl-2-yl]-nicotinamide (DB820), exhibiting plasma Cmax values of 430 and 190 nM for DB844 and DB820, respectively, after the 14th dose at 6 mg/kg qd. A 100-fold reduction in blood trypanosome counts was observed within 24 h of the third dose and, at the end of treatment evaluation performed four days post the last drug dose, trypanosomes were not detected in the blood or cerebrospinal fluid of any monkey. However, some animals relapsed during the 300 days of post treatment monitoring, resulting in a cure rate of 3/8 (37.5%) and 3/7 (42.9%) for the 5 mg/kg×10 days and the 6 mg/kg×14 days dose regimens respectively. These DB844 efficacy data were an improvement compared with pentamidine and pafuramidine both of which were previously shown to be non-curative in this model of CNS stage HAT. These data show that synthesis of novel diamidines with improved activity against CNS-stage HAT was possible. PMID:22848769

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

    Science.gov (United States)

    Pandey, Ram Vinay; Nolte, Viola; Boenigk, Jens; Schlötterer, Christian

    2011-06-30

    Next generation sequencing (NGS) is widely used in metagenomic and transcriptomic analyses in biodiversity. The ease of data generation provided by NGS platforms has allowed researchers to perform these analyses on their particular study systems. In particular the 454 platform has become the preferred choice for PCR amplicon based biodiversity surveys because it generates the longest sequence reads. Nevertheless, the handling and organization of massive amounts of sequencing data poses a major problem for the research community, particularly when multiple researchers are involved in data acquisition and analysis. An integrated and user-friendly tool, which performs quality control, read trimming, PCR primer removal, and data organization is desperately needed, therefore, to make data interpretation fast and manageable. We developed CANGS DB (Cleaning and Analyzing Next Generation Sequences DataBase) a flexible, stand alone and user-friendly integrated database tool. CANGS DB is specifically designed to organize and manage the massive amount of sequencing data arising from various NGS projects. CANGS DB also provides an intuitive user interface for sequence trimming and quality control, taxonomy analysis and rarefaction analysis. Our database tool can be easily adapted to handle multiple sequencing projects in parallel with different sample information, amplicon sizes, primer sequences, and quality thresholds, which makes this software especially useful for non-bioinformaticians. Furthermore, CANGS DB is especially suited for projects where multiple users need to access the data. CANGS DB is available at http://code.google.com/p/cangsdb/. CANGS DB provides a simple and user-friendly solution to process, store and analyze 454 sequencing data. Being a local database that is accessible through a user-friendly interface, CANGS DB provides the perfect tool for collaborative amplicon based biodiversity surveys without requiring prior bioinformatics skills.

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

    Directory of Open Access Journals (Sweden)

    Schlötterer Christian

    2011-06-01

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

  19. SynapticDB, effective web-based management and sharing of data from serial section electron microscopy.

    Science.gov (United States)

    Shi, Bitao; Bourne, Jennifer; Harris, Kristen M

    2011-03-01

    Serial section electron microscopy (ssEM) is rapidly expanding as a primary tool to investigate synaptic circuitry and plasticity. The ultrastructural images collected through ssEM are content rich and their comprehensive analysis is beyond the capacity of an individual laboratory. Hence, sharing ultrastructural data is becoming crucial to visualize, analyze, and discover the structural basis of synaptic circuitry and function in the brain. We devised a web-based management system called SynapticDB (http://synapses.clm.utexas.edu/synapticdb/) that catalogues, extracts, analyzes, and shares experimental data from ssEM. The management strategy involves a library with check-in, checkout and experimental tracking mechanisms. We developed a series of spreadsheet templates (MS Excel, Open Office spreadsheet, etc) that guide users in methods of data collection, structural identification, and quantitative analysis through ssEM. SynapticDB provides flexible access to complete templates, or to individual columns with instructional headers that can be selected to create user-defined templates. New templates can also be generated and uploaded. Research progress is tracked via experimental note management and dynamic PDF forms that allow new investigators to follow standard protocols and experienced researchers to expand the range of data collected and shared. The combined use of templates and tracking notes ensures that the supporting experimental information is populated into the database and associated with the appropriate ssEM images and analyses. We anticipate that SynapticDB will serve future meta-analyses towards new discoveries about the composition and circuitry of neurons and glia, and new understanding about structural plasticity during development, behavior, learning, memory, and neuropathology.

  20. dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder.

    Science.gov (United States)

    Zhang, Shuyun; Deng, Libin; Jia, Qiyue; Huang, Shaoting; Gu, Junwang; Zhou, Fankun; Gao, Meng; Sun, Xinyi; Feng, Chang; Fan, Guangqin

    2017-11-16

    Autism spectrum disorders (ASD) are hereditary, heterogeneous and biologically complex neurodevelopmental disorders. Individual studies on gene expression in ASD cannot provide clear consensus conclusions. Therefore, a systematic review to synthesize the current findings from brain tissues and a search tool to share the meta-analysis results are urgently needed. Here, we conducted a meta-analysis of brain gene expression profiles in the current reported human ASD expression datasets (with 84 frozen male cortex samples, 17 female cortex samples, 32 cerebellum samples and 4 formalin fixed samples) and knock-out mouse ASD model expression datasets (with 80 collective brain samples). Then, we applied R language software and developed an interactive shared and updated database (dbMDEGA) displaying the results of meta-analysis of data from ASD studies regarding differentially expressed genes (DEGs) in the brain. This database, dbMDEGA ( https://dbmdega.shinyapps.io/dbMDEGA/ ), is a publicly available web-portal for manual annotation and visualization of DEGs in the brain from data from ASD studies. This database uniquely presents meta-analysis values and homologous forest plots of DEGs in brain tissues. Gene entries are annotated with meta-values, statistical values and forest plots of DEGs in brain samples. This database aims to provide searchable meta-analysis results based on the current reported brain gene expression datasets of ASD to help detect candidate genes underlying this disorder. This new analytical tool may provide valuable assistance in the discovery of DEGs and the elucidation of the molecular pathogenicity of ASD. This database model may be replicated to study other disorders.