Large scale EMF in current sheets induced by tearing modes

NASA Astrophysics Data System (ADS)

Mizerski, Krzysztof A.

2018-02-01

An extension of the analysis of resistive instabilities of a sheet pinch from a famous work by Furth et al (1963 Phys. Fluids 6 459) is presented here, to study the mean electromotive force (EMF) generated by the developing instability. In a Cartesian configuration and in the presence of a current sheet first the boundary layer technique is used to obtain global, matched asymptotic solutions for the velocity and magnetic field and then the solutions are used to calculate the large-scale EMF in the system. It is reported, that in the bulk the curl of the mean EMF is linear in {{j}}0\\cdot {{B}}0, a simple pseudo-scalar quantity constructed from the large-scale quantities.

Thermal emf generated by laser emission along thin metal films

NASA Astrophysics Data System (ADS)

Konov, V. I.; Nikitin, P. I.; Satiukov, D. G.; Uglov, S. A.

1991-07-01

Substantial pulse thermal emf values (about 1.5 V) have been detected along the substrate during the interaction of laser emission with thin metal films (Ni, Ti, and Bi) sprayed on corrugated substrates. Relationships are established between the irradiation conditions and parameters of the generated electrical signals. Possible mechanisms of thermal emf generation and promising applications are discussed.

Design and fabrication of a microplatform for the proximity effect study of localized ELF-EMF on the growth of in vitro HeLa and PC-12 cells

NASA Astrophysics Data System (ADS)

Chen, Y. C.; Chen, C. C.; Tu, W.; Cheng, Y. T.; Tseng, F. G.

2010-12-01

This paper presents a platform technology with experimental results that show the scientists and biologists a way to rapidly investigate and analyze the biological effects of localized extremely low frequency (ELF) electromagnetic field (EMF) on living cells. The proximity effect of the localized ELF-EMF on living cells is revealed using the bio-compatible microplatform on which an on-glass inductive coil array, the source of the localized ELF-EMF in micro scale, is designed, fabricated and operated with a field strength of 1.2 ± 0.1 mT at 60 Hz for cell culturing study. After a 72 h ELF-EMF exposure, HeLa (human cervical cancer) and PC-12 (rat pheochromocytoma) cells exhibit about 18.4% and 12.9% cell proliferation rate reduction, respectively. Furthermore, according to the presented dynamic model, the reduction of the proliferation can be attributed to the interference of signal transduction processes due to the tangential currents induced around the cells.

Electromagnetic fields and the public: EMF standards and estimation of risk

NASA Astrophysics Data System (ADS)

Grigoriev, Yury

2010-04-01

Mobile communications are a relatively new and additional source of electromagnetic exposure for the population. Standard daily mobile-phone use is known to increase RF-EMF (radiofrequency electromagnetic field) exposure to the brains of users of all ages, whilst mobile-phone base stations, and base station units for cordless phones, can regularly increase the exposures of large numbers of the population to RF-EMF radiation in everyday life. The need to determine appropriate standards stipulating the maximum acceptable short-term and long-term RF-EMF levels encountered by the public, and set such levels as general guidelines, is of great importance in order to help preserve the general public's health and that of the next generation of humanity.

Optimization of a therapeutic electromagnetic field (EMF) to retard breast cancer tumor growth and vascularity.

PubMed

Cameron, Ivan L; Markov, Marko S; Hardman, W Elaine

2014-01-01

This study provided additional data on the effects of a therapeutic electromagnetic field (EMF) device on growth and vascularization of murine 16/C mammary adenocarcinoma cells implanted in C3H/HeJ mice. The therapeutic EMF device generated a defined 120 Hz semi sine wave pulse signal of variable intensity. Murine 16/C mammary adenocarcinoma tumor fragments were implanted subcutaneously between the scapulae of syngeneic C3H mice. Once the tumor grew to 100 mm(3), daily EMF treatments were started by placing the cage of mice within the EMF field. Treatment ranged from 10 to 20 milli-Tesla (mT) and was given for 3 to 80 minutes either once or twice a day for 12 days. Tumors were measured and volumes calculated each 3-4 days. Therapeutic EMF treatment significantly suppressed tumor growth in all 7 EMF treated groups. Exposure to 20mT for 10 minutes twice a day was the most effective tumor growth suppressor. The effect of EMF treatment on extent of tumor vascularization, necrosis and viable area was determined after euthanasia. The EMF reduced the vascular (CD31 immunohistochemically positive) volume fraction and increased the necrotic volume of the tumor. Treatment with 15 mT for 10 min/d gave the maximum anti-angiogenic effect. Lack of a significant correlation between tumor CD 31 positive area and tumor growth rate indicates a mechanism for suppression of tumor growth in addition to suppression of tumor vascularization. It is proposed that EMF therapy aimed at suppression of tumor growth and vascularization may prove a safe alternative for patients whether they are or are not candidates for conventional cancer therapy.

Review of the epidemiologic literature on EMF and Health.

PubMed Central

Ahlbom, I C; Cardis, E; Green, A; Linet, M; Savitz, D; Swerdlow, A

2001-01-01

Exposures to extremely low-frequency electric and magnetic fields (EMF) emanating from the generation, transmission, and use of electricity are a ubiquitous part of modern life. Concern about potential adverse health effects was initially brought to prominence by an epidemiologic report two decades ago from Denver on childhood cancer. We reviewed the now voluminous epidemiologic literature on EMF and risks of chronic disease and conclude the following: a) The quality of epidemiologic studies on this topic has improved over time and several of the recent studies on childhood leukemia and on cancer associated with occupational exposure are close to the limit of what can realistically be achieved in terms of size of study and methodological rigor. b) Exposure assessment is a particular difficulty of EMF epidemiology, in several respects: i) The exposure is imperceptible, ubiquitous, has multiple sources, and can vary greatly over time and short distances. ii) The exposure period of relevance is before the date at which measurements can realistically be obtained and of unknown duration and induction period. iii) The appropriate exposure metric is not known and there are no biological data from which to impute it. c) In the absence of experimental evidence and given the methodological uncertainties in the epidemiologic literature, there is no chronic disease for which an etiological relation to EMF can be regarded as established. d) There has been a large body of high quality data for childhood cancer, and also for adult leukemia and brain tumor in relation to occupational exposure. Among all the outcomes evaluated in epidemiologic studies of EMF, childhood leukemia in relation to postnatal exposures above 0.4 microT is the one for which there is most evidence of an association. The relative risk has been estimated at 2.0 (95% confidence limit: 1.27-3.13) in a large pooled analysis. This is unlikely to be due to chance but, may be, in part, due to bias. This is

Safety of High Speed Guided Ground Transportation Systems - EMF Exposure Environments Summary Reports

DOT National Transportation Integrated Search

1993-08-01

This paper presents an overview of American exposure assessments for electric and magnetic fields (EMF) in the frequency : range from 0 to 3 kHz. The exposure information available is very limited for all but a few occupations and sources of : EMF. M...

The impact of background radiation, illumination and temperature on EMF-induced changes of aqua medium properties.

PubMed

Naira, Baghdasaryan; Yerazik, Mikayelyan; Anna, Nikoghosyan; Sinerik, Ayrapetyan

2013-09-01

The effects of extremely low frequency electromagnetic field (ELF EMF) on physicochemical properties of physiological solution at different environmental media were studied. The existence of frequency "windows" at 4 and 8 Hz frequencies of ELF EMF having effects on heat fusion period, hydrogen peroxide (H2O2) formation and oxygen (O2) content of water solution and different dependency on temperature, background radiation and illumination was shown. Obtained data allow us to suggest that EMF-induced effect on water physicochemical properties depends on abovementioned environmental factors. As cell bathing medium is a target for biological effects of ELF EMF, the variability of experimental data on biological effects of EMF, obtained in different laboratories, can be explained by different environmental conditions of experiments, which very often are not considered adequately.

Thermodynamic properties of calcium-bismuth alloys determined by emf measurements

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

Kim, H; Boysen, DA; Bradwell, DJ

2012-01-15

The thermodynamic properties of Ca-Bi alloys were determined by electromotive force (emf) measurements to assess the suitability of Ca-Bi electrodes for electrochemical energy storage applications. Emf was measured at ambient pressure as a function of temperature between 723 K and 1173 K using a Ca(s)vertical bar CaF2(s)vertical bar Ca(in Bi) cell for twenty different Ca-Bi alloys spanning the entire range of composition from chi(Ca) = 0 to 1. Reported are the temperature-independent partial molar entropy and enthalpy of calcium for each Ca-Bi alloy. Also given are the measured activities of calcium, the excess partial molar Gibbs energy of bismuth estimatedmore » from the Gibbs-Duhem equation, and the integral change in Gibbs energy for each Ca-Bi alloy at 873 K, 973 K, and 1073 K. Calcium activities at 973 K were found to be nearly constant at a value a(Ca) = 1 x 10(-8) over the composition range chi(Ca) = 0.32-0.56, yielding an emf of similar to 0.77 V. Above chi(Ca) = 0.62 and coincident with Ca5Bi3 formation, the calcium activity approached unity. The Ca-Bi system was also characterized by differential scanning calorimetry over the entire range of composition. Based upon these data along with the emf measurements, a revised Ca-Bi binary phase diagram is proposed. (C) 2011 Elsevier Ltd. All rights reserved.« less

Rate of rotation measurement using back-EMFS associated with windings of a brushless DC motor

NASA Technical Reports Server (NTRS)

Howard, David E. (Inventor)

2000-01-01

A system and method are provided for measuring rate of rotation. A brushless DC motor is rotated and produces a back electromagnetic force (emf) on each winding thereof. Each winding's back-emf is integrated and multiplied by the back-emf associated with an adjacent winding. The multiplied outputs associated with each winding are combined to produce a directionally sensitive DC output proportional only to the rate of rotation of the motor's shaft.

mTOR Activation by PI3K/Akt and ERK Signaling in Short ELF-EMF Exposed Human Keratinocytes

PubMed Central

Patruno, Antonia; Pesce, Mirko; Grilli, Alfredo; Speranza, Lorenza; Franceschelli, Sara; De Lutiis, Maria Anna; Vianale, Giovina; Costantini, Erica; Amerio, Paolo; Muraro, Raffaella; Felaco, Mario; Reale, Marcella

2015-01-01

Several reports suggest that ELF-EMF exposures interact with biological processes including promotion of cell proliferation. However, the molecular mechanisms by which ELF-EMF controls cell growth are not completely understood. The present study aimed to investigate the effect of ELF-EMF on keratinocytes proliferation and molecular mechanisms involved. Effect of ELF-EMF (50 Hz, 1 mT) on HaCaT cell cycle and cells growth and viability was monitored by FACS analysis and BrdU assay. Gene expression profile by microarray and qRT-PCR validation was performed in HaCaT cells exposed or not to ELF-EMF. mTOR, Akt and MAPKs expressions were evaluated by Western blot analysis. In HaCaT cells, short ELF-EMF exposure modulates distinct patterns of gene expression involved in cell proliferation and in the cell cycle. mTOR activation resulted the main molecular target of ELF-EMF on HaCaT cells. Our data showed the increase of the canonical pathway of mTOR regulation (PI3K/Akt) and activation of ERK signaling pathways. Our results indicate that ELF-EMF selectively modulated the expression of multiple genes related to pivotal biological processes and functions that play a key role in physio-pathological mechanisms such as wound healing. PMID:26431550

[Optimization of measurement methods for a multi-frequency electromagnetic field from mobile phone base station using broadband EMF meter].

PubMed

Bieńkowski, Paweł; Cała, Paweł; Zubrzak, Bartłomiej

2015-01-01

This paper presents the characteristics of the mobile phone base station (BS) as an electromagnetic field (EMF) source. The most common system configurations with their construction are described. The parameters of radiated EMF in the context of the access to methods and other parameters of the radio transmission are discussed. Attention was also paid to antennas that are used in this technology. The influence of individual components of a multi-frequency EMF, most commonly found in the BS surroundings, on the resultant EMF strength value indicated by popular broadband EMF meters was analyzed. The examples of metrological characteristics of the most common EMF probes and 2 measurement scenarios of the multisystem base station, with and without microwave relays, are shown. The presented method for measuring the multi-frequency EMF using 2 broadband probes allows for the significant minimization of measurement uncertainty. Equations and formulas that can be used to calculate the actual EMF intensity from multi-frequency sources are shown. They have been verified in the laboratory conditions on a specific standard setup as well as in real conditions in a survey of the existing base station with microwave relays. Presented measurement methodology of multi-frequency EMF from BS with microwave relays, validated both in laboratory and real conditions. It has been proven that the described measurement methodology is the optimal approach to the evaluation of EMF exposure in BS surrounding. Alternative approaches with much greater uncertainty (precaution method) or more complex measuring procedure (sources exclusion method) are also presented). This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

Rrsm: The European Rapid Raw Strong-Motion Database

NASA Astrophysics Data System (ADS)

Cauzzi, C.; Clinton, J. F.; Sleeman, R.; Domingo Ballesta, J.; Kaestli, P.; Galanis, O.

2014-12-01

We introduce the European Rapid Raw Strong-Motion database (RRSM), a Europe-wide system that provides parameterised strong motion information, as well as access to waveform data, within minutes of the occurrence of strong earthquakes. The RRSM significantly differs from traditional earthquake strong motion dissemination in Europe, which has focused on providing reviewed, processed strong motion parameters, typically with significant delays. As the RRSM provides rapid open access to raw waveform data and metadata and does not rely on external manual waveform processing, RRSM information is tailored to seismologists and strong-motion data analysts, earthquake and geotechnical engineers, international earthquake response agencies and the educated general public. Access to the RRSM database is via a portal at http://www.orfeus-eu.org/rrsm/ that allows users to query earthquake information, peak ground motion parameters and amplitudes of spectral response; and to select and download earthquake waveforms. All information is available within minutes of any earthquake with magnitude ≥ 3.5 occurring in the Euro-Mediterranean region. Waveform processing and database population are performed using the waveform processing module scwfparam, which is integrated in SeisComP3 (SC3; http://www.seiscomp3.org/). Earthquake information is provided by the EMSC (http://www.emsc-csem.org/) and all the seismic waveform data is accessed at the European Integrated waveform Data Archive (EIDA) at ORFEUS (http://www.orfeus-eu.org/index.html), where all on-scale data is used in the fully automated processing. As the EIDA community is continually growing, the already significant number of strong motion stations is also increasing and the importance of this product is expected to also increase. Real-time RRSM processing started in June 2014, while past events have been processed in order to provide a complete database back to 2005.

Three-phase power factor controller with induced EMF sensing

NASA Technical Reports Server (NTRS)

Nola, F. J. (Inventor)

1984-01-01

A power factor controller for an ac induction motor is provided which is of the type comprising thyristor switches connected in series with the motor, phase detectors for sensing the motor current and voltage and providing an output proportional to the phase difference between the motor voltage and current, and a control circuit, responsive to the output of the phase detector and to a power factor command signal, for controlling switching of the thyristor. The invention involves sensing the induced emf produced by the motor during the time interval when the thyristor is off and for producing a corresponding feedback signal for controlling switching of the thyristor. The sensed emf is also used to enhance soft starting of the motor.

Rapid-onset/offset, variably scheduled 60 Hz electric and magnetic field exposure reduces nocturnal serum melatonin concentration in nonhuman primates

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

Rogers, W.R.; Smith, H.D.; Reiter, R.J.

Experiments with rodents indicate that power-frequency electric field (EF) or magnetic field (MF) exposure can suppress the normal nocturnal increase in melatonin concentration in pineal gland and blood. In a separate set of three experiments conducted with nonhuman primates, the authors did not observe melatonin suppression as a result of 6 weeks of day-time exposure to combined 60 Hz electric and magnetic fields (E/MF) with regularly schedule ``slow`` E/MF onsets/offsets. The study described here used a different exposure paradigm in which two baboons were exposed to E/MF with ``rapid`` E/MF onsets/offsets accompanied by EF transients not found with slowly rampedmore » E/MF onset/offset; profound reductions in nocturnal serum melatonin concentration were observed in this experiment. If replicated in a more extensive experiment, the observation of melatonin suppression only in the presence of E/MF transients would suggest that very specific exposure parameters determine the effects of 60 Hz E/MF on melatonin.« less

Comparison of a triaxial fluxgate magnetometer and Toftness sensometer for body surface EMF measurement.

PubMed

Zhang, John; Toftness, Dave; Snyder, Brian; Nosco, Dennis; Balcavage, Walter; Nindl, Gabi

2004-12-01

The use of magnetic fields to treat disease has intrigued mankind since the time of the ancient Greeks. More recently it has been shown that electromagnetic field (EMF) treatment aids bone healing, and repetitive transcranial magnetic stimulation (rTMS) appears to be beneficial in treating schizophrenia and depression. Since external EMFs influence internal body processes, we hypothesized that measurement of body surface EMFs might be used to detect disease states and direct the course of subsequent therapy. However, measurement of minute body surface EMFs requires use of a sensitive and well documented magnetometer. In this study we evaluated the sensitivity and frequency response of a fluxgate magnetometer with a triaxial probe for use in detecting body surface EMF and we compared the magnetometer readings with a signal from a Toftness Sensometer, operated by an experienced clinician, in the laboratory and in a clinical setting. A Peavy Audio Amplifier and variable power output Telulex signal generator were used to develop 50 microT EMFs in a three coil Merritt coil system. A calibrated magnetometer was used to set a 60 Hz 50 microT field in the coil and an ammeter was used to measure the current required to develop the 50 microT field. At frequencies other than 60 Hz, the field strength was maintained at 50 microT by adjusting the Telulex signal output to keep the current constant. The field generated was monitored using a 10 turn coil connected to an oscilloscope. The oscilloscope reading indicated that the field strength was the same at all frequencies tested. To determine if there was a correspondence between the signals detected by a fluxgate magnetometer (FGM1) and the Toftness Sensometer both devices were placed in the Merritt coil and readings were recorded from the FGM1 and compared with the ability of a highly experienced Toftness operator to detect the 50 microT field. Subsequently, in a clinical setting, FGM1 readings made by an FGM1 technician and

Comparison of a triaxial fluxgate magnetometer and Toftness sensometer for body surface EMF measurement

PubMed Central

Zhang, John; Toftness, Dave; Snyder, Brian; Nosco, Dennis; Balcavage, Walter; Nindl, Gabi

2004-01-01

Introduction The use of magnetic fields to treat disease has intrigued mankind since the time of the ancient Greeks. More recently it has been shown that electromagnetic field (EMF) treatment aids bone healing, and repetitive transcranial magnetic stimulation (rTMS) appears to be beneficial in treating schizophrenia and depression. Since external EMFs influence internal body processes, we hypothesized that measurement of body surface EMFs might be used to detect disease states and direct the course of subsequent therapy. However, measurement of minute body surface EMFs requires use of a sensitive and well documented magnetometer. In this study we evaluated the sensitivity and frequency response of a fluxgate magnetometer with a triaxial probe for use in detecting body surface EMF and we compared the magnetometer readings with a signal from a Toftness Sensometer, operated by an experienced clinician, in the laboratory and in a clinical setting. Methods A Peavy Audio Amplifier and variable power output Telulex signal generator were used to develop 50 μT EMFs in a three coil Merritt coil system. A calibrated magnetometer was used to set a 60 Hz 50 μT field in the coil and an ammeter was used to measure the current required to develop the 50 μT field. At frequencies other than 60 Hz, the field strength was maintained at 50 μT by adjusting the Telulex signal output to keep the current constant. The field generated was monitored using a 10 turn coil connected to an oscilloscope. The oscilloscope reading indicated that the field strength was the same at all frequencies tested. To determine if there was a correspondence between the signals detected by a fluxgate magnetometer (FGM1) and the Toftness Sensometer both devices were placed in the Merritt coil and readings were recorded from the FGM1 and compared with the ability of a highly experienced Toftness operator to detect the 50 μT field. Subsequently, in a clinical setting, FGM1 readings made by an FGM1 technician

Extremely low frequency electromagnetic field (ELF-EMF) reduces oxidative stress and improves functional and psychological status in ischemic stroke patients.

PubMed

Cichoń, Natalia; Bijak, Michał; Miller, Elżbieta; Saluk, Joanna

2017-07-01

As a result of ischaemia/reperfusion, massive generation of reactive oxygen species occurs, followed by decreased activity of antioxidant enzymes. Extremely low frequency electromagnetic fields (ELF-EMF) can modulate oxidative stress, but there are no clinical antioxidant studies in brain stroke patients. The aim of our study was to investigate the effect of ELF-EMF on clinical and antioxidant status in post-stroke patients. Fifty-seven patients were divided into two groups: ELF-EMF and non-ELF-EMF. Both groups underwent the same 4-week rehabilitation program. Additionally, the ELF-EMF group was exposed to an ELF-EMF field of 40 Hz, 7 mT for 15 min/day for 4 weeks (5 days a week). The activity of catalase and superoxide dismutase was measured in hemolysates, and total antioxidant status (TAS) determined in plasma. Functional status was assessed before and after the series of treatments using Activities of Daily Living (ADL), Mini-Mental State Examination (MMSE), and Geriatric Depression Scale (GDS). Applied ELF-EMF significantly increased enzymatic antioxidant activity; however, TAS levels did not change in either group. Results show that ELF-EMF induced a significant improvement in functional (ADL) and mental (MMSE, GDS) status. Clinical parameters had positive correlation with the level of enzymatic antioxidant protection. Bioelectromagnetics. 38:386-396, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Residential exposure from extremely low frequency electromagnetic field (ELF EMF) radiation

NASA Astrophysics Data System (ADS)

Parthasarathy, Shamesh Raj; Tukimin, Roha

2018-01-01

ELF EMF radiation have received considerable attention as a potential threat to the safety and health of people living in the vicinity of high voltage transmission lines, electric distribution substations, power stations and even in close proximity to electronics and electrical household appliances. The paper highlights the study on the ELF EMF safety assessment performed at residences comprising of an owner-occupied house, a completed vacant house and an under construction condominium. The objectives of this study were to determine the ELF EMF radiation exposure level from the high voltage transmission line, electric distribution substation, power station and electrical household appliances in the residences, and to assess the potential exposure received by the occupants at the assessed locations. The results were logged in the electric and magnetic field strength with the units of volt per meter (V/m) and miliGauss (mG) respectively. The instrument setup and measurement protocols during the assessment were adopted from standard measurement method and procedures stipulated under the Institute of Electrical and Electronics Engineers (IEEE) Standard. The results were compared with the standards recommended in the International Commission on Non-Ionizing Radiation Protection (ICNIRP) guidelines.

Melatonin and puberty in female lambs exposed to EMF: A replicate study

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

Lee, J.M. Jr.; Stormshak, F.; Thompson, J.M.

1995-06-01

In an earlier study, the authors found no effects of 60 Hz electric and magnetic fields (EMF) from a 500 kV transmission line on serum melatonin patterns or on puberty in ten female Suffolk lambs (Ovis aries). The authors conducted a larger replicate study of 15 lambs exposed to a mean electric field of 6.3 kV/m and a mean magnetic field of 3.77 {mu}T and 15 controls exposed to EMF two orders of magnitude weaker than in the line area. The replicate produced essentially the same results as their previous study.

Transparent Democratic Foresight Strategies in the California EMF Program.

PubMed

Neutra, Raymond Richard; Delpizzo, Vincent

2002-01-01

A California Department of Health Services program dealt with possible health effects from Electric and Magnetic Fields (EMF) from power lines. With the advice of stakeholders, and well before any risk determinations were made, transparent policy analyses about the power grid and schools asked the question, "How confident must one be of how big an effect before one would adopt cheap or expensive EMF avoidance measures?" A risk evaluation was carried out with features that promoted transparency. It was formatted to provide a policy-neutral "degree of certainty of causality" to adherents of utilitarian, environmental justice, and libertarian policy frameworks. Though the program had many features advocated by adherents of the precautionary principle, it might be better characterized as following "Transparent Democratic Foresight Strategies," since no single principle justifies the strategies used in this participatory program, and it examined the pros and cons of options but made no recommendations, precautionary or otherwise.

Genotoxic effects of exposure to radiofrequency electromagnetic fields (RF-EMF) in HL-60 cells are not reproducible.

PubMed

Speit, Günter; Gminski, Richard; Tauber, Rudolf

2013-08-15

Conflicting results have been published regarding the induction of genotoxic effects by exposure to radiofrequency electromagnetic fields (RF-EMF). Various results indicating a genotoxic potential of RF-EMF were reported by the collaborative EU-funded REFLEX (Risk Evaluation of Potential Environmental Hazards From Low Energy Electromagnetic Field Exposure Using Sensitive in vitro Methods) project. There has been a long-lasting scientific debate about the reliability of the reported results and an attempt to reproduce parts of the results obtained with human fibroblasts failed. Another part of the REFLEX study was performed in Berlin with the human lymphoblastoid cell line HL-60; genotoxic effects of RF-EMF were measured by means of the comet assay and the micronucleus test. The plausibility and reliability of these results were also questioned. In order to contribute to a clarification of the biological significance of the reported findings, a repeat study was performed, involving scientists of the original study. Comet-assay experiments and micronucleus tests were performed under the same experimental conditions that had led to genotoxic effects in the REFLEX study. Here we report that the attempts to reproduce the induction of genotoxic effects by RF-EMF in HL-60 cells failed. No genotoxic effects of RF-EMF were measured in the repeat experiments. We could not find an explanation for the conflicting results. However, the negative repeat experiments suggest that the biological significance of genotoxic effects of RF-EMF reported by the REFLEX study should be re-assessed. Copyright © 2013 Elsevier B.V. All rights reserved.

The role of the JAK2-STAT3 pathway in pro-inflammatory responses of EMF-stimulated N9 microglial cells

PubMed Central

2010-01-01

Background In several neuropathological conditions, microglia can become overactivated and cause neurotoxicity by initiating neuronal damage in response to pro-inflammatory stimuli. Our previous studies have shown that exposure to electromagnetic fields (EMF) activates cultured microglia to produce tumor necrosis factor (TNF)-α and nitric oxide (NO) through signal transduction involving the activator of transcription STAT3. Here, we investigated the role of STAT3 signaling in EMF-induced microglial activation and pro-inflammatory responses in more detail than the previous study. Methods N9 microglial cells were treated with EMF exposure or a sham treatment, with or without pretreatment with an inhibitor (Pyridone 6, P6) of the Janus family of tyrosine kinases (JAK). The activation state of microglia was assessed via immunoreaction using the microglial marker CD11b. Levels of inducible nitric oxide synthase (iNOS), TNF-α and NO were measured using real-time reverse transcription-polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA) and the nitrate reductase method. Activation of JAKs and STAT3 proteins was evaluated by western blotting for specific tyrosine phosphorylation. The ability of STAT3 to bind to DNA was detected with an electrophoresis mobility shift assay (EMSA). Results EMF was found to significantly induce phosphorylation of JAK2 and STAT3, and DNA-binding ability of STAT3 in N9 microglia. In addition, EMF dramatically increased the expression of CD11b, TNF-α and iNOS, and the production of NO. P6 strongly suppressed the phosphorylation of JAK2 and STAT3 and diminished STAT3 activity in EMF-stimulated microglia. Interestingly, expression of CD11b as well as gene expression and production of TNF-α and iNOS were suppressed by P6 at 12 h, but not at 3 h, after EMF exposure. Conclusions EMF exposure directly triggers initial activation of microglia and produces a significant pro-inflammatory response. Our findings confirm that

Fluctuation driven EMFs in the Madison Dynamo Experiment

NASA Astrophysics Data System (ADS)

Kaplan, Elliot; Brown, Ben; Clark, Mike; Nornberg, Mark; Rahbarnia, Kian; Rasmus, Alex; Taylor, Zane; Forest, Cary

2013-04-01

The Madison Dynamo Experiment is a 1 m diameter sphere filled with liquid Sodium designed to study MHD in a simply connected geometry. Two impellers drive a two-vortex flow, based on the calculations of Dudley and James, intended to excite system-scale dynamo instability. We present a collection of results from experiments measuring hydrodynamic fluctuations and their MHD effects. An equatorial baffle was added to the experiment in order to diminish the large-eddy hydrodynamic fluctuations by stabilizing the shear layer between the two counter-rotating flow cells. The change in the fluctuation levels was inferred from the change in the spatial spectrum of the induced magnetic field. This reduction correlated with a 2.4 times increase in the induced toroidal magnetic field (a proxy measure of the effective resistivity). Furthermore, the local velocity fluctuations were directly measured by the addition of a 3-d emf probe (a strong permanent magnet inserted into the flow with electrical leads to measure the induced voltage, and magnetic probes to determine the magnetic fluctuations). The measured emfs are consistent with the enhanced magnetic diffusivity interpretation of mean-field MHD.

High reliability sheathed, beryllia insulated, tungsten-rhenium alloy thermocouple assemblies; their fabrication and EMF stability

NASA Technical Reports Server (NTRS)

Burns, G. W.; Hurst, W. S.; Scroger, M. G.

1974-01-01

Tantalum sheathed, BeO insulated, W-3% Re/W-25% Re thermocouple assemblies were fabricated and their emf drift determined during 2059 hours of exposure at 2073 K in a gaseous helium environment. The sheathed thermocouple assemblies were constructed from aged thermoelements, specially heat-treated BeO insulators, and specially cleaned and etched tantalum sheaths. Their thermal emf drifts ranged from the equivalent of only -0.3 to -0.8 K drift per 1000 hours of exposure at 2073 K. No evidence of any gross chemical attack or degradation of the component materials was found. The emf drift and material behavior of some unsheathed, BeO insulated, W-3% Re/W-25% Re thermocouples at 2250 and 2400 K were also determined. Unsheathed thermocouples tested in an argon environment at 2250 K for 1100 hours and at 2400 K for 307 hours exhibited changes in thermal emf that typically ranged from the equivalent of a few degrees K to as much as +11 K. Post-test examinations of these thermocouples revealed some undesirable material degradation and interaction which included erosion of the BeO insulators and contamination of the thermoelements by tantalum from the tantalum blackbody enclosure in which the thermocouples were contained.

Five years later: the current status of the use of proteomics and transcriptomics in EMF research.

PubMed

Leszczynski, Dariusz; de Pomerai, David; Koczan, Dirk; Stoll, Dieter; Franke, Helmut; Albar, Juan Pablo

2012-08-01

The World Health Organization's and Radiation and Nuclear Safety Authority's "Workshop on Application of Proteomics and Transcriptomics in Electromagnetic Fields Research" was held in Helsinki in the October/November 2005. As a consequence of this meeting, Proteomics journal published in 2006 a special issue "Application of Proteomics and Transcriptomics in EMF Research" (Vol. 6 No. 17; Guest Editor: D. Leszczynski). This Proteomics issue presented the status of research, of the effects of electromagnetic fields (EMF) using proteomics and transcriptomics methods, present in 2005. The current overview/opinion article presents the status of research in this area by reviewing all studies that were published by the end of 2010. The review work was a part of the European Cooperation in the Field of Scientific and Technical Research (COST) Action BM0704 that created a structure in which researchers in the field of EMF and health shared knowledge and information. The review was prepared by the members of the COST Action BM0704 task group on the high-throughput screening techniques and electromagnetic fields (TG-HTST-EMF). © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

New bimetallic EMF cell shows promise in direct energy conversion

NASA Technical Reports Server (NTRS)

Hesson, J. C.; Shimotake, H.

1968-01-01

Concentration cell, based upon a thermally regenerative cell principle, produces electrical energy from any large heat source. This experimental bimetallic EMF cell uses a sodium-bismuth alloy cathode and a pure liquid sodium anode. The cell exhibits reliability, corrosion resistance, and high current density performance.

EMF Monitoring on Amtrak's Northeast Corridor : Post-Electrification Measurement and Analysis

DOT National Transportation Integrated Search

2006-10-01

This survey of electromagnetic fields (EMF) and radiation (EMR) due to the electrification infrastructure and operations of Amtrak Acela trains on the Northeast Corridor from New Haven, CT, to Boston, MA, was performed by Electric Research & Manageme...

Database Development for Ocean Impacts: Imaging, Outreach, and Rapid Response

DTIC Science & Technology

2012-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Database Development for Ocean Impacts: Imaging, Outreach...Development for Ocean Impacts: Imaging, Outreach, and Rapid Response 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d...hoses ( Applied Ocean Physics & Engineering department, WHOI, to evaluate wear and locate in mooring optical cables used in the Right Whale monitoring

No effects of intermittent 50 Hz EMF on cytoplasmic free calcium and on the mitochondrial membrane potential in human diploid fibroblasts.

PubMed

Pilger, Alexander; Ivancsits, Sabine; Diem, Elisabeth; Steffens, Melanie; Kolb, Hans-Albert; Rüdiger, Hugo W

2004-09-01

The recently described increase in DNA strand breaks of cultured human diploid fibroblasts after intermittent exposure to extremely-low-frequency electromagnetic fields (ELF-EMF) of more than about 70 microT ELF-EMF is difficult to explain by a direct induction of covalent bond disruption. Therefore the hypothesis has been tested that ELF-EMF-induced DNA strand breaks might be mediated by cellular processes that cause alteration of the intracellular concentration of free calcium ([Ca2+]i) and/or the membrane potential (DeltaPsi(m)). [Ca2+]i was determined by the ratiometric fura-2 technique. Changes in DeltaPsi(m) were assessed by using the potential-dependent lipophilic cationic probe JC-1. Human fibroblasts were exposed to intermittent ELF-EMF (50 Hz, 1000 microT). Although exposure of fiboblasts to ELF-EMF resulted in a highly significant increase in DNA strand breaks as determined by the comet assay, no effect on JC-1 fluorescence emission or on [Ca2+]i has been observed when comparing exposed with sham-exposed cells. Therefore, it is suggested that ELF-EMF-induced DNA strand breaks are unlikely to be caused by intracellular changes that affect [Ca2+]i and/or DeltaPsi(m).

A novel database of bio-effects from non-ionizing radiation.

PubMed

Leach, Victor; Weller, Steven; Redmayne, Mary

2018-06-06

A significant amount of electromagnetic field/electromagnetic radiation (EMF/EMR) research is available that examines biological and disease associated endpoints. The quantity, variety and changing parameters in the available research can be challenging when undertaking a literature review, meta-analysis, preparing a study design, building reference lists or comparing findings between relevant scientific papers. The Oceania Radiofrequency Scientific Advisory Association (ORSAA) has created a comprehensive, non-biased, multi-categorized, searchable database of papers on non-ionizing EMF/EMR to help address these challenges. It is regularly added to, freely accessible online and designed to allow data to be easily retrieved, sorted and analyzed. This paper demonstrates the content and search flexibility of the ORSAA database. Demonstration searches are presented by Effect/No Effect; frequency-band/s; in vitro; in vivo; biological effects; study type; and funding source. As of the 15th September 2017, the clear majority of 2653 papers captured in the database examine outcomes in the 300 MHz-3 GHz range. There are 3 times more biological "Effect" than "No Effect" papers; nearly a third of papers provide no funding statement; industry-funded studies more often than not find "No Effect", while institutional funding commonly reveal "Effects". Country of origin where the study is conducted/funded also appears to have a dramatic influence on the likely result outcome.

Universal 'imaginary closed circuit method' and formula for determination of direction of induced emf/current

NASA Astrophysics Data System (ADS)

Balaram Atram, Dattatraya

2011-01-01

Fleming's right-hand rule and the right-flat-hand rule are generally applied for determining the direction of flow of induced emf/current in straight conductors. The right-hand-fingers rule is applied for coils only. The right-hand-thumb rule can be applied for either straight conductors or coils. Different rules have to be applied for different situations. Also, a formula for determining the direction of induced emf/current does not exist on the basis of these rules. In this article, based on Faraday's law of electromagnetic induction and Lenz's law, an 'imaginary closed circuit method' and a formula for determination of direction of induced emf/current has been proposed. The method is universal in the sense that it is applicable for conductors of any shape, for any kind of relative motion of the conductor with respect to the magnetic flux, and moreover it is applicable for the case of varying magnetic flux.

The amelioration of phagocytic ability in microglial cells by curcumin through the inhibition of EMF-induced pro-inflammatory responses

PubMed Central

2014-01-01

Background Insufficient clearance by microglial cells, prevalent in several neurological conditions and diseases, is intricately intertwined with MFG-E8 expression and inflammatory responses. Electromagnetic field (EMF) exposure can elicit the pro-inflammatory activation and may also trigger an alteration of the clearance function in microglial cells. Curcumin has important roles in the anti-inflammatory and phagocytic process. Here, we evaluated the ability of curcumin to ameliorate the phagocytic ability of EMF-exposed microglial cells (N9 cells) and documented relative pathways. Methods N9 cells were pretreated with or without recombinant murine MFG-E8 (rmMFG-E8), curcumin and an antibody of toll-like receptor 4 (anti-TLR4), and subsequently treated with EMF or a sham exposure. Their phagocytic ability was evaluated using phosphatidylserine-containing fluorescent bioparticles. The pro-inflammatory activation of microglia was assessed via CD11b immunoreactivity and the production of tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β) and nitric oxide (NO) via the enzyme-linked immunosorbent assay or the Griess test. We evaluated the ability of curcumin to ameliorate the phagocytic ability of EMF-exposed N9 cells, including checking the expression of MFG-E8, αvβ3 integrin, TLR4, nuclear factor-κB (NF-κB) and signal transducer and activator of transcription 3 (STAT3) using Western blotting. Results EMF exposure dramatically enhanced the expression of CD11b and depressed the phagocytic ability of N9 cells. rmMFG-E8 could clearly ameliorate the phagocytic ability of N9 cells after EMF exposure. We also found that EMF exposure significantly increased the secretion of pro-inflammatory cytokines (TNF-α, IL-6 and IL-1β) and the production of NO; however, these increases were efficiently chilled by the addition of curcumin to the culture medium. This reduction led to the amelioration of the phagocytic ability of EMF-exposed N9 cells

Effects of EMF emissions from undersea electric cables on coral reef fish.

PubMed

Kilfoyle, Audie K; Jermain, Robert F; Dhanak, Manhar R; Huston, Joseph P; Spieler, Richard E

2018-01-01

The objective of this study was to determine if electromagnetic field (EMF) emissions from undersea power cables impacted local marine life, with an emphasis on coral reef fish. The work was done at the South Florida Ocean Measurement Facility of Naval Surface Warfare Center in Broward County, Florida, which has a range of active undersea detection and data transmission cables. EMF emissions from a selected cable were created during non-destructive visual fish surveys on SCUBA. During surveys, the transmission of either alternating current (AC), direct current (DC), or none (OFF) was randomly initiated by the facility at a specified time. Visual surveys were conducted using standardized transect and point-count methods to acquire reef fish abundances and species richness prior to and immediately after a change in transmission frequency. The divers were also tasked to note the reaction of the reef fish to the immediate change in EMF during a power transition. In general, analysis of the data did not find statistical differences among power states and any variables. However, this may be a Type II error as there are strong indications of a potential difference of a higher abundance of reef fish at the sites when the power was off, and further study is warranted. Bioelectromagnetics. 39:35-52, 2018. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Scientific method discourses in the construction of 'EMF' science: interests, resources and rhetoric in submissions to a public inquiry.

PubMed

Mercer, David

2002-04-01

Since the late 1970s, there has been considerable debate surrounding the question of whether or not exposures to non-ionizing radiation and electric and magnetic fields (EMF), produced by powerlines and electrical and telecommunications technologies, are harmful to health. Whilst there has been some recent evidence of regulatory fatigue, and attempts to enforce closure, the EMF debate nevertheless still continues. This paper will explore the rôle played by competing images of scientific method in the argumentative strategies used by two of the main protagonists in an Australian public inquiry (held in 1990-91) which investigated the EMF issue: 'Inquiry into Community Needs and High Voltage (132kv and above) Transmission Line Development', the so-called Gibbs Inquiry. Apart from documenting some of the epistemologically intricate features of the EMF controversy, the following discussion will also consider the way scientific method discourses can contribute to enhancing the durability of knowledge claims in legal and regulatory settings.

A Meta-Analysis on the Relationship between Exposure to ELF-EMFs and the Risk of Female Breast Cancer

PubMed Central

Chen, Qingsong; Lang, Li; Wu, Wenzhe; Xu, Guoyong; Zhang, Xiao; Li, Tao; Huang, Hanlin

2013-01-01

Objective To comprehensively analyze the relationship between exposure to extremely low frequency electromagnetic fields (ELF-EMFs) and the development of female breast cancer. Methods Reports of case-control studies published from 1990 to 2010 were analyzed. The quality effect model was chosen to calculate total odds ratio (OR) depending on the data in studies and quality scores. Subgroup analyses were also performed by the situation of menopause, estrogenic receptor and exposure assessment respectively. Results For all 23 studies the OR was 1.07, 95% CI = 1.02–1.13, for estrogen receptor positive subgroup,OR = 1.11, 95% CI = 1.03–1.20; for premenopausal subgroup, OR = 1.11, 95% CI = 1.00–1.23. The results of other subgroups showed no significant association between ELF-EMF and female breast cancer. Conclusion ELF-EMFs might be related to an increased risk for female breast cancer, especially for premenopausal and ER+ females. However, it's necessary to undertake better epidemiologic researches to verify the association between ELF-EMF and female breast cancer due to the limits of current study, especially the one on exposure assessment. PMID:23869239

Examination of the melatonin hypothesis in women exposed at night to EMF or bright light.

PubMed

Graham, C; Cook, M R; Gerkovich, M M; Sastre, A

2001-05-01

It has been hypothesized that the increased incidence of breast cancer in industrial societies is related to greater exposure to power-frequency electric and magnetic fields (EMF) and/or the presence of high levels of light at night (LAN). EMF and LAN are said to reduce circulating levels of the hormone melatonin which, in turn, allows estrogen levels to rise and stimulate the turnover of breast epithelial stem cells and increase the risk for malignant transformation. Three laboratory-based studies, in which a total of 53 healthy young women were exposed at night to EMF or to LAN under controlled exposure conditions, were performed to determine whether such exposures reduce melatonin and are associated with further alterations in estrogen. All-night exposure to industrial-strength magnetic fields (60 Hz, 28.3 microT) had no effect on the blood levels of melatonin or estradiol. In contrast, nocturnal melatonin levels were profoundly suppressed, and the time of peak concentration was significantly delayed in women exposed to LAN, regardless of whether they were in the follicular or luteal phase of the menstrual cycle. These changes, however, were not associated with alterations in point-for-point matching measures of estradiol. Women who chronically secrete high or low amounts of melatonin each night (area-under-curve range: 86-1,296 pg/mL) also did not differ in their blood levels of estradiol. Taken together, these results are consistent with a growing body of evidence which generally suggests that environmental EMF exposure has little or no effect on the parameters measured in this report.

Correction for Thermal EMFs in Thermocouple Feedthroughs

NASA Technical Reports Server (NTRS)

Ziemke, Robert A.

2006-01-01

A straightforward measurement technique provides for correction of thermal-electromotive-force (thermal-EMF) errors introduced by temperature gradients along the pins of non-thermocouple-alloy hermetic feedthrough connectors for thermocouple extension wires that must pass through bulkheads. This technique is an alternative to the traditional technique in which the thermal-EMF errors are eliminated by use of custom-made multipin hermetic feedthrough connectors that contain pins made of the same alloys as those of the thermocouple extension wires. One disadvantage of the traditional technique is that it is expensive and time-consuming to fabricate multipin custom thermocouple connectors. In addition, the thermocouple-alloy pins in these connectors tend to corrode easily and/or tend to be less rugged compared to the non-thermocouple-alloy pins of ordinary connectors. As the number of thermocouples (and thus pins) is increased in a given setup, the magnitude of these disadvantages increases accordingly. The present technique is implemented by means of a little additional hardware and software, the cost of which is more than offset by the savings incurred through the use of ordinary instead of thermocouple connectors. The figure schematically depicts a typical measurement setup to which the technique is applied. The additional hardware includes an isothermal block (made of copper) instrumented with a reference thermocouple and a compensation thermocouple. The reference thermocouple is connected to an external data-acquisition system (DAS) through a two-pin thermocouple-alloy hermetic feedthrough connector, but this is the only such connector in the apparatus. The compensation thermocouple is connected to the DAS through two pins of the same ordinary multipin connector that connects the measurement thermocouples to the DAS.

Effects of four kinds of electromagnetic fields (EMF) with different frequency spectrum bands on ovariectomized osteoporosis in mice.

PubMed

Lei, Tao; Li, Feijiang; Liang, Zhuowen; Tang, Chi; Xie, Kangning; Wang, Pan; Dong, Xu; Shan, Shuai; Liu, Juan; Xu, Qiaoling; Luo, Erping; Shen, Guanghao

2017-04-03

Electromagnetic fields (EMF) was considered as a non-invasive modality for treatment of osteoporosis while the effects were diverse with EMF parameters in time domain. In present study, we extended analysis of EMF characteristics from time domain to frequency domain, aiming to investigate effects of four kinds of EMF (LP (1-100 Hz), BP (100-3,000 Hz), HP (3,000-50,000 Hz) and AP (1-50,000 Hz)) on ovariectomized (OVX) osteoporosis (OP) in mice. Forty-eight 3-month-old female BALB/c mice were equally assigned to Sham, OVX, OVX + LP, OVX + BP, OVX + HP and OVX + AP groups (n = 8). After 8-week exposure (3 h/day), LP and BP significantly increased serum bone formation markers and osteogenesis-related gene expressions compared with OVX. Bedsides, LP and BP also slightly increased bone resorption activity compared with OVX, evidenced by increased RANKL/OPG ratio. HP sharply decreased serum bone formation and resporption markers and osteogenesis and osteoclastogenesis related gene expressions compared with OVX. AP had accumulative effects of LP, BP and HP, which significantly increased bone formation and decreased bone resporption activity compared with OVX. As a result, LP, BP and HP exposure did not later deterioration of bone mass, microarchitecture and mechanical strength in OVX mice with OP. However, AP stimulation attenuated OVX-induced bone loss.

qEMF3, a novel QTL for the early-morning flowering trait from wild rice, Oryza officinalis, to mitigate heat stress damage at flowering in rice, O. sativa

PubMed Central

Hirabayashi, Hideyuki; Sasaki, Kazuhiro; Kambe, Takashi; Gannaban, Ritchel B.; Miras, Monaliza A.; Mendioro, Merlyn S.; Simon, Eliza V.; Lumanglas, Patrick D.; Fujita, Daisuke; Takemoto-Kuno, Yoko; Takeuchi, Yoshinobu; Kaji, Ryota; Kondo, Motohiko; Kobayashi, Nobuya; Ogawa, Tsugufumi; Ando, Ikuo; Jagadish, Krishna S. V.; Ishimaru, Tsutomu

2015-01-01

A decline in rice (Oryza sativa L.) production caused by heat stress is one of the biggest concerns resulting from future climate change. Rice spikelets are most susceptible to heat stress at flowering. The early-morning flowering (EMF) trait mitigates heat-induced spikelet sterility at the flowering stage by escaping heat stress during the daytime. We attempted to develop near-isogenic lines (NILs) for EMF in the indica-type genetic background by exploiting the EMF locus from wild rice, O. officinalis (CC genome). A stable quantitative trait locus (QTL) for flower opening time (FOT) was detected on chromosome 3. A QTL was designated as qEMF3 and it shifted FOT by 1.5–2.0h earlier for cv. Nanjing 11 in temperate Japan and cv. IR64 in the Philippine tropics. NILs for EMF mitigated heat-induced spikelet sterility under elevated temperature conditions completing flower opening before reaching 35°C, a general threshold value leading to spikelet sterility. Quantification of FOT of cultivars popular in the tropics and subtropics did not reveal the EMF trait in any of the cultivars tested, suggesting that qEMF3 has the potential to advance FOT of currently popular cultivars to escape heat stress at flowering under future hotter climates. This is the first report to examine rice with the EMF trait through marker-assisted breeding using wild rice as a genetic resource. PMID:25534925

Measurement of the 100 MHz EMF radiation in vivo effects on zebrafish D. rerio embryonic development: A multidisciplinary study.

PubMed

Piccinetti, Chiara Carla; De Leo, Alfredo; Cosoli, Gloria; Scalise, Lorenzo; Randazzo, Basilio; Cerri, Graziano; Olivotto, Ike

2018-06-15

The augmented exposure of both environment and human being to electromagnetic waves and the concomitant lack of an unequivocal knowledge about biological consequences of these radiations, raised public interest on electromagnetic pollution. In this context, the present study aims to evaluate the biological effects on zebrafish (ZF) embryos of 100 MHz radiofrequency electromagnetic field (RF-EMF) exposure through a multidisciplinary protocol. Because of the shared synteny between human and ZF genomes that validated its use in biomedical research, toxicology and developmental biology studies, ZF was here selected as experimental model and a measurement protocol and biological analyses have been set up to clearly discriminate between RF-EMF biological and thermal effects. The results showed that a 100 MHz EMF was able to affect ZF embryonic development, from 24 to 72 h post fertilization (hpf) in all the analyzed pathways. Particularly, at the 48 hpf stage, a reduced growth, an increased transcription of oxidative stress genes, the onset of apoptotic/autophagic processes and a modification in cholesterol metabolism were detected. ZF embryos faced stress induced by EMF radiation by triggering detoxification mechanisms and at 72 hpf they partially recovered from stress reaching the hatching time in a comparable way respect to the control group. Data here obtained showed unequivocally the in vivo effects of RF-EMF on an animal model, excluding thermal outcomes and thus represents the starting point for more comprehensive studies on dose response effects of electromagnetic fields radiations consequences. Copyright © 2018 Elsevier Inc. All rights reserved.

qEMF3, a novel QTL for the early-morning flowering trait from wild rice, Oryza officinalis, to mitigate heat stress damage at flowering in rice, O. sativa.

PubMed

Hirabayashi, Hideyuki; Sasaki, Kazuhiro; Kambe, Takashi; Gannaban, Ritchel B; Miras, Monaliza A; Mendioro, Merlyn S; Simon, Eliza V; Lumanglas, Patrick D; Fujita, Daisuke; Takemoto-Kuno, Yoko; Takeuchi, Yoshinobu; Kaji, Ryota; Kondo, Motohiko; Kobayashi, Nobuya; Ogawa, Tsugufumi; Ando, Ikuo; Jagadish, Krishna S V; Ishimaru, Tsutomu

2015-03-01

A decline in rice (Oryza sativa L.) production caused by heat stress is one of the biggest concerns resulting from future climate change. Rice spikelets are most susceptible to heat stress at flowering. The early-morning flowering (EMF) trait mitigates heat-induced spikelet sterility at the flowering stage by escaping heat stress during the daytime. We attempted to develop near-isogenic lines (NILs) for EMF in the indica-type genetic background by exploiting the EMF locus from wild rice, O. officinalis (CC genome). A stable quantitative trait locus (QTL) for flower opening time (FOT) was detected on chromosome 3. A QTL was designated as qEMF3 and it shifted FOT by 1.5-2.0 h earlier for cv. Nanjing 11 in temperate Japan and cv. IR64 in the Philippine tropics. NILs for EMF mitigated heat-induced spikelet sterility under elevated temperature conditions completing flower opening before reaching 35°C, a general threshold value leading to spikelet sterility. Quantification of FOT of cultivars popular in the tropics and subtropics did not reveal the EMF trait in any of the cultivars tested, suggesting that qEMF3 has the potential to advance FOT of currently popular cultivars to escape heat stress at flowering under future hotter climates. This is the first report to examine rice with the EMF trait through marker-assisted breeding using wild rice as a genetic resource. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Impact of a Small Cell on the RF-EMF Exposure in a Train

PubMed Central

Aerts, Sam; Plets, David; Thielens, Arno; Martens, Luc; Joseph, Wout

2015-01-01

The deployment of a miniature mobile-phone base station or small cell in a train car significantly improves the coverage and the capacity of a mobile network service on the train. However, the impact of the small cell on the passengers’ exposure to radio-frequency electromagnetic fields (RF-EMF) is unknown. In this study, we assessed experimentally the RF-EMF exposure of a mobile-phone user who is either connected to the outdoor macrocell network or to an in-train small cell, while traveling on the train, by means of the absorbed-dose concept, which combines the base station downlink exposure with the mobile-phone uplink exposure. For Global System for Mobile Communications (GSM) technology at 1800 MHz, we found that by connecting to a small cell, the brain exposure of the user could realistically be reduced by a factor 35 and the whole-body exposure by a factor 11. PMID:25734793

Development of an RF-EMF Exposure Surrogate for Epidemiologic Research.

PubMed

Roser, Katharina; Schoeni, Anna; Bürgi, Alfred; Röösli, Martin

2015-05-22

Exposure assessment is a crucial part in studying potential effects of RF-EMF. Using data from the HERMES study on adolescents, we developed an integrative exposure surrogate combining near-field and far-field RF-EMF exposure in a single brain and whole-body exposure measure. Contributions from far-field sources were modelled by propagation modelling and multivariable regression modelling using personal measurements. Contributions from near-field sources were assessed from both, questionnaires and mobile phone operator records. Mean cumulative brain and whole-body doses were 1559.7 mJ/kg and 339.9 mJ/kg per day, respectively. 98.4% of the brain dose originated from near-field sources, mainly from GSM mobile phone calls (93.1%) and from DECT phone calls (4.8%). Main contributors to the whole-body dose were GSM mobile phone calls (69.0%), use of computer, laptop and tablet connected to WLAN (12.2%) and data traffic on the mobile phone via WLAN (6.5%). The exposure from mobile phone base stations contributed 1.8% to the whole-body dose, while uplink exposure from other people's mobile phones contributed 3.6%. In conclusion, the proposed approach is considered useful to combine near-field and far-field exposure to an integrative exposure surrogate for exposure assessment in epidemiologic studies. However, substantial uncertainties remain about exposure contributions from various near-field and far-field sources.

DIRECT OBSERVATION OF THE TURBULENT emf AND TRANSPORT OF MAGNETIC FIELD IN A LIQUID SODIUM EXPERIMENT

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

Rahbarnia, Kian; Brown, Benjamin P.; Clark, Mike M.

2012-11-10

For the first time, we have directly measured the transport of a vector magnetic field by isotropic turbulence in a high Reynolds number liquid metal flow. In analogy with direct measurements of the turbulent Reynolds stress (turbulent viscosity) that governs momentum transport, we have measured the turbulent electromotive force (emf) by simultaneously measuring three components of velocity and magnetic fields, and computed the correlations that lead to mean-field current generation. Furthermore, we show that this turbulent emf tends to oppose and cancel out the local current, acting to increase the effective resistivity of the medium, i.e., it acts as anmore » enhanced magnetic diffusivity. This has important implications for turbulent transport in astrophysical objects, particularly in dynamos and accretion disks.« less

Safety of High Speed Guided Ground Transportation Systems : Review of Existing EMF Guidelines, Standards and Regulations

DOT National Transportation Integrated Search

1993-08-01

To assess the state of knowledge about anticipated electric and magnetic field (EMF) exposures from electrical transportation systems, including electrically powered rail and magnetically levitated (maglev), research concerning biological effects of ...

Vitamin C and Vitamin E Protected B95-8 and Balb/c-3T3 Cells from Apoptosis Induced by Intermittent 50Hz ELF-EMF Radiation

PubMed Central

DING, Zhen; LI, Jintao; LI, Fan; MEPHRYAR, Mohammadreza Mohammadzad; WU, Shuicai; ZHANG, Chen; ZENG, Yi

2017-01-01

Background: The extremely low-frequency electromagnetic field (ELF-EMF), mainly emitted by electric transmission lines and household electronic appliances, is becoming a worldwide health risk. It is imperative to investigate the biological impacts of ELF-EMF and to identify products that are resistant to the radiation from 50 Hz ELF-EMF. In this study, we investigated the biological impacts of apoptosis caused by 50 Hz Power line ELF-EMF and the protective effects of Vit C and Vit E. Methods: We conducted this study in Beijing, China in 2013. B95-8 and Balb/c-3T3 cells were divided into a sham group, an expo group and 3 expo groups in which the cells were preincubated with various concentrations of Vit C and Vit E. Then, all of the cells were exposed to 50 Hz Power line ELF-EMF and examined for apoptosis. The cells were collected for apoptosis detection after exposure. Results: The percent of cells that undergoing apoptosis and preincubated with various concentrations of Vit C and Vit E were significantly lower than in the Expo group. Conclusion: Vit C and Vit E exert significant protective effects from 50 Hz ELF-EMF radiation. The optimal protective concentrations of Vit C and Vit E are 10 μmol/L and 25 μmol/L, respectively. The protective effect of vitamins was more apparent for Balb/c-3T3 cells than B95-8 cells. PMID:28451526

Vitamin C and Vitamin E Protected B95-8 and Balb/c-3T3 Cells from Apoptosis Induced by Intermittent 50Hz ELF-EMF Radiation.

PubMed

Ding, Zhen; Li, Jintao; Li, Fan; Mephryar, Mohammadreza Mohammadzad; Wu, Shuicai; Zhang, Chen; Zeng, Yi

2017-01-01

The extremely low-frequency electromagnetic field (ELF-EMF), mainly emitted by electric transmission lines and household electronic appliances, is becoming a worldwide health risk. It is imperative to investigate the biological impacts of ELF-EMF and to identify products that are resistant to the radiation from 50 Hz ELF-EMF. In this study, we investigated the biological impacts of apoptosis caused by 50 Hz Power line ELF-EMF and the protective effects of Vit C and Vit E. We conducted this study in Beijing, China in 2013. B 95-8 and Balb/c-3T3 cells were divided into a sham group, an expo group and 3 expo groups in which the cells were preincubated with various concentrations of Vit C and Vit E. Then, all of the cells were exposed to 50 Hz Power line ELF-EMF and examined for apoptosis. The cells were collected for apoptosis detection after exposure. The percent of cells that undergoing apoptosis and preincubated with various concentrations of Vit C and Vit E were significantly lower than in the Expo group. Vit C and Vit E exert significant protective effects from 50 Hz ELF-EMF radiation. The optimal protective concentrations of Vit C and Vit E are 10 μmol/L and 25 μmol/L, respectively. The protective effect of vitamins was more apparent for Balb/c-3T3 cells than B 95-8 cells.

Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists

PubMed Central

Wiley, Laura K.; Sivley, R. Michael; Bush, William S.

2013-01-01

Efficient storage and retrieval of genomic annotations based on range intervals is necessary, given the amount of data produced by next-generation sequencing studies. The indexing strategies of relational database systems (such as MySQL) greatly inhibit their use in genomic annotation tasks. This has led to the development of stand-alone applications that are dependent on flat-file libraries. In this work, we introduce MyNCList, an implementation of the NCList data structure within a MySQL database. MyNCList enables the storage, update and rapid retrieval of genomic annotations from the convenience of a relational database system. Range-based annotations of 1 million variants are retrieved in under a minute, making this approach feasible for whole-genome annotation tasks. Database URL: https://github.com/bushlab/mynclist PMID:23894185

Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists.

PubMed

Wiley, Laura K; Sivley, R Michael; Bush, William S

2013-01-01

Efficient storage and retrieval of genomic annotations based on range intervals is necessary, given the amount of data produced by next-generation sequencing studies. The indexing strategies of relational database systems (such as MySQL) greatly inhibit their use in genomic annotation tasks. This has led to the development of stand-alone applications that are dependent on flat-file libraries. In this work, we introduce MyNCList, an implementation of the NCList data structure within a MySQL database. MyNCList enables the storage, update and rapid retrieval of genomic annotations from the convenience of a relational database system. Range-based annotations of 1 million variants are retrieved in under a minute, making this approach feasible for whole-genome annotation tasks. Database URL: https://github.com/bushlab/mynclist.

Development of an RF-EMF Exposure Surrogate for Epidemiologic Research

PubMed Central

Roser, Katharina; Schoeni, Anna; Bürgi, Alfred; Röösli, Martin

2015-01-01

Exposure assessment is a crucial part in studying potential effects of RF-EMF. Using data from the HERMES study on adolescents, we developed an integrative exposure surrogate combining near-field and far-field RF-EMF exposure in a single brain and whole-body exposure measure. Contributions from far-field sources were modelled by propagation modelling and multivariable regression modelling using personal measurements. Contributions from near-field sources were assessed from both, questionnaires and mobile phone operator records. Mean cumulative brain and whole-body doses were 1559.7 mJ/kg and 339.9 mJ/kg per day, respectively. 98.4% of the brain dose originated from near-field sources, mainly from GSM mobile phone calls (93.1%) and from DECT phone calls (4.8%). Main contributors to the whole-body dose were GSM mobile phone calls (69.0%), use of computer, laptop and tablet connected to WLAN (12.2%) and data traffic on the mobile phone via WLAN (6.5%). The exposure from mobile phone base stations contributed 1.8% to the whole-body dose, while uplink exposure from other people’s mobile phones contributed 3.6%. In conclusion, the proposed approach is considered useful to combine near-field and far-field exposure to an integrative exposure surrogate for exposure assessment in epidemiologic studies. However, substantial uncertainties remain about exposure contributions from various near-field and far-field sources. PMID:26006132

Electrode Processes and Aspects Relating to Cell EMF, Current, and Cell Components in Operating Electrochemical Cells: Precollege and College Student Interpretation

NASA Astrophysics Data System (ADS)

Ogude, N. A.; Bradleu, J. D.

1996-12-01

Four areas that present difficulty among high school pupils and tertiary level students in relation to the processes that take place in operating electrochemical cells were identified (1). These are (i) conduction in the electrolyte, (ii) electrical neutrality, (iii) electrode processes and terminology, and (iv) aspects relating to cell emf, current, and cell components. A 20-item questionnaire was designed to determine how widespread misconceptions in these areas were. The prevalence and possible causes of misconceptions in two of the four areas - namely, conduction in the electrolyte and electrical neutrality - were reported (2). In this paper, we report on the difficulties experienced by students in relation to electrode processes and terminology and aspects of cell components, cell emf, and current. In relation to electrode processes and terminology, excerpts from interviews with precollege and college students as well as the responses of a larger group of students are discussed. The discussion relating to cell components, cell emf, and current presents a response to standard textbook questions by precollege and college students and interviews conducted with postgraduate higher diploma in education (HDE-PG) students. The interviews were conducted with postgraduate students after the precollege and college students were unable to verbalize their views, especially on cell emf and current. The possible causes of the misunderstandings and the questions used to elicit the misunderstandings in these two areas are presented.

Higher order concentration moments collapse in the expected mass fraction (EMF) based risk assessment

NASA Astrophysics Data System (ADS)

Srzic, Veljko; Gotovac, Hrvoje; Cvetkovic, Vladimir; Andricevic, Roko

2014-05-01

In this work Langrangian framework is used for conservative tracer transport simulations through 2-D extremely heterogeneous porous media. Conducted numerical simulations enable large sets of concentration values in both spatial and temporal domains. In addition to the advection, which acts on all scales, an additional mechanism considered is local scale dispersion (LSD), accounting for both mechanical dispersion and molecular diffusion. The ratio between these two mechanisms is quantified by the Peclet (Pe) number. In its base, the work gives answers to concentration scalar features when influenced by: i) different log-conductivity variance; ii) log-conductivity structures defined by the same global variogram but with different log conductivity patterns correlated; and iii) for a wide range of Peclet values. Results conducted by Monte Carlo analysis show a complex interplay between the aforementioned parameters, indicating the influence of aquifer properties to temporal LSD evolution. A remarkable collapse of higher order to second-order concentration moments [Yee, 2009] leads to the conclusion that only two concentration moments are required for an accurate description of concentration fluctuations. This explicitly holds for the pure advection case, while in the case of LSD presence the moment deriving function(MDF) is involved to ensure the moment collapse validity. An inspection of the Beta distribution leads to the conclusion that the two-parametric distribution can be used for concentration fluctuation characterization even in cases of high aquifer heterogeneity and/or for different log-conductivity structures, independent of the sampling volume used. Furthermore, the expected mass fraction (EMF) [Heagy & Sullivan, 1996] concept is applied in groundwater transport. In its origin, EMF is function of the concentration but with lower number of realizations needed for its determination, compared to the one point PDF. From practical point of view, EMF excludes

Are media warnings about the adverse health effects of modern life self-fulfilling? An experimental study on idiopathic environmental intolerance attributed to electromagnetic fields (IEI-EMF).

PubMed

Witthöft, Michael; Rubin, G James

2013-03-01

Medically unsubstantiated 'intolerances' to foods, chemicals and environmental toxins are common and are frequently discussed in the media. Idiopathic environmental intolerance attributed to electromagnetic fields (IEI-EMF) is one such condition and is characterized by symptoms that are attributed to exposure to electromagnetic fields (EMF). In this experiment, we tested whether media reports promote the development of this condition. Participants (N=147) were randomly assigned to watch a television report about the adverse health effects of WiFi (n=76) or a control film (n=71). After watching their film, participants received a sham exposure to a WiFi signal (15 min). The principal outcome measure was symptom reports following the sham exposure. Secondary outcomes included worries about the health effects of EMF, attributing symptoms to the sham exposure and increases in perceived sensitivity to EMF. 82 (54%) of the 147 participants reported symptoms which they attributed to the sham exposure. The experimental film increased: EMF related worries (β=0.19; P=.019); post sham exposure symptoms among participants with high pre-existing anxiety (β=0.22; P=.008); the likelihood of symptoms being attributed to the sham exposure among people with high anxiety (β=.31; P=.001); and the likelihood of people who attributed their symptoms to the sham exposure believing themselves to be sensitive to EMF (β=0.16; P=.049). Media reports about the adverse effects of supposedly hazardous substances can increase the likelihood of experiencing symptoms following sham exposure and developing an apparent sensitivity to it. Greater engagement between journalists and scientists is required to counter these negative effects. Copyright © 2012 Elsevier Inc. All rights reserved.

Standard Gibbs energy of formation of Mo 3Te 4 by emf measurements

NASA Astrophysics Data System (ADS)

Mallika, C.; Sreedharan, O. M.

1990-03-01

The emf of the galvanic cells Pt, Mo, MoO 2¦8 YSZ¦'FeO', Fe, Pt (I) and Pt, Fe,'FeO' ¦8 YSZ¦MoO 2, Mo 3Te 4, MoTe 2(α), C, Pt (II) were measured over the temperature ranges 837 to 1151 K and 775 to 1196 K, respectively, using 8 mass% yttria-stabilized zirconia (8 YSZ) as the solid electrolyte. From the emf values, the partial molar Gibbs energy of solution of molybdenum in Mo 3Te 4/MoTe 2(α), Δ ḠMo was found to be Δ ḠMo ± 1.19 ( kJ/mol) = -025.08 + 0.00420T(K) . Using the literature data for the Gibbs energy of formation of MoTe 2(α). the expression ΔG° f( Mo3Te4, s) ± 5.97 (kj/mol) = -253.58 + 0.09214 T( K) was derived for the range 775 to 1196 K. A third-law analysis yielded a value of -209 ± 10 kJ/mol for ΔH° f.298o of Mo 3Te 4(s).

Rapid response of soil fungal communities to low and high intensity fire

NASA Astrophysics Data System (ADS)

Smith, Jane E.; Cowan, Ariel D.; Reazin, Chris; Jumpponen, Ari

2016-04-01

burned soils within one growing season. Community results from both burn treatments suggest an increase in patchy spatial distribution of EMF. The importance of incorporating mixed fire effects in fuel management practices will help to provide EMF refugia for dry forest regeneration. Our studies highlight the strong and rapid fungal community responses to fires and differences among fires of different severities. We theorize that quick initiation of EMF recolonization is possible depending on the size of high burn patches, proximity of low and unburned soil, and survival of nearby hosts.

Safety of High Speed Guided Ground Transportation Systems. Broadband Magnetic Fields : Their Possible Role in EMF Associated Bioeffects

DOT National Transportation Integrated Search

1993-08-01

This report reviews electric and magnetic field (EMF) exposures from electrical transportation systems, including : electrically powered rail and magnetic levitation (maglev). Material also covered includes research concerning : biological effects of...

DroSpeGe: rapid access database for new Drosophila species genomes.

PubMed

Gilbert, Donald G

2007-01-01

The Drosophila species comparative genome database DroSpeGe (http://insects.eugenes.org/DroSpeGe/) provides genome researchers with rapid, usable access to 12 new and old Drosophila genomes, since its inception in 2004. Scientists can use, with minimal computing expertise, the wealth of new genome information for developing new insights into insect evolution. New genome assemblies provided by several sequencing centers have been annotated with known model organism gene homologies and gene predictions to provided basic comparative data. TeraGrid supplies the shared cyberinfrastructure for the primary computations. This genome database includes homologies to Drosophila melanogaster and eight other eukaryote model genomes, and gene predictions from several groups. BLAST searches of the newest assemblies are integrated with genome maps. GBrowse maps provide detailed views of cross-species aligned genomes. BioMart provides for data mining of annotations and sequences. Common chromosome maps identify major synteny among species. Potential gain and loss of genes is suggested by Gene Ontology groupings for genes of the new species. Summaries of essential genome statistics include sizes, genes found and predicted, homology among genomes, phylogenetic trees of species and comparisons of several gene predictions for sensitivity and specificity in finding new and known genes.

Universal "Imaginary Closed Circuit Method" and Formula for Determination of Direction of Induced EMF/Current

ERIC Educational Resources Information Center

Atram, Dattatraya Balaram

2011-01-01

Fleming's right-hand rule and the right-flat-hand rule are generally applied for determining the direction of flow of induced emf/current in straight conductors. The right-hand-fingers rule is applied for coils only. The right-hand-thumb rule can be applied for either straight conductors or coils. Different rules have to be applied for different…

Synergistic effect of EMF-BEMER-type pulsed weak electromagnetic field and HPMA-bound doxorubicin on mouse EL4 T-cell lymphoma.

PubMed

Říhová, Blanka; Etrych, Tomáš; Šírová, Milada; Tomala, Jakub; Ulbrich, Karel; Kovář, Marek

2011-12-01

We have investigated the effects of low-frequency pulsed electromagnetic field (LF-EMF) produced by BEMER device on experimental mouse T-cell lymphoma EL4 growing on conventional and/or athymic (nude) mice. Exposure to EMF-BEMER slowed down the growth of tumor mass and prolonged the survival of experimental animals. The effect was more pronounced in immuno-compromised nude mice compared to conventional ones. Acceleration of tumor growth was never observed. No measurable levels of Hsp 70 or increased levels of specific anti-EL4 antibodies were detected in the serum taken from experimental mice before and at different intervals during the experiment, i.e. before solid tumor appeared, at the time of its aggressive growth, and at the terminal stage of the disease. A significant synergizing antitumor effect was seen when EL4 tumor-bearing mice were simultaneously exposed to EMF-BEMER and treated with suboptimal dose of synthetic HPMA copolymer-based doxorubicin, DOX(HYD)-HPMA. Such a combination may be especially useful for heavily treated patients suffering from advanced tumor and requiring additional aggressive chemotherapy which, however, at that time could represent almost life-threatening way of medication.

Does EMF Emitted from In Situ Subsea Power Cables Affect the Composition of Deep Benthic Fish and Invertebrate Communities?

NASA Astrophysics Data System (ADS)

Bull, A. S.; Nishimoto, M.; Love, M.; Schroeder, D. M.

2016-02-01

A network of power cables is an important component of any offshore renewable energy generation facilities (e.g., wind and wave). The cables laid on the seafloor carry current that produces both electric and magnetic fields; the magnetic field, here called an electromagnetic field (EMF), is what is emitted from shielded cables. The cables, themselves, add hard, low-relief structure to what is typically soft-bottom habitat (mud or sand). Given that laboratory experiments show EMF can affect the behavior of some marine vertebrates and invertebrates, concern is raised over the potential ecological impacts of in situ power cables. Here we report an unusual comparative study of the effect of EMF emitted from in situ power cables on the fish and invertebrate communities of the deep coastal shelf environment. In the Santa Barbara Channel of southern California, subsea power cables, similar to those used in the offshore renewable energy industry, transmit electricity from shore to offshore oil and gas production platforms. A non-energized cable in the vicinity of energized cables afforded us the unusual opportunity to control for the effect of cable as hard, low relief habitat. We conducted three annual submersible surveys in October, 2012- 2014, at depths from 75 m to 210 m. We present results comparing observations along the energized and nonenergized cables and on the adjacent natural substrate.

Biogenic Magnetite and EMF Effects

NASA Astrophysics Data System (ADS)

Kirschvink, Joseph L.

1996-03-01

Magnetite biomineralization is a genetically-controlled biochemical process through which organisms make perfect ferrimagnetic crystals, usually of single magnetic domain size. This process is an ancient one, having evolved about 2 billion years ago in the magnetotactic bacteria, and presumably was incorporated in the genome of higher organisms, including humans. During this time, DNA replication, protein synthesis, and many other biochemical processes have functioned in the presence of strong static fields of up to 400 mT adjacent to these magnetosomes without any obvious deleterious effects. Recent behavioral experiments using short but strong magnetic pulses in honeybees and birds demonstrates that ferromagnetic materials are involved in the sensory transduction of geomagnetic field information to the nervous system, and both behavioral and direct electrophysiological experiments indicate sensitivity thresholds to DC magnetic fields down to a few nT. However, far more biogenic magnetite is present in animal tissues than is needed for magnetoreception, and the biological function of this extra material is unknown. The presence of ferromagnetic materials in biological systems could provide physical transduction mechanisms for ELF magnetic fields, as well for microwave radiation in the .5 to 10 GHz band where magnetite has its peak ferromagnetic resonance. Elucidation of the cellular ultrastructure and biological function(s) of magnetite might help resolve the question of whether anthropogenic EMFs can cause deleterious biological effects. This work has been supported by grants from the NIH and EPRI.

Assessment and comparison of total RF-EMF exposure in femtocell and macrocell base station scenarios.

PubMed

Aerts, Sam; Plets, David; Verloock, Leen; Martens, Luc; Joseph, Wout

2014-12-01

The indoor coverage of a mobile service can be drastically improved by deployment of an indoor femtocell base station (FBS). However, the impact of its proximity on the total exposure of the human body to radio-frequency (RF) electromagnetic fields (EMFs) is unknown. Using a framework designed for the combination of near-field and far-field exposure, the authors assessed and compared the RF-EMF exposure of a mobile-phone (MP) user that is either connected to an FBS or a conventional macrocell base station while in an office environment. It is found that, in average macrocell coverage and MP use-time conditions and for Universal Mobile Telecommunications System technology, the total exposure can be reduced by a factor of 20-40 by using an FBS, mostly due to the significant decrease in the output power of the MP. In general, the framework presented in this study can be used for any exposure scenario, featuring any number of technologies, base stations and/or access points, users and duration. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Review of Studies Concerning Electromagnetic Field (EMF) Exposure Assessment in Europe: Low Frequency Fields (50 Hz–100 kHz)

PubMed Central

Gajšek, Peter; Ravazzani, Paolo; Grellier, James; Samaras, Theodoros; Bakos, József; Thuróczy, György

2016-01-01

We aimed to review the findings of exposure assessment studies done in European countries on the exposure of the general public to low frequency electric and magnetic fields (EMFs) of various frequencies. The study shows that outdoor average extremely low frequency magnetic fields (ELF-MF) in public areas in urban environments range between 0.05 and 0.2 µT in terms of flux densities, but stronger values (of the order of a few µT) may occur directly beneath high-voltage power lines, at the walls of transformer buildings, and at the boundary fences of substations. In the indoor environment, high values have been measured close to several domestic appliances (up to the mT range), some of which are held close to the body, e.g., hair dryers, electric shavers. Common sources of exposure to intermediate frequencies (IF) include induction cookers, compact fluorescent lamps, inductive charging systems for electric cars and security or anti-theft devices. No systematic measurement surveys or personal exposimetry data for the IF range have been carried out and only a few reports on measurements of EMFs around such devices are mentioned. According to the available European exposure assessment studies, three population exposure categories were classified by the authors regarding the possible future risk analysis. This classification should be considered a crucial advancement for exposure assessment, which is a mandatory step in any future health risk assessment of EMFs exposure. PMID:27598182

Review of Studies Concerning Electromagnetic Field (EMF) Exposure Assessment in Europe: Low Frequency Fields (50 Hz-100 kHz).

PubMed

Gajšek, Peter; Ravazzani, Paolo; Grellier, James; Samaras, Theodoros; Bakos, József; Thuróczy, György

2016-09-01

We aimed to review the findings of exposure assessment studies done in European countries on the exposure of the general public to low frequency electric and magnetic fields (EMFs) of various frequencies. The study shows that outdoor average extremely low frequency magnetic fields (ELF-MF) in public areas in urban environments range between 0.05 and 0.2 µT in terms of flux densities, but stronger values (of the order of a few µT) may occur directly beneath high-voltage power lines, at the walls of transformer buildings, and at the boundary fences of substations. In the indoor environment, high values have been measured close to several domestic appliances (up to the mT range), some of which are held close to the body, e.g., hair dryers, electric shavers. Common sources of exposure to intermediate frequencies (IF) include induction cookers, compact fluorescent lamps, inductive charging systems for electric cars and security or anti-theft devices. No systematic measurement surveys or personal exposimetry data for the IF range have been carried out and only a few reports on measurements of EMFs around such devices are mentioned. According to the available European exposure assessment studies, three population exposure categories were classified by the authors regarding the possible future risk analysis. This classification should be considered a crucial advancement for exposure assessment, which is a mandatory step in any future health risk assessment of EMFs exposure.

Comprehensive personal RF-EMF exposure map and its potential use in epidemiological studies.

PubMed

Gonzalez-Rubio, Jesus; Najera, Alberto; Arribas, Enrique

2016-08-01

In recent years, numerous epidemiological studies, which deal with the potential effects of mobile phone antennas on health, have almost exclusively focused on their distance to mobile phone base stations. Although it is known that this is not the best approach to the problem, this situation occurs due to the numerous difficulties when determining the personal exposure to the radiofrequency electromagnetic fields (RF-EMF). However, due to the rise of personal exposimeters, the evolution of spatial statistics, the development of geographical information systems and the use of powerful software, new alternatives are available to deal with these epidemiological studies and thus overcome the aforementioned difficulties. Using these tools, this paper presents a lattice map of personal RF-EMF exposure from exterior mobile phone base stations, covering the entire 110 administrative regions in the city of Albacete (Spain). For this purpose, we used a personal exposimeter, Satimo EME Spy 140 model, performing measurements every 4s The exposimeter was located inside the plastic basket of a bicycle, whose versatility permitted the access to all the zones of the city. Once the exposure map was prepared, its relation with the known antenna locations was studied. The 64 mobile telephone antennas of the city were also georeferenced; the randomness of both variables (exposure and antennas) were studied by means of the Moran's I test. Results showed that the distribution of the antennas follows a grouped pattern (p<0.001), while the distribution of the average exposure values have a random distribution (p=0.618). In addition, we showed two Spearman correlation studies: the first between the average exposure values and the number of mobile telephone antennas per administrative region, and the second, also considering the antennas of the neighbouring regions. No substantial correlation was detected in either of the two cases. This study also reveals the weaknesses of the

Ge/Si(001) heterostructures with dense arrays of Ge quantum dots: morphology, defects, photo-emf spectra and terahertz conductivity.

PubMed

Yuryev, Vladimir A; Arapkina, Larisa V; Storozhevykh, Mikhail S; Chapnin, Valery A; Chizh, Kirill V; Uvarov, Oleg V; Kalinushkin, Victor P; Zhukova, Elena S; Prokhorov, Anatoly S; Spektor, Igor E; Gorshunov, Boris P

2012-07-23

: Issues of Ge hut cluster array formation and growth at low temperatures on the Ge/Si(001) wetting layer are discussed on the basis of explorations performed by high resolution STM and in-situ RHEED. Dynamics of the RHEED patterns in the process of Ge hut array formation is investigated at low and high temperatures of Ge deposition. Different dynamics of RHEED patterns during the deposition of Ge atoms in different growth modes is observed, which reflects the difference in adatom mobility and their 'condensation' fluxes from Ge 2D gas on the surface for different modes, which in turn control the nucleation rates and densities of Ge clusters. Data of HRTEM studies of multilayer Ge/Si heterostructures are presented with the focus on low-temperature formation of perfect films.Heteroepitaxial Si p-i-n-diodes with multilayer stacks of Ge/Si(001) quantum dot dense arrays built in intrinsic domains have been investigated and found to exhibit the photo-emf in a wide spectral range from 0.8 to 5 μm. An effect of wide-band irradiation by infrared light on the photo-emf spectra has been observed. Photo-emf in different spectral ranges has been found to be differently affected by the wide-band irradiation. A significant increase in photo-emf is observed in the fundamental absorption range under the wide-band irradiation. The observed phenomena are explained in terms of positive and neutral charge states of the quantum dot layers and the Coulomb potential of the quantum dot ensemble. A new design of quantum dot infrared photodetectors is proposed.By using a coherent source spectrometer, first measurements of terahertz dynamical conductivity (absorptivity) spectra of Ge/Si(001) heterostructures were performed at frequencies ranged from 0.3 to 1.2 THz in the temperature interval from 300 to 5 K. The effective dynamical conductivity of the heterostructures with Ge quantum dots has been discovered to be significantly higher than that of the structure with the same amount of bulk

The Seminole Serpent Warrior At Miramar, FL, Shows Settlement Locations Enabled Environmental Monitoring Reminiscent Of the Four-corners Kokopelli-like EMF Phenomena, and Related to Earthquakes, Tornados and Hurricanes.

NASA Astrophysics Data System (ADS)

Balam Matagamon, Chan; Pawa Matagamon, Sagamo

2004-03-01

Certain Native Americans of the past seem to have correctly deduced that significant survival information for their tradition-respecting cultures resided in EMF-based phenomena that they were monitoring. This is based upon their myths and the place or cult-hero names they bequeathed us. The sites we have located in FL have been detectable by us visually, usually by faint blue light, or by the elicitation of pin-like prickings, by somewhat intense nervous-system response, by EMF interactions with aural electrochemical systems that can elicit tinitus, and other ways. In the northeast, Cautantowit served as a harbinger of Indian summer, and appears to be another alter ego of the EMF. The Miami, FL Tequesta site along the river clearly correlates with tornado, earthquake and hurricane locations. Sites like the Mohave Deserts giant man may have had similar significance.

EMF radiations (1800 MHz)-inhibited early seedling growth of maize (Zea mays) involves alterations in starch and sucrose metabolism.

PubMed

Kumar, Arvind; Singh, Harminder Pal; Batish, Daizy R; Kaur, Shalinder; Kohli, Ravinder Kumar

2016-07-01

The present study investigated the impact of 1800-MHz electromagnetic field radiations (EMF-r), widely used in mobile communication, on the growth and activity of starch-, sucrose-, and phosphate-hydrolyzing enzymes in Zea mays seedlings. We exposed Z. mays to modulated continuous wave homogenous EMF-r at specific absorption rate (SAR) of 1.69±0.0 × 10(-1) W kg(-1) for ½, 1, 2, and 4 h. The analysis of seedlings after 7 days revealed that short-term exposure did not induce any significant change, while longer exposure of 4 h caused significant growth and biochemical alterations. There was a reduction in the root and coleoptile length with more pronounced effect on coleoptile growth (23 % reduction on 4-h exposure). The contents of photosynthetic pigments and total carbohydrates declined by 13 and 18 %, respectively, in 4-h exposure treatments compared to unexposed control. The activity of starch-hydrolyzing enzymes-α- and β-amylases-increased by ∼92 and 94 %, respectively, at an exposure duration of 4 h, over that in the control. In response to 4-h exposure treatment, the activity of sucrolytic enzymes-acid invertases and alkaline invertases-was increased by 88 and 266 %, whereas the specific activities of phosphohydrolytic enzymes (acid phosphatases and alkaline phosphatases) showed initial increase up to ≤2 h duration and then declined at >2 h exposure duration. The study concludes that EMF-r-inhibited seedling growth of Z. mays involves interference with starch and sucrose metabolism.

Ge/Si(001) heterostructures with dense arrays of Ge quantum dots: morphology, defects, photo-emf spectra and terahertz conductivity

PubMed Central

2012-01-01

Issues of Ge hut cluster array formation and growth at low temperatures on the Ge/Si(001) wetting layer are discussed on the basis of explorations performed by high resolution STM and in-situ RHEED. Dynamics of the RHEED patterns in the process of Ge hut array formation is investigated at low and high temperatures of Ge deposition. Different dynamics of RHEED patterns during the deposition of Ge atoms in different growth modes is observed, which reflects the difference in adatom mobility and their ‘condensation’ fluxes from Ge 2D gas on the surface for different modes, which in turn control the nucleation rates and densities of Ge clusters. Data of HRTEM studies of multilayer Ge/Si heterostructures are presented with the focus on low-temperature formation of perfect films. Heteroepitaxial Si p–i–n-diodes with multilayer stacks of Ge/Si(001) quantum dot dense arrays built in intrinsic domains have been investigated and found to exhibit the photo-emf in a wide spectral range from 0.8 to 5 μm. An effect of wide-band irradiation by infrared light on the photo-emf spectra has been observed. Photo-emf in different spectral ranges has been found to be differently affected by the wide-band irradiation. A significant increase in photo-emf is observed in the fundamental absorption range under the wide-band irradiation. The observed phenomena are explained in terms of positive and neutral charge states of the quantum dot layers and the Coulomb potential of the quantum dot ensemble. A new design of quantum dot infrared photodetectors is proposed. By using a coherent source spectrometer, first measurements of terahertz dynamical conductivity (absorptivity) spectra of Ge/Si(001) heterostructures were performed at frequencies ranged from 0.3 to 1.2 THz in the temperature interval from 300 to 5 K. The effective dynamical conductivity of the heterostructures with Ge quantum dots has been discovered to be significantly higher than that of the structure with the same amount

Robust laser-based detection of Lamb waves using photo-EMF sensors

NASA Astrophysics Data System (ADS)

Klein, Marvin B.; Bacher, Gerald D.

1998-03-01

Lamb waves are easily generated and detected using laser techniques. It has been shown that both symmetric and antisymmetric modes can be produced, using single-spot and phased array generation. Detection has been demonstrated with Michelson interferometers, but these instruments can not function effectively on rough surfaces. By contrast, the confocal Fabry-Perot interferometer can interrogate rough surfaces, but generally is not practical for operation below 300 kHz. In this paper we will present Lamb wave data on a number of parts using a robust, adaptive receiver based on photo-emf detection. This receiver has useful sensitivity down to at least 100 kHz, can process speckled beams and can be easily configured to measure both out-of-plane and in- plane motion with a single probe beam.

Rapid Tsunami Inundation Forecast from Near-field or Far-field Earthquakes using Pre-computed Tsunami Database: Pelabuhan Ratu, Indonesia

NASA Astrophysics Data System (ADS)

Gusman, A. R.; Setiyono, U.; Satake, K.; Fujii, Y.

2017-12-01

We built pre-computed tsunami inundation database in Pelabuhan Ratu, one of tsunami-prone areas on the southern coast of Java, Indonesia. The tsunami database can be employed for a rapid estimation of tsunami inundation during an event. The pre-computed tsunami waveforms and inundations are from a total of 340 scenarios ranging from 7.5 to 9.2 in moment magnitude scale (Mw), including simple fault models of 208 thrust faults and 44 tsunami earthquakes on the plate interface, as well as 44 normal faults and 44 reverse faults in the outer-rise region. Using our tsunami inundation forecasting algorithm (NearTIF), we could rapidly estimate the tsunami inundation in Pelabuhan Ratu for three different hypothetical earthquakes. The first hypothetical earthquake is a megathrust earthquake type (Mw 9.0) offshore Sumatra which is about 600 km from Pelabuhan Ratu to represent a worst-case event in the far-field. The second hypothetical earthquake (Mw 8.5) is based on a slip deficit rate estimation from geodetic measurements and represents a most likely large event near Pelabuhan Ratu. The third hypothetical earthquake is a tsunami earthquake type (Mw 8.1) which often occur south off Java. We compared the tsunami inundation maps produced by the NearTIF algorithm with results of direct forward inundation modeling for the hypothetical earthquakes. The tsunami inundation maps produced from both methods are similar for the three cases. However, the tsunami inundation map from the inundation database can be obtained in much shorter time (1 min) than the one from a forward inundation modeling (40 min). These indicate that the NearTIF algorithm based on pre-computed inundation database is reliable and useful for tsunami warning purposes. This study also demonstrates that the NearTIF algorithm can work well even though the earthquake source is located outside the area of fault model database because it uses a time shifting procedure for the best-fit scenario searching.

Radio-frequency electromagnetic field (RF-EMF) exposure levels in different European outdoor urban environments in comparison with regulatory limits.

PubMed

Urbinello, Damiano; Joseph, Wout; Huss, Anke; Verloock, Leen; Beekhuizen, Johan; Vermeulen, Roel; Martens, Luc; Röösli, Martin

2014-07-01

Concerns of the general public about potential adverse health effects caused by radio-frequency electromagnetic fields (RF-EMFs) led authorities to introduce precautionary exposure limits, which vary considerably between regions. It may be speculated that precautionary limits affect the base station network in a manner that mean population exposure unintentionally increases. The objectives of this multicentre study were to compare mean exposure levels in outdoor areas across four different European cities and to compare with regulatory RF-EMF exposure levels in the corresponding areas. We performed measurements in the cities of Amsterdam (the Netherlands, regulatory limits for mobile phone base station frequency bands: 41-61 V/m), Basel (Switzerland, 4-6 V/m), Ghent (Belgium, 3-4.5 V/m) and Brussels (Belgium, 2.9-4.3 V/m) using a portable measurement device. Measurements were conducted in three different types of outdoor areas (central and non-central residential areas and downtown), between 2011 and 2012 at 12 different days. On each day, measurements were taken every 4s for approximately 15 to 30 min per area. Measurements per urban environment were repeated 12 times during 1 year. Arithmetic mean values for mobile phone base station exposure ranged between 0.22 V/m (Basel) and 0.41 V/m (Amsterdam) in all outdoor areas combined. The 95th percentile for total RF-EMF exposure varied between 0.46 V/m (Basel) and 0.82 V/m (Amsterdam) and the 99th percentile between 0.81 V/m (Basel) and 1.20 V/m (Brussels). All exposure levels were far below international reference levels proposed by ICNIRP (International Commission on Non-Ionizing Radiation Protection). Our study did not find indications that lowering the regulatory limit results in higher mobile phone base station exposure levels. Copyright © 2014 Elsevier Ltd. All rights reserved.

Photo-EMF sensitivity of porous silicon thin layer-crystalline silicon heterojunction to ammonia adsorption.

PubMed

Vashpanov, Yuriy; Jung, Jae Il; Kwack, Kae Dal

2011-01-01

A new method of using photo-electromotive force in detecting gas and controlling sensitivity is proposed. Photo-electromotive force on the heterojunction between porous silicon thin layer and crystalline silicon wafer depends on the concentration of ammonia in the measurement chamber. A porous silicon thin layer was formed by electrochemical etching on p-type silicon wafer. A gas and light transparent electrical contact was manufactured to this porous layer. Photo-EMF sensitivity corresponding to ammonia concentration in the range from 10 ppm to 1,000 ppm can be maximized by controlling the intensity of illumination light.

Photo-EMF Sensitivity of Porous Silicon Thin Layer–Crystalline Silicon Heterojunction to Ammonia Adsorption

PubMed Central

Vashpanov, Yuriy; Jung, Jae Il; Kwack, Kae Dal

2011-01-01

A new method of using photo-electromotive force in detecting gas and controlling sensitivity is proposed. Photo-electromotive force on the heterojunction between porous silicon thin layer and crystalline silicon wafer depends on the concentration of ammonia in the measurement chamber. A porous silicon thin layer was formed by electrochemical etching on p-type silicon wafer. A gas and light transparent electrical contact was manufactured to this porous layer. Photo-EMF sensitivity corresponding to ammonia concentration in the range from 10 ppm to 1,000 ppm can be maximized by controlling the intensity of illumination light. PMID:22319353

Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments.

PubMed

Zani, Carlos L; Carroll, Anthony R

2017-06-23

The discovery of novel and/or new bioactive natural products from biota sources is often confounded by the reisolation of known natural products. Dereplication strategies that involve the analysis of NMR and MS spectroscopic data to infer structural features present in purified natural products in combination with database searches of these substructures provide an efficient method to rapidly identify known natural products. Unfortunately this strategy has been hampered by the lack of publically available and comprehensive natural product databases and open source cheminformatics tools. A new platform, DEREP-NP, has been developed to help solve this problem. DEREP-NP uses the open source cheminformatics program DataWarrior to generate a database containing counts of 65 structural fragments present in 229 358 natural product structures derived from plants, animals, and microorganisms, published before 2013 and freely available in the nonproprietary Universal Natural Products Database (UNPD). By counting the number of times one or more of these structural features occurs in an unknown compound, as deduced from the analysis of its NMR ( 1 H, HSQC, and/or HMBC) and/or MS data, matching structures carrying the same numeric combination of searched structural features can be retrieved from the database. Confirmation that the matching structure is the same compound can then be verified through literature comparison of spectroscopic data. This methodology can be applied to both purified natural products and fractions containing a small number of individual compounds that are often generated as screening libraries. The utility of DEREP-NP has been verified through the analysis of spectra derived from compounds (and fractions containing two or three compounds) isolated from plant, marine invertebrate, and fungal sources. DEREP-NP is freely available at https://github.com/clzani/DEREP-NP and will help to streamline the natural product discovery process.

Numerous Sinusoidal and Other EMF Phenomena, At Present and Former Native American Sites, May Be Superimposing Themselves onto Regional Power Grids.

NASA Astrophysics Data System (ADS)

Cadran, Lawrence R.; Mc Leod, Roger D.; Mc Leod, David M.

2003-10-01

Periodic electromagnetic field signals (EMF), sometimes noticeable as faint blue-light or other phenomena, frequently are also detected at sites associated with Native Americans. We first noticed this sort of information in the vicinity of Wendell, MA about fourteen years ago. Similar and other signals are apparent at Americas Stonehenge, AS, in North Salem, NH. Connecticut provided our first evidence of superposition of two such waves at the Gungywamp site north of Groton, CT. A Maine location first showed orthogonally oriented trajectories in neighborhoods formerly frequented by Molocket and Metallak and their relatives near Rumford and Rangeley, ME. Florida exhibits similar signals in the vicinity of Hollywood and at Miamis Tequesta instrument, as does a separate site in CT. Powerful thunderstorms in the vicinity of a stone serpent effigy in Ohio cause EMF pulsations. Such signals are possibly superimposing themselves onto power-grids, where frequency changes and system instabilities may occur, according to the elementary physics involved.

Environmental Metabolic Footprinting (EMF) vs. half-life: a new and integrative proxy for the discrimination between control and pesticides exposed sediments in order to further characterise pesticides' environmental impact.

PubMed

Salvia, Marie-Virginie; Ben Jrad, Amani; Raviglione, Delphine; Zhou, Yuxiang; Bertrand, Cédric

2017-06-28

Pesticides are regularly used for a variety of applications and are disseminated throughout the environment. These substances may have significant negative impacts. To date, the half-life, t 1/2 , was often used to study the fate of pesticides in environmental matrices (water, soil, sediment). However, this value gives limited information. First, it does not evaluate the formation of by-products, resulting in the need for additional experiments to be performed to evaluate biodegradation and biotransformation products. T 1/2 also fails to consider the chemical's impact on biodiversity. Resilience time, a new and integrative proxy, was recently proposed as an alternative to t 1/2 , with the potential to evaluate all the post-application effects of the chemical on the environment. The 'Environmental Metabolic Footprinting' (EMF) approach, giving an idea of the resilience time, was used to evaluate the impact of botanicals on soil. The goal is to optimise the EMF to study the impact of a microbial insecticide, the Bacillus thuringiensis israelensis (Bti), on sediment. The difficulty of this work lies in the commercial solution of Bti that is really complex, and this complexity yields chromatograms that are extremely difficult to interpret; t 1/2 cannot be used. No methodologies currently exist to monitor the impact of these compounds on the environment. We will test the EMF to determine if it is sensitive enough to tolerate such complex mixtures. A pure chemical insecticide, the α-cypermethrin, will be also studied. The article shows that the EMF is able to distinguish meta-metabolome differences between control and exposed (with Bti) sediments.

Effect of occupational EMF exposure from radar at two different frequency bands on plasma melatonin and serotonin levels.

PubMed

Singh, Sarika; Mani, Kumar Vyonkesh; Kapoor, Neeru

2015-05-01

To delineate the effect of chronic electromagnetic field (EMF) exposure from radar on plasma melatonin and serotonin levels in occupationally exposed military personnel. A total of 166 male military personnel participated in the study out of which only 155 joined for blood draw. They were divided into three sets: Control group (n = 68), exposure group I (n = 40) exposed to 8-12 GHz and exposure group II (n = 58) working with radar at 12.5-18 GHz frequency. The three groups were further split into two groups according to their years of service (up to 10 years and > 10 years) in order to investigate the effect of years of exposure from radar. Melatonin and serotonin levels were estimated by enzyme immunoassay in fasting blood samples collected from 06:00-07:00 h. EMF measurements were recorded at different locations using Satimo EME Guard 'Personal Exposure Meter' and Narda 'Broad Band Field Meter'. The group I exposed population registered a minor though not significant decrease in plasma melatonin concentration while the other group II exposed population registered statistically significant decline in melatonin concentration when compared with controls. Highly significant increase in plasma serotonin levels was found in exposure group II when compared to control whereas marginal non-significant rise was also registered in exposure group I in comparison to control. Exposure in terms of length of service up to 10 years did not produce any significant effect in the indoleamine levels in both the exposure groups when they were compared with their respective control groups. Whereas, length of service greater than 10 years was observed to decrease and increase respectively the melatonin and serotonin concentration significantly in exposure group II but not in exposure group I. However, correlation test did not yield any significant association between years of service and melatonin or serotonin levels respectively in both the exposure sets I and II. No significant

Effects of time-variant extremely low-frequency (ELF) electromagnetic fields (EMF) on cholinesterase activity in Dictyostelium discoideum (Protista).

PubMed

Amaroli, Andrea; Trielli, Francesca; Bianco, Bruno; Giordano, Stefano; Moggia, Elsa; Corrado, Maria U Delmonte

2005-12-15

Recently, we detected propionylcholinesterase (PrChE) activity in single-cell amoebae of Dictyostelium discoideum using cytochemical, electrophoretic, and spectrophotometric methods. The involvement of this enzyme activity in cell-cell and cell-environment interactions was suggested. In this work, we found that exposure of single-cell amoebae to an extremely low-frequency electromagnetic fields (ELF-EMF) of 300 microT, 50 Hz, from 1 h up to 48 h at 21 +/- 1 degrees C affected PrChE activity.

Occupational EMF exposure from radar at X and Ku frequency band and plasma catecholamine levels.

PubMed

Singh, Sarika; Kapoor, Neeru

2015-09-01

Workers in certain occupations such as the military may be exposed to technical radiofrequency radiation exposure above current limits, which may pose a health risk. The present investigation intended to find the effect of chronic electromagnetic field (EMF) exposure from radar on plasma catecholamines in the military workforce. In the study, 166 male personnel selected randomly were categorized into three groups: control (n = 68), exposure group-I (X-band, 8-12 GHz, n = 40), and exposure group-II (Ku-band, 12.5-18 GHz, n = 58). The three clusters were further divided into two groups according to their years of service (YOS) (up to 9 years and ≥10 years) to study the effect of years of radar exposure. Enzyme immunoassay was employed to assess catecholamine concentrations. EMF levels were recorded at different occupational distances from radar. Significant adrenaline diminution was registered in exposure group-II with no significant difference in exposure group-I when both groups were weighed against control. Nor-adrenaline and dopamine levels did not vary significantly in both exposure groups when compared to controls. Exposure in terms of YOS also did not yield any significant alteration in any of the catecholamines and in any of the exposure groups when compared with their respective control groups. The shift from baseline catecholamine values due to stress has immense significance for health and well-being. Their continual alteration may prove harmful in due course. Suitable follow-up studies are needed to further strengthen these preliminary observations and for now, exposures should be limited as much as possible with essential safeguards. © 2015 Wiley Periodicals, Inc.

ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding.

PubMed

Guhlin, Joseph; Silverstein, Kevin A T; Zhou, Peng; Tiffin, Peter; Young, Nevin D

2017-08-10

Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data. The Omics Database Generator (ODG) allows users to create customized databases that utilize published genomics data integrated with experimental data which can be queried using a flexible graph database. When provided with omics and experimental data, ODG will create a comparative, multi-dimensional graph database. ODG can import definitions and annotations from other sources such as InterProScan, the Gene Ontology, ENZYME, UniPathway, and others. This annotation data can be especially useful for studying new or understudied species for which transcripts have only been predicted, and rapidly give additional layers of annotation to predicted genes. In better studied species, ODG can perform syntenic annotation translations or rapidly identify characteristics of a set of genes or nucleotide locations, such as hits from an association study. ODG provides a web-based user-interface for configuring the data import and for querying the database. Queries can also be run from the command-line and the database can be queried directly through programming language hooks available for most languages. ODG supports most common genomic formats as well as generic, easy to use tab-separated value format for user-provided annotations. ODG is a user-friendly database generation and query tool that adapts to the supplied data to produce a comparative genomic database or multi-layered annotation database. ODG provides rapid comparative genomic annotation and is therefore particularly useful for non-model or

A Database Management System Application for the Graduate Programs Office of the School of Systems and Logistics. Volume 2. Technical Reference Manual

DTIC Science & Technology

1988-09-01

CIT C 15 Name of local city. InCSrATE C 2 Name of local state as tw letter abbreviatiom. SIC ZIP C 10 Loa ZIP code. Five or nine digits . InC_ PHKtE C 15...record: 10 Database Dictimary for C: \\ BASE\\PAS1E.MF Field Nane Type Width Decimal Coments PMSCODE C 2 Third and fourth digits of PAS code. ON C 3...Version: 3.01 Date: 09/01/88 Time: 21:34 Report Libary : C: ASE\\GPO.RP1 Date: 08/28/88 Time: 11:32 PRMNT OFTICNS CflRL-PRINrM Nmber of copies: 1 Starting

A case study for a digital seabed database: Bohai Sea engineering geology database

NASA Astrophysics Data System (ADS)

Tianyun, Su; Shikui, Zhai; Baohua, Liu; Ruicai, Liang; Yanpeng, Zheng; Yong, Wang

2006-07-01

This paper discusses the designing plan of ORACLE-based Bohai Sea engineering geology database structure from requisition analysis, conceptual structure analysis, logical structure analysis, physical structure analysis and security designing. In the study, we used the object-oriented Unified Modeling Language (UML) to model the conceptual structure of the database and used the powerful function of data management which the object-oriented and relational database ORACLE provides to organize and manage the storage space and improve its security performance. By this means, the database can provide rapid and highly effective performance in data storage, maintenance and query to satisfy the application requisition of the Bohai Sea Oilfield Paradigm Area Information System.

Database recovery using redundant disk arrays

NASA Technical Reports Server (NTRS)

Mourad, Antoine N.; Fuchs, W. K.; Saab, Daniel G.

1992-01-01

Redundant disk arrays provide a way for achieving rapid recovery from media failures with a relatively low storage cost for large scale database systems requiring high availability. In this paper a method is proposed for using redundant disk arrays to support rapid-recovery from system crashes and transaction aborts in addition to their role in providing media failure recovery. A twin page scheme is used to store the parity information in the array so that the time for transaction commit processing is not degraded. Using an analytical model, it is shown that the proposed method achieves a significant increase in the throughput of database systems using redundant disk arrays by reducing the number of recovery operations needed to maintain the consistency of the database.

Influence of the on-line ELF-EMF stimulation on the electrophysiological properties of the rat hippocampal CA1 neurons in vitro

NASA Astrophysics Data System (ADS)

Zheng, Yu; Ma, Wei; Dong, Lei; Dou, Jun-rong; Gao, Yang; Xue, Jing

2017-10-01

The extremely low frequency electromagnetic fields (ELF-EMFs) have been shown to have an environmentally negative effect on humans' health; however, its treatment effect is beneficial for patients suffering from neurological disorders. Despite this success, the application of ELF-EMF has exceeded in the understanding of its internal mechanism. Recently, it was found that on-line magnetic stimulation may offer advantages over off-line magnetic exposure and has proven to be effective in activating the prefrontal cortex pyramidal neurons in vitro. Here, we perform computational simulations of the stimulation coils in COMSOL modeling to describe the uniformity of the distribution of the on-line magnetic field. Interestingly, the modeling data and actual measurements showed that the densities of the magnetic flux that was generated by the on-line stimulation coils were similar. The on-line magnetic stimulator induced sodium channel currents as well as field excitatory postsynaptic potentials of the rat hippocampal CA1 neurons and successfully demonstrated its extensive applications to activate neuronal tissue. These findings further raise the possibility that the instrument of on-line magnetic stimulation may be an effective alternative for studies in the field of bioelectromagnetics.

Architecture Knowledge for Evaluating Scalable Databases

DTIC Science & Technology

2015-01-16

problems, arising from the proliferation of new data models and distributed technologies for building scalable, available data stores . Architects must...longer are relational databases the de facto standard for building data repositories. Highly distributed, scalable “ NoSQL ” databases [11] have emerged...This is especially challenging at the data storage layer. The multitude of competing NoSQL database technologies creates a complex and rapidly

WHO Meeting on EMF Biological Effects and Standards Harmonization in Asia and Oceania, 22-24 October, 2001, Shilla Hotel, Seoul, Korea

DTIC Science & Technology

2001-10-24

thermoelastic waves in the have been developed in several laboratories. head to stimulate auditory system. This hypothesis has been examined theoretically...country, thus stimulating the study on the EMF influence on human body. In closing, I extend my sincere appreciation to all presenters and...various systems of direct stimulation of nerves and other excitable cells the body, particularly the nervous, endocrine and using electrodes. immune

Thermodynamic Properties of AgIn2Te3I and AgIn2Te3Br, Determined by EMF Method

NASA Astrophysics Data System (ADS)

Moroz, M. V.; Prokhorenko, M. V.; Prokhorenko, S. V.; Yatskov, M. V.; Reshetnyak, O. V.

2018-01-01

Differential thermal analysis (DTA), X-ray diffraction (XRD), and electromotive force (EMF) are used to triangulate Ag-In-Te-I(Br) systems in the vicinity of compounds AgIn2Te3I and AgIn2Te3Br. The three-dimensional position of the AgIn2Te3I-InTe-Ag2Te-AgI and AgIn2Te3Br-InTe-Ag3TeBr phase areas with respect to the figurative points of silver is used to create equations of potential-determining chemical reactions. The potential-determining reactions are conducted in (-)C|Ag|Ag3GeS3I(Br) glass|D|C(+) electrochemical cells (ECCs), where C stands for inert (graphite) electrodes, Ag and D are ECC electrodes (D denotes alloys of one-, three-, and four-phase areas), and Ag3GeS3I and Ag3GeS3Br glasses are membranes with purely ionic Ag+ conductivity. Linear parts of the temperature dependences of the cell EMFs are used to calculate the standard integral thermodynamic functions of saturated solid solutions based on AgIn2Te3I and AgIn2Te3Br, and the relative partial thermodynamic functions of silver in the stoichiometric quaternary compounds.

Supporting the operational use of process based hydrological models and NASA Earth Observations for use in land management and post-fire remediation through a Rapid Response Erosion Database (RRED).

NASA Astrophysics Data System (ADS)

Miller, M. E.; Elliot, W.; Billmire, M.; Robichaud, P. R.; Banach, D. M.

2017-12-01

We have built a Rapid Response Erosion Database (RRED, http://rred.mtri.org/rred/) for the continental United States to allow land managers to access properly formatted spatial model inputs for the Water Erosion Prediction Project (WEPP). Spatially-explicit process-based models like WEPP require spatial inputs that include digital elevation models (DEMs), soil, climate and land cover. The online database delivers either a 10m or 30m USGS DEM, land cover derived from the Landfire project, and soil data derived from SSURGO and STATSGO datasets. The spatial layers are projected into UTM coordinates and pre-registered for modeling. WEPP soil parameter files are also created along with linkage files to match both spatial land cover and soils data with the appropriate WEPP parameter files. Our goal is to make process-based models more accessible by preparing spatial inputs ahead of time allowing modelers to focus on addressing scenarios of concern. The database provides comprehensive support for post-fire hydrological modeling by allowing users to upload spatial soil burn severity maps, and within moments returns spatial model inputs. Rapid response is critical following natural disasters. After moderate and high severity wildfires, flooding, erosion, and debris flows are a major threat to life, property and municipal water supplies. Mitigation measures must be rapidly implemented if they are to be effective, but they are expensive and cannot be applied everywhere. Fire, runoff, and erosion risks also are highly heterogeneous in space, creating an urgent need for rapid, spatially-explicit assessment. The database has been used to help assess and plan remediation on over a dozen wildfires in the Western US. Future plans include expanding spatial coverage, improving model input data and supporting additional models. Our goal is to facilitate the use of the best possible datasets and models to support the conservation of soil and water.

Improving Precautionary Communication in the EMF Field? Effects of Making Messages Consistent and Explaining the Effectiveness of Precautions.

PubMed

Boehmert, Christoph; Wiedemann, Peter; Croft, Rodney

2016-10-09

Many radiation health agencies communicate precautionary measures regarding the use of mobile communication devices, e.g. the use of a headset while talking on the phone. These precautionary messages have, however, been shown to unintentionally increase risk perceptions about radiofrequency electromagnetic fields (RF-EMFs). The current study tested two potential ways of amending precautionary messages in order to minimise this unintentional effect. Firstly, the messages' potential to be perceived as inconsistent and thereby raise suspicions was addressed; secondly, the effectiveness of the precautions was explained. An experimental design was applied in which a quota sample of 1717 Australian residents was randomly assigned to one of six message conditions. Three different risk perception measures served as dependent variables, two of them are conditional measures. The original effect of precautionary messages to amplify risk perceptions could not be replicated. Furthermore, amending precautionary messages in favour of more consistency had no effect, while explaining the effectiveness of the precautions increased conditional risk perception under the condition that no precautions are taken. This was contrary to our assumptions. We infer from these results that changing precautionary messages in terms of consistency and effectiveness in order to reduce risk perception is hardly possible. The use of conditional risk perception measures seems fruitful for studies looking at the effects of precautionary or protective messages, given that previous studies have only investigated effects on unconditional risk perception. However, the present results should not be over-interpreted as the measures' validity in the EMF context still needs further investigation.

Improving Precautionary Communication in the EMF Field? Effects of Making Messages Consistent and Explaining the Effectiveness of Precautions

PubMed Central

Boehmert, Christoph; Wiedemann, Peter; Croft, Rodney

2016-01-01

Many radiation health agencies communicate precautionary measures regarding the use of mobile communication devices, e.g. the use of a headset while talking on the phone. These precautionary messages have, however, been shown to unintentionally increase risk perceptions about radiofrequency electromagnetic fields (RF-EMFs). The current study tested two potential ways of amending precautionary messages in order to minimise this unintentional effect. Firstly, the messages’ potential to be perceived as inconsistent and thereby raise suspicions was addressed; secondly, the effectiveness of the precautions was explained. An experimental design was applied in which a quota sample of 1717 Australian residents was randomly assigned to one of six message conditions. Three different risk perception measures served as dependent variables, two of them are conditional measures. The original effect of precautionary messages to amplify risk perceptions could not be replicated. Furthermore, amending precautionary messages in favour of more consistency had no effect, while explaining the effectiveness of the precautions increased conditional risk perception under the condition that no precautions are taken. This was contrary to our assumptions. We infer from these results that changing precautionary messages in terms of consistency and effectiveness in order to reduce risk perception is hardly possible. The use of conditional risk perception measures seems fruitful for studies looking at the effects of precautionary or protective messages, given that previous studies have only investigated effects on unconditional risk perception. However, the present results should not be over-interpreted as the measures’ validity in the EMF context still needs further investigation. PMID:27735851

In Situ California Bearing Ration Database

DTIC Science & Technology

2007-10-01

for use in this investigation ( Berney and Wahl 2007). The goal of the JRAC effort is to enable a rapid assessment of a soil with a miniaturized...variability - Benalla test section. Research Report ARR 220. Victoria, Australia: Australian Road Research Board. Berney , E.S., and R.E. Wahl. 2007. Rapid...number given to each unique soil that was identified in the Joint Rapid Airfield Construction program’s database ( Berney and Wahl 2007). Test or

RF EMF Risk Perception Revisited: Is the Focus on Concern Sufficient for Risk Perception Studies?

PubMed Central

Wiedemann, Peter M.; Freudenstein, Frederik; Böhmert, Christoph; Wiart, Joe; Croft, Rodney J.

2017-01-01

An implicit assumption of risk perception studies is that concerns expressed in questionnaires reflect concerns in everyday life. The aim of the present study is to check this assumption, i.e., the extrapolability of risk perceptions expressed in a survey, to risk perceptions in everyday life. To that end, risk perceptions were measured by a multidimensional approach. In addition to the traditional focus on measuring the magnitude of risk perceptions, the thematic relevance (how often people think about a risk issue) and the discursive relevance (how often people think about or discuss a risk issue) of risk perceptions were also collected. Taking into account this extended view of risk perception, an online survey was conducted in six European countries with 2454 respondents, referring to radio frequency electromagnetic field (RF EMF) risk potentials from base stations, and access points, such as WiFi routers and cell phones. The findings reveal that the present study’s multidimensional approach to measuring risk perception provides a more differentiated understanding of RF EMF risk perception. High levels of concerns expressed in questionnaires do not automatically imply that these concerns are thematically relevant in everyday life. We use thematic relevance to distinguish between enduringly concerned (high concern according to both questionnaire and thematic relevance) and not enduringly concerned participants (high concern according to questionnaire but no thematic relevance). Furthermore, we provide data for the empirical value of this distinction: Compared to other participants, enduringly concerned subjects consider radio frequency electromagnetic field exposure to a greater extent as a moral and affective issue. They also see themselves as highly exposed to radio frequency electromagnetic fields. However, despite these differences, subjects with high levels of thematic relevance are nevertheless sensitive to exposure reduction as a means for improving the

RF EMF Risk Perception Revisited: Is the Focus on Concern Sufficient for Risk Perception Studies?

PubMed

Wiedemann, Peter M; Freudenstein, Frederik; Böhmert, Christoph; Wiart, Joe; Croft, Rodney J

2017-06-08

An implicit assumption of risk perception studies is that concerns expressed in questionnaires reflect concerns in everyday life. The aim of the present study is to check this assumption, i.e., the extrapolability of risk perceptions expressed in a survey, to risk perceptions in everyday life. To that end, risk perceptions were measured by a multidimensional approach. In addition to the traditional focus on measuring the magnitude of risk perceptions, the thematic relevance (how often people think about a risk issue) and the discursive relevance (how often people think about or discuss a risk issue) of risk perceptions were also collected. Taking into account this extended view of risk perception, an online survey was conducted in six European countries with 2454 respondents, referring to radio frequency electromagnetic field (RF EMF) risk potentials from base stations, and access points, such as WiFi routers and cell phones. The findings reveal that the present study's multidimensional approach to measuring risk perception provides a more differentiated understanding of RF EMF risk perception. High levels of concerns expressed in questionnaires do not automatically imply that these concerns are thematically relevant in everyday life. We use thematic relevance to distinguish between enduringly concerned (high concern according to both questionnaire and thematic relevance) and not enduringly concerned participants (high concern according to questionnaire but no thematic relevance). Furthermore, we provide data for the empirical value of this distinction: Compared to other participants, enduringly concerned subjects consider radio frequency electromagnetic field exposure to a greater extent as a moral and affective issue. They also see themselves as highly exposed to radio frequency electromagnetic fields. However, despite these differences, subjects with high levels of thematic relevance are nevertheless sensitive to exposure reduction as a means for improving the

Heterogeneous database integration in biomedicine.

PubMed

Sujansky, W

2001-08-01

The rapid expansion of biomedical knowledge, reduction in computing costs, and spread of internet access have created an ocean of electronic data. The decentralized nature of our scientific community and healthcare system, however, has resulted in a patchwork of diverse, or heterogeneous, database implementations, making access to and aggregation of data across databases very difficult. The database heterogeneity problem applies equally to clinical data describing individual patients and biological data characterizing our genome. Specifically, databases are highly heterogeneous with respect to the data models they employ, the data schemas they specify, the query languages they support, and the terminologies they recognize. Heterogeneous database systems attempt to unify disparate databases by providing uniform conceptual schemas that resolve representational heterogeneities, and by providing querying capabilities that aggregate and integrate distributed data. Research in this area has applied a variety of database and knowledge-based techniques, including semantic data modeling, ontology definition, query translation, query optimization, and terminology mapping. Existing systems have addressed heterogeneous database integration in the realms of molecular biology, hospital information systems, and application portability.

The Israel DNA database--the establishment of a rapid, semi-automated analysis system.

PubMed

Zamir, Ashira; Dell'Ariccia-Carmon, Aviva; Zaken, Neomi; Oz, Carla

2012-03-01

The Israel Police DNA database, also known as IPDIS (Israel Police DNA Index System), has been operating since February 2007. During that time more than 135,000 reference samples have been uploaded and more than 2000 hits reported. We have developed an effective semi-automated system that includes two automated punchers, three liquid handler robots and four genetic analyzers. An inhouse LIMS program enables full tracking of every sample through the entire process of registration, pre-PCR handling, analysis of profiles, uploading to the database, hit reports and ultimately storage. The LIMS is also responsible for the future tracking of samples and their profiles to be expunged from the database according to the Israeli DNA legislation. The database is administered by an in-house developed software program, where reference and evidentiary profiles are uploaded, stored, searched and matched. The DNA database has proven to be an effective investigative tool which has gained the confidence of the Israeli public and on which the Israel National Police force has grown to rely. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Recovery issues in databases using redundant disk arrays

NASA Technical Reports Server (NTRS)

Mourad, Antoine N.; Fuchs, W. K.; Saab, Daniel G.

1993-01-01

Redundant disk arrays provide a way for achieving rapid recovery from media failures with a relatively low storage cost for large scale database systems requiring high availability. In this paper we propose a method for using redundant disk arrays to support rapid recovery from system crashes and transaction aborts in addition to their role in providing media failure recovery. A twin page scheme is used to store the parity information in the array so that the time for transaction commit processing is not degraded. Using an analytical model, we show that the proposed method achieves a significant increase in the throughput of database systems using redundant disk arrays by reducing the number of recovery operations needed to maintain the consistency of the database.

Setting up an off-site emergency mortuary facility (EMF) to deal with a DVI incident: disaster victim management (DVM).

PubMed

Eitzen, David; Zimmermann, Alex

2012-06-01

Forensic mortuaries in all Australian jurisdictions are dealing with increasing workloads, with routine cases regularly occupying greater than 50%, and often as much as 85%, of existing cold room body storage capacity, particularly over long weekends and during seasonal increases in respiratory infections. Hence the need to deal with a sudden influx of deceased persons or multiple body parts in a mass fatality incident would overwhelm most Australian forensic mortuaries, thereby requiring other means of body storage and processing. Exercise "Construct" was a joint South Australian Police (SAPol) and Forensic Science South Australia exercise designed to practice the establishment and construction of an emergency mortuary facility (EMF) to deal with a mass fatality incident and the subsequent disaster victim identification process. The aims of the exercise were to test preparedness, activation and construction processes relative to the establishment of an EMF. The exercise provided the opportunity to identify gaps in the capacity to successfully complete the tasks within the allotted time frames. The exercise reinforced the need to have a comprehensive and clearly documented process which must include a current list of suppliers who can deliver goods and services in a timely manner. The aim of this paper is to report on the exercise findings and share the experience with other jurisdictions. It will also provide other jurisdictions with the opportunity to consider whether the South Australian model will be useful to them in improving their own response when confronted with a mass fatality incident that may overwhelm existing local mortuary capacities and capabilities.

Rapid production of optimal-quality reduced-resolution representations of very large databases

DOEpatents

Sigeti, David E.; Duchaineau, Mark; Miller, Mark C.; Wolinsky, Murray; Aldrich, Charles; Mineev-Weinstein, Mark B.

2001-01-01

View space representation data is produced in real time from a world space database representing terrain features. The world space database is first preprocessed. A database is formed having one element for each spatial region corresponding to a finest selected level of detail. A multiresolution database is then formed by merging elements and a strict error metric is computed for each element at each level of detail that is independent of parameters defining the view space. The multiresolution database and associated strict error metrics are then processed in real time for real time frame representations. View parameters for a view volume comprising a view location and field of view are selected. The error metric with the view parameters is converted to a view-dependent error metric. Elements with the coarsest resolution are chosen for an initial representation. Data set first elements from the initial representation data set are selected that are at least partially within the view volume. The first elements are placed in a split queue ordered by the value of the view-dependent error metric. If the number of first elements in the queue meets or exceeds a predetermined number of elements or whether the largest error metric is less than or equal to a selected upper error metric bound, the element at the head of the queue is force split and the resulting elements are inserted into the queue. Force splitting is continued until the determination is positive to form a first multiresolution set of elements. The first multiresolution set of elements is then outputted as reduced resolution view space data representing the terrain features.

Dynamic Control of Adsorption Sensitivity for Photo-EMF-Based Ammonia Gas Sensors Using a Wireless Network

PubMed Central

Vashpanov, Yuriy; Choo, Hyunseung; Kim, Dongsoo Stephen

2011-01-01

This paper proposes an adsorption sensitivity control method that uses a wireless network and illumination light intensity in a photo-electromagnetic field (EMF)-based gas sensor for measurements in real time of a wide range of ammonia concentrations. The minimum measurement error for a range of ammonia concentration from 3 to 800 ppm occurs when the gas concentration magnitude corresponds with the optimal intensity of the illumination light. A simulation with LabView-engineered modules for automatic control of a new intelligent computer system was conducted to improve measurement precision over a wide range of gas concentrations. This gas sensor computer system with wireless network technology could be useful in the chemical industry for automatic detection and measurement of hazardous ammonia gas levels in real time. PMID:22346680

CD-ROM-aided Databases

NASA Astrophysics Data System (ADS)

Masuyama, Keiichi

CD-ROM has rapidly evolved as a new information medium with large capacity, In the U.S. it is predicted that it will become two hundred billion yen market in three years, and thus CD-ROM is strategic target of database industry. Here in Japan the movement toward its commercialization has been active since this year. Shall CD-ROM bussiness ever conquer information market as an on-disk database or electronic publication? Referring to some cases of the applications in the U.S. the author views marketability and the future trend of this new optical disk medium.

Run-Time Support for Rapid Prototyping

DTIC Science & Technology

1988-12-01

prototyping. One such system is the Computer-Aided Proto- typing System (CAPS). It combines rapid prototypng with automatic program generation. Some of the...a design database, and a design management system [Ref. 3:p. 66. By using both rapid prototyping and automatic program genera- tion. CAPS will be...Most proto- typing systems perform these functions. CAPS is different in that it combines rapid prototyping with a variant of automatic program

[Assessment of 10 years of memory consultations in the Franche-Comté: Description and analysis of the RAPID regional database].

PubMed

Bereau, M; Sylvestre, G; Mauny, F; Puyraveau, M; Baudier, F; Magnin, E; Berger, E; Vandel, P; Galmiche, J; Chopard, G

2015-09-01

The aim of this study was to evaluate the impact, on a regional scale (Franche-Comté), of 3 National Alzheimer care plans, particularly concerning the development of the offer of care management by clinicians as well as the panel of diagnoses concerned. Data on sociodemographic, neuropsychological and diagnostic characteristics were retrieved from the RAPID regional database between 1st January 2003 and 31st December 2012. These analyses focused exclusively on patients who had an initial consultation (n=12,017) during the same period. The existence of a previously established health network capable of carrying out governmental health plans has produced an effective interface between regional administrative structures responsible for the implementation of these plans and health professionals responsible for carrying out them out. This network study, the use of a battery of tests and a common software database have enabled the development of patient care management throughout the Franche-Comté region. It also showed the diversification of diagnoses mentioned over the past years as well as changes in clinical practices on how to address the issue of cognitive impairment. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Establishment of a matrix-assisted laser desorption ionization time-of-flight mass spectrometry database for rapid identification of infectious achlorophyllous green micro-algae of the genus Prototheca.

PubMed

Murugaiyan, J; Ahrholdt, J; Kowbel, V; Roesler, U

2012-05-01

The possibility of using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of pathogenic and non-pathogenic species of the genus Prototheca has been recently demonstrated. A unique reference database of MALDI-TOF MS profiles for type and reference strains of the six generally accepted Prototheca species was established. The database quality was reinforced after the acquisition of 27 spectra for selected Prototheca strains, with three biological and technical replicates for each of 18 type and reference strains of Prototheca and four strains of Chlorella. This provides reproducible and unique spectra covering a wide m/z range (2000-20 000 Da) for each of the strains used in the present study. The reproducibility of the spectra was further confirmed by employing composite correlation index calculation and main spectra library (MSP) dendrogram creation, available with MALDI Biotyper software. The MSP dendrograms obtained were comparable with the 18S rDNA sequence-based dendrograms. These reference spectra were successfully added to the Bruker database, and the efficiency of identification was evaluated by cross-reference-based and unknown Prototheca identification. It is proposed that the addition of further strains would reinforce the reference spectra library for rapid identification of Prototheca strains to the genus and species/genotype level. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

[The electromagnetic fields of the base stations of mobile radio communication and ecology. The estimation of danger of the base station EMF for population and for bioecosystems].

PubMed

Grigor'ev, Iu G; Grigor'ev, K A

2005-01-01

The estimation of the danger for the population and for the bioecosistems of the electromagnetic conditions around of the base stations was given. The insufficiency of the scientific knowledge does not allow to guarantee the safety of the population and of the bioecosystems in the conditions of a round-the-clock long-term influence of EMF RF. WHO recommends to use "Precautionary principle".

Utility of rapid database searching for quality assurance: 'detective work' in uncovering radiology coding and billing errors

NASA Astrophysics Data System (ADS)

Horii, Steven C.; Kim, Woojin; Boonn, William; Iyoob, Christopher; Maston, Keith; Coleman, Beverly G.

2011-03-01

When the first quarter of 2010 Department of Radiology statistics were provided to the Section Chiefs, the authors (SH, BC) were alarmed to discover that Ultrasound showed a decrease of 2.5 percent in billed examinations. This seemed to be in direct contradistinction to the experience of the ultrasound faculty members and sonographers. Their experience was that they were far busier than during the same quarter of 2009. The one exception that all acknowledged was the month of February, 2010 when several major winter storms resulted in a much decreased Hospital admission and Emergency Department visit rate. Since these statistics in part help establish priorities for capital budget items, professional and technical staffing levels, and levels of incentive salary, they are taken very seriously. The availability of a desktop, Web-based RIS database search tool developed by two of the authors (WK, WB) and built-in database functions of the ultrasound miniPACS, made it possible for us very rapidly to develop and test hypotheses for why the number of billable examinations was declining in the face of what experience told the authors was an increasing number of examinations being performed. Within a short time, we identified the major cause as errors on the part of the company retained to verify billable Current Procedural Terminology (CPT) codes against ultrasound reports. This information is being used going forward to recover unbilled examinations and take measures to reduce or eliminate the types of coding errors that resulted in the problem.

Molecular Identification and Databases in Fusarium

USDA-ARS?s Scientific Manuscript database

DNA sequence-based methods for identifying pathogenic and mycotoxigenic Fusarium isolates have become the gold standard worldwide. Moreover, fusarial DNA sequence data are increasing rapidly in several web-accessible databases for comparative purposes. Unfortunately, the use of Basic Alignment Sea...

ReprDB and panDB: minimalist databases with maximal microbial representation.

PubMed

Zhou, Wei; Gay, Nicole; Oh, Julia

2018-01-18

Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes. We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets. reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.

Electromagnetic field and brain development.

PubMed

Kaplan, Suleyman; Deniz, Omur Gulsum; Önger, Mehmet Emin; Türkmen, Aysın Pınar; Yurt, Kıymet Kübra; Aydın, Işınsu; Altunkaynak, Berrin Zuhal; Davis, Devra

2016-09-01

Rapid advances in technology involve increased exposures to radio-frequency/microwave radiation from mobile phones and other wireless transmitting devices. As cell phones are held close to the head during talking and often stored next to the reproductive organs, studies are mostly focused on the brain. In fact, more research is especially needed to investigate electromagnetic field (EMF)'s effects on the central nervous system (CNS). Several studies clearly demonstrate that EMF emitted by cell phones could affect a range of body systems and functions. Recent work has demonstrated that EMF inhibit the formation and differentiation of neural stem cells during embryonic development and also affect reproductive and neurological health of adults that have undergone prenatal exposure. The aim of this review is to discuss the developing CNS and explain potential impacts of EMF on this system. Copyright © 2015 Elsevier B.V. All rights reserved.

Determination of torque speed current characteristics of a brushless DC motor by utilizing back-EMF of non-energized phase

NASA Astrophysics Data System (ADS)

Jang, G. H.; Yeom, J. H.; Kim, M. G.

2007-03-01

This paper presents a method to determine the torque constant and the torque-speed-current characteristics of a brushless DC (BLDC) motor by utilizing back-EMF variation of nonenergized phase. It also develops a BLDC motor controller with a digital signal processor (DSP) to monitor its current, voltage and speed in real time. Torque-speed-current characteristics of a BLDC motor are determined by using the proposed method and the developed controller. They are compared with the torque-speed-current characteristics measured by dynamometer experimentally. This research shows that the proposed method is an effective method to determine the torque constant and the torque-speed-current characteristics of the BLDC motor without using dynamometer.

Scale out databases for CERN use cases

NASA Astrophysics Data System (ADS)

Baranowski, Zbigniew; Grzybek, Maciej; Canali, Luca; Lanza Garcia, Daniel; Surdy, Kacper

2015-12-01

Data generation rates are expected to grow very fast for some database workloads going into LHC run 2 and beyond. In particular this is expected for data coming from controls, logging and monitoring systems. Storing, administering and accessing big data sets in a relational database system can quickly become a very hard technical challenge, as the size of the active data set and the number of concurrent users increase. Scale-out database technologies are a rapidly developing set of solutions for deploying and managing very large data warehouses on commodity hardware and with open source software. In this paper we will describe the architecture and tests on database systems based on Hadoop and the Cloudera Impala engine. We will discuss the results of our tests, including tests of data loading and integration with existing data sources and in particular with relational databases. We will report on query performance tests done with various data sets of interest at CERN, notably data from the accelerator log database.

The Sequenced Angiosperm Genomes and Genome Databases.

PubMed

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

The Sequenced Angiosperm Genomes and Genome Databases

PubMed Central

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology. PMID:29706973

Distributed databases for materials study of thermo-kinetic properties

NASA Astrophysics Data System (ADS)

Toher, Cormac

2015-03-01

High-throughput computational materials science provides researchers with the opportunity to rapidly generate large databases of materials properties. To rapidly add thermal properties to the AFLOWLIB consortium and Materials Project repositories, we have implemented an automated quasi-harmonic Debye model, the Automatic GIBBS Library (AGL). This enables us to screen thousands of materials for thermal conductivity, bulk modulus, thermal expansion and related properties. The search and sort functions of the online database can then be used to identify suitable materials for more in-depth study using more precise computational or experimental techniques. AFLOW-AGL source code is public domain and will soon be released within the GNU-GPL license.

DMTB: the magnetotactic bacteria database

NASA Astrophysics Data System (ADS)

Pan, Y.; Lin, W.

2012-12-01

Magnetotactic bacteria (MTB) are of interest in biogeomagnetism, rock magnetism, microbiology, biomineralization, and advanced magnetic materials because of their ability to synthesize highly ordered intracellular nano-sized magnetic minerals, magnetite or greigite. Great strides for MTB studies have been made in the past few decades. More than 600 articles concerning MTB have been published. These rapidly growing data are stimulating cross disciplinary studies in such field as biogeomagnetism. We have compiled the first online database for MTB, i.e., Database of Magnestotactic Bacteria (DMTB, http://database.biomnsl.com). It contains useful information of 16S rRNA gene sequences, oligonucleotides, and magnetic properties of MTB, and corresponding ecological metadata of sampling sites. The 16S rRNA gene sequences are collected from the GenBank database, while all other data are collected from the scientific literature. Rock magnetic properties for both uncultivated and cultivated MTB species are also included. In the DMTB database, data are accessible through four main interfaces: Site Sort, Phylo Sort, Oligonucleotides, and Magnetic Properties. References in each entry serve as links to specific pages within public databases. The online comprehensive DMTB will provide a very useful data resource for researchers from various disciplines, e.g., microbiology, rock magnetism and paleomagnetism, biogeomagnetism, magnetic material sciences and others.

Enhanced DIII-D Data Management Through a Relational Database

NASA Astrophysics Data System (ADS)

Burruss, J. R.; Peng, Q.; Schachter, J.; Schissel, D. P.; Terpstra, T. B.

2000-10-01

A relational database is being used to serve data about DIII-D experiments. The database is optimized for queries across multiple shots, allowing for rapid data mining by SQL-literate researchers. The relational database relates different experiments and datasets, thus providing a big picture of DIII-D operations. Users are encouraged to add their own tables to the database. Summary physics quantities about DIII-D discharges are collected and stored in the database automatically. Meta-data about code runs, MDSplus usage, and visualization tool usage are collected, stored in the database, and later analyzed to improve computing. Documentation on the database may be accessed through programming languages such as C, Java, and IDL, or through ODBC compliant applications such as Excel and Access. A database-driven web page also provides a convenient means for viewing database quantities through the World Wide Web. Demonstrations will be given at the poster.

Implementation of a MFAC based position sensorless drive for high speed BLDC motors with nonideal back EMF.

PubMed

Li, Haitao; Ning, Xin; Li, Wenzhuo

2017-03-01

In order to improve the reliability and reduce power consumption of the high speed BLDC motor system, this paper presents a model free adaptive control (MFAC) based position sensorless drive with only a dc-link current sensor. The initial commutation points are obtained by detecting the phase of EMF zero-crossing point and then delaying 30 electrical degrees. According to the commutation error caused by the low pass filter (LPF) and other factors, the relationship between commutation error angle and dc-link current is analyzed, a corresponding MFAC based control method is proposed, and the commutation error can be corrected by the controller in real time. Both the simulation and experimental results show that the proposed correction method can achieve ideal commutation effect within the entire operating speed range. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Study of Belousov—Zhabotinsky oscillators in water—acetonitrile medium employing EMF and EPR techniques with o-vanillin, p-vanillin and adrenaline as substrates

NASA Astrophysics Data System (ADS)

Lalitha, P. V.; Ramaswamy, R.; Ramakrishnan, Geetha; Rao, P. Sambasiva

1994-12-01

The oscillatory behaviour of three substrates, ortho-vanillin, para-vanillin and adrenaline, in mixed media (water plus 20% acetonitrile) has been investigated using EPR and EMF techniques. All these substrates exhibit two types of oscillation involving Br 2/Br - and Mn(III)/Mn(II) redox couples. From the oscillatory characteristics (total time, number of oscillations and time per oscillation) obtained by employing these techniques, the reactivities of the vanillins have been correlated. The Field—Koros—Noyes mechanism, suggested for catalysed systems in pure aqueous medium, is established to be applicable even in mixed media.

Controversies related to electromagnetic field exposure on peripheral nerves.

PubMed

Say, Ferhat; Altunkaynak, Berrin Zuhal; Coşkun, Sina; Deniz, Ömür Gülsüm; Yıldız, Çağrı; Altun, Gamze; Kaplan, Arife Ahsen; Kaya, Sefa Ersan; Pişkin, Ahmet

2016-09-01

Electromagnetic field (EMF) is a pervasive environmental presence in modern society. In recent years, mobile phone usage has increased rapidly throughout the world. As mobile phones are generally held close to the head while talking, studies have mostly focused on the central and peripheral nervous system. There is a need for further research to ascertain the real effect of EMF exposure on the nervous system. Several studies have clearly demonstrated that EMF emitted by cell phones could affect the systems of the body as well as functions. However, the adverse effects of EMF emitted by mobile phones on the peripheral nerves are still controversial. Therefore, this review summarizes current knowledge on the possible positive or negative effects of electromagnetic field on peripheral nerves. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of electromagnetic fields emitted by GSM phones on working memory: a meta-analysis.

PubMed

Zubko, O; Gould, R L; Gay, H C; Cox, H J; Coulson, M C; Howard, R J

2017-02-01

Current treatments for Alzheimer's Disease (AD) do not affect the course of the illness and brain stimulation techniques are increasingly promoted as potential therapeutic interventions for AD. This study reviews the effects of electromagnetic field (EMF) exposure versus sham exposure on working memory (WM) performance of healthy human participants. Online literature databases and previous systematic reviews were searched for studies of EMF and WM in participants without reported memory problems. Two thousand eight hundred and fifty seven studies were identified, and 10 studies met the inclusion criteria. An assessment of study quality was completed, and separate, random effects meta-analyses were conducted for each of the three WM tasks included: n-back, substitution and digit span forward. No differences were found between participants exposed to active EMF versus sham conditions in any of the three working memory tasks examined. Results indicate that EMF does not affect WM during the n-back, substitution and digit-span tasks. Future studies should focus on the possible effects of chronic exposure to EMF in older adults with AD using a battery of comparable WM and attention tasks, before EMF can be seriously considered as a potential modulator of WM in AD. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

WGE: a CRISPR database for genome engineering.

PubMed

Hodgkins, Alex; Farne, Anna; Perera, Sajith; Grego, Tiago; Parry-Smith, David J; Skarnes, William C; Iyer, Vivek

2015-09-15

The rapid development of CRISPR-Cas9 mediated genome editing techniques has given rise to a number of online and stand-alone tools to find and score CRISPR sites for whole genomes. Here we describe the Wellcome Trust Sanger Institute Genome Editing database (WGE), which uses novel methods to compute, visualize and select optimal CRISPR sites in a genome browser environment. The WGE database currently stores single and paired CRISPR sites and pre-calculated off-target information for CRISPRs located in the mouse and human exomes. Scoring and display of off-target sites is simple, and intuitive, and filters can be applied to identify high-quality CRISPR sites rapidly. WGE also provides a tool for the design and display of gene targeting vectors in the same genome browser, along with gene models, protein translation and variation tracks. WGE is open, extensible and can be set up to compute and present CRISPR sites for any genome. The WGE database is freely available at www.sanger.ac.uk/htgt/wge : vvi@sanger.ac.uk or skarnes@sanger.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Biological agents database in the armed forces.

PubMed

Niemcewicz, Marcin; Kocik, Janusz; Bielecka, Anna; Wierciński, Michał

2014-10-01

Rapid detection and identification of the biological agent during both, natural or deliberate outbreak is crucial for implementation of appropriate control measures and procedures in order to mitigate the spread of disease. Determination of pathogen etiology may not only support epidemiological investigation and safety of human beings, but also enhance forensic efforts in pathogen tracing, collection of evidences and correct inference. The article presents objectives of the Biological Agents Database, which was developed for the purpose of the Ministry of National Defense of the Republic of Poland under the European Defence Agency frame. The Biological Agents Database is an electronic catalogue of genetic markers of highly dangerous pathogens and biological agents of weapon of mass destruction concern, which provides full identification of biological threats emerging in Poland and in locations of activity of Polish troops. The Biological Agents Database is a supportive tool used for tracing biological agents' origin as well as rapid identification of agent causing the disease of unknown etiology. It also provides support in diagnosis, analysis, response and exchange of information between institutions that use information contained in it. Therefore, it can be used not only for military purposes, but also in a civilian environment.

MIPS: a database for genomes and protein sequences.

PubMed Central

Mewes, H W; Heumann, K; Kaps, A; Mayer, K; Pfeiffer, F; Stocker, S; Frishman, D

1999-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried near Munich, Germany, develops and maintains genome oriented databases. It is commonplace that the amount of sequence data available increases rapidly, but not the capacity of qualified manual annotation at the sequence databases. Therefore, our strategy aims to cope with the data stream by the comprehensive application of analysis tools to sequences of complete genomes, the systematic classification of protein sequences and the active support of sequence analysis and functional genomics projects. This report describes the systematic and up-to-date analysis of genomes (PEDANT), a comprehensive database of the yeast genome (MYGD), a database reflecting the progress in sequencing the Arabidopsis thaliana genome (MATD), the database of assembled, annotated human EST clusters (MEST), and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). MIPS provides access through its WWW server (http://www.mips.biochem.mpg.de) to a spectrum of generic databases, including the above mentioned as well as a database of protein families (PROTFAM), the MITOP database, and the all-against-all FASTA database. PMID:9847138

Investigating short-term exposure to electromagnetic fields on reproductive capacity of invertebrates in the field situation.

PubMed

Vijver, Martina G; Bolte, John F B; Evans, Tracy R; Tamis, Wil L M; Peijnenburg, Willie J G M; Musters, C J M; de Snoo, Geert R

2014-01-01

Organisms are exposed to electromagnetic fields from the introduction of wireless networks that send information all over the world. In this study we examined the impact of exposure to the fields from mobile phone base stations (GSM 900 MHz) on the reproductive capacity of small, virgin, invertebrates. A field experiment was performed exposing four different invertebrate species at different distances from a radiofrequency electromagnetic fields (RF EMF) transmitter for a 48-h period. The control groups were isolated from EMF exposure by use of Faraday cages. The response variables as measured in the laboratory were fecundity and number of offspring. Results showed that distance was not an adequate proxy to explain dose-response regressions. No significant impact of the exposure matrices, measures of central tendency and temporal variability of EMF, on reproductive endpoints was found. Finding no impact on reproductive capacity does not fully exclude the existence of EMF impact, since mechanistically models hypothesizing non-thermal-induced biological effects from RF exposure are still to be developed. The exposure to RF EMF is ubiquitous and is still increasing rapidly over large areas. We plea for more attention toward the possible impacts of EMF on biodiversity.

The Danish Microbiology Database (MiBa) 2010 to 2013.

PubMed

Voldstedlund, M; Haarh, M; Mølbak, K

2014-01-09

The Danish Microbiology Database (MiBa) is a national database that receives copies of reports from all Danish departments of clinical microbiology. The database was launched in order to provide healthcare personnel with nationwide access to microbiology reports and to enable real-time surveillance of communicable diseases and microorganisms. The establishment and management of MiBa has been a collaborative process among stakeholders, and the present paper summarises lessons learned from this nationwide endeavour which may be relevant to similar projects in the rapidly changing landscape of health informatics.

The NCBI BioCollections Database

PubMed Central

Sharma, Shobha; Ciufo, Stacy; Starchenko, Elena; Darji, Dakshesh; Chlumsky, Larry; Karsch-Mizrachi, Ilene

2018-01-01

Abstract The rapidly growing set of GenBank submissions includes sequences that are derived from vouchered specimens. These are associated with culture collections, museums, herbaria and other natural history collections, both living and preserved. Correct identification of the specimens studied, along with a method to associate the sample with its institution, is critical to the outcome of related studies and analyses. The National Center for Biotechnology Information BioCollections Database was established to allow the association of specimen vouchers and related sequence records to their home institutions. This process also allows cross-linking from the home institution for quick identification of all records originating from each collection. Database URL: https://www.ncbi.nlm.nih.gov/biocollections PMID:29688360

The Future of Database Information Services.

ERIC Educational Resources Information Center

Auld, Dennis

Changes affecting the delivery of information over the next 10 years are going to be more numerous, farther reaching, and more rapid than those experienced in the last 10 years. Technological, legislative, economic, and sociological factors are all playing vital roles in shaping the environment within which database information services operate.…

Simple re-instantiation of small databases using cloud computing.

PubMed

Tan, Tin Wee; Xie, Chao; De Silva, Mark; Lim, Kuan Siong; Patro, C Pawan K; Lim, Shen Jean; Govindarajan, Kunde Ramamoorthy; Tong, Joo Chuan; Choo, Khar Heng; Ranganathan, Shoba; Khan, Asif M

2013-01-01

Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear.

Simple re-instantiation of small databases using cloud computing

PubMed Central

2013-01-01

Background Small bioinformatics databases, unlike institutionally funded large databases, are vulnerable to discontinuation and many reported in publications are no longer accessible. This leads to irreproducible scientific work and redundant effort, impeding the pace of scientific progress. Results We describe a Web-accessible system, available online at http://biodb100.apbionet.org, for archival and future on demand re-instantiation of small databases within minutes. Depositors can rebuild their databases by downloading a Linux live operating system (http://www.bioslax.com), preinstalled with bioinformatics and UNIX tools. The database and its dependencies can be compressed into an ".lzm" file for deposition. End-users can search for archived databases and activate them on dynamically re-instantiated BioSlax instances, run as virtual machines over the two popular full virtualization standard cloud-computing platforms, Xen Hypervisor or vSphere. The system is adaptable to increasing demand for disk storage or computational load and allows database developers to use the re-instantiated databases for integration and development of new databases. Conclusions Herein, we demonstrate that a relatively inexpensive solution can be implemented for archival of bioinformatics databases and their rapid re-instantiation should the live databases disappear. PMID:24564380

Are Naturopathic Universities ``The Natural Places'' to investigate Attention-Deficit Type Disorders, with Possible Linkages to Cultural Patterns and the EMF?

NASA Astrophysics Data System (ADS)

de Souza, Beatriz; Balam Matagamon, Chan; Pawa Matagamon, Sagamo

2006-03-01

We desire serious investigations of behavioral impacts of certain localized or larger-scale environmental elements, such as the electromagnetic spectrum as detected by us at some sites. One author was impacted by the earth's EMF to such an extent in FL that it falsely convinced him that he was having a heart attack more severe than his nearly fatal one. Instead, it preceded an earthquake he then predicted six hours in advance. Chitto Tustenugee's `everglades' site, in Miramar FL, evokes tinnitus. Elsewhere, unease, terror, inappropriate behavior or sporadic loss of attention occurs where it can impact runway or roadway safety. Physics and Naturopathic Universities could be appropriate partners for understanding, preventing or curing these.

Choice of osteoblast model critical for studying the effects of electromagnetic stimulation on osteogenesis in vitro.

PubMed

Bique, Anna-Maria; Kaivosoja, Emilia; Mikkonen, Marko; Paulasto-Kröckel, Mervi

2016-01-01

The clinical benefits of electromagnetic field (EMF) therapy in enhancing osteogenesis have been acknowledged for decades, but agreement regarding the underlying mechanisms continues to be sought. Studies have shown EMFs to promote osteoblast-like cell proliferation, or contrarily, to induce differentiation and enhance mineralization. Typically these disparities have been attributed to methodological differences. The present paper argues the possibility that the chosen osteoblast model impacts stimulation outcome. Phenotypically immature cells, particularly at low seeding densities, appear to be prone to EMF-amplified proliferation. Conversely, mature cells at higher densities seem to be predisposed to earlier onset differentiation and mineralization. This suggests that EMFs augment ongoing processes in cell populations. To test this hypothesis, mature SaOS-2 cells and immature MC3T3-E1 cells at various densities, with or without osteo-induction, were exposed to sinusoidal 50 Hz EMF. The exposure stimulated the proliferation of MC3T3-E1 and inhibited the proliferation of SaOS-2 cells. Baseline alkaline phosphatase (ALP) expression of SaOS-2 cells was high and rapidly further increased with EMF exposure, whereas ALP effects in MC3T3-E1 cells were not seen until the second week. Thus both cell types responded differently to EMF stimulation, corroborating the hypothesis that the phenotypic maturity and culture stage of cells influence stimulation outcome.

Determining if an axially rotated solenoid will induce a radial EMF

NASA Astrophysics Data System (ADS)

MacDermott, Dustin R.

The nature of the electromagnetic field of an axially rotated solenoid or magnet is investigated. The investigations reviewed suggest the possibility of a radially emitted electric field by either: axially rotated magnetic field lines, or a relativistic change in charge of the electron. For a very long solenoid a relativistic change in charge leaves no electric field inside while leaving an electric field outside. The concept of axially rotating magnetic field lines gives an opposite prediction. They both seem to be in contradiction to the standard model of induction, which gives no change in the electric field for a rotated solenoid or magnet. An experiment by Joseph B. Tate [48], [49] conducted in 1968 seemed to have measured a change in charge outside of a rotated solenoid. Another experiment by Barnett [3] in 1912 reported measuring no electric field inside of a rotated solenoid. Further experimentation was decided necessary and the method decided upon to attempt detection of the radial E or EMF induced by an axially rotating B field or change in charge is two concentric capacitor plates, one inside and the other outside an axially rotated solenoid. The solenoid was rotated on a lathe for the test. A concentric capacitor around an axially rotated permanent neodymium magnet was also used as a test. These experiments proved very challenging because of the small magnitude of the predicted effect. Nevertheless, the bulk of the evidence obtained indicates that no induced E arises when a magnetic source is rotated about its magnetic axis, thus supporting the standard field model of electromagnetic induction, and casting doubt on the alternative theories of magnetic field line rotation or relativistic charge enhancement.

CHRONIS: an animal chromosome image database.

PubMed

Toyabe, Shin-Ichi; Akazawa, Kouhei; Fukushi, Daisuke; Fukui, Kiichi; Ushiki, Tatsuo

2005-01-01

We have constructed a database system named CHRONIS (CHROmosome and Nano-Information System) to collect images of animal chromosomes and related nanotechnological information. CHRONIS enables rapid sharing of information on chromosome research among cell biologists and researchers in other fields via the Internet. CHRONIS is also intended to serve as a liaison tool for researchers who work in different centers. The image database contains more than 3,000 color microscopic images, including karyotypic images obtained from more than 1,000 species of animals. Researchers can browse the contents of the database using a usual World Wide Web interface in the following URL: http://chromosome.med.niigata-u.ac.jp/chronis/servlet/chronisservlet. The system enables users to input new images into the database, to locate images of interest by keyword searches, and to display the images with detailed information. CHRONIS has a wide range of applications, such as searching for appropriate probes for fluorescent in situ hybridization, comparing various kinds of microscopic images of a single species, and finding researchers working in the same field of interest.

Construction of In-house Databases in a Corporation

NASA Astrophysics Data System (ADS)

Dezaki, Kyoko; Saeki, Makoto

Rapid progress in advanced informationalization has increased need to enforce documentation activities in industries. Responding to it Tokin Corporation has been engaged in database construction for patent information, technical reports and so on accumulated inside the Company. Two results are obtained; One is TOPICS, inhouse patent information management system, the other is TOMATIS, management and technical information system by use of personal computers and all-purposed relational database software. These systems aim at compiling databases of patent and technological management information generated internally and externally by low labor efforts as well as low cost, and providing for comprehensive information company-wide. This paper introduces the outline of these systems and how they are actually used.

Construction of image database for newspapaer articles using CTS

NASA Astrophysics Data System (ADS)

Kamio, Tatsuo

Nihon Keizai Shimbun, Inc. developed a system of making articles' image database automatically by use of CTS (Computer Typesetting System). Besides the articles and the headlines inputted in CTS, it reproduces the image of elements of such as photography and graphs by article in accordance with information of position on the paper. So to speak, computer itself clips the articles out of the newspaper. Image database is accumulated in magnetic file and optical file and is output to the facsimile of users. With diffusion of CTS, newspaper companies which start to have structure of articles database are increased rapidly, the said system is the first attempt to make database automatically. This paper describes the device of CTS which supports this system and outline.

Object-oriented parsing of biological databases with Python.

PubMed

Ramu, C; Gemünd, C; Gibson, T J

2000-07-01

While database activities in the biological area are increasing rapidly, rather little is done in the area of parsing them in a simple and object-oriented way. We present here an elegant, simple yet powerful way of parsing biological flat-file databases. We have taken EMBL, SWISSPROT and GENBANK as examples. EMBL and SWISS-PROT do not differ much in the format structure. GENBANK has a very different format structure than EMBL and SWISS-PROT. Extracting the desired fields in an entry (for example a sub-sequence with an associated feature) for later analysis is a constant need in the biological sequence-analysis community: this is illustrated with tools to make new splice-site databases. The interface to the parser is abstract in the sense that the access to all the databases is independent from their different formats, since parsing instructions are hidden.

Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library.

PubMed

Lee, Hyeyoung; Cuthbertson, Daniel J; Otter, Don E; Barile, Daniela

2016-08-17

A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching.

Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library

PubMed Central

Lee, Hyeyoung; Cuthbertson, Daniel J.; Otter, Don E.; Barile, Daniela

2018-01-01

A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching. PMID:27428379

A Chronostratigraphic Relational Database Ontology

NASA Astrophysics Data System (ADS)

Platon, E.; Gary, A.; Sikora, P.

2005-12-01

A chronostratigraphic research database was donated by British Petroleum to the Stratigraphy Group at the Energy and Geoscience Institute (EGI), University of Utah. These data consists of over 2,000 measured sections representing over three decades of research into the application of the graphic correlation method. The data are global and includes both microfossil (foraminifera, calcareous nannoplankton, spores, pollen, dinoflagellate cysts, etc) and macrofossil data. The objective of the donation was to make the research data available to the public in order to encourage additional chronostratigraphy studies, specifically regarding graphic correlation. As part of the National Science Foundation's Cyberinfrastructure for the Geosciences (GEON) initiative these data have been made available to the public at http://css.egi.utah.edu. To encourage further research using the graphic correlation method, EGI has developed a software package, StrataPlot that will soon be publicly available from the GEON website as a standalone software download. The EGI chronostratigraphy research database, although relatively large, has many data holes relative to some paleontological disciplines and geographical areas, so the challenge becomes how do we expand the data available for chronostratigrahic studies using graphic correlation. There are several public or soon-to-be public databases available to chronostratigraphic research, but they have their own data structures and modes of presentation. The heterogeneous nature of these database schemas hinders their integration and makes it difficult for the user to retrieve and consolidate potentially valuable chronostratigraphic data. The integration of these data sources would facilitate rapid and comprehensive data searches, thus helping advance studies in chronostratigraphy. The GEON project will host a number of databases within the geology domain, some of which contain biostratigraphic data. Ontologies are being developed to provide

Bio-effects of non-ionizing electromagnetic fields in context of cancer therapy.

PubMed

Saliev, Timur; Tachibana, Katsuro; Bulanin, Denis; Mikhalovsky, Sergey; Whitby, Ray D L

2014-01-01

Bio-effects mediated by non-ionizing electromagnetic fields (EMF) have become a hot topic of research in the last decades. This interest has been triggered by a growing public concern about the rapid expansion of telecommunication devices and possible consequences of their use on human health. Despite a feasibility study of potential negative impacts, the therapeutic advantages of EMF could be effectively harnessed for the treatment of cancer and other diseases. This review aims to examine recent findings relating to the mechanisms of action underlying the bio-effects induced by non-ionizing EMF. The potential of non-thermal and thermal effects is discussed in the context of possible applications for the induction of apoptosis, formation of reactive oxygen species, and increase of membrane permeability in malignant cells. A special emphasis has been put on the combination of EMF with magnetic nano-particles and ultrasound for cancer treatment. The review encompasses both human and animal studies.

Stability of Tungsten-Rhenium Thermocouples in the Range from 0 °C to 1500 °C

NASA Astrophysics Data System (ADS)

Ogura, H.; Izuchi, M.; Tamba, J.

2011-12-01

The effect of exposure up to 1500 °C on emf values of type C (95 % tungsten 5 % rhenium vs. 74 % tungsten 26 % rhenium) thermocouples were evaluated. Three thermocouples consisting of thermocouple wires of 0.5 mm diameter, twin-bore beryllia tubes, and tantalum sheaths were prepared. After three type C thermocouples were calibrated in the range from 0 °C to 1550 °C, which confirmed insignificant difference among them, the drifts of two among them were measured at the palladium-carbon (Pd-C) eutectic point (1492 °C). They indicated a similar tendency, where the emf of thermocouples increased rapidly within the first 30 h, and after that, decreased gradually. To investigate the mechanism of the drift, the inhomogeneities of thermocouples were examined at 160 °C using a water heat-pipe furnace during the drift measurements at the Pd-C eutectic point. It was found that the increase of emf within the first 30 h exposure at around 1500 °C was caused by the emf change due to inhomogeneity above 700 °C, and after that, the decrease of emf was caused by that around 1400 °C.

Network Configuration of Oracle and Database Programming Using SQL

NASA Technical Reports Server (NTRS)

Davis, Melton; Abdurrashid, Jibril; Diaz, Philip; Harris, W. C.

2000-01-01

A database can be defined as a collection of information organized in such a way that it can be retrieved and used. A database management system (DBMS) can further be defined as the tool that enables us to manage and interact with the database. The Oracle 8 Server is a state-of-the-art information management environment. It is a repository for very large amounts of data, and gives users rapid access to that data. The Oracle 8 Server allows for sharing of data between applications; the information is stored in one place and used by many systems. My research will focus primarily on SQL (Structured Query Language) programming. SQL is the way you define and manipulate data in Oracle's relational database. SQL is the industry standard adopted by all database vendors. When programming with SQL, you work on sets of data (i.e., information is not processed one record at a time).

Simrank: Rapid and sensitive general-purpose k-mer search tool

PubMed Central

2011-01-01

Background Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project http://nihroadmap.nih.gov/hmp. Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Results Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Conclusions Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity. PMID:21524302

Concentrations of indoor pollutants database: User's manual

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

Not Available

1992-05-01

This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author's last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user's needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

Toward unification of taxonomy databases in a distributed computer environment

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

Kitakami, Hajime; Tateno, Yoshio; Gojobori, Takashi

1994-12-31

All the taxonomy databases constructed with the DNA databases of the international DNA data banks are powerful electronic dictionaries which aid in biological research by computer. The taxonomy databases are, however not consistently unified with a relational format. If we can achieve consistent unification of the taxonomy databases, it will be useful in comparing many research results, and investigating future research directions from existent research results. In particular, it will be useful in comparing relationships between phylogenetic trees inferred from molecular data and those constructed from morphological data. The goal of the present study is to unify the existent taxonomymore » databases and eliminate inconsistencies (errors) that are present in them. Inconsistencies occur particularly in the restructuring of the existent taxonomy databases, since classification rules for constructing the taxonomy have rapidly changed with biological advancements. A repair system is needed to remove inconsistencies in each data bank and mismatches among data banks. This paper describes a new methodology for removing both inconsistencies and mismatches from the databases on a distributed computer environment. The methodology is implemented in a relational database management system, SYBASE.« less

Rapid identification of anonymous subjects in large criminal databases: problems and solutions in IAFIS III/FBI subject searches

NASA Astrophysics Data System (ADS)

Kutzleb, C. D.

1997-02-01

The high incidence of recidivism (repeat offenders) in the criminal population makes the use of the IAFIS III/FBI criminal database an important tool in law enforcement. The problems and solutions employed by IAFIS III/FBI criminal subject searches are discussed for the following topics: (1) subject search selectivity and reliability; (2) the difficulty and limitations of identifying subjects whose anonymity may be a prime objective; (3) database size, search workload, and search response time; (4) techniques and advantages of normalizing the variability in an individual's name and identifying features into identifiable and discrete categories; and (5) the use of database demographics to estimate the likelihood of a match between a search subject and database subjects.

Evaluating the Cassandra NoSQL Database Approach for Genomic Data Persistency.

PubMed

Aniceto, Rodrigo; Xavier, Rene; Guimarães, Valeria; Hondo, Fernanda; Holanda, Maristela; Walter, Maria Emilia; Lifschitz, Sérgio

2015-01-01

Rapid advances in high-throughput sequencing techniques have created interesting computational challenges in bioinformatics. One of them refers to management of massive amounts of data generated by automatic sequencers. We need to deal with the persistency of genomic data, particularly storing and analyzing these large-scale processed data. To find an alternative to the frequently considered relational database model becomes a compelling task. Other data models may be more effective when dealing with a very large amount of nonconventional data, especially for writing and retrieving operations. In this paper, we discuss the Cassandra NoSQL database approach for storing genomic data. We perform an analysis of persistency and I/O operations with real data, using the Cassandra database system. We also compare the results obtained with a classical relational database system and another NoSQL database approach, MongoDB.

Evaluating the Cassandra NoSQL Database Approach for Genomic Data Persistency

PubMed Central

Aniceto, Rodrigo; Xavier, Rene; Guimarães, Valeria; Hondo, Fernanda; Holanda, Maristela; Walter, Maria Emilia; Lifschitz, Sérgio

2015-01-01

Rapid advances in high-throughput sequencing techniques have created interesting computational challenges in bioinformatics. One of them refers to management of massive amounts of data generated by automatic sequencers. We need to deal with the persistency of genomic data, particularly storing and analyzing these large-scale processed data. To find an alternative to the frequently considered relational database model becomes a compelling task. Other data models may be more effective when dealing with a very large amount of nonconventional data, especially for writing and retrieving operations. In this paper, we discuss the Cassandra NoSQL database approach for storing genomic data. We perform an analysis of persistency and I/O operations with real data, using the Cassandra database system. We also compare the results obtained with a classical relational database system and another NoSQL database approach, MongoDB. PMID:26558254

The Coral Trait Database, a curated database of trait information for coral species from the global oceans

NASA Astrophysics Data System (ADS)

Madin, Joshua S.; Anderson, Kristen D.; Andreasen, Magnus Heide; Bridge, Tom C. L.; Cairns, Stephen D.; Connolly, Sean R.; Darling, Emily S.; Diaz, Marcela; Falster, Daniel S.; Franklin, Erik C.; Gates, Ruth D.; Hoogenboom, Mia O.; Huang, Danwei; Keith, Sally A.; Kosnik, Matthew A.; Kuo, Chao-Yang; Lough, Janice M.; Lovelock, Catherine E.; Luiz, Osmar; Martinelli, Julieta; Mizerek, Toni; Pandolfi, John M.; Pochon, Xavier; Pratchett, Morgan S.; Putnam, Hollie M.; Roberts, T. Edward; Stat, Michael; Wallace, Carden C.; Widman, Elizabeth; Baird, Andrew H.

2016-03-01

Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism’s function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.

The Coral Trait Database, a curated database of trait information for coral species from the global oceans

PubMed Central

Madin, Joshua S.; Anderson, Kristen D.; Andreasen, Magnus Heide; Bridge, Tom C.L.; Cairns, Stephen D.; Connolly, Sean R.; Darling, Emily S.; Diaz, Marcela; Falster, Daniel S.; Franklin, Erik C.; Gates, Ruth D.; Hoogenboom, Mia O.; Huang, Danwei; Keith, Sally A.; Kosnik, Matthew A.; Kuo, Chao-Yang; Lough, Janice M.; Lovelock, Catherine E.; Luiz, Osmar; Martinelli, Julieta; Mizerek, Toni; Pandolfi, John M.; Pochon, Xavier; Pratchett, Morgan S.; Putnam, Hollie M.; Roberts, T. Edward; Stat, Michael; Wallace, Carden C.; Widman, Elizabeth; Baird, Andrew H.

2016-01-01

Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism’s function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research. PMID:27023900

The Coral Trait Database, a curated database of trait information for coral species from the global oceans.

PubMed

Madin, Joshua S; Anderson, Kristen D; Andreasen, Magnus Heide; Bridge, Tom C L; Cairns, Stephen D; Connolly, Sean R; Darling, Emily S; Diaz, Marcela; Falster, Daniel S; Franklin, Erik C; Gates, Ruth D; Harmer, Aaron; Hoogenboom, Mia O; Huang, Danwei; Keith, Sally A; Kosnik, Matthew A; Kuo, Chao-Yang; Lough, Janice M; Lovelock, Catherine E; Luiz, Osmar; Martinelli, Julieta; Mizerek, Toni; Pandolfi, John M; Pochon, Xavier; Pratchett, Morgan S; Putnam, Hollie M; Roberts, T Edward; Stat, Michael; Wallace, Carden C; Widman, Elizabeth; Baird, Andrew H

2016-03-29

Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism's function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.

The EU Physical Agents (EMF) Directive and its impact on MRI imaging in animal experiments: a submission by FRAME to the HSE.

PubMed

Hudson, Michelle

2006-06-01

The EU Physical Agents (EMF) Directive, Directive 2004/40/EC, which threatens to greatly restrict the use of magnetic resonance imaging (MRI) in both clinical and research situations, will come into force on 30 April 2008. This could severely affect experimental animal welfare and scientific progress, as well as patient care. FRAME made a submission to a Health and Safety Executive round-table discussion about the Directive, held in January 2006, detailing concerns about the implications that the legislation would have on implementing the Three Rs in animal-based research and testing, and the subsequent consequences for animal welfare and the quality of scientific output. The submission is reproduced here, with additional comments on the outcome of the meeting and recommendations for further research into the consequences of the Directive.

The AMMA database

NASA Astrophysics Data System (ADS)

Boichard, Jean-Luc; Brissebrat, Guillaume; Cloche, Sophie; Eymard, Laurence; Fleury, Laurence; Mastrorillo, Laurence; Moulaye, Oumarou; Ramage, Karim

2010-05-01

The AMMA project includes aircraft, ground-based and ocean measurements, an intensive use of satellite data and diverse modelling studies. Therefore, the AMMA database aims at storing a great amount and a large variety of data, and at providing the data as rapidly and safely as possible to the AMMA research community. In order to stimulate the exchange of information and collaboration between researchers from different disciplines or using different tools, the database provides a detailed description of the products and uses standardized formats. The AMMA database contains: - AMMA field campaigns datasets; - historical data in West Africa from 1850 (operational networks and previous scientific programs); - satellite products from past and future satellites, (re-)mapped on a regular latitude/longitude grid and stored in NetCDF format (CF Convention); - model outputs from atmosphere or ocean operational (re-)analysis and forecasts, and from research simulations. The outputs are processed as the satellite products are. Before accessing the data, any user has to sign the AMMA data and publication policy. This chart only covers the use of data in the framework of scientific objectives and categorically excludes the redistribution of data to third parties and the usage for commercial applications. Some collaboration between data producers and users, and the mention of the AMMA project in any publication is also required. The AMMA database and the associated on-line tools have been fully developed and are managed by two teams in France (IPSL Database Centre, Paris and OMP, Toulouse). Users can access data of both data centres using an unique web portal. This website is composed of different modules : - Registration: forms to register, read and sign the data use chart when an user visits for the first time - Data access interface: friendly tool allowing to build a data extraction request by selecting various criteria like location, time, parameters... The request can

Academic impact of a public electronic health database: bibliometric analysis of studies using the general practice research database.

PubMed

Chen, Yu-Chun; Wu, Jau-Ching; Haschler, Ingo; Majeed, Azeem; Chen, Tzeng-Ji; Wetter, Thomas

2011-01-01

Studies that use electronic health databases as research material are getting popular but the influence of a single electronic health database had not been well investigated yet. The United Kingdom's General Practice Research Database (GPRD) is one of the few electronic health databases publicly available to academic researchers. This study analyzed studies that used GPRD to demonstrate the scientific production and academic impact by a single public health database. A total of 749 studies published between 1995 and 2009 with 'General Practice Research Database' as their topics, defined as GPRD studies, were extracted from Web of Science. By the end of 2009, the GPRD had attracted 1251 authors from 22 countries and been used extensively in 749 studies published in 193 journals across 58 study fields. Each GPRD study was cited 2.7 times by successive studies. Moreover, the total number of GPRD studies increased rapidly, and it is expected to reach 1500 by 2015, twice the number accumulated till the end of 2009. Since 17 of the most prolific authors (1.4% of all authors) contributed nearly half (47.9%) of GPRD studies, success in conducting GPRD studies may accumulate. The GPRD was used mainly in, but not limited to, the three study fields of "Pharmacology and Pharmacy", "General and Internal Medicine", and "Public, Environmental and Occupational Health". The UK and United States were the two most active regions of GPRD studies. One-third of GRPD studies were internationally co-authored. A public electronic health database such as the GPRD will promote scientific production in many ways. Data owners of electronic health databases at a national level should consider how to reduce access barriers and to make data more available for research.

Rapid Model Fabrication and Testing for Aerospace Vehicles

NASA Technical Reports Server (NTRS)

Buck, Gregory M.

2000-01-01

Advanced methods for rapid fabrication and instrumentation of hypersonic wind tunnel models are being developed and evaluated at NASA Langley Research Center. Rapid aeroheating model fabrication and measurement techniques using investment casting of ceramic test models and thermographic phosphors are reviewed. More accurate model casting techniques for fabrication of benchmark metal and ceramic test models are being developed using a combination of rapid prototype patterns and investment casting. White light optical scanning is used for coordinate measurements to evaluate the fabrication process and verify model accuracy to +/- 0.002 inches. Higher-temperature (<210C) luminescent coatings are also being developed for simultaneous pressure and temperature mapping, providing global pressure as well as global aeroheating measurements. Together these techniques will provide a more rapid and complete experimental aerodynamic and aerothermodynamic database for future aerospace vehicles.

The Gene Expression Omnibus Database.

PubMed

Clough, Emily; Barrett, Tanya

2016-01-01

The Gene Expression Omnibus (GEO) database is an international public repository that archives and freely distributes high-throughput gene expression and other functional genomics data sets. Created in 2000 as a worldwide resource for gene expression studies, GEO has evolved with rapidly changing technologies and now accepts high-throughput data for many other data applications, including those that examine genome methylation, chromatin structure, and genome-protein interactions. GEO supports community-derived reporting standards that specify provision of several critical study elements including raw data, processed data, and descriptive metadata. The database not only provides access to data for tens of thousands of studies, but also offers various Web-based tools and strategies that enable users to locate data relevant to their specific interests, as well as to visualize and analyze the data. This chapter includes detailed descriptions of methods to query and download GEO data and use the analysis and visualization tools. The GEO homepage is at http://www.ncbi.nlm.nih.gov/geo/.

The Gene Expression Omnibus database

PubMed Central

Clough, Emily; Barrett, Tanya

2016-01-01

The Gene Expression Omnibus (GEO) database is an international public repository that archives and freely distributes high-throughput gene expression and other functional genomics data sets. Created in 2000 as a worldwide resource for gene expression studies, GEO has evolved with rapidly changing technologies and now accepts high-throughput data for many other data applications, including those that examine genome methylation, chromatin structure, and genome–protein interactions. GEO supports community-derived reporting standards that specify provision of several critical study elements including raw data, processed data, and descriptive metadata. The database not only provides access to data for tens of thousands of studies, but also offers various Web-based tools and strategies that enable users to locate data relevant to their specific interests, as well as to visualize and analyze the data. This chapter includes detailed descriptions of methods to query and download GEO data and use the analysis and visualization tools. The GEO homepage is at http://www.ncbi.nlm.nih.gov/geo/. PMID:27008011

Concentrations of indoor pollutants database: User`s manual

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

Not Available

1992-05-01

This manual describes the computer-based database on indoor air pollutants. This comprehensive database alloys helps utility personnel perform rapid searches on literature related to indoor air pollutants. Besides general information, it provides guidance for finding specific information on concentrations of indoor air pollutants. The manual includes information on installing and using the database as well as a tutorial to assist the user in becoming familiar with the procedures involved in doing bibliographic and summary section searches. The manual demonstrates how to search for information by going through a series of questions that provide search parameters such as pollutants type, year,more » building type, keywords (from a specific list), country, geographic region, author`s last name, and title. As more and more parameters are specified, the list of references found in the data search becomes smaller and more specific to the user`s needs. Appendixes list types of information that can be input into the database when making a request. The CIP database allows individual utilities to obtain information on indoor air quality based on building types and other factors in their own service territory. This information is useful for utilities with concerns about indoor air quality and the control of indoor air pollutants. The CIP database itself is distributed by the Electric Power Software Center and runs on IBM PC-compatible computers.« less

Floridas Miami Tequesta Indian Site, Its Calusa Indian Locations, the Matacumbe Keys, and Orlandos Wikiwa Springs Generate Environmentally Significant EMFs.

NASA Astrophysics Data System (ADS)

Mac Dougall, Jean S.; Mc Leod, Roger D.; Mc Leod, David M.

2003-10-01

Florida purchased the Tequesta ([Langue] doc Christ Spirit-signal) Indian site along the Miami River site that vigorously pulsates with even minor rainstorms entering or leaving the area. Although there is a laughable chimera of a fountain of youth associated with Ponce de Leons discovery of the Florida peninsula in about AD 1513, the Calusa (Royal Christ Jesus Spirit-signal) Indian Nation has an associated significance with EMF signals they possibly monitored throughout their area of activity. Our efforts have also led to the investigation of cultural and other influences implied by the Matacumbe Keys that indicate a shared commonality of awareness with Native Americans of the northeast such as Metacomet, or regions like Maines Grand Lake Matagamon and its associated electromagnetic Spirit Signal. Wikiwa Springs near Orlando shares much with Massachusetts (adherent of serpent Jesus Christ Spirit-signal) Natick, and New Hampshires Naticook Island. These are the locales of environmentally sensitive instrumentation.

AgdbNet – antigen sequence database software for bacterial typing

PubMed Central

Jolley, Keith A; Maiden, Martin CJ

2006-01-01

Background Bacterial typing schemes based on the sequences of genes encoding surface antigens require databases that provide a uniform, curated, and widely accepted nomenclature of the variants identified. Due to the differences in typing schemes, imposed by the diversity of genes targeted, creating these databases has typically required the writing of one-off code to link the database to a web interface. Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. Results Databases are described by XML files that are parsed by a Perl CGI script. Each database can have any number of loci, which may be defined by nucleotide and/or peptide sequences. The software is currently in use on at least five public databases for the typing of Neisseria meningitidis, Campylobacter jejuni and Streptococcus equi and can be set up to query internal isolate tables or suitably-configured external isolate databases, such as those used for multilocus sequence typing. The style of the resulting website can be fully configured by modifying stylesheets and through the use of customised header and footer files that surround the output of the script. Conclusion The software provides a rapid means of setting up customised Internet antigen sequence databases. The flexible configuration options enable typing schemes with differing requirements to be accommodated. PMID:16790057

The Revised Electromagnetic Fields Directive and Worker Exposure in Environments With High Magnetic Flux Densities

PubMed Central

Stam, Rianne

2014-01-01

Some of the strongest electromagnetic fields (EMF) are found in the workplace. A European Directive sets limits to workers’ exposure to EMF. This review summarizes its origin and contents and compares magnetic field exposure levels in high-risk workplaces with the limits set in the revised Directive. Pubmed, Scopus, grey literature databases, and websites of organizations involved in occupational exposure measurements were searched. The focus was on EMF with frequencies up to 10 MHz, which can cause stimulation of the nervous system. Selected studies had to provide individual maximum exposure levels at the workplace, either in terms of the external magnetic field strength or flux density or as induced electric field strength or current density. Indicative action levels and the corresponding exposure limit values for magnetic fields in the revised European Directive will be higher than those in the previous version. Nevertheless, magnetic flux densities in excess of the action levels for peripheral nerve stimulation are reported for workers involved in welding, induction heating, transcranial magnetic stimulation, and magnetic resonance imaging (MRI). The corresponding health effects exposure limit values for the electric fields in the worker’s body can be exceeded for welding and MRI, but calculations for induction heating and transcranial magnetic stimulation are lacking. Since the revised European Directive conditionally exempts MRI-related activities from the exposure limits, measures to reduce exposure may be necessary for welding, induction heating, and transcranial nerve stimulation. Since such measures can be complicated, there is a clear need for exposure databases for different workplace scenarios with significant EMF exposure and guidance on good practices. PMID:24557933

The revised electromagnetic fields directive and worker exposure in environments with high magnetic flux densities.

PubMed

Stam, Rianne

2014-06-01

Some of the strongest electromagnetic fields (EMF) are found in the workplace. A European Directive sets limits to workers' exposure to EMF. This review summarizes its origin and contents and compares magnetic field exposure levels in high-risk workplaces with the limits set in the revised Directive. Pubmed, Scopus, grey literature databases, and websites of organizations involved in occupational exposure measurements were searched. The focus was on EMF with frequencies up to 10 MHz, which can cause stimulation of the nervous system. Selected studies had to provide individual maximum exposure levels at the workplace, either in terms of the external magnetic field strength or flux density or as induced electric field strength or current density. Indicative action levels and the corresponding exposure limit values for magnetic fields in the revised European Directive will be higher than those in the previous version. Nevertheless, magnetic flux densities in excess of the action levels for peripheral nerve stimulation are reported for workers involved in welding, induction heating, transcranial magnetic stimulation, and magnetic resonance imaging (MRI). The corresponding health effects exposure limit values for the electric fields in the worker's body can be exceeded for welding and MRI, but calculations for induction heating and transcranial magnetic stimulation are lacking. Since the revised European Directive conditionally exempts MRI-related activities from the exposure limits, measures to reduce exposure may be necessary for welding, induction heating, and transcranial nerve stimulation. Since such measures can be complicated, there is a clear need for exposure databases for different workplace scenarios with significant EMF exposure and guidance on good practices. © The Author 2014. Published by Oxford University Press on behalf of the British Occupational Hygiene Society.

Influence of Inner Transducer Properties on EMF Response and Stability of Solid-Contact Anion Selective Membrane Electrodes Based on Metalloporphyrin Ionophores

PubMed Central

Górski, Łukasz; Matusevich, Alexey; Pietrzak, Mariusz; Wang, Lin; Meyerhoff, Mark E.; Malinowska, Elżbieta

2010-01-01

The performance of solid-contact/coated wire type electrodes with plasticized PVC membranes containing metalloporphyrins as anion selective ionophores is reported. The membranes are deposited on transducers based on graphite pastes and graphite rods. The hydrophobicity of the underlying conductive transducer surface is found to be a key factor that influences the formation of an aqueous layer beneath the polymer film. Elimination of this ill-defined water layer greatly improves the electrochemical properties of the ion-sensors, such as EMF stability and life-time. Only highly lipophilic electrode substrates, namely graphite paste with mineral oil, were shown to prevent the formation of aqueous layer underneath the ion-sensing membrane. The possibility of employing Co(III)-tetraphenylporphyrin both as NO2− selective ionophore and as electron/ion conducting species to ensure ion-to-electron translation was also discussed based on the results of preliminary experiments. PMID:20357903

Private and Efficient Query Processing on Outsourced Genomic Databases.

PubMed

Ghasemi, Reza; Al Aziz, Md Momin; Mohammed, Noman; Dehkordi, Massoud Hadian; Jiang, Xiaoqian

2017-09-01

Applications of genomic studies are spreading rapidly in many domains of science and technology such as healthcare, biomedical research, direct-to-consumer services, and legal and forensic. However, there are a number of obstacles that make it hard to access and process a big genomic database for these applications. First, sequencing genomic sequence is a time consuming and expensive process. Second, it requires large-scale computation and storage systems to process genomic sequences. Third, genomic databases are often owned by different organizations, and thus, not available for public usage. Cloud computing paradigm can be leveraged to facilitate the creation and sharing of big genomic databases for these applications. Genomic data owners can outsource their databases in a centralized cloud server to ease the access of their databases. However, data owners are reluctant to adopt this model, as it requires outsourcing the data to an untrusted cloud service provider that may cause data breaches. In this paper, we propose a privacy-preserving model for outsourcing genomic data to a cloud. The proposed model enables query processing while providing privacy protection of genomic databases. Privacy of the individuals is guaranteed by permuting and adding fake genomic records in the database. These techniques allow cloud to evaluate count and top-k queries securely and efficiently. Experimental results demonstrate that a count and a top-k query over 40 Single Nucleotide Polymorphisms (SNPs) in a database of 20 000 records takes around 100 and 150 s, respectively.

Private and Efficient Query Processing on Outsourced Genomic Databases

PubMed Central

Ghasemi, Reza; Al Aziz, Momin; Mohammed, Noman; Dehkordi, Massoud Hadian; Jiang, Xiaoqian

2017-01-01

Applications of genomic studies are spreading rapidly in many domains of science and technology such as healthcare, biomedical research, direct-to-consumer services, and legal and forensic. However, there are a number of obstacles that make it hard to access and process a big genomic database for these applications. First, sequencing genomic sequence is a time-consuming and expensive process. Second, it requires large-scale computation and storage systems to processes genomic sequences. Third, genomic databases are often owned by different organizations and thus not available for public usage. Cloud computing paradigm can be leveraged to facilitate the creation and sharing of big genomic databases for these applications. Genomic data owners can outsource their databases in a centralized cloud server to ease the access of their databases. However, data owners are reluctant to adopt this model, as it requires outsourcing the data to an untrusted cloud service provider that may cause data breaches. In this paper, we propose a privacy-preserving model for outsourcing genomic data to a cloud. The proposed model enables query processing while providing privacy protection of genomic databases. Privacy of the individuals is guaranteed by permuting and adding fake genomic records in the database. These techniques allow cloud to evaluate count and top-k queries securely and efficiently. Experimental results demonstrate that a count and a top-k query over 40 SNPs in a database of 20,000 records takes around 100 and 150 seconds, respectively. PMID:27834660

Academic Impact of a Public Electronic Health Database: Bibliometric Analysis of Studies Using the General Practice Research Database

PubMed Central

Chen, Yu-Chun; Wu, Jau-Ching; Haschler, Ingo; Majeed, Azeem; Chen, Tzeng-Ji; Wetter, Thomas

2011-01-01

Background Studies that use electronic health databases as research material are getting popular but the influence of a single electronic health database had not been well investigated yet. The United Kingdom's General Practice Research Database (GPRD) is one of the few electronic health databases publicly available to academic researchers. This study analyzed studies that used GPRD to demonstrate the scientific production and academic impact by a single public health database. Methodology and Findings A total of 749 studies published between 1995 and 2009 with ‘General Practice Research Database’ as their topics, defined as GPRD studies, were extracted from Web of Science. By the end of 2009, the GPRD had attracted 1251 authors from 22 countries and been used extensively in 749 studies published in 193 journals across 58 study fields. Each GPRD study was cited 2.7 times by successive studies. Moreover, the total number of GPRD studies increased rapidly, and it is expected to reach 1500 by 2015, twice the number accumulated till the end of 2009. Since 17 of the most prolific authors (1.4% of all authors) contributed nearly half (47.9%) of GPRD studies, success in conducting GPRD studies may accumulate. The GPRD was used mainly in, but not limited to, the three study fields of “Pharmacology and Pharmacy”, “General and Internal Medicine”, and “Public, Environmental and Occupational Health”. The UK and United States were the two most active regions of GPRD studies. One-third of GRPD studies were internationally co-authored. Conclusions A public electronic health database such as the GPRD will promote scientific production in many ways. Data owners of electronic health databases at a national level should consider how to reduce access barriers and to make data more available for research. PMID:21731733

Rapid identification of fatty acid methyl esters using a multidimensional gas chromatography-mass spectrometry database.

PubMed

Härtig, Claus

2008-01-04

A multidimensional approach for the identification of fatty acid methyl esters (FAME) based on GC/MS analysis is described. Mass spectra and retention data of more than 130 FAME from various sources (chain lengths in the range from 4 to 24 carbon atoms) were collected in a database. Hints for the interpretation of FAME mass spectra are given and relevant diagnostic marker ions are deduced indicating specific groups of fatty acids. To verify the identity of single species and to ensure an optimized chromatographic resolution, the database was compiled with retention data libraries acquired on columns of different polarity (HP-5, DB-23, and HP-88). For a combined use of mass spectra and retention data standardized methods of measurement for each of these columns are required. Such master methods were developed and always applied under the conditions of retention time locking (RTL) which allowed an excellent reproducibility and comparability of absolute retention times. Moreover, as a relative retention index system, equivalent chain lengths (ECL) of FAME were determined by linear interpolation. To compare and to predict ECL values by means of structural features, fractional chain lengths (FCL) were calculated and fitted as well. As shown in an example, the use of retention data and mass spectral information together in a database search leads to an improved and reliable identification of FAME (including positional and geometrical isomers) without further derivatizations.

Quality Matters: Systematic Analysis of Endpoints Related to “Cellular Life” in Vitro Data of Radiofrequency Electromagnetic Field Exposure

PubMed Central

Simkó, Myrtill; Remondini, Daniel; Zeni, Olga; Scarfi, Maria Rosaria

2016-01-01

Possible hazardous effects of radiofrequency electromagnetic fields (RF-EMF) at low exposure levels are controversially discussed due to inconsistent study findings. Therefore, the main focus of the present study is to detect if any statistical association exists between RF-EMF and cellular responses, considering cell proliferation and apoptosis endpoints separately and with both combined as a group of “cellular life” to increase the statistical power of the analysis. We searched for publications regarding RF-EMF in vitro studies in the PubMed database for the period 1995–2014 and extracted the data to the relevant parameters, such as cell culture type, frequency, exposure duration, SAR, and five exposure-related quality criteria. These parameters were used for an association study with the experimental outcome in terms of the defined endpoints. We identified 104 published articles, from which 483 different experiments were extracted and analyzed. Cellular responses after exposure to RF-EMF were significantly associated to cell lines rather than to primary cells. No other experimental parameter was significantly associated with cellular responses. A highly significant negative association with exposure condition-quality and cellular responses was detected, showing that the more the quality criteria requirements were satisfied, the smaller the number of detected cellular responses. According to our knowledge, this is the first systematic analysis of specific RF-EMF bio-effects in association to exposure quality, highlighting the need for more stringent quality procedures for the exposure conditions. PMID:27420084

Database on Performance of Neutron Irradiated FeCrAl Alloys

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

Field, Kevin G.; Briggs, Samuel A.; Littrell, Ken

The present report summarizes and discusses the database on radiation tolerance for Generation I, Generation II, and commercial FeCrAl alloys. This database has been built upon mechanical testing and microstructural characterization on selected alloys irradiated within the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL) up to doses of 13.8 dpa at temperatures ranging from 200°C to 550°C. The structure and performance of these irradiated alloys were characterized using advanced microstructural characterization techniques and mechanical testing. The primary objective of developing this database is to enhance the rapid development of a mechanistic understanding on the radiation tolerancemore » of FeCrAl alloys, thereby enabling informed decisions on the optimization of composition and microstructure of FeCrAl alloys for application as an accident tolerant fuel (ATF) cladding. This report is structured to provide a brief summary of critical results related to the database on radiation tolerance of FeCrAl alloys.« less

Adding Impacts and Mitigation Measures to OpenEI's RAPID Toolkit

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

Vogel, Erin

The Open Energy Information platform hosts the Regulatory and Permitting Information Desktop (RAPID) Toolkit to provide renewable energy permitting information on federal and state regulatory processes. One of the RAPID Toolkit's functions is to help streamline the geothermal permitting processes outlined in the National Environmental Policy Act (NEPA). This is particularly important in the geothermal energy sector since each development phase requires separate land analysis to acquire exploration, well field drilling, and power plant construction permits. Using the Environmental Assessment documents included in RAPID's NEPA Database, the RAPID team identified 37 resource categories that a geothermal project may impact. Examplesmore » include impacts to geology and minerals, nearby endangered species, or water quality standards. To provide federal regulators, project developers, consultants, and the public with typical impacts and mitigation measures for geothermal projects, the RAPID team has provided overview webpages of each of these 37 resource categories with a sidebar query to reference related NEPA documents in the NEPA Database. This project is an expansion of a previous project that analyzed the time to complete NEPA environmental review for various geothermal activities. The NEPA review not only focused on geothermal projects within the Bureau of Land Management and U.S. Forest Service managed lands, but also projects funded by the Department of Energy. Timeline barriers found were: extensive public comments and involvement; content overlap in NEPA documents, and discovery of impacted resources such as endangered species or cultural sites.« less

Current situation and future usage of anticancer drug databases.

PubMed

Wang, Hongzhi; Yin, Yuanyuan; Wang, Peiqi; Xiong, Chenyu; Huang, Lingyu; Li, Sijia; Li, Xinyi; Fu, Leilei

2016-07-01

Cancer is a deadly disease with increasing incidence and mortality rates and affects the life quality of millions of people per year. The past 15 years have witnessed the rapid development of targeted therapy for cancer treatment, with numerous anticancer drugs, drug targets and related gene mutations been identified. The demand for better anticancer drugs and the advances in database technologies have propelled the development of databases related to anticancer drugs. These databases provide systematic collections of integrative information either directly on anticancer drugs or on a specific type of anticancer drugs with their own emphases on different aspects, such as drug-target interactions, the relationship between mutations in drug targets and drug resistance/sensitivity, drug-drug interactions, natural products with anticancer activity, anticancer peptides, synthetic lethality pairs and histone deacetylase inhibitors. We focus on a holistic view of the current situation and future usage of databases related to anticancer drugs and further discuss their strengths and weaknesses, in the hope of facilitating the discovery of new anticancer drugs with better clinical outcomes.

ClusterMine360: a database of microbial PKS/NRPS biosynthesis

PubMed Central

Conway, Kyle R.; Boddy, Christopher N.

2013-01-01

ClusterMine360 (http://www.clustermine360.ca/) is a database of microbial polyketide and non-ribosomal peptide gene clusters. It takes advantage of crowd-sourcing by allowing members of the community to make contributions while automation is used to help achieve high data consistency and quality. The database currently has >200 gene clusters from >185 compound families. It also features a unique sequence repository containing >10 000 polyketide synthase/non-ribosomal peptide synthetase domains. The sequences are filterable and downloadable as individual or multiple sequence FASTA files. We are confident that this database will be a useful resource for members of the polyketide synthases/non-ribosomal peptide synthetases research community, enabling them to keep up with the growing number of sequenced gene clusters and rapidly mine these clusters for functional information. PMID:23104377

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

PubMed

Mo, Fan; Hong, Xu; Gao, Feng; Du, Lin; Wang, Jun; Omenn, Gilbert S; Lin, Biaoyang

2008-12-16

Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data.

The effect of low-frequency electromagnetic field on human bone marrow stem/progenitor cell differentiation

PubMed Central

Ross, Christina L.; Siriwardane, Mevan; Almeida-Porada, Graça; Porada, Christopher D.; Brink, Peter; Christ, George J.; Harrison, Benjamin S.

2015-01-01

Human bone marrow stromal cells (hBMSCs, also known as bone marrow-derived mesenchymal stem cells) are a population of progenitor cells that contain a subset of skeletal stem cells (hSSCs), able to recreate cartilage, bone, stroma that supports hematopoiesis and marrow adipocytes. As such, they have become an important resource in developing strategies for regenerative medicine and tissue engineering due to their self-renewal and differentiation capabilities. The differentiation of SSCs/BMSCs is dependent on exposure to biophysical and biochemical stimuli that favor early and rapid activation of the in vivo tissue repair process. Exposure to exogenous stimuli such as an electromagnetic field (EMF) can promote differentiation of SSCs/BMSCs via ion dynamics and small signaling molecules. The plasma membrane is often considered to be the main target for EMF signals and most results point to an effect on the rate of ion or ligand binding due to a receptor site acting as a modulator of signaling cascades. Ion fluxes are closely involved in differentiation control as stem cells move and grow in specific directions to form tissues and organs. EMF affects numerous biological functions such as gene expression, cell fate, and cell differentiation, but will only induce these effects within a certain range of low frequencies as well as low amplitudes. EMF has been reported to be effective in the enhancement of osteogenesis and chondrogenesis of hSSCs/BMSCs with no documented negative effects. Studies show specific EMF frequencies enhance hSSC/BMSC adherence, proliferation, differentiation, and viability, all of which play a key role in the use of hSSCs/BMSCs for tissue engineering. While many EMF studies report significant enhancement of the differentiation process, results differ depending on the experimental and environmental conditions. Here we review how specific EMF parameters (frequency, intensity, and time of exposure) significantly regulate hSSC/BMSC differentiation in

Amplatzer vascular plug for rapid vessel occlusion in interventional neuroradiology

PubMed Central

Banfield, Jillian C

2016-01-01

The purpose of this paper is to report different uses of endovascular Amplatzer vascular plug (AVP) treatment for rapid vessel occlusion in the field of interventional neuroradiology. We retrospectively reviewed our interventional neuroradiology database from November 2010 to July 2015 and found nine patients who were treated with endovascular AVP. AVP was used for rapid vessel occlusion of common carotid artery (1 patient), internal carotid artery (5 patients), vertebral artery (2 patients), and internal jugular vein (1 patient). A median of three AVPs were used with almost immediate occlusion and no thromboembolic complications. Use of AVP is feasible, safe, rapid, and potentially cost-effective method for rapid occlusion of larger size vessels in the head and neck region for different indications. PMID:26515699

JICST Factual Database JICST DNA Database

NASA Astrophysics Data System (ADS)

Shirokizawa, Yoshiko; Abe, Atsushi

Japan Information Center of Science and Technology (JICST) has started the on-line service of DNA database in October 1988. This database is composed of EMBL Nucleotide Sequence Library and Genetic Sequence Data Bank. The authors outline the database system, data items and search commands. Examples of retrieval session are presented.

Evaluation of relational and NoSQL database architectures to manage genomic annotations.

PubMed

Schulz, Wade L; Nelson, Brent G; Felker, Donn K; Durant, Thomas J S; Torres, Richard

2016-12-01

While the adoption of next generation sequencing has rapidly expanded, the informatics infrastructure used to manage the data generated by this technology has not kept pace. Historically, relational databases have provided much of the framework for data storage and retrieval. Newer technologies based on NoSQL architectures may provide significant advantages in storage and query efficiency, thereby reducing the cost of data management. But their relative advantage when applied to biomedical data sets, such as genetic data, has not been characterized. To this end, we compared the storage, indexing, and query efficiency of a common relational database (MySQL), a document-oriented NoSQL database (MongoDB), and a relational database with NoSQL support (PostgreSQL). When used to store genomic annotations from the dbSNP database, we found the NoSQL architectures to outperform traditional, relational models for speed of data storage, indexing, and query retrieval in nearly every operation. These findings strongly support the use of novel database technologies to improve the efficiency of data management within the biological sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

Geothermal NEPA Database on OpenEI (Poster)

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

Young, K. R.; Levine, A.

2014-09-01

The National Renewable Energy Laboratory (NREL) developed the Geothermal National Environmental Policy Act (NEPA) Database as a platform for government agencies and industry to access and maintain information related to geothermal NEPA documents. The data were collected to inform analyses of NEPA timelines, and the collected data were made publically available via this tool in case others might find the data useful. NREL staff and contractors collected documents from agency websites, during visits to the two busiest Bureau of Land Management (BLM) field offices for geothermal development, and through email and phone call requests from other BLM field offices. Theymore » then entered the information into the database, hosted by Open Energy Information (http://en.openei.org/wiki/RAPID/NEPA). The long-term success of the project will depend on the willingness of federal agencies, industry, and others to populate the database with NEPA and related documents, and to use the data for their own analyses. As the information and capabilities of the database expand, developers and agencies can save time on new NEPA reports by accessing a single location to research related activities, their potential impacts, and previously proposed and imposed mitigation measures. NREL used a wiki platform to allow industry and agencies to maintain the content in the future so that it continues to provide relevant and accurate information to users.« less

yStreX: yeast stress expression database

PubMed Central

Wanichthanarak, Kwanjeera; Nookaew, Intawat; Petranovic, Dina

2014-01-01

Over the past decade genome-wide expression analyses have been often used to study how expression of genes changes in response to various environmental stresses. Many of these studies (such as effects of oxygen concentration, temperature stress, low pH stress, osmotic stress, depletion or limitation of nutrients, addition of different chemical compounds, etc.) have been conducted in the unicellular Eukaryal model, yeast Saccharomyces cerevisiae. However, the lack of a unifying or integrated, bioinformatics platform that would permit efficient and rapid use of all these existing data remain an important issue. To facilitate research by exploiting existing transcription data in the field of yeast physiology, we have developed the yStreX database. It is an online repository of analyzed gene expression data from curated data sets from different studies that capture genome-wide transcriptional changes in response to diverse environmental transitions. The first aim of this online database is to facilitate comparison of cross-platform and cross-laboratory gene expression data. Additionally, we performed different expression analyses, meta-analyses and gene set enrichment analyses; and the results are also deposited in this database. Lastly, we constructed a user-friendly Web interface with interactive visualization to provide intuitive access and to display the queried data for users with no background in bioinformatics. Database URL: http://www.ystrexdb.com PMID:25024351

An Introduction to Database Structure and Database Machines.

ERIC Educational Resources Information Center

Detweiler, Karen

1984-01-01

Enumerates principal management objectives of database management systems (data independence, quality, security, multiuser access, central control) and criteria for comparison (response time, size, flexibility, other features). Conventional database management systems, relational databases, and database machines used for backend processing are…

The Structural Ceramics Database: Technical Foundations

PubMed Central

Munro, R. G.; Hwang, F. Y.; Hubbard, C. R.

1989-01-01

The development of a computerized database on advanced structural ceramics can play a critical role in fostering the widespread use of ceramics in industry and in advanced technologies. A computerized database may be the most effective means of accelerating technology development by enabling new materials to be incorporated into designs far more rapidly than would have been possible with traditional information transfer processes. Faster, more efficient access to critical data is the basis for creating this technological advantage. Further, a computerized database provides the means for a more consistent treatment of data, greater quality control and product reliability, and improved continuity of research and development programs. A preliminary system has been completed as phase one of an ongoing program to establish the Structural Ceramics Database system. The system is designed to be used on personal computers. Developed in a modular design, the preliminary system is focused on the thermal properties of monolithic ceramics. The initial modules consist of materials specification, thermal expansion, thermal conductivity, thermal diffusivity, specific heat, thermal shock resistance, and a bibliography of data references. Query and output programs also have been developed for use with these modules. The latter program elements, along with the database modules, will be subjected to several stages of testing and refinement in the second phase of this effort. The goal of the refinement process will be the establishment of this system as a user-friendly prototype. Three primary considerations provide the guidelines to the system’s development: (1) The user’s needs; (2) The nature of materials properties; and (3) The requirements of the programming language. The present report discusses the manner and rationale by which each of these considerations leads to specific features in the design of the system. PMID:28053397

BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources.

PubMed

Lim, Jeongheui; Kim, Sang-Yoon; Kim, Sungmin; Eo, Hae-Seok; Kim, Chang-Bae; Paek, Woon Kee; Kim, Won; Bhak, Jong

2009-12-03

DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on Earth, particularly when DNA sequencing technology is cheaply available. There are many nations in Asia with many biodiversity resources that need to be mapped and registered in databases. We have built a general DNA barcode data processing system, BioBarcode, with open source software - which is a general purpose database and server. It uses mySQL RDBMS 5.0, BLAST2, and Apache httpd server. An exemplary database of BioBarcode has around 11,300 specimen entries (including GenBank data) and registers the biological species to map their genetic relationships. The BioBarcode database contains a chromatogram viewer which improves the performance in DNA sequence analyses. Asia has a very high degree of biodiversity and the BioBarcode database server system aims to provide an efficient bioinformatics protocol that can be freely used by Asian researchers and research organizations interested in DNA barcoding. The BioBarcode promotes the rapid acquisition of biological species DNA sequence data that meet global standards by providing specialized services, and provides useful tools that will make barcoding cheaper and faster in the biodiversity community such as standardization, depository, management, and analysis of DNA barcode data. The system can be downloaded upon request, and an exemplary server has been constructed with which to build an Asian biodiversity system http://www.asianbarcode.org.

Rhinoplasty perioperative database using a personal digital assistant.

PubMed

Kotler, Howard S

2004-01-01

To construct a reliable, accurate, and easy-to-use handheld computer database that facilitates the point-of-care acquisition of perioperative text and image data specific to rhinoplasty. A user-modified database (Pendragon Forms [v.3.2]; Pendragon Software Corporation, Libertyville, Ill) and graphic image program (Tealpaint [v.4.87]; Tealpaint Software, San Rafael, Calif) were used to capture text and image data, respectively, on a Palm OS (v.4.11) handheld operating with 8 megabytes of memory. The handheld and desktop databases were maintained secure using PDASecure (v.2.0) and GoldSecure (v.3.0) (Trust Digital LLC, Fairfax, Va). The handheld data were then uploaded to a desktop database of either FileMaker Pro 5.0 (v.1) (FileMaker Inc, Santa Clara, Calif) or Microsoft Access 2000 (Microsoft Corp, Redmond, Wash). Patient data were collected from 15 patients undergoing rhinoplasty in a private practice outpatient ambulatory setting. Data integrity was assessed after 6 months' disk and hard drive storage. The handheld database was able to facilitate data collection and accurately record, transfer, and reliably maintain perioperative rhinoplasty data. Query capability allowed rapid search using a multitude of keyword search terms specific to the operative maneuvers performed in rhinoplasty. Handheld computer technology provides a method of reliably recording and storing perioperative rhinoplasty information. The handheld computer facilitates the reliable and accurate storage and query of perioperative data, assisting the retrospective review of one's own results and enhancement of surgical skills.

MICA: desktop software for comprehensive searching of DNA databases

PubMed Central

Stokes, William A; Glick, Benjamin S

2006-01-01

Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software. PMID:17018144

Exposure to 50 Hz electromagnetic radiation promote early maturation and differentiation in newborn rat cerebellar granule neurons.

PubMed

Lisi, A; Ciotti, M T; Ledda, M; Pieri, M; Zona, C; Mercanti, D; Rieti, S; Giuliani, L; Grimaldi, S

2005-08-01

The wish of this work is the study of the effect of electromagnetic (EMF) radiations at a frequency of 50 Hz on the development of cerebellar granule neurons (CGN). Granule neurons, prepared from newborn rat cerebellum (8 days after birth), were cultured after plate-seeding in the presence of EMF radiations, with the plan of characterizing their cellular and molecular biochemistry, after exposure to the electromagnetic stimulus. Five days challenge to EMF radiations showed, by the cytotoxic glutamate (Glu) pulse test, a 30% decrease of cells survival, while only 5% of mortality was reported for unexposed sample. Moreover, blocking the glutamate receptor (GluR) with the Glu competitor MK-801, no toxicity effect after CGN challenge to EMF radiations and Glu was detected. By patch-clamp recording technique, the Kainate-induced currents from 6 days old exposed CGN exhibited a significant increase with respect to control cells. Western blot and reverse transcription-polymerase chain reaction (RT-PCR) analyses show that EMF exposure of rats CGN, induces a change in both GluRs proteins and mRNAs expression with respect to control. In addition, the use of monoclonal antibody raised against neurofilament protein (NF-200) reveals an increase in NF-200 synthesis in the exposed CGN. All these results indicate that exposure to non-ionizing radiations contribute to a premature expression of GluRs reducing the life span of CGN, leading to a more rapid cell maturation. (c) 2005 Wiley-Liss, Inc.

A comprehensive and scalable database search system for metaproteomics.

PubMed

Chatterjee, Sandip; Stupp, Gregory S; Park, Sung Kyu Robin; Ducom, Jean-Christophe; Yates, John R; Su, Andrew I; Wolan, Dennis W

2016-08-16

Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metaproteomic analysis method (ComPIL) that addresses protein database size limitations. Our approach to overcome this significant limitation in metaproteomics was to design a scalable set of sequence databases assembled for optimal library querying speeds. ComPIL was integrated with a modified version of the search engine ProLuCID (termed "Blazmass") to permit rapid matching of experimental spectra. Proof-of-principle analysis of human HEK293 lysate with a ComPIL database derived from high-quality genomic libraries was able to detect nearly all of the same peptides as a search with a human database (~500x fewer peptides in the database), with a small reduction in sensitivity. We were also able to detect proteins from the adenovirus used to immortalize these cells. We applied our method to a set of healthy human gut microbiome proteomic samples and showed a substantial increase in the number of identified peptides and proteins compared to previous metaproteomic analyses, while retaining a high degree of protein identification accuracy and allowing for a more in-depth characterization of the functional landscape of the samples. The combination of ComPIL with Blazmass allows proteomic searches to be performed with database sizes much larger than previously possible. These large database searches can be applied to complex meta-samples with unknown composition or proteomic samples where unexpected proteins may be identified. The protein database, proteomic search engine, and the proteomic data files for

Application of cloud database in the management of clinical data of patients with skin diseases.

PubMed

Mao, Xiao-fei; Liu, Rui; DU, Wei; Fan, Xue; Chen, Dian; Zuo, Ya-gang; Sun, Qiu-ning

2015-04-01

To evaluate the needs and applications of using cloud database in the daily practice of dermatology department. The cloud database was established for systemic scleroderma and localized scleroderma. Paper forms were used to record the original data including personal information, pictures, specimens, blood biochemical indicators, skin lesions,and scores of self-rating scales. The results were input into the cloud database. The applications of the cloud database in the dermatology department were summarized and analyzed. The personal and clinical information of 215 systemic scleroderma patients and 522 localized scleroderma patients were included and analyzed using the cloud database. The disease status,quality of life, and prognosis were obtained by statistical calculations. The cloud database can efficiently and rapidly store and manage the data of patients with skin diseases. As a simple, prompt, safe, and convenient tool, it can be used in patients information management, clinical decision-making, and scientific research.

ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.

PubMed

Konc, Janez; Cesnik, Tomo; Konc, Joanna Trykowska; Penca, Matej; Janežič, Dušanka

2012-02-27

ProBiS-Database is a searchable repository of precalculated local structural alignments in proteins detected by the ProBiS algorithm in the Protein Data Bank. Identification of functionally important binding regions of the protein is facilitated by structural similarity scores mapped to the query protein structure. PDB structures that have been aligned with a query protein may be rapidly retrieved from the ProBiS-Database, which is thus able to generate hypotheses concerning the roles of uncharacterized proteins. Presented with uncharacterized protein structure, ProBiS-Database can discern relationships between such a query protein and other better known proteins in the PDB. Fast access and a user-friendly graphical interface promote easy exploration of this database of over 420 million local structural alignments. The ProBiS-Database is updated weekly and is freely available online at http://probis.cmm.ki.si/database.

[Role and management of cancer clinical database in the application of gastric cancer precision medicine].

PubMed

Li, Yuanfang; Zhou, Zhiwei

2016-02-01

Precision medicine is a new medical concept and medical model, which is based on personalized medicine, rapid progress of genome sequencing technology and cross application of biological information and big data science. Precision medicine improves the diagnosis and treatment of gastric cancer to provide more convenience through more profound analyses of characteristics, pathogenesis and other core issues in gastric cancer. Cancer clinical database is important to promote the development of precision medicine. Therefore, it is necessary to pay close attention to the construction and management of the database. The clinical database of Sun Yat-sen University Cancer Center is composed of medical record database, blood specimen bank, tissue bank and medical imaging database. In order to ensure the good quality of the database, the design and management of the database should follow the strict standard operation procedure(SOP) model. Data sharing is an important way to improve medical research in the era of medical big data. The construction and management of clinical database must also be strengthened and innovated.

Research on keyword retrieval method of HBase database based on index structure

NASA Astrophysics Data System (ADS)

Gong, Pijin; Lv, Congmin; Gong, Yongsheng; Ma, Haozhi; Sun, Yang; Wang, Lu

2017-10-01

With the rapid development of manned spaceflight engineering, the scientific experimental data in space application system is increasing rapidly. How to efficiently query the specific data in the mass data volume has become a problem. In this paper, a method of retrieving the object data based on the object attribute as the keyword is proposed. The HBase database is used to store the object data and object attributes, and the secondary index is constructed. The research shows that this method is a good way to retrieve specified data based on object attributes.

Enhancing the Utility of the Rapid Environmental Assessment Database Through the Use of In Situ and Modelled Data Sets During Q316

DTIC Science & Technology

2008-11-01

17ºC; red: 17-18ºC. Although the image produced in Figure 9 is useful, the image itself is not the most important aspect of the process . Two...climatology for the Scotian Shelf. The database is intended for use while ashore and also while at-sea. Trial Q316 was the maiden voyage of the database...to the process of data transfer from external sources to the database, and also how the database can be restructured to be more accommodating of

Analysis of Rapidly Developing Low Cloud Ceilings in a Stable Environment

NASA Technical Reports Server (NTRS)

Bauman, William H., III; Barrett, Joe H., III; Case, Jonathan L.; Wheeler, Mark M.; Baggett, G. Wayne

2006-01-01

Forecasters at the Space Meteorology Group (SMG) issue 30 to 90 minute forecasts for low cloud ceilings at the Space Shuttle Landing Facility (TTS) to support Space Shuttle landings. Mission verification statistics have shown ceilings to be the number one forecast challenge for SMG. More specifically, forecasters at SMG are concerned with any rapidly developing clouds/ceilings below 8000 ft in a stable, capped thermodynamic environment. Therefore, the Applied Meteorology Unit (AMU) was tasked to examine archived events of rapid stable cloud formation resulting in ceilings below 8000 ft, and document the atmospheric regimes favoring this type of cloud development. The AMU examined the cool season months of November to March during the years of 1993-2003 for days that had low-level inversions and rapid, stable low cloud formation that resulted in ceilings violating the Space Shuttle Flight Rules. The AMU wrote and modified existing code to identify inversions from the morning (-10 UTC) Cape Canaveral, FL rawinsonde (XMR) during the cool season and output pertinent sounding information. They parsed all days with cloud ceilings below 8000 ft at TTS, forming a database of possible rapidly-developing low ceiling events. Days with precipitation or noticeable fog burn-off situations were excluded from the database. In the first phase of this work, only the daytime hours were examined for possible ceiling development events since low clouds are easier to diagnose with visible satellite imagery. Phase II of this work includes expanding the database to include nighttime cases which is underway as this abstract is being written. For the nighttime cases, the AMU will analyze both the 00 UTC soundings and the 10 UTC soundings to examine those data for the presence of a low-level inversion. The 00 UTC soundings will probably not have a surface-based inversion, but the presence of inversions or "neutral" layers aloft and below 8,000 ft will most likely help define the stable

BioBarcode: a general DNA barcoding database and server platform for Asian biodiversity resources

PubMed Central

2009-01-01

Background DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on Earth, particularly when DNA sequencing technology is cheaply available. There are many nations in Asia with many biodiversity resources that need to be mapped and registered in databases. Results We have built a general DNA barcode data processing system, BioBarcode, with open source software - which is a general purpose database and server. It uses mySQL RDBMS 5.0, BLAST2, and Apache httpd server. An exemplary database of BioBarcode has around 11,300 specimen entries (including GenBank data) and registers the biological species to map their genetic relationships. The BioBarcode database contains a chromatogram viewer which improves the performance in DNA sequence analyses. Conclusion Asia has a very high degree of biodiversity and the BioBarcode database server system aims to provide an efficient bioinformatics protocol that can be freely used by Asian researchers and research organizations interested in DNA barcoding. The BioBarcode promotes the rapid acquisition of biological species DNA sequence data that meet global standards by providing specialized services, and provides useful tools that will make barcoding cheaper and faster in the biodiversity community such as standardization, depository, management, and analysis of DNA barcode data. The system can be downloaded upon request, and an exemplary server has been constructed with which to build an Asian biodiversity system http://www.asianbarcode.org. PMID:19958506

Databases on biotechnology and biosafety of GMOs.

PubMed

Degrassi, Giuliano; Alexandrova, Nevena; Ripandelli, Decio

2003-01-01

Due to the involvement of scientific, industrial, commercial and public sectors of society, the complexity of the issues concerning the safety of genetically modified organisms (GMOs) for the environment, agriculture, and human and animal health calls for a wide coverage of information. Accordingly, development of the field of biotechnology, along with concerns related to the fate of released GMOs, has led to a rapid development of tools for disseminating such information. As a result, there is a growing number of databases aimed at collecting and storing information related to GMOs. Most of the sites deal with information on environmental releases, field trials, transgenes and related sequences, regulations and legislation, risk assessment documents, and literature. Databases are mainly established and managed by scientific, national or international authorities, and are addressed towards scientists, government officials, policy makers, consumers, farmers, environmental groups and civil society representatives. This complexity can lead to an overlapping of information. The purpose of the present review is to analyse the relevant databases currently available on the web, providing comments on their vastly different information and on the structure of the sites pertaining to different users. A preliminary overview on the development of these sites during the last decade, at both the national and international level, is also provided.

Mt Pamola, the Electromagnetic Field, EMF, Thunderbird, Mothman and Environmental Monitoring Signals Via the Southern Constellation Phoenix As Detectable In Potato Cave, Acton, MA.

NASA Astrophysics Data System (ADS)

Pecora, Andrea S.; Pawa Matagamon, Sagamo

2004-03-01

Just below the peak of Mt Pamola in ME, at the juncture with the Knife Edge, downwardly arcing segments of Earths EMF, are manifested by a faint lotus-blossom-blue, neon-like glow at 3 pm some sunny afternoons. Similarly hued glows, and horizontal but variable-arced segmented trajectories, are somewhat periodically detectable under certain conditions in chambers at Acton, MA. These phenomena curiously have the filled-in profile that precisely matches the outline of the southern constellation Phoenix, which is never visible above the nighttime horizon locally. The stick-figure representation of the constellation Canis Major can also be detected in a chamber at Americas Stonehenge, two hours before it has arisen, at certain times. The sequence of phenomena visible at Acton correctly correlates with eclipses and other alignments of our solar system. Phoenix, a.k.a. Thunderbird and Mothman, is detectable elsewhere in MA.

Large-scale annotation of small-molecule libraries using public databases.

PubMed

Zhou, Yingyao; Zhou, Bin; Chen, Kaisheng; Yan, S Frank; King, Frederick J; Jiang, Shumei; Winzeler, Elizabeth A

2007-01-01

While many large publicly accessible databases provide excellent annotation for biological macromolecules, the same is not true for small chemical compounds. Commercial data sources also fail to encompass an annotation interface for large numbers of compounds and tend to be cost prohibitive to be widely available to biomedical researchers. Therefore, using annotation information for the selection of lead compounds from a modern day high-throughput screening (HTS) campaign presently occurs only under a very limited scale. The recent rapid expansion of the NIH PubChem database provides an opportunity to link existing biological databases with compound catalogs and provides relevant information that potentially could improve the information garnered from large-scale screening efforts. Using the 2.5 million compound collection at the Genomics Institute of the Novartis Research Foundation (GNF) as a model, we determined that approximately 4% of the library contained compounds with potential annotation in such databases as PubChem and the World Drug Index (WDI) as well as related databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) and ChemIDplus. Furthermore, the exact structure match analysis showed 32% of GNF compounds can be linked to third party databases via PubChem. We also showed annotations such as MeSH (medical subject headings) terms can be applied to in-house HTS databases in identifying signature biological inhibition profiles of interest as well as expediting the assay validation process. The automated annotation of thousands of screening hits in batch is becoming feasible and has the potential to play an essential role in the hit-to-lead decision making process.

An annotated database of Arabidopsis mutants of acyl lipid metabolism

DOE PAGES

McGlew, Kathleen; Shaw, Vincent; Zhang, Meng; ...

2014-12-10

Mutants have played a fundamental role in gene discovery and in understanding the function of genes involved in plant acyl lipid metabolism. The first mutant in Arabidopsis lipid metabolism ( fad4) was described in 1985. Since that time, characterization of mutants in more than 280 genes associated with acyl lipid metabolism has been reported. This review provides a brief background and history on identification of mutants in acyl lipid metabolism, an analysis of the distribution of mutants in different areas of acyl lipid metabolism and presents an annotated database (ARALIPmutantDB) of these mutants. The database provides information on the phenotypesmore » of mutants, pathways and enzymes/proteins associated with the mutants, and allows rapid access via hyperlinks to summaries of information about each mutant and to literature that provides information on the lipid composition of the mutants. Mutants for at least 30 % of the genes in the database have multiple names, which have been compiled here to reduce ambiguities in searches for information. Furthermore, the database should also provide a tool for exploring the relationships between mutants in acyl lipid-related genes and their lipid phenotypes and point to opportunities for further research.« less

Rapid identification of dairy lactic acid bacteria by M13-generated, RAPD-PCR fingerprint databases.

PubMed

Rossetti, Lia; Giraffa, Giorgio

2005-11-01

About a thousand lactic acid bacteria (LAB) isolated from dairy products, especially cheeses, were identified and typed by species-specific PCR and RAPD-PCR, respectively. RAPD-PCR profiles, which were obtained by using the M13 sequence as a primer, allowed us to implement a large database of different fingerprints, which were analysed by BioNumerics software. Cluster analysis of the combined RAPD-PCR fingerprinting profiles enabled us to implement a library, which is a collection of library units, which in turn is a selection of representative database entries. A library unit, in this case, can be considered to be a definable taxon. The strains belonged to 11 main RAPD-PCR fingerprinting library units identified as Lactobacillus casei/paracasei, Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacillus helveticus, Lactobacillus delbrueckii, Lactobacillus fermentum, Lactobacillus brevis, Enterococcus faecium, Enterococcus faecalis, Streptococcus thermophilus and Lactococcus lactis. The possibility to routinely identify newly typed, bacterial isolates by consulting the library of the software was valued. The proposed method could be suggested to refine previous strain identifications, eliminate redundancy and dispose of a technologically useful LAB strain collection. The same approach could also be applied to identify LAB strains isolated from other food ecosystems.

Exposure to 900 MHz electromagnetic fields activates the mkp-1/ERK pathway and causes blood-brain barrier damage and cognitive impairment in rats.

PubMed

Tang, Jun; Zhang, Yuan; Yang, Liming; Chen, Qianwei; Tan, Liang; Zuo, Shilun; Feng, Hua; Chen, Zhi; Zhu, Gang

2015-03-19

With the rapid increase in the number of mobile phone users, the potential adverse effects of the electromagnetic field radiation emitted by a mobile phone has become a serious concern. This study demonstrated, for the first time, the blood-brain barrier and cognitive changes in rats exposed to 900 MHz electromagnetic field (EMF) and aims to elucidate the potential molecular pathway underlying these changes. A total of 108 male Sprague-Dawley rats were exposed to a 900 MHz, 1 mW/cm(2) EMF or sham (unexposed) for 14 or 28 days (3h per day). The specific energy absorption rate (SAR) varied between 0.016 (whole body) and 2 W/kg (locally in the head). In addition, the Morris water maze test was used to examine spatial memory performance determination. Morphological changes were investigated by examining ultrastructural changes in the hippocampus and cortex, and the Evans Blue assay was used to assess blood brain barrier (BBB) damage. Immunostaining was performed to identify heme oxygenase-1 (HO-1)-positive neurons and albumin extravasation detection. Western blot was used to determine HO-1 expression, phosphorylated ERK expression and the upstream mediator, mkp-1 expression. We found that the frequency of crossing platforms and the percentage of time spent in the target quadrant were lower in rats exposed to EMF for 28 days than in rats exposed to EMF for 14 days and unexposed rats. Moreover, 28 days of EMF exposure induced cellular edema and neuronal cell organelle degeneration in the rat. In addition, damaged BBB permeability, which resulted in albumin and HO-1 extravasation were observed in the hippocampus and cortex. Thus, for the first time, we found that EMF exposure for 28 days induced the expression of mkp-1, resulting in ERK dephosphorylation. Taken together, these results demonstrated that exposure to 900 MHz EMF radiation for 28 days can significantly impair spatial memory and damage BBB permeability in rat by activating the mkp-1/ERK pathway. Copyright �

Neuronal Cellular Responses to Extremely Low Frequency Electromagnetic Field Exposure: Implications Regarding Oxidative Stress and Neurodegeneration

PubMed Central

Reale, Marcella; Kamal, Mohammad A.; Patruno, Antonia; Costantini, Erica; D'Angelo, Chiara; Pesce, Miko; Greig, Nigel H.

2014-01-01

Neurodegenerative diseases comprise both hereditary and sporadic conditions characterized by an identifying progressive nervous system dysfunction and distinctive neuopathophysiology. The majority are of non-familial etiology and hence environmental factors and lifestyle play key roles in their pathogenesis. The extensive use of and ever increasing worldwide demand for electricity has stimulated societal and scientific interest on the environmental exposure to low frequency electromagnetic fields (EMFs) on human health. Epidemiological studies suggest a positive association between 50/60-Hz power transmission fields and leukemia or lymphoma development. Consequent to the association between EMFs and induction of oxidative stress, concerns relating to development of neurodegenerative diseases, such as Alzheimer disease (AD), have been voiced as the brain consumes the greatest fraction of oxygen and is particularly vulnerable to oxidative stress. Exposure to extremely low frequency (ELF)-EMFs are reported to alter animal behavior and modulate biological variables, including gene expression, regulation of cell survival, promotion of cellular differentiation, and changes in cerebral blood flow in aged AD transgenic mice. Alterations in inflammatory responses have also been reported, but how these actions impact human health remains unknown. We hence evaluated the effects of an electromagnetic wave (magnetic field intensity 1mT; frequency, 50-Hz) on a well-characterized immortalized neuronal cell model, human SH-SY5Y cells. ELF-EMF exposure elevated the expession of NOS and O2 −, which were countered by compensatory changes in antioxidant catylase (CAT) activity and enzymatic kinetic parameters related to CYP-450 and CAT activity. Actions of ELF-EMFs on cytokine gene expression were additionally evaluated and found rapidly modified. Confronted with co-exposure to H2O2-induced oxidative stress, ELF-EMF proved not as well counteracted and resulted in a decline in CAT

Analysis of Rapidly Developing Low Cloud Ceilings in a Stable Environment

NASA Technical Reports Server (NTRS)

Wheeler, Mark M.; Case, Jonathan L.

2005-01-01

This report describes the work done by the Applied Meteorology Unit (AMU) in developing a database of days that experienced rapid (< 90 minutes) low cloud formation in a stable atmosphere, resulting in ceilings at the Shuttle Landing Facility (TTS) that violated Space Shuttle Flight Rules (FR). The meteorological conditions favoring the rapid formation of low ceilings include the presence of any inversion below 8000 ft, high relative humidity beneath the inversion, and a clockwise turning of the winds from the surface to the middle troposphere (approx. 15000 ft). The AMU compared and contrasted the atmospheric and thermodynamic conditions between days with rapid low ceiling formation and days with low ceiling resulting from other mechanism. The AMU found that the vertical wind profile is the probable discerning factor between the rapidly-forming ceiling days and other low ceiling days at TTS. Most rapidly-developing low ceiling days had a clockwise turning of the winds with height, whereas other low ceiling days typically had a counter-clockwise turning of the winds with height or negligible vertical wind shear. Forecasters at the Space Meteorology Group (SMG) issue 30 to 90 minute forecasts for low cloud ceilings at TTS to support Space Shuttle landings. Mission verification statistics have shown ceilings to be the number one forecast challenge. More specifically, forecasters at SMG are concerned with any rapidly developing clouds ceilings below 8000 ft in a stable, capped thermodynamic environment, Therefore, the AMU was tasked to examine archived events of rapid stable cloud formation resulting in ceilings below 8000 ft, and document the atmospheric regimes favoring this type of cloud development. The AMU examined the cool season months of November to March during the years of 1993-2003 for days that had low-level inversions and rapid, stable low cloud formation that resulted in ceilings violating the Space Shuttle FR. The AMU wrote and modified existing code to

Brain Topography of Emf-Induced Eeg-Changes in Restful Wakefulness: Tracing Current Effects, Targeting Future Prospects.

PubMed

Gjoneska, Biljana; Markovska-Simoska, Simona; Hinrikus, Hiie; Pop-Jordanova, Nada; Pop-Jordanov, Jordan

2015-01-01

Covering a handful of decades but spanning across two centuries, mobile phones announced the dawn of the technological revolution, standing at the forefront as its' most prominent symbol. Over the course of their sovereign dominance, human generations born with the birth of the mobile phone reached the age of maturity, while scientific community started reaching for experience-based perceptivity. The following review serves as a short-cut across a half-decade old research gap, and a clear-cut analysis on the cutting-edge knowledge of the EMF induced EEG changes. The selection covers 28 articles about mobile phone effects on resting wakeful EEG in humans conducted over the last two decades, across three continents and 12 countries, of which 75% had positive findings. At present, the general protocol of a typical study includes investigations on adults (20-60 yrs) grouped in smaller samples and exposed to shorter intervals of GSM-like pulse-modulated signal (10-30 subjects/minutes). The assessment usually involves linear methods for quantitative analysis, while the results mostly revolve around posterior increase in alpha and beta frequency range. The qualitative variations, however, remain open to interpretation. Future research may benefit from multiplication of sub-specific studies leading to replication of more consistent results. The long-term and large-size epidemiologic studies, stratified by age and gender, may also improve the expected outcomes. Regarding the interpretation, non-linear methods could be employed for assessment of individual variations. The emphasis should be placed on theories/measures for better understanding of the subtle interplay between the spectral individualities and mobile phone radiation specifics.

Contamination of sequence databases with adaptor sequences

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

Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D.

Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable ofmore » transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.« less

A scoping review of rapid review methods.

PubMed

Tricco, Andrea C; Antony, Jesmin; Zarin, Wasifa; Strifler, Lisa; Ghassemi, Marco; Ivory, John; Perrier, Laure; Hutton, Brian; Moher, David; Straus, Sharon E

2015-09-16

Rapid reviews are a form of knowledge synthesis in which components of the systematic review process are simplified or omitted to produce information in a timely manner. Although numerous centers are conducting rapid reviews internationally, few studies have examined the methodological characteristics of rapid reviews. We aimed to examine articles, books, and reports that evaluated, compared, used or described rapid reviews or methods through a scoping review. MEDLINE, EMBASE, the Cochrane Library, internet websites of rapid review producers, and reference lists were searched to identify articles for inclusion. Two reviewers independently screened literature search results and abstracted data from included studies. Descriptive analysis was conducted. We included 100 articles plus one companion report that were published between 1997 and 2013. The studies were categorized as 84 application papers, seven development papers, six impact papers, and four comparison papers (one was included in two categories). The rapid reviews were conducted between 1 and 12 months, predominantly in Europe (58 %) and North America (20 %). The included studies failed to report 6 % to 73 % of the specific systematic review steps examined. Fifty unique rapid review methods were identified; 16 methods occurred more than once. Streamlined methods that were used in the 82 rapid reviews included limiting the literature search to published literature (24 %) or one database (2 %), limiting inclusion criteria by date (68 %) or language (49 %), having one person screen and another verify or screen excluded studies (6 %), having one person abstract data and another verify (23 %), not conducting risk of bias/quality appraisal (7 %) or having only one reviewer conduct the quality appraisal (7 %), and presenting results as a narrative summary (78 %). Four case studies were identified that compared the results of rapid reviews to systematic reviews. Three studies found that the conclusions between

SQL is Dead; Long-live SQL: Relational Database Technology in Science Contexts

NASA Astrophysics Data System (ADS)

Howe, B.; Halperin, D.

2014-12-01

Relational databases are often perceived as a poor fit in science contexts: Rigid schemas, poor support for complex analytics, unpredictable performance, significant maintenance and tuning requirements --- these idiosyncrasies often make databases unattractive in science contexts characterized by heterogeneous data sources, complex analysis tasks, rapidly changing requirements, and limited IT budgets. In this talk, I'll argue that although the value proposition of typical relational database systems are weak in science, the core ideas that power relational databases have become incredibly prolific in open source science software, and are emerging as a universal abstraction for both big data and small data. In addition, I'll talk about two open source systems we are building to "jailbreak" the core technology of relational databases and adapt them for use in science. The first is SQLShare, a Database-as-a-Service system supporting collaborative data analysis and exchange by reducing database use to an Upload-Query-Share workflow with no installation, schema design, or configuration required. The second is Myria, a service that supports much larger scale data, complex analytics, and supports multiple back end systems. Finally, I'll describe some of the ways our collaborators in oceanography, astronomy, biology, fisheries science, and more are using these systems to replace script-based workflows for reasons of performance, flexibility, and convenience.

Application of GIS Rapid Mapping Technology in Disaster Monitoring

NASA Astrophysics Data System (ADS)

Wang, Z.; Tu, J.; Liu, G.; Zhao, Q.

2018-04-01

With the rapid development of GIS and RS technology, especially in recent years, GIS technology and its software functions have been increasingly mature and enhanced. And with the rapid development of mathematical statistical tools for spatial modeling and simulation, has promoted the widespread application and popularization of quantization in the field of geology. Based on the investigation of field disaster and the construction of spatial database, this paper uses remote sensing image, DEM and GIS technology to obtain the data information of disaster vulnerability analysis, and makes use of the information model to carry out disaster risk assessment mapping.Using ArcGIS software and its spatial data modeling method, the basic data information of the disaster risk mapping process was acquired and processed, and the spatial data simulation tool was used to map the disaster rapidly.

Calcium spiking activity and baseline calcium levels in ROS 17/2.8 cells exposed to extremely low frequency electromagnetic fields (ELF EMF).

PubMed

Shahidain, R; Mullins, R D; Sisken, J E

2001-02-01

To determine whether extremely low frequency electromagnetic fields can alter average free cytosolic calcium ion concentrations [Ca2+]i and transient increases in [Ca2+]i in populations of ROS 17/2.8 cells. Cells loaded with the calcium-selective luminescent photoprotein, aequorin, were placed in the bottom of a sample chamber, which was inserted into the gap of a previously described air gap reactor system where they were exposed either to sinusoidal magnetic fields at a variety of frequencies and flux densities or to sham conditions. Real-time recordings of photon counts due to aequorin luminescence were obtained and data were analysed with the use of probit plots. Probit plots of data obtained from cells exposed to the various magnetic fields were virtually superimposable over the data obtained for the same cultures during pre- and post-exposure sham or no-field periods. These experiments provided no evidence for any effects of ELF EMF, either positive or negative, on either average [Ca2+]i or on transient increases in [Ca2+]i.

Utilizing Arc Marine Concepts for Designing a Geospatially Enabled Database to Support Rapid Environmental Assessment

DTIC Science & Technology

2009-07-01

data were recognized as being largely geospatial and thus a GIS was considered the most reasonable way to proceed. The Postgre suite of software also...for the ESRI (2009) geodatabase environment but is applicable for this Postgre -based system. We then introduce and discuss spatial reference...PostgreSQL database using a Postgre ODBC connection. This procedure identified 100 tables with 737 columns. This is after the removal of two

Passenger baggage object database (PBOD)

NASA Astrophysics Data System (ADS)

Gittinger, Jaxon M.; Suknot, April N.; Jimenez, Edward S.; Spaulding, Terry W.; Wenrich, Steve A.

2018-04-01

Detection of anomalies of interest in x-ray images is an ever-evolving problem that requires the rapid development of automatic detection algorithms. Automatic detection algorithms are developed using machine learning techniques, which would require developers to obtain the x-ray machine that was used to create the images being trained on, and compile all associated metadata for those images by hand. The Passenger Baggage Object Database (PBOD) and data acquisition application were designed and developed for acquiring and persisting 2-D and 3-D x-ray image data and associated metadata. PBOD was specifically created to capture simulated airline passenger "stream of commerce" luggage data, but could be applied to other areas of x-ray imaging to utilize machine-learning methods.

Challenges in developing medicinal plant databases for sharing ethnopharmacological knowledge.

PubMed

Ningthoujam, Sanjoy Singh; Talukdar, Anupam Das; Potsangbam, Kumar Singh; Choudhury, Manabendra Dutta

2012-05-07

Major research contributions in ethnopharmacology have generated vast amount of data associated with medicinal plants. Computerized databases facilitate data management and analysis making coherent information available to researchers, planners and other users. Web-based databases also facilitate knowledge transmission and feed the circle of information exchange between the ethnopharmacological studies and public audience. However, despite the development of many medicinal plant databases, a lack of uniformity is still discernible. Therefore, it calls for defining a common standard to achieve the common objectives of ethnopharmacology. The aim of the study is to review the diversity of approaches in storing ethnopharmacological information in databases and to provide some minimal standards for these databases. Survey for articles on medicinal plant databases was done on the Internet by using selective keywords. Grey literatures and printed materials were also searched for information. Listed resources were critically analyzed for their approaches in content type, focus area and software technology. Necessity for rapid incorporation of traditional knowledge by compiling primary data has been felt. While citation collection is common approach for information compilation, it could not fully assimilate local literatures which reflect traditional knowledge. Need for defining standards for systematic evaluation, checking quality and authenticity of the data is felt. Databases focussing on thematic areas, viz., traditional medicine system, regional aspect, disease and phytochemical information are analyzed. Issues pertaining to data standard, data linking and unique identification need to be addressed in addition to general issues like lack of update and sustainability. In the background of the present study, suggestions have been made on some minimum standards for development of medicinal plant database. In spite of variations in approaches, existence of many overlapping

Rapid-Learning System for Cancer Care

PubMed Central

Abernethy, Amy P.; Etheredge, Lynn M.; Ganz, Patricia A.; Wallace, Paul; German, Robert R.; Neti, Chalapathy; Bach, Peter B.; Murphy, Sharon B.

2010-01-01

Compelling public interest is propelling national efforts to advance the evidence base for cancer treatment and control measures and to transform the way in which evidence is aggregated and applied. Substantial investments in health information technology, comparative effectiveness research, health care quality and value, and personalized medicine support these efforts and have resulted in considerable progress to date. An emerging initiative, and one that integrates these converging approaches to improving health care, is “rapid-learning health care.” In this framework, routinely collected real-time clinical data drive the process of scientific discovery, which becomes a natural outgrowth of patient care. To better understand the state of the rapid-learning health care model and its potential implications for oncology, the National Cancer Policy Forum of the Institute of Medicine held a workshop entitled “A Foundation for Evidence-Driven Practice: A Rapid-Learning System for Cancer Care” in October 2009. Participants examined the elements of a rapid-learning system for cancer, including registries and databases, emerging information technology, patient-centered and -driven clinical decision support, patient engagement, culture change, clinical practice guidelines, point-of-care needs in clinical oncology, and federal policy issues and implications. This Special Article reviews the activities of the workshop and sets the stage to move from vision to action. PMID:20585094

Database Access Systems.

ERIC Educational Resources Information Center

Dalrymple, Prudence W.; Roderer, Nancy K.

1994-01-01

Highlights the changes that have occurred from 1987-93 in database access systems. Topics addressed include types of databases, including CD-ROMs; enduser interface; database selection; database access management, including library instruction and use of primary literature; economic issues; database users; the search process; and improving…

"Mr. Database" : Jim Gray and the History of Database Technologies.

PubMed

Hanwahr, Nils C

2017-12-01

Although the widespread use of the term "Big Data" is comparatively recent, it invokes a phenomenon in the developments of database technology with distinct historical contexts. The database engineer Jim Gray, known as "Mr. Database" in Silicon Valley before his disappearance at sea in 2007, was involved in many of the crucial developments since the 1970s that constitute the foundation of exceedingly large and distributed databases. Jim Gray was involved in the development of relational database systems based on the concepts of Edgar F. Codd at IBM in the 1970s before he went on to develop principles of Transaction Processing that enable the parallel and highly distributed performance of databases today. He was also involved in creating forums for discourse between academia and industry, which influenced industry performance standards as well as database research agendas. As a co-founder of the San Francisco branch of Microsoft Research, Gray increasingly turned toward scientific applications of database technologies, e. g. leading the TerraServer project, an online database of satellite images. Inspired by Vannevar Bush's idea of the memex, Gray laid out his vision of a Personal Memex as well as a World Memex, eventually postulating a new era of data-based scientific discovery termed "Fourth Paradigm Science". This article gives an overview of Gray's contributions to the development of database technology as well as his research agendas and shows that central notions of Big Data have been occupying database engineers for much longer than the actual term has been in use.

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.

PubMed

Laukens, Kris; Hollunder, Jens; Dang, Thanh Hai; De Jaeger, Geert; Kuiper, Martin; Witters, Erwin; Verschoren, Alain; Van Leemput, Koenraad

2010-07-01

Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file formats, or directly from external databases through specialized third party plugins. However, molecular data are often stored in relational databases with their own specific structure, for which dedicated plugins do not exist. Therefore, a more generic solution is presented. A new Cytoscape plugin 'CytoSQL' is developed to connect Cytoscape to any relational database. It allows to launch SQL ('Structured Query Language') queries from within Cytoscape, with the option to inject node or edge features of an existing network as SQL arguments, and to convert the retrieved data to Cytoscape network components. Supported by a set of case studies we demonstrate the flexibility and the power of the CytoSQL plugin in converting specific data subsets into meaningful network representations. CytoSQL offers a unified approach to let Cytoscape interact with relational databases. Thanks to the power of the SQL syntax, this tool can rapidly generate and enrich networks according to very complex criteria. The plugin is available at http://www.ptools.ua.ac.be/CytoSQL.

Clinical utility of RapidArc™ radiotherapy technology

PubMed Central

Infusino, Erminia

2015-01-01

RapidArc™ is a radiation technique that delivers highly conformal dose distributions through the complete rotation (360°) and speed variation of the linear accelerator gantry. This technique, called volumetric modulated arc therapy (VMAT), compared with conventional radiotherapy techniques, can achieve high-target volume coverage and sparing damage to normal tissues. RapidArc delivers precise dose distribution and conformity similar to or greater than intensity-modulated radiation therapy in a short time, generally a few minutes, to which image-guided radiation therapy is added. RapidArc has become a currently used technology in many centers, which use RapidArc technology to treat a large number of patients. Large and small hospitals use it to treat the most challenging cases, but more and more frequently for the most common cancers. The clinical use of RapidArc and VMAT technology is constantly growing. At present, a limited number of clinical data are published, mostly concerning planning and feasibility studies. Clinical outcome data are increasing for a few tumor sites, even if only a little. The purpose of this work is to discuss the current status of VMAT techniques in clinical use through a review of the published data of planning systems and clinical outcomes in several tumor sites. The study consisted of a systematic review based on analysis of manuscripts retrieved from the PubMed, BioMed Central, and Scopus databases by searching for the keywords “RapidArc”, “Volumetric modulated arc radiotherapy”, and “Intensity-modulated radiotherapy”. PMID:26648755

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.

PubMed

Toofanny, Rudesh D; Simms, Andrew M; Beck, David A C; Daggett, Valerie

2011-08-10

and visualization of contacts and rapid cross simulation analysis for knowledge discovery. Using page compression for the atomic coordinate tables and indexes saves ~36% of disk space without any significant decrease in calculation time and should be considered for other non-transactional databases in MS SQL SERVER 2008.

Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

PubMed Central

2011-01-01

enables on-the-fly calculation and visualization of contacts and rapid cross simulation analysis for knowledge discovery. Using page compression for the atomic coordinate tables and indexes saves ~36% of disk space without any significant decrease in calculation time and should be considered for other non-transactional databases in MS SQL SERVER 2008. PMID:21831299

Pathogen Research Databases

Science.gov Websites

Hepatitis C Virus (HCV) database project is funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID). The HCV database project started as a spin-off from the HIV database project. There are two databases for HCV, a sequence database

MIPS: a database for protein sequences, homology data and yeast genome information.

PubMed Central

Mewes, H W; Albermann, K; Heumann, K; Liebl, S; Pfeiffer, F

1997-01-01

The MIPS group (Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, collects, processes and distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence Database (,). MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Database. The database is distributed on CD-ROM together with PATCHX, an exhaustive supplement of unique, unverified protein sequences from external sources compiled by MIPS. Through its WWW server (http://www.mips.biochem.mpg.de/ ) MIPS permits internet access to sequence databases, homology data and to yeast genome information. (i) Sequence similarity results from the FASTA program () are stored in the FASTA database for all proteins from PIR-International and PATCHX. The database is dynamically maintained and permits instant access to FASTA results. (ii) Starting with FASTA database queries, proteins have been classified into families and superfamilies (PROT-FAM). (iii) The HPT (hashed position tree) data structure () developed at MIPS is a new approach for rapid sequence and pattern searching. (iv) MIPS provides access to the sequence and annotation of the complete yeast genome (), the functional classification of yeast genes (FunCat) and its graphical display, the 'Genome Browser' (). A CD-ROM based on the JAVA programming language providing dynamic interactive access to the yeast genome and the related protein sequences has been compiled and is available on request. PMID:9016498

An algorithm of discovering signatures from DNA databases on a computer cluster.

PubMed

Lee, Hsiao Ping; Sheu, Tzu-Fang

2014-10-05

Signatures are short sequences that are unique and not similar to any other sequence in a database that can be used as the basis to identify different species. Even though several signature discovery algorithms have been proposed in the past, these algorithms require the entirety of databases to be loaded in the memory, thus restricting the amount of data that they can process. It makes those algorithms unable to process databases with large amounts of data. Also, those algorithms use sequential models and have slower discovery speeds, meaning that the efficiency can be improved. In this research, we are debuting the utilization of a divide-and-conquer strategy in signature discovery and have proposed a parallel signature discovery algorithm on a computer cluster. The algorithm applies the divide-and-conquer strategy to solve the problem posed to the existing algorithms where they are unable to process large databases and uses a parallel computing mechanism to effectively improve the efficiency of signature discovery. Even when run with just the memory of regular personal computers, the algorithm can still process large databases such as the human whole-genome EST database which were previously unable to be processed by the existing algorithms. The algorithm proposed in this research is not limited by the amount of usable memory and can rapidly find signatures in large databases, making it useful in applications such as Next Generation Sequencing and other large database analysis and processing. The implementation of the proposed algorithm is available at http://www.cs.pu.edu.tw/~fang/DDCSDPrograms/DDCSD.htm.

MAGIC database and interfaces: an integrated package for gene discovery and expression.

PubMed

Cordonnier-Pratt, Marie-Michèle; Liang, Chun; Wang, Haiming; Kolychev, Dmitri S; Sun, Feng; Freeman, Robert; Sullivan, Robert; Pratt, Lee H

2004-01-01

The rapidly increasing rate at which biological data is being produced requires a corresponding growth in relational databases and associated tools that can help laboratories contend with that data. With this need in mind, we describe here a Modular Approach to a Genomic, Integrated and Comprehensive (MAGIC) Database. This Oracle 9i database derives from an initial focus in our laboratory on gene discovery via production and analysis of expressed sequence tags (ESTs), and subsequently on gene expression as assessed by both EST clustering and microarrays. The MAGIC Gene Discovery portion of the database focuses on information derived from DNA sequences and on its biological relevance. In addition to MAGIC SEQ-LIMS, which is designed to support activities in the laboratory, it contains several additional subschemas. The latter include MAGIC Admin for database administration, MAGIC Sequence for sequence processing as well as sequence and clone attributes, MAGIC Cluster for the results of EST clustering, MAGIC Polymorphism in support of microsatellite and single-nucleotide-polymorphism discovery, and MAGIC Annotation for electronic annotation by BLAST and BLAT. The MAGIC Microarray portion is a MIAME-compliant database with two components at present. These are MAGIC Array-LIMS, which makes possible remote entry of all information into the database, and MAGIC Array Analysis, which provides data mining and visualization. Because all aspects of interaction with the MAGIC Database are via a web browser, it is ideally suited not only for individual research laboratories but also for core facilities that serve clients at any distance.

Development of a source-exposure matrix for occupational exposure assessment of electromagnetic fields in the INTEROCC study.

PubMed

Vila, Javier; Bowman, Joseph D; Figuerola, Jordi; Moriña, David; Kincl, Laurel; Richardson, Lesley; Cardis, Elisabeth

2017-07-01

To estimate occupational exposures to electromagnetic fields (EMF) for the INTEROCC study, a database of source-based measurements extracted from published and unpublished literature resources had been previously constructed. The aim of the current work was to summarize these measurements into a source-exposure matrix (SEM), accounting for their quality and relevance. A novel methodology for combining available measurements was developed, based on order statistics and log-normal distribution characteristics. Arithmetic and geometric means, and estimates of variability and maximum exposure were calculated by EMF source, frequency band and dosimetry type. The mean estimates were weighted by our confidence in the pooled measurements. The SEM contains confidence-weighted mean and maximum estimates for 312 EMF exposure sources (from 0 Hz to 300 GHz). Operator position geometric mean electric field levels for radiofrequency (RF) sources ranged between 0.8 V/m (plasma etcher) and 320 V/m (RF sealer), while magnetic fields ranged from 0.02 A/m (speed radar) to 0.6 A/m (microwave heating). For extremely low frequency sources, electric fields ranged between 0.2 V/m (electric forklift) and 11,700 V/m (high-voltage transmission line-hotsticks), whereas magnetic fields ranged between 0.14 μT (visual display terminals) and 17 μT (tungsten inert gas welding). The methodology developed allowed the construction of the first EMF-SEM and may be used to summarize similar exposure data for other physical or chemical agents.

Development of a source-exposure matrix for occupational exposure assessment of electromagnetic fields in the INTEROCC study

PubMed Central

Vila, Javier; Bowman, Joseph D; Figuerola, Jordi; Moriña, David; Kincl, Laurel; Richardson, Lesley; Cardis, Elisabeth

2017-01-01

Introduction To estimate occupational exposures to electromagnetic fields (EMF) for the INTEROCC study, a database of source-based measurements extracted from published and unpublished literature resources had been previously constructed. The aim of the current work was to summarize these measurements into a source-exposure matrix (SEM), accounting for their quality and relevance. Methods A novel methodology for combining available measurements was developed, based on order statistics and log-normal distribution characteristics. Arithmetic and geometric means, and estimates of variability and maximum exposure were calculated by EMF source, frequency band and dosimetry type. Mean estimates were weighted by our confidence on the pooled measurements. Results The SEM contains confidence-weighted mean and maximum estimates for 312 EMF exposure sources (from 0 Hz to 300 GHz). Operator position geometric mean electric field levels for RF sources ranged between 0.8 V/m (plasma etcher) and 320 V/m (RF sealer), while magnetic fields ranged from 0.02 A/m (speed radar) to 0.6 A/m (microwave heating). For ELF sources, electric fields ranged between 0.2 V/m (electric forklift) and 11,700 V/m (HVTL-hotsticks), while magnetic fields ranged between 0.14 μT (visual display terminals) and 17 μT (TIG welding). Conclusion The methodology developed allowed the construction of the first EMF-SEM and may be used to summarize similar exposure data for other physical or chemical agents. PMID:27827378

Aptamer Database

PubMed Central

Lee, Jennifer F.; Hesselberth, Jay R.; Meyers, Lauren Ancel; Ellington, Andrew D.

2004-01-01

The aptamer database is designed to contain comprehensive sequence information on aptamers and unnatural ribozymes that have been generated by in vitro selection methods. Such data are not normally collected in ‘natural’ sequence databases, such as GenBank. Besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility, the database serves as a valuable resource for theoretical biologists who describe and explore fitness landscapes. The database is updated monthly and is publicly available at http://aptamer.icmb.utexas.edu/. PMID:14681367

Efficacy of concurrent treatments in idiopathic pulmonary fibrosis patients with a rapid progression of respiratory failure: an analysis of a national administrative database in Japan.

PubMed

Oda, Keishi; Yatera, Kazuhiro; Fujino, Yoshihisa; Ishimoto, Hiroshi; Nakao, Hiroyuki; Hanaka, Tetsuya; Ogoshi, Takaaki; Kido, Takashi; Fushimi, Kiyohide; Matsuda, Shinya; Mukae, Hiroshi

2016-06-08

Some IPF patients show a rapid progression of respiratory failure. Most patients are treated with high-dose corticosteroids. However, no large clinical studies have investigated the prognosis or efficacy of combined treatments including high-dose corticosteroids in IPF patients with a rapid progression of respiratory failure. We enrolled IPF patients who received mechanical ventilation and high-dose corticosteroids between April 2010 and March 2013. Records were extracted from a Japanese nationwide inpatient database. We conducted a retrospective epidemiologic and prognostic analysis. Two hundred nine patients receiving an average of 12.8 days of ventilatory support were enrolled. There were 138 (66 %) fatal cases; the median survival was 21 days. The short-term (within 30 days) and long-term (within 90 days) survival rates were 44.6 and 24.6 %, respectively. The average monthly admission rate among the IPF patients with the rapid progression of respiratory failure in the winter was significantly higher than that in spring (p = 0.018). Survival did not differ to a statistically significant extent in the different geographic areas of Japan. Survivors were significantly younger (p = 0.002) with higher rates of mild dyspnea on admission (p = 0.012), they more frequently underwent bronchoscopy (p < 0.001), and received anticoagulants (p = 0.027), co-trimoxazole (p < 0.001) and macrolide (p = 0.02) more frequently than non-survivors. A multivariate logistic analysis demonstrated that two factors were significantly associated with a poor prognosis: >80 years of age (OR = 2.94, 95 % Cl 1.044-8.303; p = 0.041) and the intravenous administration of high-dose cyclophosphamide (OR = 3.17, 95 % Cl 1.101-9.148; p = 0.033). Undergoing bronchoscopy during intubation (OR = 0.25, 95 % Cl 0.079-0.798; p = 0.019) and the administration of co-trimoxazole (OR = 0.28, 95 % Cl 0.132-0.607; p = 0.001) and macrolides

Solving Relational Database Problems with ORDBMS in an Advanced Database Course

ERIC Educational Resources Information Center

Wang, Ming

2011-01-01

This paper introduces how to use the object-relational database management system (ORDBMS) to solve relational database (RDB) problems in an advanced database course. The purpose of the paper is to provide a guideline for database instructors who desire to incorporate the ORDB technology in their traditional database courses. The paper presents…

Generalized Database Management System Support for Numeric Database Environments.

ERIC Educational Resources Information Center

Dominick, Wayne D.; Weathers, Peggy G.

1982-01-01

This overview of potential for utilizing database management systems (DBMS) within numeric database environments highlights: (1) major features, functions, and characteristics of DBMS; (2) applicability to numeric database environment needs and user needs; (3) current applications of DBMS technology; and (4) research-oriented and…

Mining the Galaxy Zoo Database: Machine Learning Applications

NASA Astrophysics Data System (ADS)

Borne, Kirk D.; Wallin, J.; Vedachalam, A.; Baehr, S.; Lintott, C.; Darg, D.; Smith, A.; Fortson, L.

2010-01-01

The new Zooniverse initiative is addressing the data flood in the sciences through a transformative partnership between professional scientists, volunteer citizen scientists, and machines. As part of this project, we are exploring the application of machine learning techniques to data mining problems associated with the large and growing database of volunteer science results gathered by the Galaxy Zoo citizen science project. We will describe the basic challenge, some machine learning approaches, and early results. One of the motivators for this study is the acquisition (through the Galaxy Zoo results database) of approximately 100 million classification labels for roughly one million galaxies, yielding a tremendously large and rich set of training examples for improving automated galaxy morphological classification algorithms. In our first case study, the goal is to learn which morphological and photometric features in the Sloan Digital Sky Survey (SDSS) database correlate most strongly with user-selected galaxy morphological class. As a corollary to this study, we are also aiming to identify which galaxy parameters in the SDSS database correspond to galaxies that have been the most difficult to classify (based upon large dispersion in their volunter-provided classifications). Our second case study will focus on similar data mining analyses and machine leaning algorithms applied to the Galaxy Zoo catalog of merging and interacting galaxies. The outcomes of this project will have applications in future large sky surveys, such as the LSST (Large Synoptic Survey Telescope) project, which will generate a catalog of 20 billion galaxies and will produce an additional astronomical alert database of approximately 100 thousand events each night for 10 years -- the capabilities and algorithms that we are exploring will assist in the rapid characterization and classification of such massive data streams. This research has been supported in part through NSF award #0941610.

Toward Phase IV, Populating the WOVOdat Database

NASA Astrophysics Data System (ADS)

Ratdomopurbo, A.; Newhall, C. G.; Schwandner, F. M.; Selva, J.; Ueda, H.

2009-12-01

One of challenges for volcanologists is the fact that more and more people are likely to live on volcanic slopes. Information about volcanic activity during unrest should be accurate and rapidly distributed. As unrest may lead to eruption, evacuation may be necessary to minimize damage and casualties. The decision to evacuate people is usually based on the interpretation of monitoring data. Over the past several decades, monitoring volcanoes has used more and more sophisticated instruments. A huge volume of data is collected in order to understand the state of activity and behaviour of a volcano. WOVOdat, The World Organization of Volcano Observatories (WOVO) Database of Volcanic Unrest, will provide context within which scientists can interpret the state of their own volcano, during and between crises. After a decision during the 2000 IAVCEI General Assembly to create WOVOdat, development has passed through several phases, from Concept Development (Phase-I in 2000-2002), Database Design (Phase-II, 2003-2006) and Pilot Testing (Phase-III in 2007-2008). For WOVOdat to be operational, there are still two (2) steps to complete, which are: Database Population (Phase-IV) and Enhancement and Maintenance (Phase-V). Since January 2009, the WOVOdat project is hosted by Earth Observatory of Singapore for at least a 5-year period. According to the original planning in 2002, this 5-year period will be used for completing the Phase-IV. As the WOVOdat design is not yet tested for all types of data, 2009 is still reserved for building the back-end relational database management system (RDBMS) of WOVOdat and testing it with more complex data. Fine-tuning of the WOVOdat’s RDBMS design is being done with each new upload of observatory data. The next and main phase of WOVOdat development will be data population, managing data transfer from multiple observatory formats to WOVOdat format. Data population will depend on two important things, the availability of SQL database in volcano

Idiopathic environmental intolerance attributed to electromagnetic fields: a content analysis of British newspaper reports.

PubMed

Eldridge-Thomas, Buffy; Rubin, G James

2013-01-01

Idiopathic environmental intolerance attributed to electromagnetic fields (IEI-EMF) is a controversial condition in which people describe symptoms following exposure to electromagnetic fields from everyday electrical devices. However, double-blind experiments have found no convincing evidence that electromagnetic fields cause these symptoms. In this study, we assessed whether recent newspaper reporting in the UK reflected this scientific evidence. We searched a database of newspaper articles to identify all those that contained IEI-EMF related keywords and selected a random sample of 60 for content analysis. For our primary outcomes, we assessed how many articles mainly or wholly presented an electromagnetic cause for IEI-EMF and how many discussed unproven treatments for the condition such as strategies intended to reduce exposure to electromagnetic fields or the use of complementary and alternative therapies. We also assessed whether the type of information source used by a newspaper article (e.g. scientist, person with IEI-EMF, politician) or the type of newspaper (broadsheet, tabloid, local or regional) was associated with either outcome. Of the 60 articles, 43 (71.7%) presented a mainly electromagnetic cause, compared to 13 (21.7%) which presented mainly non-electromagnetic causes and 4 (6.7%) which did not discuss a cause. 29 (48.3%) did not mention any potential treatment, while 24 (40.0%) mentioned eletromagnetic field related strategies and 12 (20.0%) mentioned complementary or alternative therapies. Articles which quoted someone with IEI-EMF were significantly more likely to report an electromagnetic cause and to present unproven treatments. Those which used a scientist as a source were more likely to present a non-electromagnetic cause for the condition. The widespread poor reporting we identified is disappointing and has the potential for to encourage more people to misattribute their symptoms to electromagnetic fields. Scientists should remain engaged

“Triple M” Effect: A Proposed Mechanism to Explain Increased Dental Amalgam Microleakage after Exposure to Radiofrequency Electromagnetic Radiation

PubMed Central

Mortazavi, Gh.; Mortazavi, S.A.R.; Mehdizadeh, A.R.

2018-01-01

A large body of evidence now indicates that the amount of mercury released from dental amalgam fillings can be significantly accelerated by exposure to radiofrequency electromagnetic fields (RF-EMFs) such as common mobile phones and magnetic resonance imaging (MRI). Studies performed on the increased microleakage of dental amalgam restorations after exposure to RF-EMFs have further supported these findings. Although the accelerated microleakage induced by RF-EMFs is clinically significant, the entire mechanisms of this phenomenon are not clearly understood. In this paper, we introduce “Triple M” effect, a new evidence-based theory which can explain the accelerated microleakage of dental amalgam fillings after exposure to different sources of electromagnetic radiation. Based on this theory, there are saliva-filled tiny spaces between amalgam and the tooth. Exposure of the oral cavity to RF-EMFs increases the energy of these small amounts of saliva. Due to the small mass of saliva in these tiny spaces, a small amount of energy will be required for heating. Moreover, reflection of the radiofrequency radiation on the inner walls of the tiny spaces causes interference which in turn produces some “hot spots” in these spaces. Finally, formation of gas bubbles in response to increased temperature and very rapid expansion of these bubbles will accelerate the microleakage of amalgam. Experiments that confirm the validity of this theory are discussed. PMID:29732349

"Triple M" Effect: A Proposed Mechanism to Explain Increased Dental Amalgam Microleakage after Exposure to Radiofrequency Electromagnetic Radiation.

PubMed

Mortazavi, Gh; Mortazavi, S A R; Mehdizadeh, A R

2018-03-01

A large body of evidence now indicates that the amount of mercury released from dental amalgam fillings can be significantly accelerated by exposure to radiofrequency electromagnetic fields (RF-EMFs) such as common mobile phones and magnetic resonance imaging (MRI). Studies performed on the increased microleakage of dental amalgam restorations after exposure to RF-EMFs have further supported these findings. Although the accelerated microleakage induced by RF-EMFs is clinically significant, the entire mechanisms of this phenomenon are not clearly understood. In this paper, we introduce "Triple M" effect, a new evidence-based theory which can explain the accelerated microleakage of dental amalgam fillings after exposure to different sources of electromagnetic radiation. Based on this theory, there are saliva-filled tiny spaces between amalgam and the tooth. Exposure of the oral cavity to RF-EMFs increases the energy of these small amounts of saliva. Due to the small mass of saliva in these tiny spaces, a small amount of energy will be required for heating. Moreover, reflection of the radiofrequency radiation on the inner walls of the tiny spaces causes interference which in turn produces some "hot spots" in these spaces. Finally, formation of gas bubbles in response to increased temperature and very rapid expansion of these bubbles will accelerate the microleakage of amalgam. Experiments that confirm the validity of this theory are discussed.

Intraoperative observation of changes in cochlear nerve action potentials during exposure to electromagnetic fields generated by mobile phones.

PubMed

Colletti, Vittorio; Mandalà, Marco; Manganotti, Paolo; Ramat, Stefano; Sacchetto, Luca; Colletti, Liliana

2011-07-01

The rapid spread of devices generating electromagnetic fields (EMF) has raised concerns as to the possible effects of this technology on humans. The auditory system is the neural organ most frequently and directly exposed to electromagnetic activity owing to the daily use of mobile phones. In recent publications, a possible correlation between mobile phone usage and central nervous system tumours has been detected. Very recently a deterioration in otoacoustic emissions and in the auditory middle latency responses after intensive and long-term magnetic field exposure in humans has been demonstrated. To determine with objective observations if exposure to mobile phone EMF affects acoustically evoked cochlear nerve compound action potentials, seven patients suffering from Ménière's disease and undergoing retrosigmoid vestibular neurectomy were exposed to the effects of mobile phone placed over the craniotomy for 5 min. All patients showed a substantial decrease in amplitude and a significant increase in latency of cochlear nerve compound action potentials during the 5 min of exposure to EMF. These changes lasted for a period of around 5 min after exposure. The possibility that EMF can produce relatively long-lasting effects on cochlear nerve conduction is discussed and analysed in light of contrasting previous literature obtained under non-surgical conditions. Limitations of this novel approach, including the effects of the anaesthetics, craniotomy and surgical procedure, are presented in detail.

Database Administrator

ERIC Educational Resources Information Center

Moore, Pam

2010-01-01

The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

FIREMON Database

Treesearch

John F. Caratti

2006-01-01

The FIREMON database software allows users to enter data, store, analyze, and summarize plot data, photos, and related documents. The FIREMON database software consists of a Java application and a Microsoft® Access database. The Java application provides the user interface with FIREMON data through data entry forms, data summary reports, and other data management tools...

Influence of Radiofrequency Electromagnetic Fields on the Fertility System: Protocol for a Systematic Review and Meta-Analysis.

PubMed

Roozbeh, Nasibeh; Abdi, Fatemeh; Amraee, Azadeh; Atarodi Kashani, Zahra; Darvish, Leili

2018-02-08

Due to the increased number of users of mobile phones, tablets, and other devices over the past few years, concerns about the potential impact of mobile phones on health are growing. The influence of mobile phone exposure on male fertility has been studied in recent years. Other research has shown that electromagnetic fields (EMFs) increase macrophages in the corpus luteum and growing follicles. Due to conflicting results among studies and since no systematic review has been performed to analyze the effects of radiofrequency EMF exposure from electronic devices on the fertility system in recent years, this evidence-based study is necessary. The main objectives of this study are to determine the best evidence associated with the influence of radiofrequency EMFs on the fertility system and to provide insight into a potential mechanism using our observations. In this systematic review, the databases and gray literature will be searched with no language and date limitation. The following databases will be searched: Cochrane Library, MEDLINE, PubMed, EMBASE, CINAHL, ProQuest, Scopus, Science Direct, Google Scholar, and other Persian databases. The combination of the Medical Subject Heading terms "radiofrequency electromagnetic" and "male reproductive system" or "female reproductive system" will be searched. Observational study designs will be included but case reports, case series, reviews, and letters to the editor will be excluded. Papers selected for retrieval will be evaluated by two independent referees for methodological validation before entering a review using the Newcastle-Ottawa Scale for nonrandomized studies and cohort studies. The results of this study will be submitted to a peer-reviewed journal for publication and also presented at PROSPERO. This systematic review will provide evidence-based data on the effect of radiofrequency EMFs on the fertility system. This article will also classify the harmful effect of radiofrequency waves on primary and

RAPADAPTE for rapid guideline development: high-quality clinical guidelines can be rapidly developed with limited resources.

PubMed

Alper, Brian S; Tristan, Mario; Ramirez-Morera, Anggie; Vreugdenhil, Maria M T; Van Zuuren, Esther J; Fedorowicz, Zbys

2016-06-01

Guideline development is challenging, expensive and labor-intensive. A high-quality guideline with 90 recommendations for breast cancer treatment was developed within 6 months with limited resources in Costa Rica. We describe the experience and propose a process others can use and adapt.The ADAPTE method (using existing guidelines to minimize repeating work that has been done) was used but existing guidelines were not current. The method was extended to use databases that systematically identify, appraise and synthesize evidence for clinical application (DynaMed, EBM Guidelines) to provide current evidence searches and critical appraisal of evidence. The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to rate the quality of evidence and the strength of recommendations. Draft recommendations with supporting evidence were provided to panel members for facilitated voting to target panel discussion to areas necessary for reaching consensus.Training panelists in guideline development methodology facilitated rapid consensus development. Extending 'guideline adaptation' to 'evidence database adaptation' was highly effective and efficient. Methods were created to simplify mapping DynaMed evidence ratings to GRADE ratings. Twelve steps are presented to facilitate rapid guideline development and enable further adaptation by others.This is a case report and the RAPADAPTE method was retrospectively derived. Prospective replication and validation will support advances for the guideline development community. If guideline development can be accelerated without compromising validity and relevance of the resulting recommendations this would greatly improve our ability to impact clinical care. © The Author 2016. Published by Oxford University Press in association with the International Society for Quality in Health Care; all rights reserved.

The BioGRID Interaction Database: 2011 update

PubMed Central

Stark, Chris; Breitkreutz, Bobby-Joe; Chatr-aryamontri, Andrew; Boucher, Lorrie; Oughtred, Rose; Livstone, Michael S.; Nixon, Julie; Van Auken, Kimberly; Wang, Xiaodong; Shi, Xiaoqi; Reguly, Teresa; Rust, Jennifer M.; Winter, Andrew; Dolinski, Kara; Tyers, Mike

2011-01-01

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (http://www.thebiogrid.org). BioGRID currently holds 347 966 interactions (170 162 genetic, 177 804 protein) curated from both high-throughput data sets and individual focused studies, as derived from over 23 000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana), and efforts to expand curation across multiple metazoan species are underway. The BioGRID houses 48 831 human protein interactions that have been curated from 10 247 publications. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.0 web interface contains new search and display features that enable rapid queries across multiple data types and sources. An automated Interaction Management System (IMS) is used to prioritize, coordinate and track curation across international sites and projects. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including PSI MI XML. Source code for BioGRID 3.0 is freely available without any restrictions. PMID:21071413

Comparison of the NCI open database with seven large chemical structural databases.

PubMed

Voigt, J H; Bienfait, B; Wang, S; Nicklaus, M C

2001-01-01

Eight large chemical databases have been analyzed and compared to each other. Central to this comparison is the open National Cancer Institute (NCI) database, consisting of approximately 250 000 structures. The other databases analyzed are the Available Chemicals Directory ("ACD," from MDL, release 1.99, 3D-version); the ChemACX ("ACX," from CamSoft, Version 4.5); the Maybridge Catalog and the Asinex database (both as distributed by CamSoft as part of ChemInfo 4.5); the Sigma-Aldrich Catalog (CD-ROM, 1999 Version); the World Drug Index ("WDI," Derwent, version 1999.03); and the organic part of the Cambridge Crystallographic Database ("CSD," from Cambridge Crystallographic Data Center, 1999 Version 5.18). The database properties analyzed are internal duplication rates; compounds unique to each database; cumulative occurrence of compounds in an increasing number of databases; overlap of identical compounds between two databases; similarity overlap; diversity; and others. The crystallographic database CSD and the WDI show somewhat less overlap with the other databases than those with each other. In particular the collections of commercial compounds and compilations of vendor catalogs have a substantial degree of overlap among each other. Still, no database is completely a subset of any other, and each appears to have its own niche and thus "raison d'être". The NCI database has by far the highest number of compounds that are unique to it. Approximately 200 000 of the NCI structures were not found in any of the other analyzed databases.

PrimateLit Database

Science.gov Websites

Primate Info Net Related Databases NCRR PrimateLit: A bibliographic database for primatology Top of any problems with this service. We welcome your feedback. The PrimateLit database is no longer being Resources, National Institutes of Health. The database is a collaborative project of the Wisconsin Primate

Rapid Response Tools and Datasets for Post-fire Hydrological Modeling

NASA Astrophysics Data System (ADS)

Miller, Mary Ellen; MacDonald, Lee H.; Billmire, Michael; Elliot, William J.; Robichaud, Pete R.

2016-04-01

Rapid response is critical following natural disasters. Flooding, erosion, and debris flows are a major threat to life, property and municipal water supplies after moderate and high severity wildfires. The problem is that mitigation measures must be rapidly implemented if they are to be effective, but they are expensive and cannot be applied everywhere. Fires, runoff, and erosion risks also are highly heterogeneous in space, so there is an urgent need for a rapid, spatially-explicit assessment. Past post-fire modeling efforts have usually relied on lumped, conceptual models because of the lack of readily available, spatially-explicit data layers on the key controls of topography, vegetation type, climate, and soil characteristics. The purpose of this project is to develop a set of spatially-explicit data layers for use in process-based models such as WEPP, and to make these data layers freely available. The resulting interactive online modeling database (http://geodjango.mtri.org/geowepp/) is now operational and publically available for 17 western states in the USA. After a fire, users only need to upload a soil burn severity map, and this is combined with the pre-existing data layers to generate the model inputs needed for spatially explicit models such as GeoWEPP (Renschler, 2003). The development of this online database has allowed us to predict post-fire erosion and various remediation scenarios in just 1-7 days for six fires ranging in size from 4-540 km2. These initial successes have stimulated efforts to further improve the spatial extent and amount of data, and add functionality to support the USGS debris flow model, batch processing for Disturbed WEPP (Elliot et al., 2004) and ERMiT (Robichaud et al., 2007), and to support erosion modeling for other land uses, such as agriculture or mining. The design and techniques used to create the database and the modeling interface are readily repeatable for any area or country that has the necessary topography

Genome databases

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

Courteau, J.

1991-10-11

Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts inmore » the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.« less

GPCR & company: databases and servers for GPCRs and interacting partners.

PubMed

Kowalsman, Noga; Niv, Masha Y

2014-01-01

G-protein-coupled receptors (GPCRs) are a large superfamily of membrane receptors that are involved in a wide range of signaling pathways. To fulfill their tasks, GPCRs interact with a variety of partners, including small molecules, lipids and proteins. They are accompanied by different proteins during all phases of their life cycle. Therefore, GPCR interactions with their partners are of great interest in basic cell-signaling research and in drug discovery.Due to the rapid development of computers and internet communication, knowledge and data can be easily shared within the worldwide research community via freely available databases and servers. These provide an abundance of biological, chemical and pharmacological information.This chapter describes the available web resources for investigating GPCR interactions. We review about 40 freely available databases and servers, and provide a few sentences about the essence and the data they supply. For simplification, the databases and servers were grouped under the following topics: general GPCR-ligand interactions; particular families of GPCRs and their ligands; GPCR oligomerization; GPCR interactions with intracellular partners; and structural information on GPCRs. In conclusion, a multitude of useful tools are currently available. Summary tables are provided to ease navigation between the numerous and partially overlapping resources. Suggestions for future enhancements of the online tools include the addition of links from general to specialized databases and enabling usage of user-supplied template for GPCR structural modeling.

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

PubMed Central

2010-01-01

Background Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file formats, or directly from external databases through specialized third party plugins. However, molecular data are often stored in relational databases with their own specific structure, for which dedicated plugins do not exist. Therefore, a more generic solution is presented. Results A new Cytoscape plugin 'CytoSQL' is developed to connect Cytoscape to any relational database. It allows to launch SQL ('Structured Query Language') queries from within Cytoscape, with the option to inject node or edge features of an existing network as SQL arguments, and to convert the retrieved data to Cytoscape network components. Supported by a set of case studies we demonstrate the flexibility and the power of the CytoSQL plugin in converting specific data subsets into meaningful network representations. Conclusions CytoSQL offers a unified approach to let Cytoscape interact with relational databases. Thanks to the power of the SQL syntax, this tool can rapidly generate and enrich networks according to very complex criteria. The plugin is available at http://www.ptools.ua.ac.be/CytoSQL. PMID:20594316

Application of the ToxMiner Database: Network Analysis ...

EPA Pesticide Factsheets

The US EPA ToxCast program is using in vitro HTS (High-Throughput Screening) methods to profile and model bioactivity of environmental chemicals. The main goals of the ToxCast program are to generate predictive signatures of toxicity, and ultimately provide rapid and cost-effective alternatives to animal testing. The chemicals selected for Phase I are composed largely by a diverse set of pesticide active ingredients, which had sufficient supporting in vivo data included as part of their registration process with the EPA. Other miscellaneous chemicals of environmental concern were also included. Application of HTS to environmental toxicants is a novel approach to predictive toxicology and health risk assessment, and differs from what is required for drug efficacy screening in that biochemical interaction of environmental chemicals are sometimes weaker than that seen with drugs and their intended targets. Additionally, the chemical space covered by environmental chemicals is much broader compared to that of pharmaceuticals. The ToxMiner database has been created and added to the EPA’s ACToR (Aggregated Computational Toxicology Resource) chemical database. One purpose of the ToxMiner database is to link biological, metabolic, and cellular pathway data to genes and in vitro assay data for the initial subset of chemicals screened in the ToxCast Phase I HTS assays. Also included in ToxMiner is human disease information, which correlates with ToxCast assays that ta

DataBase on Demand

NASA Astrophysics Data System (ADS)

Gaspar Aparicio, R.; Gomez, D.; Coterillo Coz, I.; Wojcik, D.

2012-12-01

At CERN a number of key database applications are running on user-managed MySQL database services. The database on demand project was born out of an idea to provide the CERN user community with an environment to develop and run database services outside of the actual centralised Oracle based database services. The Database on Demand (DBoD) empowers the user to perform certain actions that had been traditionally done by database administrators, DBA's, providing an enterprise platform for database applications. It also allows the CERN user community to run different database engines, e.g. presently open community version of MySQL and single instance Oracle database server. This article describes a technology approach to face this challenge, a service level agreement, the SLA that the project provides, and an evolution of possible scenarios.

Molecular and Functional Characterization of Broccoli EMBRYONIC FLOWER 2 Genes

PubMed Central

Chen, Long-Fang O.; Lin, Chun-Hung; Lai, Ying-Mi; Huang, Jia-Yuan; Sung, Zinmay Renee

2012-01-01

Polycomb group (PcG) proteins regulate major developmental processes in Arabidopsis. EMBRYONIC FLOWER 2 (EMF2), the VEFS domain-containing PcG gene, regulates diverse genetic pathways and is required for vegetative development and plant survival. Despite widespread EMF2-like sequences in plants, little is known about their function other than in Arabidopsis and rice. To study the role of EMF2 in broccoli (Brassica oleracea var. italica cv. Elegance) development, we identified two broccoli EMF2 (BoEMF2) genes with sequence homology to and a similar gene expression pattern to that in Arabidopsis (AtEMF2). Reducing their expression in broccoli resulted in aberrant phenotypes and gene expression patterns. BoEMF2 regulates genes involved in diverse developmental and stress programs similar to AtEMF2 in Arabidopsis. However, BoEMF2 differs from AtEMF2 in the regulation of flower organ identity, cell proliferation and elongation, and death-related genes, which may explain the distinct phenotypes. The expression of BoEMF2.1 in the Arabidopsis emf2 mutant (Rescued emf2) partially rescued the mutant phenotype and restored the gene expression pattern to that of the wild type. Many EMF2-mediated molecular and developmental functions are conserved in broccoli and Arabidopsis. Furthermore, the restored gene expression pattern in Rescued emf2 provides insights into the molecular basis of PcG-mediated growth and development. PMID:22537758

The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses.

PubMed

Kuiken, Carla; Thurmond, Jim; Dimitrijevic, Mira; Yoon, Hyejin

2012-01-01

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55,000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52-61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38-D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov.

The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses

PubMed Central

Kuiken, Carla; Thurmond, Jim; Dimitrijevic, Mira; Yoon, Hyejin

2012-01-01

Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55 000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52–61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38–D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov. PMID:22064861

Using a Semi-Realistic Database to Support a Database Course

ERIC Educational Resources Information Center

Yue, Kwok-Bun

2013-01-01

A common problem for university relational database courses is to construct effective databases for instructions and assignments. Highly simplified "toy" databases are easily available for teaching, learning, and practicing. However, they do not reflect the complexity and practical considerations that students encounter in real-world…

A new version of the RDP (Ribosomal Database Project)

NASA Technical Reports Server (NTRS)

Maidak, B. L.; Cole, J. R.; Parker, C. T. Jr; Garrity, G. M.; Larsen, N.; Li, B.; Lilburn, T. G.; McCaughey, M. J.; Olsen, G. J.; Overbeek, R.;

A tuberculosis biomarker database: the key to novel TB diagnostics.

PubMed

Yerlikaya, Seda; Broger, Tobias; MacLean, Emily; Pai, Madhukar; Denkinger, Claudia M

2017-03-01

New diagnostic innovations for tuberculosis (TB), including point-of-care solutions, are critical to reach the goals of the End TB Strategy. However, despite decades of research, numerous reports on new biomarker candidates, and significant investment, no well-performing, simple and rapid TB diagnostic test is yet available on the market, and the search for accurate, non-DNA biomarkers remains a priority. To help overcome this 'biomarker pipeline problem', FIND and partners are working on the development of a well-curated and user-friendly TB biomarker database. The web-based database will enable the dynamic tracking of evidence surrounding biomarker candidates in relation to target product profiles (TPPs) for needed TB diagnostics. It will be able to accommodate raw datasets and facilitate the verification of promising biomarker candidates and the identification of novel biomarker combinations. As such, the database will simplify data and knowledge sharing, empower collaboration, help in the coordination of efforts and allocation of resources, streamline the verification and validation of biomarker candidates, and ultimately lead to an accelerated translation into clinically useful tools. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Evolution of the use of relational and NoSQL databases in the ATLAS experiment

NASA Astrophysics Data System (ADS)

Barberis, D.

2016-09-01

The ATLAS experiment used for many years a large database infrastructure based on Oracle to store several different types of non-event data: time-dependent detector configuration and conditions data, calibrations and alignments, configurations of Grid sites, catalogues for data management tools, job records for distributed workload management tools, run and event metadata. The rapid development of "NoSQL" databases (structured storage services) in the last five years allowed an extended and complementary usage of traditional relational databases and new structured storage tools in order to improve the performance of existing applications and to extend their functionalities using the possibilities offered by the modern storage systems. The trend is towards using the best tool for each kind of data, separating for example the intrinsically relational metadata from payload storage, and records that are frequently updated and benefit from transactions from archived information. Access to all components has to be orchestrated by specialised services that run on front-end machines and shield the user from the complexity of data storage infrastructure. This paper describes this technology evolution in the ATLAS database infrastructure and presents a few examples of large database applications that benefit from it.

NATIVE HEALTH DATABASES: NATIVE HEALTH RESEARCH DATABASE (NHRD)

EPA Science Inventory

The Native Health Databases contain bibliographic information and abstracts of health-related articles, reports, surveys, and other resource documents pertaining to the health and health care of American Indians, Alaska Natives, and Canadian First Nations. The databases provide i...

JetWeb: A WWW interface and database for Monte Carlo tuning and validation

NASA Astrophysics Data System (ADS)

Butterworth, J. M.; Butterworth, S.

2003-06-01

A World Wide Web interface to a Monte Carlo tuning facility is described. The aim of the package is to allow rapid and reproducible comparisons to be made between detailed measurements at high-energy physics colliders and general physics simulation packages. The package includes a relational database, a Java servlet query and display facility, and clean interfaces to simulation packages and their parameters.

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

PubMed

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

2013-01-01

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

MIPS PlantsDB: a database framework for comparative plant genome research

PubMed Central

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

2013-01-01

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB–plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834–D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB. PMID:23203886

Spatial electromagnetic field intensity modelling of global system for mobile communication base stations in the Istanbul Technical University Ayazaga campus area.

PubMed

Boz, Kubra; Denli, Hayri Hakan

2018-05-07

The rapid development of the global system for mobile communication services and the consequent increased electromagnetic field (EMF) exposure to the human body have generated debate on the potential danger with respect to human health. The many research studies focused on this subject have, however, not provided any certain evidence about harmful consequences due to mobile communication systems. On the other hand, there are still views suggesting such exposure might affect the human body in different ways. To reduce such effects to a minimum, the International Commission on Non-Ionizing Radiation Protection (ICNIRP) has declared boundary values for the energy released by the base stations, which are the main source of the electromagnetic fields. These values are accepted by many countries in various parts of the world. The aim of this study was to create EMF intensity maps for the area covered by Istanbul Technical University (ITU) and find areas of potential risk with regard to health considering the current situation and future trends. In this study, the field intensities of electromagnetic signals issued at the frequencies of 900 and 1800 MHz were measured in V/m at 29 pre-specified survey points using a spectrum analyzer (Spectran HF-6065). Geographic information systems and spatial interpolation techniques were used to produce EMF intensity maps. Three different spatial interpolation methods, minimum mean square error, Radial Basis and Empirical Bayesian Kriging, were compared. The results were geographically analyzed and the measurements expressed as heat maps covering the study area. Using these maps, the values measured were compared with the EMF intensity standards issued by ICNIRP. The results showed that the exposure levels to the EMF intensities were all within the ICNIRP limits at the ITU study area. However, since the EMF intensity level with respect to human health is not known, it is not possible to confirm if these levels are safe or not.

Molecular Imaging and Contrast Agent Database (MICAD): evolution and progress.

PubMed

Chopra, Arvind; Shan, Liang; Eckelman, W C; Leung, Kam; Latterner, Martin; Bryant, Stephen H; Menkens, Anne

2012-02-01

The purpose of writing this review is to showcase the Molecular Imaging and Contrast Agent Database (MICAD; www.micad.nlm.nih.gov ) to students, researchers, and clinical investigators interested in the different aspects of molecular imaging. This database provides freely accessible, current, online scientific information regarding molecular imaging (MI) probes and contrast agents (CA) used for positron emission tomography, single-photon emission computed tomography, magnetic resonance imaging, X-ray/computed tomography, optical imaging and ultrasound imaging. Detailed information on >1,000 agents in MICAD is provided in a chapter format and can be accessed through PubMed. Lists containing >4,250 unique MI probes and CAs published in peer-reviewed journals and agents approved by the United States Food and Drug Administration as well as a comma separated values file summarizing all chapters in the database can be downloaded from the MICAD homepage. Users can search for agents in MICAD on the basis of imaging modality, source of signal/contrast, agent or target category, pre-clinical or clinical studies, and text words. Chapters in MICAD describe the chemical characteristics (structures linked to PubChem), the in vitro and in vivo activities, and other relevant information regarding an imaging agent. All references in the chapters have links to PubMed. A Supplemental Information Section in each chapter is available to share unpublished information regarding an agent. A Guest Author Program is available to facilitate rapid expansion of the database. Members of the imaging community registered with MICAD periodically receive an e-mail announcement (eAnnouncement) that lists new chapters uploaded to the database. Users of MICAD are encouraged to provide feedback, comments, or suggestions for further improvement of the database by writing to the editors at micad@nlm.nih.gov.

Molecular Imaging and Contrast Agent Database (MICAD): Evolution and Progress

PubMed Central

Chopra, Arvind; Shan, Liang; Eckelman, W. C.; Leung, Kam; Latterner, Martin; Bryant, Stephen H.; Menkens, Anne

2011-01-01

The purpose of writing this review is to showcase the Molecular Imaging and Contrast Agent Database (MICAD; www.micad.nlm.nih.gov) to students, researchers and clinical investigators interested in the different aspects of molecular imaging. This database provides freely accessible, current, online scientific information regarding molecular imaging (MI) probes and contrast agents (CA) used for positron emission tomography, single-photon emission computed tomography, magnetic resonance imaging, x-ray/computed tomography, optical imaging and ultrasound imaging. Detailed information on >1000 agents in MICAD is provided in a chapter format and can be accessed through PubMed. Lists containing >4250 unique MI probes and CAs published in peer-reviewed journals and agents approved by the United States Food and Drug Administration (FDA) as well as a CSV file summarizing all chapters in the database can be downloaded from the MICAD homepage. Users can search for agents in MICAD on the basis of imaging modality, source of signal/contrast, agent or target category, preclinical or clinical studies, and text words. Chapters in MICAD describe the chemical characteristics (structures linked to PubChem), the in vitro and in vivo activities and other relevant information regarding an imaging agent. All references in the chapters have links to PubMed. A Supplemental Information Section in each chapter is available to share unpublished information regarding an agent. A Guest Author Program is available to facilitate rapid expansion of the database. Members of the imaging community registered with MICAD periodically receive an e-mail announcement (eAnnouncement) that lists new chapters uploaded to the database. Users of MICAD are encouraged to provide feedback, comments or suggestions for further improvement of the database by writing to the editors at: micad@nlm.nih.gov PMID:21989943

Drug residues in urban water: A database for ecotoxicological risk management.

PubMed

Destrieux, Doriane; Laurent, François; Budzinski, Hélène; Pedelucq, Julie; Vervier, Philippe; Gerino, Magali

2017-12-31

Human-use drug residues (DR) are only partially eliminated by waste water treatment plants (WWTPs), so that residual amounts can reach natural waters and cause environmental hazards. In order to properly manage these hazards in the aquatic environment, a database is made available that integrates the concentration ranges for DR, which cause adverse effects for aquatic organisms, and the temporal variations of the ecotoxicological risks. To implement this database for the ecotoxicological risk assessment (ERA database), the required information for each DR is the predicted no effect concentrations (PNECs), along with the predicted environmental concentrations (PECs). The risk assessment is based on the ratio between the PNECs and the PECs. Adverse effect data or PNECs have been found in the publicly available literature for 45 substances. These ecotoxicity test data have been extracted from 125 different sources. This ERA database contains 1157 adverse effect data and 287 PNECs. The efficiency of this ERA database was tested with a data set coming from a simultaneous survey of WWTPs and the natural environment. In this data set, 26 DR were searched for in two WWTPs and in the river. On five sampling dates, concentrations measured in the river for 10 DR could pose environmental problems of which 7 were measured only downstream of WWTP outlets. From scientific literature and measurements, data implementation with unit homogenisation in a single database facilitates the actual ecotoxicological risk assessment, and may be useful for further risk coming from data arising from the future field survey. Moreover, the accumulation of a large ecotoxicity data set in a single database should not only improve knowledge of higher risk molecules but also supply an objective tool to help the rapid and efficient evaluation of the risk. Copyright © 2017 Elsevier B.V. All rights reserved.

Initial Assessment of a Rapid Method of Calculating CEV Environmental Heating

NASA Technical Reports Server (NTRS)

Pickney, John T.; Milliken, Andrew H.

2010-01-01

An innovative method for rapidly calculating spacecraft environmental absorbed heats in planetary orbit is described. The method employs reading a database of pre-calculated orbital absorbed heats and adjusting those heats for desired orbit parameters. The approach differs from traditional Monte Carlo methods that are orbit based with a planet centered coordinate system. The database is based on a spacecraft centered coordinated system where the range of all possible sun and planet look angles are evaluated. In an example case 37,044 orbit configurations were analyzed for average orbital heats on selected spacecraft surfaces. Calculation time was under 2 minutes while a comparable Monte Carlo evaluation would have taken an estimated 26 hours

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

PubMed Central

Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T.; Arenillas, David; Zhao, Xiaobei; Valen, Eivind; Yusuf, Dimas; Lenhard, Boris; Wasserman, Wyeth W.; Sandelin, Albin

2010-01-01

JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database to date: the database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. The introduction of a yeast division brings the convenience of JASPAR to an active research community. As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family. The changes in the database set the system ready for more rapid acquisition of new high-throughput data sources. Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches. PMID:19906716

Rapid learning: a breakthrough agenda.

PubMed

Etheredge, Lynn M

2014-07-01

A "rapid-learning health system" was proposed in a 2007 thematic issue of Health Affairs. The system was envisioned as one that uses evidence-based medicine to quickly determine the best possible treatments for patients. It does so by drawing on electronic health records and the power of big data to access large volumes of information from a variety of sources at high speed. The foundation for a rapid-learning health system was laid during 2007-13 by workshops, policy papers, large public investments in databases and research programs, and developing learning systems. Challenges now include implementing a new clinical research system with several hundred million patients, modernizing clinical trials and registries, devising and funding research on national priorities, and analyzing genetic and other factors that influence diseases and responses to treatment. Next steps also should aim to improve comparative effectiveness research; build on investments in health information technology to standardize handling of genetic information and support information exchange through apps and software modules; and develop new tools, data, and information for clinical decision support. Further advances will require commitment, leadership, and public-private and global collaboration. Project HOPE—The People-to-People Health Foundation, Inc.

Omics databases on kidney disease: where they can be found and how to benefit from them.

PubMed

Papadopoulos, Theofilos; Krochmal, Magdalena; Cisek, Katryna; Fernandes, Marco; Husi, Holger; Stevens, Robert; Bascands, Jean-Loup; Schanstra, Joost P; Klein, Julie

2016-06-01

In the recent decades, the evolution of omics technologies has led to advances in all biological fields, creating a demand for effective storage, management and exchange of rapidly generated data and research discoveries. To address this need, the development of databases of experimental outputs has become a common part of scientific practice in order to serve as knowledge sources and data-sharing platforms, providing information about genes, transcripts, proteins or metabolites. In this review, we present omics databases available currently, with a special focus on their application in kidney research and possibly in clinical practice. Databases are divided into two categories: general databases with a broad information scope and kidney-specific databases distinctively concentrated on kidney pathologies. In research, databases can be used as a rich source of information about pathophysiological mechanisms and molecular targets. In the future, databases will support clinicians with their decisions, providing better and faster diagnoses and setting the direction towards more preventive, personalized medicine. We also provide a test case demonstrating the potential of biological databases in comparing multi-omics datasets and generating new hypotheses to answer a critical and common diagnostic problem in nephrology practice. In the future, employment of databases combined with data integration and data mining should provide powerful insights into unlocking the mysteries of kidney disease, leading to a potential impact on pharmacological intervention and therapeutic disease management.

The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

PubMed

Galperin, Michael Y; Rigden, Daniel J; Fernández-Suárez, Xosé M

2015-01-01

The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Energy Consumption Database

Science.gov Websites

Consumption Database The California Energy Commission has created this on-line database for informal reporting ) classifications. The database also provides easy downloading of energy consumption data into Microsoft Excel (XLSX

Human Mitochondrial Protein Database

National Institute of Standards and Technology Data Gateway

SRD 131 Human Mitochondrial Protein Database (Web, free access)   The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases.

Inhibition of cancer cell growth by exposure to a specific time-varying electromagnetic field involves T-type calcium channels.

PubMed

Buckner, Carly A; Buckner, Alison L; Koren, Stan A; Persinger, Michael A; Lafrenie, Robert M

2015-01-01

Electromagnetic field (EMF) exposures affect many biological systems. The reproducibility of these effects is related to the intensity, duration, frequency, and pattern of the EMF. We have shown that exposure to a specific time-varying EMF can inhibit the growth of malignant cells. Thomas-EMF is a low-intensity, frequency-modulated (25-6 Hz) EMF pattern. Daily, 1 h, exposures to Thomas-EMF inhibited the growth of malignant cell lines including B16-BL6, MDA-MB-231, MCF-7, and HeLa cells but did not affect the growth of non-malignant cells. Thomas-EMF also inhibited B16-BL6 cell proliferation in vivo. B16-BL6 cells implanted in syngeneic C57b mice and exposed daily to Thomas-EMF produced smaller tumours than in sham-treated controls. In vitro studies showed that exposure of malignant cells to Thomas-EMF for > 15 min promoted Ca(2+) influx which could be blocked by inhibitors of voltage-gated T-type Ca(2+) channels. Blocking Ca(2+) uptake also blocked Thomas-EMF-dependent inhibition of cell proliferation. Exposure to Thomas-EMF delayed cell cycle progression and altered cyclin expression consistent with the decrease in cell proliferation. Non-malignant cells did not show any EMF-dependent changes in Ca(2+) influx or cell growth. These data confirm that exposure to a specific EMF pattern can affect cellular processes and that exposure to Thomas-EMF may provide a potential anti-cancer therapy.

Inhibition of Cancer Cell Growth by Exposure to a Specific Time-Varying Electromagnetic Field Involves T-Type Calcium Channels

PubMed Central

Buckner, Carly A.; Buckner, Alison L.; Koren, Stan A.; Persinger, Michael A.; Lafrenie, Robert M.

2015-01-01

Electromagnetic field (EMF) exposures affect many biological systems. The reproducibility of these effects is related to the intensity, duration, frequency, and pattern of the EMF. We have shown that exposure to a specific time-varying EMF can inhibit the growth of malignant cells. Thomas-EMF is a low-intensity, frequency-modulated (25-6 Hz) EMF pattern. Daily, 1 h, exposures to Thomas-EMF inhibited the growth of malignant cell lines including B16-BL6, MDA-MB-231, MCF-7, and HeLa cells but did not affect the growth of non-malignant cells. Thomas-EMF also inhibited B16-BL6 cell proliferation in vivo. B16-BL6 cells implanted in syngeneic C57b mice and exposed daily to Thomas-EMF produced smaller tumours than in sham-treated controls. In vitro studies showed that exposure of malignant cells to Thomas-EMF for > 15 min promoted Ca2+ influx which could be blocked by inhibitors of voltage-gated T-type Ca2+ channels. Blocking Ca2+ uptake also blocked Thomas-EMF-dependent inhibition of cell proliferation. Exposure to Thomas-EMF delayed cell cycle progression and altered cyclin expression consistent with the decrease in cell proliferation. Non-malignant cells did not show any EMF-dependent changes in Ca2+ influx or cell growth. These data confirm that exposure to a specific EMF pattern can affect cellular processes and that exposure to Thomas-EMF may provide a potential anti-cancer therapy. PMID:25875081

Perception of health risks of electromagnetic fields by MRI radiographers and airport security officers compared to the general Dutch working population: a cross sectional analysis

PubMed Central

2011-01-01

Background The amount of exposure to electromagnetic fields (EMF) at work is mainly determined by an individual's occupation and may differ from exposure at home. It is, however, unknown how different occupational groups perceive possible adverse health effects of EMF. Methods Three occupational groups, the general Dutch working population (n = 567), airport security officers who work with metal detectors (n = 106), and MRI radiographers who work with MRI (n = 193), were compared on perceived risk of and positive and negative feelings towards EMF in general and of different EMF sources, and health concerns by using analyses of variances. Data were collected via an internet survey. Results Overall, MRI radiographers had a lower perceived risk, felt less negative, and more positive towards EMF and different sources of EMF than the general working population and the security officers. For security officers, feeling more positive about EMF was not significantly related to perceived risk of EMF in general or EMF of domestic sources. Feeling positive about a source did not generalize to a lower perceived risk, while negative feelings were stronger related to perceived risk. MRI radiographers had fewer health concerns regarding EMF than the other two groups, although they considered it more likely that EMF could cause physical complaints. Conclusions These data show that although differences in occupation appear to be reflected in different perceptions of EMF, the level of occupational exposure to EMF as such does not predict the perceived health risk of EMF. PMID:22070906

Rapid Polymer Sequencer

NASA Technical Reports Server (NTRS)

Stolc, Viktor (Inventor); Brock, Mathew W. (Inventor)

2011-01-01

Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal or transverse direction at the tip, a polymer sequence is passed through the tip, and a change in an electrical current signal is measured as each polymer component passes through the tip. Each measured change in electrical current signals is compared with a database of reference signals, with each reference signal identified with a polymer component, to identify the unknown polymer component. The tip preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

Biofuel Database

National Institute of Standards and Technology Data Gateway

Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

Teaching Case: Adapting the Access Northwind Database to Support a Database Course

ERIC Educational Resources Information Center

Dyer, John N.; Rogers, Camille

2015-01-01

A common problem encountered when teaching database courses is that few large illustrative databases exist to support teaching and learning. Most database textbooks have small "toy" databases that are chapter objective specific, and thus do not support application over the complete domain of design, implementation and management concepts…

BoreholeAR: A mobile tablet application for effective borehole database visualization using an augmented reality technology

NASA Astrophysics Data System (ADS)

Lee, Sangho; Suh, Jangwon; Park, Hyeong-Dong

2015-03-01

Boring logs are widely used in geological field studies since the data describes various attributes of underground and surface environments. However, it is difficult to manage multiple boring logs in the field as the conventional management and visualization methods are not suitable for integrating and combining large data sets. We developed an iPad application to enable its user to search the boring log rapidly and visualize them using the augmented reality (AR) technique. For the development of the application, a standard borehole database appropriate for a mobile-based borehole database management system was designed. The application consists of three modules: an AR module, a map module, and a database module. The AR module superimposes borehole data on camera imagery as viewed by the user and provides intuitive visualization of borehole locations. The map module shows the locations of corresponding borehole data on a 2D map with additional map layers. The database module provides data management functions for large borehole databases for other modules. Field survey was also carried out using more than 100,000 borehole data.

Applications of GIS and database technologies to manage a Karst Feature Database

USGS Publications Warehouse

Gao, Y.; Tipping, R.G.; Alexander, E.C.

2006-01-01

This paper describes the management of a Karst Feature Database (KFD) in Minnesota. Two sets of applications in both GIS and Database Management System (DBMS) have been developed for the KFD of Minnesota. These applications were used to manage and to enhance the usability of the KFD. Structured Query Language (SQL) was used to manipulate transactions of the database and to facilitate the functionality of the user interfaces. The Database Administrator (DBA) authorized users with different access permissions to enhance the security of the database. Database consistency and recovery are accomplished by creating data logs and maintaining backups on a regular basis. The working database provides guidelines and management tools for future studies of karst features in Minnesota. The methodology of designing this DBMS is applicable to develop GIS-based databases to analyze and manage geomorphic and hydrologic datasets at both regional and local scales. The short-term goal of this research is to develop a regional KFD for the Upper Mississippi Valley Karst and the long-term goal is to expand this database to manage and study karst features at national and global scales.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry and database for identification of Legionella species.

PubMed

He, Ying; Chang, Tsung C; Li, Haijing; Shi, Gongyi; Tang, Yi-Wei

2011-07-01

More than 20 species of Legionella have been identified in relation to human infections. Rapid detection and identification of Legionella isolates is clinically useful to differentiate between infection and contamination and to determine treatment regimens. We explored the use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) Biotyper system (Bruker Daltonik GmbH, Bremen, Germany) for the identification of Legionella species. The MALDI MS spectra were generated and compared with the Biotyper database, which includes 25 Legionella strains covering 22 species and four Legionella pneumophila serogroups. A total of 83 blind-coded Legionella strains, consisting of 54 reference and 29 clinical strains, were analyzed in the study. Overall, the Biotyper system correctly identified 51 (61.4%) of all strains and isolates to the species level. For species included in the Biotyper database, the method identified 51 (86.4%) strains out of 59 Legionella strains to the correct species level, including 24 (100%) L. pneumophila and 27 (77.1%) non-L. pneumophila strains. The remaining 24 Legionella strains, belonging to species not covered by the Biotyper database, were either identified to the Legionella genus level or had no reliable identification. The Biotyper system produces constant and reproducible MALDI MS spectra for Legionella strains and can be used for rapid and accurate Legionella identification. More Legionella strains, especially the non-L. pneumophila strains, need to be included in the current Biotyper database to cover varieties of Legionella species and to increase identification accuracy.

Open Geoscience Database

NASA Astrophysics Data System (ADS)

Bashev, A.

2012-04-01

Currently there is an enormous amount of various geoscience databases. Unfortunately the only users of the majority of the databases are their elaborators. There are several reasons for that: incompaitability, specificity of tasks and objects and so on. However the main obstacles for wide usage of geoscience databases are complexity for elaborators and complication for users. The complexity of architecture leads to high costs that block the public access. The complication prevents users from understanding when and how to use the database. Only databases, associated with GoogleMaps don't have these drawbacks, but they could be hardly named "geoscience" Nevertheless, open and simple geoscience database is necessary at least for educational purposes (see our abstract for ESSI20/EOS12). We developed a database and web interface to work with them and now it is accessible at maps.sch192.ru. In this database a result is a value of a parameter (no matter which) in a station with a certain position, associated with metadata: the date when the result was obtained; the type of a station (lake, soil etc); the contributor that sent the result. Each contributor has its own profile, that allows to estimate the reliability of the data. The results can be represented on GoogleMaps space image as a point in a certain position, coloured according to the value of the parameter. There are default colour scales and each registered user can create the own scale. The results can be also extracted in *.csv file. For both types of representation one could select the data by date, object type, parameter type, area and contributor. The data are uploaded in *.csv format: Name of the station; Lattitude(dd.dddddd); Longitude(ddd.dddddd); Station type; Parameter type; Parameter value; Date(yyyy-mm-dd). The contributor is recognised while entering. This is the minimal set of features that is required to connect a value of a parameter with a position and see the results. All the complicated data

The MAR databases: development and implementation of databases specific for marine metagenomics

PubMed Central

Klemetsen, Terje; Raknes, Inge A; Fu, Juan; Agafonov, Alexander; Balasundaram, Sudhagar V; Tartari, Giacomo; Robertsen, Espen

2018-01-01

Abstract We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. PMID:29106641

PATtyFams: Protein families for the microbial genomes in the PATRIC database

DOE PAGES

Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.; ...

2016-02-08

The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based functionmore » assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). In conclusion, this new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.« less

PATtyFams: Protein families for the microbial genomes in the PATRIC database

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

Davis, James J.; Gerdes, Svetlana; Olsen, Gary J.

The ability to build accurate protein families is a fundamental operation in bioinformatics that influences comparative analyses, genome annotation, and metabolic modeling. For several years we have been maintaining protein families for all microbial genomes in the PATRIC database (Pathosystems Resource Integration Center, patricbrc.org) in order to drive many of the comparative analysis tools that are available through the PATRIC website. However, due to the burgeoning number of genomes, traditional approaches for generating protein families are becoming prohibitive. In this report, we describe a new approach for generating protein families, which we call PATtyFams. This method uses the k-mer-based functionmore » assignments available through RAST (Rapid Annotation using Subsystem Technology) to rapidly guide family formation, and then differentiates the function-based groups into families using a Markov Cluster algorithm (MCL). In conclusion, this new approach for generating protein families is rapid, scalable and has properties that are consistent with alignment-based methods.« less

Human Thermal Model Evaluation Using the JSC Human Thermal Database

NASA Technical Reports Server (NTRS)

Bue, Grant; Makinen, Janice; Cognata, Thomas

2012-01-01

Human thermal modeling has considerable long term utility to human space flight. Such models provide a tool to predict crew survivability in support of vehicle design and to evaluate crew response in untested space environments. It is to the benefit of any such model not only to collect relevant experimental data to correlate it against, but also to maintain an experimental standard or benchmark for future development in a readily and rapidly searchable and software accessible format. The Human thermal database project is intended to do just so; to collect relevant data from literature and experimentation and to store the data in a database structure for immediate and future use as a benchmark to judge human thermal models against, in identifying model strengths and weakness, to support model development and improve correlation, and to statistically quantify a model s predictive quality. The human thermal database developed at the Johnson Space Center (JSC) is intended to evaluate a set of widely used human thermal models. This set includes the Wissler human thermal model, a model that has been widely used to predict the human thermoregulatory response to a variety of cold and hot environments. These models are statistically compared to the current database, which contains experiments of human subjects primarily in air from a literature survey ranging between 1953 and 2004 and from a suited experiment recently performed by the authors, for a quantitative study of relative strength and predictive quality of the models.

Methods for eliciting, annotating, and analyzing databases for child speech development.

PubMed

Beckman, Mary E; Plummer, Andrew R; Munson, Benjamin; Reidy, Patrick F

2017-09-01

Methods from automatic speech recognition (ASR), such as segmentation and forced alignment, have facilitated the rapid annotation and analysis of very large adult speech databases and databases of caregiver-infant interaction, enabling advances in speech science that were unimaginable just a few decades ago. This paper centers on two main problems that must be addressed in order to have analogous resources for developing and exploiting databases of young children's speech. The first problem is to understand and appreciate the differences between adult and child speech that cause ASR models developed for adult speech to fail when applied to child speech. These differences include the fact that children's vocal tracts are smaller than those of adult males and also changing rapidly in size and shape over the course of development, leading to between-talker variability across age groups that dwarfs the between-talker differences between adult men and women. Moreover, children do not achieve fully adult-like speech motor control until they are young adults, and their vocabularies and phonological proficiency are developing as well, leading to considerably more within-talker variability as well as more between-talker variability. The second problem then is to determine what annotation schemas and analysis techniques can most usefully capture relevant aspects of this variability. Indeed, standard acoustic characterizations applied to child speech reveal that adult-centered annotation schemas fail to capture phenomena such as the emergence of covert contrasts in children's developing phonological systems, while also revealing children's nonuniform progression toward community speech norms as they acquire the phonological systems of their native languages. Both problems point to the need for more basic research into the growth and development of the articulatory system (as well as of the lexicon and phonological system) that is oriented explicitly toward the construction of

Perception of health risks of electromagnetic fields by MRI radiographers and airport security officers compared to the general Dutch working population: a cross sectional analysis.

PubMed

van Dongen, Diana; Smid, Tjabe; Timmermans, Daniëlle R M

2011-11-09

The amount of exposure to electromagnetic fields (EMF) at work is mainly determined by an individual's occupation and may differ from exposure at home. It is, however, unknown how different occupational groups perceive possible adverse health effects of EMF. Three occupational groups, the general Dutch working population (n = 567), airport security officers who work with metal detectors (n = 106), and MRI radiographers who work with MRI (n = 193), were compared on perceived risk of and positive and negative feelings towards EMF in general and of different EMF sources, and health concerns by using analyses of variances. Data were collected via an internet survey. Overall, MRI radiographers had a lower perceived risk, felt less negative, and more positive towards EMF and different sources of EMF than the general working population and the security officers. For security officers, feeling more positive about EMF was not significantly related to perceived risk of EMF in general or EMF of domestic sources. Feeling positive about a source did not generalize to a lower perceived risk, while negative feelings were stronger related to perceived risk. MRI radiographers had fewer health concerns regarding EMF than the other two groups, although they considered it more likely that EMF could cause physical complaints. These data show that although differences in occupation appear to be reflected in different perceptions of EMF, the level of occupational exposure to EMF as such does not predict the perceived health risk of EMF. © 2011 van Dongen et al; licensee BioMed Central Ltd.

A Study of Rapidly Developing Low Cloud Ceilings in a Stable Atmosphere at the Florida Spaceport

NASA Technical Reports Server (NTRS)

Wheeler, Mark M.; Case, Jonathan L.; Baggett, G. Wayne

2006-01-01

Forecasters at the Space Meteorology Group (SMG) issue 30 to 90 minute forecasts for low cloud ceilings at the Shuttle Landing Facility (KTTS) in Kennedy Space Center, FL for all Space Shuttle missions. Mission verification statistics have shown cloud ceilings to be the biggest forecast challenge. SMG forecasters are especially concerned with rapidly developing cloud ceilings below 8000 ft. in a stable, capped thermodynamic environment because ceilings below 8000 ft restrict Shuttle landing operations and are the most challenging to predict accurately. This project involves the development of a database of these cases over east-central Florida in order to identify the onset, location, and if possible, dissipation times of rapidly-developing low cloud ceilings. Another goal is to document the atmospheric regimes favoring this type of cloud development to improve forecast skill of such events during Space Shuttle launch and landing operations. A 10-year database of stable, rapid low cloud development days during the daylight hours was compiled for the Florida cool-season months by examining the Cape Canaveral Air Force Station sounding data, and identifying days that had high boundary layer relative humidity associated with a thermally-capped environment below 8000 ft. Archived hourly surface observations from KTTS and Melbourne, Orlando, Sanford, and Ocala, FL were then examined for the onset of cloud ceilings below 8000 ft between 1100 and 2000 UTC. Once the database was supplemented with the hourly surface cloud observations, visible satellite imagery was examined in 30-minute intervals to confirm event occurrences. This paper will present results from some of the rapidly developing cloud ceiling cases and the prevailing meteorological conditions associated with these events, focusing on potential pre-curser information that may help improve their prediction.

Adding Hierarchical Objects to Relational Database General-Purpose XML-Based Information Managements

NASA Technical Reports Server (NTRS)

Lin, Shu-Chun; Knight, Chris; La, Tracy; Maluf, David; Bell, David; Tran, Khai Peter; Gawdiak, Yuri

2006-01-01

NETMARK is a flexible, high-throughput software system for managing, storing, and rapid searching of unstructured and semi-structured documents. NETMARK transforms such documents from their original highly complex, constantly changing, heterogeneous data formats into well-structured, common data formats in using Hypertext Markup Language (HTML) and/or Extensible Markup Language (XML). The software implements an object-relational database system that combines the best practices of the relational model utilizing Structured Query Language (SQL) with those of the object-oriented, semantic database model for creating complex data. In particular, NETMARK takes advantage of the Oracle 8i object-relational database model using physical-address data types for very efficient keyword searches of records across both context and content. NETMARK also supports multiple international standards such as WEBDAV for drag-and-drop file management and SOAP for integrated information management using Web services. The document-organization and -searching capabilities afforded by NETMARK are likely to make this software attractive for use in disciplines as diverse as science, auditing, and law enforcement.

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

PubMed

Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo; Dobson, Paul D; Dunstan, Mark; Jervis, Adrian J; Vinaixa, Maria; Williams, Alan R; Ananiadou, Sophia; Faulon, Jean-Loup; Mendes, Pedro; Kell, Douglas B; Scrutton, Nigel S; Breitling, Rainer

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and-crucially-the relationships between them. Such a resource should be extensible, such that newly discovered relationships-for example, those between novel, synthetic enzymes and non-natural products-can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists.

biochem4j: Integrated and extensible biochemical knowledge through graph databases

PubMed Central

Batista-Navarro, Riza; Dunstan, Mark; Jervis, Adrian J.; Vinaixa, Maria; Ananiadou, Sophia; Faulon, Jean-Loup; Kell, Douglas B.

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and–crucially–the relationships between them. Such a resource should be extensible, such that newly discovered relationships–for example, those between novel, synthetic enzymes and non-natural products–can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists. PMID:28708831

The MAR databases: development and implementation of databases specific for marine metagenomics.

PubMed

Klemetsen, Terje; Raknes, Inge A; Fu, Juan; Agafonov, Alexander; Balasundaram, Sudhagar V; Tartari, Giacomo; Robertsen, Espen; Willassen, Nils P

2018-01-04

We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Databases for LDEF results

NASA Technical Reports Server (NTRS)

Bohnhoff-Hlavacek, Gail

1992-01-01

One of the objectives of the team supporting the LDEF Systems and Materials Special Investigative Groups is to develop databases of experimental findings. These databases identify the hardware flown, summarize results and conclusions, and provide a system for acknowledging investigators, tracing sources of data, and future design suggestions. To date, databases covering the optical experiments, and thermal control materials (chromic acid anodized aluminum, silverized Teflon blankets, and paints) have been developed at Boeing. We used the Filemaker Pro software, the database manager for the Macintosh computer produced by the Claris Corporation. It is a flat, text-retrievable database that provides access to the data via an intuitive user interface, without tedious programming. Though this software is available only for the Macintosh computer at this time, copies of the databases can be saved to a format that is readable on a personal computer as well. Further, the data can be exported to more powerful relational databases, capabilities, and use of the LDEF databases and describe how to get copies of the database for your own research.

Databases for Microbiologists

DOE PAGES

Zhulin, Igor B.

2015-05-26

Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. Finally, the purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.

Databases for Microbiologists

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

Zhulin, Igor B.

Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. Finally, the purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.

Databases for Microbiologists

PubMed Central

2015-01-01

Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists. PMID:26013493

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system

PubMed Central

Droit, Arnaud; Hunter, Joanna M; Rouleau, Michèle; Ethier, Chantal; Picard-Cloutier, Aude; Bourgais, David; Poirier, Guy G

2007-01-01

Background In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results in an increasing amount of proteome data. This data must be archived and analysed using specialized bioinformatics tools. Description We herein describe "PARPs database," a data analysis and management pipeline for liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics. PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified. Conclusion Using this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5. PMID:18093328

Application of the ToxMiner Database: Network Analysis of ...

EPA Pesticide Factsheets

The US EPA ToxCast program is using in vitro HTS (High-Throughput Screening) methods to profile and model bioactivity of environmental chemicals. The main goals of the ToxCast program are to generate predictive signatures of toxicity, and ultimately provide rapid and cost-effective alternatives to animal testing. The chemicals selected for Phase I are composed largely by a diverse set of pesticide active ingredients, which had sufficient supporting in vivo data included as part of their registration process with the EPA. Other miscellaneous chemicals of environmental concern were also included. Application of HTS to environmental toxicants is a novel approach to predictive toxicology and health risk assessment, and differs from what is required for drug efficacy screening in that biochemical interaction of environmental chemicals are sometimes weaker than that seen with drugs and their intended targets. Additionally, the chemical space covered by environmental chemicals is much broader compared to that of pharmaceuticals. The ToxMiner database has been created and added to the EPA’s ACToR (Aggregated Computational Toxicology Resource) chemical database. One purpose of the ToxMiner database is to link biological, metabolic and cellular pathway data to genes and in vitro assay data for the initial subset of chemicals screened in the ToxCast Phase I HTS assays. Also included in ToxMiner is human disease information, which correlates with ToxCast assays that tar

Online Databases in Physics.

ERIC Educational Resources Information Center

Sievert, MaryEllen C.; Verbeck, Alison F.

1984-01-01

This overview of 47 online sources for physics information available in the United States--including sub-field databases, transdisciplinary databases, and multidisciplinary databases-- notes content, print source, language, time coverage, and databank. Two discipline-specific databases (SPIN and PHYSICS BRIEFS) are also discussed. (EJS)

Development of a personalized training system using the Lung Image Database Consortium and Image Database resource Initiative Database.

PubMed

Lin, Hongli; Wang, Weisheng; Luo, Jiawei; Yang, Xuedong

2014-12-01

The aim of this study was to develop a personalized training system using the Lung Image Database Consortium (LIDC) and Image Database resource Initiative (IDRI) Database, because collecting, annotating, and marking a large number of appropriate computed tomography (CT) scans, and providing the capability of dynamically selecting suitable training cases based on the performance levels of trainees and the characteristics of cases are critical for developing a efficient training system. A novel approach is proposed to develop a personalized radiology training system for the interpretation of lung nodules in CT scans using the Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI) database, which provides a Content-Boosted Collaborative Filtering (CBCF) algorithm for predicting the difficulty level of each case of each trainee when selecting suitable cases to meet individual needs, and a diagnostic simulation tool to enable trainees to analyze and diagnose lung nodules with the help of an image processing tool and a nodule retrieval tool. Preliminary evaluation of the system shows that developing a personalized training system for interpretation of lung nodules is needed and useful to enhance the professional skills of trainees. The approach of developing personalized training systems using the LIDC/IDRL database is a feasible solution to the challenges of constructing specific training program in terms of cost and training efficiency. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

Mycobacteriophage genome database.

PubMed

Joseph, Jerrine; Rajendran, Vasanthi; Hassan, Sameer; Kumar, Vanaja

2011-01-01

Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification in a rational way. The other objective is to browse the existing and new genomes and describe their functional annotation. The database is available for free at http://mpgdb.ibioinformatics.org/mpgdb.php.

Maize databases

USDA-ARS?s Scientific Manuscript database

This chapter is a succinct overview of maize data held in the species-specific database MaizeGDB (the Maize Genomics and Genetics Database), and selected multi-species data repositories, such as Gramene/Ensembl Plants, Phytozome, UniProt and the National Center for Biotechnology Information (NCBI), ...

Exposure to 1800 MHz radiofrequency radiation impairs neurite outgrowth of embryonic neural stem cells.

PubMed

Chen, Chunhai; Ma, Qinlong; Liu, Chuan; Deng, Ping; Zhu, Gang; Zhang, Lei; He, Mindi; Lu, Yonghui; Duan, Weixia; Pei, Liping; Li, Min; Yu, Zhengping; Zhou, Zhou

2014-05-29

A radiofrequency electromagnetic field (RF-EMF) of 1800 MHz is widely used in mobile communications. However, the effects of RF-EMFs on cell biology are unclear. Embryonic neural stem cells (eNSCs) play a critical role in brain development. Thus, detecting the effects of RF-EMF on eNSCs is important for exploring the effects of RF-EMF on brain development. Here, we exposed eNSCs to 1800 MHz RF-EMF at specific absorption rate (SAR) values of 1, 2, and 4 W/kg for 1, 2, and 3 days. We found that 1800 MHz RF-EMF exposure did not influence eNSC apoptosis, proliferation, cell cycle or the mRNA expressions of related genes. RF-EMF exposure also did not alter the ratio of eNSC differentiated neurons and astrocytes. However, neurite outgrowth of eNSC differentiated neurons was inhibited after 4 W/kg RF-EMF exposure for 3 days. Additionally, the mRNA and protein expression of the proneural genes Ngn1 and NeuroD, which are crucial for neurite outgrowth, were decreased after RF-EMF exposure. The expression of their inhibitor Hes1 was upregulated by RF-EMF exposure. These results together suggested that 1800 MHz RF-EMF exposure impairs neurite outgrowth of eNSCs. More attention should be given to the potential adverse effects of RF-EMF exposure on brain development.

Specialist Bibliographic Databases

PubMed Central

2016-01-01

Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls. PMID:27134485

Specialist Bibliographic Databases.

PubMed

Gasparyan, Armen Yuri; Yessirkepov, Marlen; Voronov, Alexander A; Trukhachev, Vladimir I; Kostyukova, Elena I; Gerasimov, Alexey N; Kitas, George D

2016-05-01

Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls.

Creating Your Own Database.

ERIC Educational Resources Information Center

Blair, John C., Jr.

1982-01-01

Outlines the important factors to be considered in selecting a database management system for use with a microcomputer and presents a series of guidelines for developing a database. General procedures, report generation, data manipulation, information storage, word processing, data entry, database indexes, and relational databases are among the…

Can Naturoptics fund Naturopathic Universities to Develop Interlocked Mentoring Relationships with Proposed Universities to Check Sensitivities of Individuals with Spina Bifida, to Environmentally Generated EMF Information about 'Quakes, Hurricanes, etc.?

NASA Astrophysics Data System (ADS)

McLeod, David M.; Ataide, Italani; McLeod, Roger D.

2006-03-01

Individuals harboring the herpes zoster virus following chicken pox, are susceptible to attacks of shingles. They may indicate peculiar awareness of pricking `pin and needle' sensations and co-symptoms of tinnitus and/or Meuniere's syndrome. RDM used similar symptoms in FL to predict the earthquake ninety miles north of Guantanamo bay in 1998. An astounding burial site in Florida from over six thousand years ago had a teenaged boy with severe spina bifida, with non-Asian genes, who could not have survived without very capable health support. Two youthful individuals likewise afflicted with spina bifida were unearthed from one site at Pompeii, entombed by the eruption of Vesuvius, August 24 and 25, CE 79. We know how to locate sites, active with EMF, which have tornado, hurricane and earthquake associations, and would like to foster joint research also involving Hawaiian and other volcanoes.

NASA STI Database, Aerospace Database and ARIN coverage of 'space law'

NASA Technical Reports Server (NTRS)

Buchan, Ronald L.

1992-01-01

The space-law coverage provided by the NASA STI Database, the Aerospace Database, and ARIN is briefly described. Particular attention is given to the space law content of the two Databases and of ARIN, the NASA Thesauras space law terminology, space law publication forms, and the availability of the space law literature.

Databases: Beyond the Basics.

ERIC Educational Resources Information Center

Whittaker, Robert

This presented paper offers an elementary description of database characteristics and then provides a survey of databases that may be useful to the teacher and researcher in Slavic and East European languages and literatures. The survey focuses on commercial databases that are available, usable, and needed. Individual databases discussed include:…

The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences.

PubMed

Fourment, Mathieu; Gibbs, Mark J

2008-02-05

Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically.

Database Dictionary for Ethiopian National Ground-Water DAtabase (ENGDA) Data Fields

USGS Publications Warehouse

Kuniansky, Eve L.; Litke, David W.; Tucci, Patrick

2007-01-01

Introduction This document describes the data fields that are used for both field forms and the Ethiopian National Ground-water Database (ENGDA) tables associated with information stored about production wells, springs, test holes, test wells, and water level or water-quality observation wells. Several different words are used in this database dictionary and in the ENGDA database to describe a narrow shaft constructed in the ground. The most general term is borehole, which is applicable to any type of hole. A well is a borehole specifically constructed to extract water from the ground; however, for this data dictionary and for the ENGDA database, the words well and borehole are used interchangeably. A production well is defined as any well used for water supply and includes hand-dug wells, small-diameter bored wells equipped with hand pumps, or large-diameter bored wells equipped with large-capacity motorized pumps. Test holes are borings made to collect information about the subsurface with continuous core or non-continuous core and/or where geophysical logs are collected. Test holes are not converted into wells. A test well is a well constructed for hydraulic testing of an aquifer in order to plan a larger ground-water production system. A water-level or water-quality observation well is a well that is used to collect information about an aquifer and not used for water supply. A spring is any naturally flowing, local, ground-water discharge site. The database dictionary is designed to help define all fields on both field data collection forms (provided in attachment 2 of this report) and for the ENGDA software screen entry forms (described in Litke, 2007). The data entered into each screen entry field are stored in relational database tables within the computer database. The organization of the database dictionary is designed based on field data collection and the field forms, because this is what the majority of people will use. After each field, however, the

General practitioners' knowledge and concern about electromagnetic fields.

PubMed

Berg-Beckhoff, Gabriele; Breckenkamp, Jürgen; Larsen, Pia Veldt; Kowall, Bernd

2014-12-01

Our aim is to explore general practitioners' (GPs') knowledge about EMF, and to assess whether different knowledge structures are related to the GPs' concern about EMF. Random samples were drawn from lists of GPs in Germany in 2008. Knowledge about EMF was assessed by seven items. A latent class analysis was conducted to identify latent structures in GPs' knowledge. Further, the GPs' concern about EMF health risk was measured using a score comprising six items. The association between GPs' concern about EMF and their knowledge was analysed using multiple linear regression. In total 435 (response rate 23.3%) GPs participated in the study. Four groups were identified by the latent class analysis: 43.1% of the GPs gave mainly correct answers; 23.7% of the GPs answered low frequency EMF questions correctly; 19.2% answered only the questions relating EMF with health risks, and 14.0% answered mostly "don't know". There was no association between GPs' latent knowledge classes or between the number of correct answers given by the GPs and their EMF concern, whereas the number of incorrect answers was associated with EMF concern. Greater EMF concern in subjects with more incorrect answers suggests paying particular attention to misconceptions regarding EMF in risk communication.

Reflective Database Access Control

ERIC Educational Resources Information Center

Olson, Lars E.

2009-01-01

"Reflective Database Access Control" (RDBAC) is a model in which a database privilege is expressed as a database query itself, rather than as a static privilege contained in an access control list. RDBAC aids the management of database access controls by improving the expressiveness of policies. However, such policies introduce new interactions…

Development and validation of an extended database for yeast identification by MALDI-TOF MS in Argentina.

PubMed

Taverna, Constanza Giselle; Mazza, Mariana; Bueno, Nadia Soledad; Alvarez, Christian; Amigot, Susana; Andreani, Mariana; Azula, Natalia; Barrios, Rubén; Fernández, Norma; Fox, Barbara; Guelfand, Liliana; Maldonado, Ivana; Murisengo, Omar Alejandro; Relloso, Silvia; Vivot, Matias; Davel, Graciela

2018-05-11

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microorganisms in clinical laboratories because it is rapid, relatively simple to use, accurate, and can be used for a wide number of microorganisms. Several studies have demonstrated the utility of this technique in the identification of yeasts; however, its performance is usually improved by the extension of the database. Here we developed an in-house database of 143 strains belonging to 42 yeast species in the MALDI Biotyper platform, and we validated the extended database with 388 regional strains and 15 reference strains belonging to 55 yeast species. We also performed an intra- and interlaboratory study to assess reproducibility and analyzed the use of the cutoff values of 1.700 and 2.000 to correctly identify at species level. The creation of an in-house database that extended the manufacturer's database was successful in view of no incorrect identification was introduced. The best performance was observed by using the extended database and a cutoff value of 1.700 with a sensitivity of .94 and specificity of .96. A reproducibility study showed utility to detect deviations and could be used for external quality control. The extended database was able to differentiate closely related species and it has potential in distinguishing the molecular genotypes of Cryptococcus neoformans and Cryptococcus gattii.

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

Human Thermal Model Evaluation Using the JSC Human Thermal Database

NASA Technical Reports Server (NTRS)

Cognata, T.; Bue, G.; Makinen, J.

2011-01-01

The human thermal database developed at the Johnson Space Center (JSC) is used to evaluate a set of widely used human thermal models. This database will facilitate a more accurate evaluation of human thermoregulatory response using in a variety of situations, including those situations that might otherwise prove too dangerous for actual testing--such as extreme hot or cold splashdown conditions. This set includes the Wissler human thermal model, a model that has been widely used to predict the human thermoregulatory response to a variety of cold and hot environments. These models are statistically compared to the current database, which contains experiments of human subjects primarily in air from a literature survey ranging between 1953 and 2004 and from a suited experiment recently performed by the authors, for a quantitative study of relative strength and predictive quality of the models. Human thermal modeling has considerable long term utility to human space flight. Such models provide a tool to predict crew survivability in support of vehicle design and to evaluate crew response in untested environments. It is to the benefit of any such model not only to collect relevant experimental data to correlate it against, but also to maintain an experimental standard or benchmark for future development in a readily and rapidly searchable and software accessible format. The Human thermal database project is intended to do just so; to collect relevant data from literature and experimentation and to store the data in a database structure for immediate and future use as a benchmark to judge human thermal models against, in identifying model strengths and weakness, to support model development and improve correlation, and to statistically quantify a model s predictive quality.

Image Databases.

ERIC Educational Resources Information Center

Pettersson, Rune

Different kinds of pictorial databases are described with respect to aims, user groups, search possibilities, storage, and distribution. Some specific examples are given for databases used for the following purposes: (1) labor markets for artists; (2) document management; (3) telling a story; (4) preservation (archives and museums); (5) research;…

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database.

PubMed

Zappia, Luke; Phipson, Belinda; Oshlack, Alicia

2018-06-25

As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for researchers. In order to better facilitate selection of appropriate analysis tools we have created the scRNA-tools database (www.scRNA-tools.org) to catalogue and curate analysis tools as they become available. Our database collects a range of information on each scRNA-seq analysis tool and categorises them according to the analysis tasks they perform. Exploration of this database gives insights into the areas of rapid development of analysis methods for scRNA-seq data. We see that many tools perform tasks specific to scRNA-seq analysis, particularly clustering and ordering of cells. We also find that the scRNA-seq community embraces an open-source and open-science approach, with most tools available under open-source licenses and preprints being extensively used as a means to describe methods. The scRNA-tools database provides a valuable resource for researchers embarking on scRNA-seq analysis and records the growth of the field over time.

Exposure to 1800 MHz radiofrequency radiation impairs neurite outgrowth of embryonic neural stem cells

PubMed Central

Chen, Chunhai; Ma, Qinlong; Liu, Chuan; Deng, Ping; Zhu, Gang; Zhang, Lei; He, Mindi; Lu, Yonghui; Duan, Weixia; Pei, Liping; Li, Min; Yu, Zhengping; Zhou, Zhou

2014-01-01

A radiofrequency electromagnetic field (RF-EMF) of 1800 MHz is widely used in mobile communications. However, the effects of RF-EMFs on cell biology are unclear. Embryonic neural stem cells (eNSCs) play a critical role in brain development. Thus, detecting the effects of RF-EMF on eNSCs is important for exploring the effects of RF-EMF on brain development. Here, we exposed eNSCs to 1800 MHz RF-EMF at specific absorption rate (SAR) values of 1, 2, and 4 W/kg for 1, 2, and 3 days. We found that 1800 MHz RF-EMF exposure did not influence eNSC apoptosis, proliferation, cell cycle or the mRNA expressions of related genes. RF-EMF exposure also did not alter the ratio of eNSC differentiated neurons and astrocytes. However, neurite outgrowth of eNSC differentiated neurons was inhibited after 4 W/kg RF-EMF exposure for 3 days. Additionally, the mRNA and protein expression of the proneural genes Ngn1 and NeuroD, which are crucial for neurite outgrowth, were decreased after RF-EMF exposure. The expression of their inhibitor Hes1 was upregulated by RF-EMF exposure. These results together suggested that 1800 MHz RF-EMF exposure impairs neurite outgrowth of eNSCs. More attention should be given to the potential adverse effects of RF-EMF exposure on brain development. PMID:24869783

The Chicago Thoracic Oncology Database Consortium: A Multisite Database Initiative.

PubMed

Won, Brian; Carey, George B; Tan, Yi-Hung Carol; Bokhary, Ujala; Itkonen, Michelle; Szeto, Kyle; Wallace, James; Campbell, Nicholas; Hensing, Thomas; Salgia, Ravi

2016-03-16

An increasing amount of clinical data is available to biomedical researchers, but specifically designed database and informatics infrastructures are needed to handle this data effectively. Multiple research groups should be able to pool and share this data in an efficient manner. The Chicago Thoracic Oncology Database Consortium (CTODC) was created to standardize data collection and facilitate the pooling and sharing of data at institutions throughout Chicago and across the world. We assessed the CTODC by conducting a proof of principle investigation on lung cancer patients who took erlotinib. This study does not look into epidermal growth factor receptor (EGFR) mutations and tyrosine kinase inhibitors, but rather it discusses the development and utilization of the database involved.  We have implemented the Thoracic Oncology Program Database Project (TOPDP) Microsoft Access, the Thoracic Oncology Research Program (TORP) Velos, and the TORP REDCap databases for translational research efforts. Standard operating procedures (SOPs) were created to document the construction and proper utilization of these databases. These SOPs have been made available freely to other institutions that have implemented their own databases patterned on these SOPs. A cohort of 373 lung cancer patients who took erlotinib was identified. The EGFR mutation statuses of patients were analyzed. Out of the 70 patients that were tested, 55 had mutations while 15 did not. In terms of overall survival and duration of treatment, the cohort demonstrated that EGFR-mutated patients had a longer duration of erlotinib treatment and longer overall survival compared to their EGFR wild-type counterparts who received erlotinib. The investigation successfully yielded data from all institutions of the CTODC. While the investigation identified challenges, such as the difficulty of data transfer and potential duplication of patient data, these issues can be resolved with greater cross-communication between

Biological aspects and candidate biomarkers for rapid-cycling in bipolar disorder: A systematic review.

PubMed

Buoli, Massimiliano; Serati, Marta; Altamura, A Carlo

2017-12-01

Rapid-cycling bipolar disorder represents a frequent severe subtype of illness which has been associated with poor response to pharmacological treatment. Aim of the present article is to provide an updated review of biological markers associated with rapid-cycling bipolar disorder. A research in the main database sources has been conducted to identify relevant papers about the topic. Rapid-cycling bipolar disorder patients seem to have a more frequent family history for bipolar spectrum disorders (d range: 0.44-0.74) as well as an increased susceptibility to DNA damage or mRNA hypo-transcription (d range: 0.78-1.67) than non rapid-cycling ones. A susceptibility to hypothyroidism, which is exacerbated by treatment with lithium, is possible in rapid-cycling bipolar disorder, but further studies are needed to draw definitive conclusions. Rapid-cycling bipolar patients might have more insuline resistance as well as more severe brain changes in frontal areas (d range: 0.82-0.94) than non rapid-cycling ones. Many questions are still open about this topic. The first is whether the rapid-cycling is inheritable or is more generally the manifestation of a severe form of bipolar disorder. The second is whether some endocrine dysfunctions (diabetes and hypothyroidism) predispose to rapid-cycling or rapid-cycling is the consequence of drug treatment or medical comorbidities (e.g. obesity). Copyright © 2017 Elsevier B.V. All rights reserved.

Cognitive and emotional functioning in binge-eating disorder: A systematic review.

PubMed

Kittel, Rebekka; Brauhardt, Anne; Hilbert, Anja

2015-09-01

Binge-eating disorder (BED) is characterized by recurrent episodes of binge eating and is associated with eating disorder and general psychopathology and overweight/obesity. Deficits in cognitive and emotional functioning for eating disorders or obesity have been reported. However, a systematic review on cognitive and emotional functioning for individuals with BED is lacking. A systematic literature search was conducted across three databases (Medline, PubMed, and PsycINFO). Overall, n = 57 studies were included in the present review. Regarding cognitive functioning (CoF), individuals with BED consistently demonstrated higher information processing biases compared to obese and normal-weight controls in the context of disorder-related stimuli (i.e., food and body cues), whereas CoF in the context of neutral stimuli appeared to be less affected. Thus, results suggest disorder-related rather than general difficulties in CoF in BED. With respect to emotional functioning (EmF), individuals with BED reported difficulties similar to individuals with other eating disorders, with a tendency to show less severe difficulties in some domains. In addition, individuals with BED reported greater emotional deficits when compared to obese and normal-weight controls. Findings suggest general difficulties in EmF in BED. Thus far, however, investigations of EmF in disorder-relevant situations are lacking. Overall, the cross-sectional findings indicate BED to be associated with difficulties in CoF and EmF. Future research should determine the nature of these difficulties, in regards to general and disorder-related stimuli, and consider interactions of both domains to foster the development and improvement of appropriate interventions in BED. © 2015 Wiley Periodicals, Inc.

Fast fingerprint database maintenance for indoor positioning based on UGV SLAM.

PubMed

Tang, Jian; Chen, Yuwei; Chen, Liang; Liu, Jingbin; Hyyppä, Juha; Kukko, Antero; Kaartinen, Harri; Hyyppä, Hannu; Chen, Ruizhi

2015-03-04

Indoor positioning technology has become more and more important in the last two decades. Utilizing Received Signal Strength Indicator (RSSI) fingerprints of Signals of OPportunity (SOP) is a promising alternative navigation solution. However, as the RSSIs vary during operation due to their physical nature and are easily affected by the environmental change, one challenge of the indoor fingerprinting method is maintaining the RSSI fingerprint database in a timely and effective manner. In this paper, a solution for rapidly updating the fingerprint database is presented, based on a self-developed Unmanned Ground Vehicles (UGV) platform NAVIS. Several SOP sensors were installed on NAVIS for collecting indoor fingerprint information, including a digital compass collecting magnetic field intensity, a light sensor collecting light intensity, and a smartphone which collects the access point number and RSSIs of the pre-installed WiFi network. The NAVIS platform generates a map of the indoor environment and collects the SOPs during processing of the mapping, and then the SOP fingerprint database is interpolated and updated in real time. Field tests were carried out to evaluate the effectiveness and efficiency of the proposed method. The results showed that the fingerprint databases can be quickly created and updated with a higher sampling frequency (5Hz) and denser reference points compared with traditional methods, and the indoor map can be generated without prior information. Moreover, environmental changes could also be detected quickly for fingerprint indoor positioning.

Fast Fingerprint Database Maintenance for Indoor Positioning Based on UGV SLAM

PubMed Central

Tang, Jian; Chen, Yuwei; Chen, Liang; Liu, Jingbin; Hyyppä, Juha; Kukko, Antero; Kaartinen, Harri; Hyyppä, Hannu; Chen, Ruizhi

2015-01-01

Indoor positioning technology has become more and more important in the last two decades. Utilizing Received Signal Strength Indicator (RSSI) fingerprints of Signals of OPportunity (SOP) is a promising alternative navigation solution. However, as the RSSIs vary during operation due to their physical nature and are easily affected by the environmental change, one challenge of the indoor fingerprinting method is maintaining the RSSI fingerprint database in a timely and effective manner. In this paper, a solution for rapidly updating the fingerprint database is presented, based on a self-developed Unmanned Ground Vehicles (UGV) platform NAVIS. Several SOP sensors were installed on NAVIS for collecting indoor fingerprint information, including a digital compass collecting magnetic field intensity, a light sensor collecting light intensity, and a smartphone which collects the access point number and RSSIs of the pre-installed WiFi network. The NAVIS platform generates a map of the indoor environment and collects the SOPs during processing of the mapping, and then the SOP fingerprint database is interpolated and updated in real time. Field tests were carried out to evaluate the effectiveness and efficiency of the proposed method. The results showed that the fingerprint databases can be quickly created and updated with a higher sampling frequency (5Hz) and denser reference points compared with traditional methods, and the indoor map can be generated without prior information. Moreover, environmental changes could also be detected quickly for fingerprint indoor positioning. PMID:25746096

MedRapid--medical community & business intelligence system.

PubMed

Finkeissen, E; Fuchs, H; Jakob, T; Wetter, T

2002-01-01

currently, it takes at least 6 months for researchers to communicate their results. This delay is caused (a) by partial lacks of machine support for both representation as well as communication and (b) by media breaks during the communication process. To make an integrated communication between researchers and practitioners possible, a general structure for medical content representation has been set up. The procedure for data entry and quality management has been generalized and implemented in a web-based authoring system. The MedRapid-system supports the medical experts in entering their knowledge into a database. Here, the level of detail is still below that of current medical guidelines representation. However, the symmetric structure for an area-wide medical knowledge representation is highly retrievable and thus can quickly be communicated into daily routine for the improvement of the treatment quality. In addition, other sources like journal articles and medical guidelines can be references within the MedRapid-system and thus be communicated into daily routine. The fundamental system for the representation of medical reference knowledge (from reference works/books) itself is not sufficient for the friction-less communication amongst medical staff. Rather, the process of (a) representing medical knowledge, (b) refereeing the represented knowledge, (c) communicating the represented knowledge, and (d) retrieving the represented knowledge has to be unified. MedRapid will soon support the whole process on one server system.

Spatial and temporal variability of personal environmental exposure to radio frequency electromagnetic fields in children in Europe.

PubMed

Birks, Laura Ellen; Struchen, Benjamin; Eeftens, Marloes; van Wel, Luuk; Huss, Anke; Gajšek, Peter; Kheifets, Leeka; Gallastegi, Mara; Dalmau-Bueno, Albert; Estarlich, Marisa; Fernandez, Mariana F; Meder, Inger Kristine; Ferrero, Amparo; Jiménez-Zabala, Ana; Torrent, Maties; Vrijkotte, Tanja G M; Cardis, Elisabeth; Olsen, Jørn; Valič, Blaž; Vermeulen, Roel; Vrijheid, Martine; Röösli, Martin; Guxens, Mònica

2018-08-01

Exposure to radiofrequency electromagnetic fields (RF-EMF) has rapidly increased and little is known about exposure levels in children. This study describes personal RF-EMF environmental exposure levels from handheld devices and fixed site transmitters in European children, the determinants of this, and the day-to-day and year-to-year repeatability of these exposure levels. Personal environmental RF-EMF exposure (μW/m 2 , power flux density) was measured in 529 children (ages 8-18 years) in Denmark, the Netherlands, Slovenia, Switzerland, and Spain using personal portable exposure meters for a period of up to three days between 2014 and 2016, and repeated in a subsample of 28 children one year later. The meters captured 16 frequency bands every 4 s and incorporated a GPS. Activity diaries and questionnaires were used to collect children's location, use of handheld devices, and presence of indoor RF-EMF sources. Six general frequency bands were defined: total, digital enhanced cordless telecommunications (DECT), television and radio antennas (broadcast), mobile phones (uplink), mobile phone base stations (downlink), and Wireless Fidelity (WiFi). We used adjusted mixed effects models with region random effects to estimate associations of handheld device use habits and indoor RF-EMF sources with personal RF-EMF exposure. Day-to-day and year-to-year repeatability of personal RF-EMF exposure were calculated through intraclass correlations (ICC). Median total personal RF-EMF exposure was 75.5 μW/m 2 . Downlink was the largest contributor to total exposure (median: 27.2 μW/m 2 ) followed by broadcast (9.9 μW/m 2 ). Exposure from uplink (4.7 μW/m 2 ) was lower. WiFi and DECT contributed very little to exposure levels. Exposure was higher during day (94.2 μW/m 2 ) than night (23.0 μW/m 2 ), and slightly higher during weekends than weekdays, although varying across regions. Median exposures were highest while children were outside (157.0 μW/m 2 ) or

Chemical Kinetics Database

National Institute of Standards and Technology Data Gateway

SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.

Rapid Polymer Sequencer

NASA Technical Reports Server (NTRS)

Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

2013-01-01

Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

sRNAdb: A small non-coding RNA database for gram-positive bacteria

PubMed Central

2012-01-01

Background The class of small non-coding RNA molecules (sRNA) regulates gene expression by different mechanisms and enables bacteria to mount a physiological response due to adaptation to the environment or infection. Over the last decades the number of sRNAs has been increasing rapidly. Several databases like Rfam or fRNAdb were extended to include sRNAs as a class of its own. Furthermore new specialized databases like sRNAMap (gram-negative bacteria only) and sRNATarBase (target prediction) were established. To the best of the authors’ knowledge no database focusing on sRNAs from gram-positive bacteria is publicly available so far. Description In order to understand sRNA’s functional and phylogenetic relationships we have developed sRNAdb and provide tools for data analysis and visualization. The data compiled in our database is assembled from experiments as well as from bioinformatics analyses. The software enables comparison and visualization of gene loci surrounding the sRNAs of interest. To accomplish this, we use a client–server based approach. Offline versions of the database including analyses and visualization tools can easily be installed locally on the user’s computer. This feature facilitates customized local addition of unpublished sRNA candidates and related information such as promoters or terminators using tab-delimited files. Conclusion sRNAdb allows a user-friendly and comprehensive comparative analysis of sRNAs from available sequenced gram-positive prokaryotic replicons. Offline versions including analysis and visualization tools facilitate complex user specific bioinformatics analyses. PMID:22883983

Database Search Strategies & Tips. Reprints from the Best of "ONLINE" [and]"DATABASE."

ERIC Educational Resources Information Center

Online, Inc., Weston, CT.

Reprints of 17 articles presenting strategies and tips for searching databases online appear in this collection, which is one in a series of volumes of reprints from "ONLINE" and "DATABASE" magazines. Edited for information professionals who use electronically distributed databases, these articles address such topics as: (1)…

Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database.

PubMed

Thai, Quan Ke; Chung, Dung Anh; Tran, Hoang-Dung

2017-06-26

Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes. The Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD. The CHD can be accessed at http://chd.vnbiology.com . It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download. The Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582 bp sequences.

A large-scale measurement of electromagnetic fields near GSM base stations in Guangxi, China for risk communication.

PubMed

Wu, Tongning; Shao, Qing; Yang, Lei; Qi, Dianyuan; Lin, Jun; Lin, Xiaojun; Yu, Zongying

2013-06-01

Radiofrequency (RF) electromagnetic field (EMF) exposure from wireless telecommunication base station antennae can lead to debates, conflicts or litigations among the adjacent residents if inappropriately managed. This paper presents a measurement campaign for the GSM band EMF exposure in the vicinity of 827 base station sites (totally 6207 measurement points) in Guangxi, China. Measurement specifications are designed for risk communication with the residents who previously complained of over-exposure. The EMF power densities with the global positioning system coordinate at each measured point were recorded. Compliance with the International Commission on Non-Ionizing Radiation Protection guidelines and Chinese environmental EMF safety standards was studied. The results show that the GSM band EMF level near the base stations is very low. The measurement results and the EMF risk communication procedures positively influence public perception of the RF EMF exposure from the base stations and promote the exchange of EMF exposure-related knowledge.

Intrusive Rock Database for the Digital Geologic Map of Utah

USGS Publications Warehouse

Nutt, C.J.; Ludington, Steve

2003-01-01

Digital geologic maps offer the promise of rapid and powerful answers to geologic questions using Geographic Information System software (GIS). Using modern GIS and database methods, a specialized derivative map can be easily prepared. An important limitation can be shortcomings in the information provided in the database associated with the digital map, a database which is often based on the legend of the original map. The purpose of this report is to show how the compilation of additional information can, when prepared as a database that can be used with the digital map, be used to create some types of derivative maps that are not possible with the original digital map and database. This Open-file Report consists of computer files with information about intrusive rocks in Utah that can be linked to the Digital Geologic Map of Utah (Hintze et al., 2000), an explanation of how to link the databases and map, and a list of references for the databases. The digital map, which represents the 1:500,000-scale Geologic Map of Utah (Hintze, 1980), can be obtained from the Utah Geological Survey (Map 179DM). Each polygon in the map has a unique identification number. We selected the polygons identified on the geologic map as intrusive rock, and constructed a database (UT_PLUT.xls) that classifies the polygons into plutonic map units (see tables). These plutonic map units are the key information that is used to relate the compiled information to the polygons on the map. The map includes a few polygons that were coded as intrusive on the state map but are largely volcanic rock; in these cases we note the volcanic rock names (rhyolite and latite) as used in the original sources Some polygons identified on the digital state map as intrusive rock were misidentified; these polygons are noted in a separate table of the database, along with some information about their true character. Fields may be empty because of lack of information from references used or difficulty in finding

Neighboring trees affect ectomycorrhizal fungal community composition in a woodland-forest ecotone.

PubMed

Hubert, Nathaniel A; Gehring, Catherine A

2008-09-01

Ectomycorrhizal fungi (EMF) are frequently species rich and functionally diverse; yet, our knowledge of the environmental factors that influence local EMF diversity and species composition remains poor. In particular, little is known about the influence of neighboring plants on EMF community structure. We tested the hypothesis that the EMF of plants with heterospecific neighbors would differ in species richness and community composition from the EMF of plants with conspecific neighbors. We conducted our study at the ecotone between pinyon (Pinus edulis)-juniper (Juniperus monosperma) woodland and ponderosa pine (Pinus ponderosa) forest in northern Arizona, USA where the dominant trees formed associations with either EMF (P. edulis and P. ponderosa) or arbuscular mycorrhizal fungi (AMF; J. monosperma). We also compared the EMF communities of pinyon and ponderosa pines where their rhizospheres overlapped. The EMF community composition, but not species richness of pinyon pines was significantly influenced by neighboring AM juniper, but not by neighboring EM ponderosa pine. Ponderosa pine EMF communities were different in species composition when growing in association with pinyon pine than when growing in association with a conspecific. The EMF communities of pinyon and ponderosa pines were similar where their rhizospheres overlapped consisting of primarily the same species in similar relative abundance. Our findings suggest that neighboring tree species identity shaped EMF community structure, but that these effects were specific to host-neighbor combinations. The overlap in community composition between pinyon pine and ponderosa pine suggests that these tree species may serve as reservoirs of EMF inoculum for one another.

Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement

PubMed Central

Govindaraj, Mahalingam

2015-01-01

The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away. PMID:25874133

The MOBI-Kids Study Protocol: Challenges in Assessing Childhood and Adolescent Exposure to Electromagnetic Fields from Wireless Telecommunication Technologies and Possible Association with Brain Tumor Risk

PubMed Central

Sadetzki, Siegal; Langer, Chelsea Eastman; Bruchim, Revital; Kundi, Michael; Merletti, Franco; Vermeulen, Roel; Kromhout, Hans; Lee, Ae-Kyoung; Maslanyj, Myron; Sim, Malcolm R.; Taki, Masao; Wiart, Joe; Armstrong, Bruce; Milne, Elizabeth; Benke, Geza; Schattner, Rosa; Hutter, Hans-Peter; Woehrer, Adelheid; Krewski, Daniel; Mohipp, Charmaine; Momoli, Franco; Ritvo, Paul; Spinelli, John; Lacour, Brigitte; Delmas, Dominique; Remen, Thomas; Radon, Katja; Weinmann, Tobias; Klostermann, Swaantje; Heinrich, Sabine; Petridou, Eleni; Bouka, Evdoxia; Panagopoulou, Paraskevi; Dikshit, Rajesh; Nagrani, Rajini; Even-Nir, Hadas; Chetrit, Angela; Maule, Milena; Migliore, Enrica; Filippini, Graziella; Miligi, Lucia; Mattioli, Stefano; Yamaguchi, Naohito; Kojimahara, Noriko; Ha, Mina; Choi, Kyung-Hwa; Mannetje, Andrea ’t; Eng, Amanda; Woodward, Alistair; Carretero, Gema; Alguacil, Juan; Aragones, Nuria; Suare-Varela, Maria Morales; Goedhart, Geertje; Schouten-van Meeteren, A. Antoinette Y. N.; Reedijk, A. Ardine M. J.; Cardis, Elisabeth

2014-01-01

The rapid increase in mobile phone use in young people has generated concern about possible health effects of exposure to radiofrequency (RF) and extremely low frequency (ELF) electromagnetic fields (EMF). MOBI-Kids, a multinational case–control study, investigates the potential effects of childhood and adolescent exposure to EMF from mobile communications technologies on brain tumor risk in 14 countries. The study, which aims to include approximately 1,000 brain tumor cases aged 10–24 years and two individually matched controls for each case, follows a common protocol and builds upon the methodological experience of the INTERPHONE study. The design and conduct of a study on EMF exposure and brain tumor risk in young people in a large number of countries is complex and poses methodological challenges. This manuscript discusses the design of MOBI-Kids and describes the challenges and approaches chosen to address them, including: (1) the choice of controls operated for suspected appendicitis, to reduce potential selection bias related to low response rates among population controls; (2) investigating a young study population spanning a relatively wide age range; (3) conducting a large, multinational epidemiological study, while adhering to increasingly stricter ethics requirements; (4) investigating a rare and potentially fatal disease; and (5) assessing exposure to EMF from communication technologies. Our experience in thus far developing and implementing the study protocol indicates that MOBI-Kids is feasible and will generate results that will contribute to the understanding of potential brain tumor risks associated with use of mobile phones and other wireless communications technologies among young people. PMID:25295243

The MOBI-Kids Study Protocol: Challenges in Assessing Childhood and Adolescent Exposure to Electromagnetic Fields from Wireless Telecommunication Technologies and Possible Association with Brain Tumor Risk.

PubMed

Sadetzki, Siegal; Langer, Chelsea Eastman; Bruchim, Revital; Kundi, Michael; Merletti, Franco; Vermeulen, Roel; Kromhout, Hans; Lee, Ae-Kyoung; Maslanyj, Myron; Sim, Malcolm R; Taki, Masao; Wiart, Joe; Armstrong, Bruce; Milne, Elizabeth; Benke, Geza; Schattner, Rosa; Hutter, Hans-Peter; Woehrer, Adelheid; Krewski, Daniel; Mohipp, Charmaine; Momoli, Franco; Ritvo, Paul; Spinelli, John; Lacour, Brigitte; Delmas, Dominique; Remen, Thomas; Radon, Katja; Weinmann, Tobias; Klostermann, Swaantje; Heinrich, Sabine; Petridou, Eleni; Bouka, Evdoxia; Panagopoulou, Paraskevi; Dikshit, Rajesh; Nagrani, Rajini; Even-Nir, Hadas; Chetrit, Angela; Maule, Milena; Migliore, Enrica; Filippini, Graziella; Miligi, Lucia; Mattioli, Stefano; Yamaguchi, Naohito; Kojimahara, Noriko; Ha, Mina; Choi, Kyung-Hwa; Mannetje, Andrea 't; Eng, Amanda; Woodward, Alistair; Carretero, Gema; Alguacil, Juan; Aragones, Nuria; Suare-Varela, Maria Morales; Goedhart, Geertje; Schouten-van Meeteren, A Antoinette Y N; Reedijk, A Ardine M J; Cardis, Elisabeth

2014-01-01

The rapid increase in mobile phone use in young people has generated concern about possible health effects of exposure to radiofrequency (RF) and extremely low frequency (ELF) electromagnetic fields (EMF). MOBI-Kids, a multinational case-control study, investigates the potential effects of childhood and adolescent exposure to EMF from mobile communications technologies on brain tumor risk in 14 countries. The study, which aims to include approximately 1,000 brain tumor cases aged 10-24 years and two individually matched controls for each case, follows a common protocol and builds upon the methodological experience of the INTERPHONE study. The design and conduct of a study on EMF exposure and brain tumor risk in young people in a large number of countries is complex and poses methodological challenges. This manuscript discusses the design of MOBI-Kids and describes the challenges and approaches chosen to address them, including: (1) the choice of controls operated for suspected appendicitis, to reduce potential selection bias related to low response rates among population controls; (2) investigating a young study population spanning a relatively wide age range; (3) conducting a large, multinational epidemiological study, while adhering to increasingly stricter ethics requirements; (4) investigating a rare and potentially fatal disease; and (5) assessing exposure to EMF from communication technologies. Our experience in thus far developing and implementing the study protocol indicates that MOBI-Kids is feasible and will generate results that will contribute to the understanding of potential brain tumor risks associated with use of mobile phones and other wireless communications technologies among young people.

A Technical Approach to the Evaluation of Radiofrequency Radiation Emissions from Mobile Telephony Base Stations

PubMed Central

Buckus, Raimondas; Strukčinskienė, Birute; Raistenskis, Juozas; Stukas, Rimantas; Šidlauskienė, Aurelija; Čerkauskienė, Rimantė; Isopescu, Dorina Nicolina; Stabryla, Jan; Cretescu, Igor

2017-01-01

During the last two decades, the number of macrocell mobile telephony base station antennas emitting radiofrequency (RF) electromagnetic radiation (EMR) in residential areas has increased significantly, and therefore much more attention is being paid to RF EMR and its effects on human health. Scientific field measurements of public exposure to RF EMR (specifically to radio frequency radiation) from macrocell mobile telephony base station antennas and RF electromagnetic field (EMF) intensity parameters in the environment are discussed in this article. The research methodology is applied according to the requirements of safety norms and Lithuanian Standards in English (LST EN). The article presents and analyses RF EMFs generated by mobile telephony base station antennas in areas accessible to the general public. Measurements of the RF electric field strength and RF EMF power density were conducted in the near- and far-fields of the mobile telephony base station antenna. Broadband and frequency-selective measurements were performed outside (on the roof and on the ground) and in a residential area. The tests performed on the roof in front of the mobile telephony base station antennas in the near-field revealed the presence of a dynamic energy interaction within the antenna electric field, which changes rapidly with distance. The RF EMF power density values on the ground at distances of 50, 100, 200, 300, 400, and 500 m from the base station are very low and are scattered within intervals of 0.002 to 0.05 μW/cm2. The results were compared with international exposure guidelines (ICNIRP). PMID:28257069

A Technical Approach to the Evaluation of Radiofrequency Radiation Emissions from Mobile Telephony Base Stations.

PubMed

Buckus, Raimondas; Strukčinskienė, Birute; Raistenskis, Juozas; Stukas, Rimantas; Šidlauskienė, Aurelija; Čerkauskienė, Rimantė; Isopescu, Dorina Nicolina; Stabryla, Jan; Cretescu, Igor

2017-03-01

During the last two decades, the number of macrocell mobile telephony base station antennas emitting radiofrequency (RF) electromagnetic radiation (EMR) in residential areas has increased significantly, and therefore much more attention is being paid to RF EMR and its effects on human health. Scientific field measurements of public exposure to RF EMR (specifically to radio frequency radiation) from macrocell mobile telephony base station antennas and RF electromagnetic field (EMF) intensity parameters in the environment are discussed in this article. The research methodology is applied according to the requirements of safety norms and Lithuanian Standards in English (LST EN). The article presents and analyses RF EMFs generated by mobile telephony base station antennas in areas accessible to the general public. Measurements of the RF electric field strength and RF EMF power density were conducted in the near- and far-fields of the mobile telephony base station antenna. Broadband and frequency-selective measurements were performed outside (on the roof and on the ground) and in a residential area. The tests performed on the roof in front of the mobile telephony base station antennas in the near-field revealed the presence of a dynamic energy interaction within the antenna electric field, which changes rapidly with distance. The RF EMF power density values on the ground at distances of 50, 100, 200, 300, 400, and 500 m from the base station are very low and are scattered within intervals of 0.002 to 0.05 μW/cm². The results were compared with international exposure guidelines (ICNIRP).

Naval Ship Database: Database Design, Implementation, and Schema

DTIC Science & Technology

2013-09-01

incoming data. The solution allows database users to store and analyze data collected by navy ships in the Royal Canadian Navy ( RCN ). The data...understanding RCN jargon and common practices on a typical RCN vessel. This experience led to the development of several error detection methods to...data to be stored in the database. Mr. Massel has also collected data pertaining to day to day activities on RCN vessels that has been imported into

Hawaii bibliographic database

USGS Publications Warehouse

Wright, T.L.; Takahashi, T.J.

1998-01-01

The Hawaii bibliographic database has been created to contain all of the literature, from 1779 to the present, pertinent to the volcanological history of the Hawaiian-Emperor volcanic chain. References are entered in a PC- and Macintosh-compatible EndNote Plus bibliographic database with keywords and abstracts or (if no abstract) with annotations as to content. Keywords emphasize location, discipline, process, identification of new chemical data or age determinations, and type of publication. The database is updated approximately three times a year and is available to upload from an ftp site. The bibliography contained 8460 references at the time this paper was submitted for publication. Use of the database greatly enhances the power and completeness of library searches for anyone interested in Hawaiian volcanism.

KaBOB: ontology-based semantic integration of biomedical databases.

PubMed

Livingston, Kevin M; Bada, Michael; Baumgartner, William A; Hunter, Lawrence E

2015-04-23

The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing resources. Despite ongoing work moving toward shared data formats and linked identifiers, significant problems persist in semantic data integration in order to establish shared identity and shared meaning across heterogeneous biomedical data sources. We present five processes for semantic data integration that, when applied collectively, solve seven key problems. These processes include making explicit the differences between biomedical concepts and database records, aggregating sets of identifiers denoting the same biomedical concepts across data sources, and using declaratively represented forward-chaining rules to take information that is variably represented in source databases and integrating it into a consistent biomedical representation. We demonstrate these processes and solutions by presenting KaBOB (the Knowledge Base Of Biomedicine), a knowledge base of semantically integrated data from 18 prominent biomedical databases using common representations grounded in Open Biomedical Ontologies. An instance of KaBOB with data about humans and seven major model organisms can be built using on the order of 500 million RDF triples. All source code for building KaBOB is available under an open-source license. KaBOB is an integrated knowledge base of biomedical data representationally based in prominent, actively maintained Open Biomedical Ontologies, thus enabling queries of the underlying data in terms of biomedical concepts (e.g., genes and gene products, interactions and processes) rather than features of source-specific data schemas or file formats. KaBOB resolves many of the issues that routinely plague biomedical researchers intending to work with data from multiple data sources and provides a platform for ongoing data integration and development and for

The Chicago Thoracic Oncology Database Consortium: A Multisite Database Initiative

PubMed Central

Carey, George B; Tan, Yi-Hung Carol; Bokhary, Ujala; Itkonen, Michelle; Szeto, Kyle; Wallace, James; Campbell, Nicholas; Hensing, Thomas; Salgia, Ravi

2016-01-01

Objective: An increasing amount of clinical data is available to biomedical researchers, but specifically designed database and informatics infrastructures are needed to handle this data effectively. Multiple research groups should be able to pool and share this data in an efficient manner. The Chicago Thoracic Oncology Database Consortium (CTODC) was created to standardize data collection and facilitate the pooling and sharing of data at institutions throughout Chicago and across the world. We assessed the CTODC by conducting a proof of principle investigation on lung cancer patients who took erlotinib. This study does not look into epidermal growth factor receptor (EGFR) mutations and tyrosine kinase inhibitors, but rather it discusses the development and utilization of the database involved. Methods:  We have implemented the Thoracic Oncology Program Database Project (TOPDP) Microsoft Access, the Thoracic Oncology Research Program (TORP) Velos, and the TORP REDCap databases for translational research efforts. Standard operating procedures (SOPs) were created to document the construction and proper utilization of these databases. These SOPs have been made available freely to other institutions that have implemented their own databases patterned on these SOPs. Results: A cohort of 373 lung cancer patients who took erlotinib was identified. The EGFR mutation statuses of patients were analyzed. Out of the 70 patients that were tested, 55 had mutations while 15 did not. In terms of overall survival and duration of treatment, the cohort demonstrated that EGFR-mutated patients had a longer duration of erlotinib treatment and longer overall survival compared to their EGFR wild-type counterparts who received erlotinib. Discussion: The investigation successfully yielded data from all institutions of the CTODC. While the investigation identified challenges, such as the difficulty of data transfer and potential duplication of patient data, these issues can be resolved

General practitioners using complementary and alternative medicine differ from general practitioners using conventional medicine in their view of the risks of electromagnetic fields: a postal survey from Germany.

PubMed

Kowall, Bernd; Breckenkamp, Jürgen; Berg-Beckhoff, Gabriele

2015-01-01

General practitioners (GPs) play a key role in consulting patients worried about health effects of electromagnetic fields (EMF). We compared GPs using conventional medicine (COM) with GPs using complementary and alternative medicine (CAM) concerning their perception of EMF risks. Moreover, we assessed whether the kind of alternative medicine has an influence on the results. A total of 2795 GPs drawn randomly from lists of German GPs were sent an either long or short self-administered postal questionnaire on EMF-related topics. Adjusted logistic regression models were fitted to assess the association of an education in alternative medicine with various aspects of perceiving EMF risks. Concern about EMF, misconceptions about EMF, and distrust toward scientific organizations are more prevalent in CAM-GPs. CAM-GPs more often falsely believed that mobile phone use can lead to head warming of more than 1°C (odds ratio [OR] = 2.2, 95% confidence interval [CI] = 1.5-3.3), more often distrusted the Federal Office for Radiation Protection (OR = 2.2, 95% CI = 1.4-3.6), were more often concerned about mobile phone base stations (OR = 2.4, 95% CI = 1.6-3.6), more often attributed own health complaints to EMF (OR = 3.2, 95% CI = 1.8-5.6), and more often reported at least 1 EMF consultation (OR = 2.5, 95% CI = 1.6-3.9). GPs using homeopathy perceived EMF as more risky than GPs using acupuncture or naturopathic treatment. Concern about common EMF sources is highly prevalent among German GPs. CAM-GPs perceive stronger associations between EMF and health problems than COM-GPs. There is a need for evidence-based information about EMF risks for GPs and particularly for CAM-GPs. This is the precondition that GPs can inform patients about EMF and health in line with current scientific knowledge. © The Author(s) 2014.

The effect of electronic monitoring feedback on medication adherence and clinical outcomes: A systematic review

PubMed Central

van den Ende, Cornelia H. M.; Houterman, Anne E. J.; Heemskerk, Charlotte P. M.; van Dulmen, Sandra; van den Bemt, Bart J. F.

2017-01-01

Objective This study aims to assess the efficacy of Electronic Monitoring Feedback (EMF) as an intervention to improve medication adherence (i.e. dose- or full adherence) and clinical outcomes in adult patients. Methods A systematic search was performed in Medline, EMBASE, PsycINFO and Web of Science and reported according to the PRISMA guidelines. Randomised controlled trials (RCTs) comparing EMF with usual care were identified to systematically summarise the evidence for use of EMF in improving medication adherence and clinical outcomes. The GRADE approach was used to assess the quality of the body of evidence. Results Of 9,993 initially-identified studies, ten studies (four of high-quality and six of low-quality) were included. The sample size of the studies included varied from 18 to 205 patients. Four of the six studies (66.7%) reported a significant positive effect of EMF on mean dose adherence levels, whereas a significant positive effect of EMF on mean full adherence levels was found in all of the included studies (100%, five out of five of the studies included). A significant positive effect of EMF on clinical outcomes was reported in one of the seven studies included. The overall effect of EMF on mean dose- and full adherence was positive and the overall effect of EMF on clinical outcomes was inconclusive. Conclusion Considering the positive effect of EMF on medication adherence, EMF might be a promising intervention to enhance medication adherence. However, the effect of EMF on clinical outcomes was inconclusive. Prior to implementing EMF in clinical practice, future research with high-quality studies (e.g. adequate sample sizes, follow-up periods and no interfering co-interventions) is required to examine the (long-term) efficacy of EMF. PMID:28991903

The effect of electronic monitoring feedback on medication adherence and clinical outcomes: A systematic review.

PubMed

van Heuckelum, Milou; van den Ende, Cornelia H M; Houterman, Anne E J; Heemskerk, Charlotte P M; van Dulmen, Sandra; van den Bemt, Bart J F

2017-01-01

This study aims to assess the efficacy of Electronic Monitoring Feedback (EMF) as an intervention to improve medication adherence (i.e. dose- or full adherence) and clinical outcomes in adult patients. A systematic search was performed in Medline, EMBASE, PsycINFO and Web of Science and reported according to the PRISMA guidelines. Randomised controlled trials (RCTs) comparing EMF with usual care were identified to systematically summarise the evidence for use of EMF in improving medication adherence and clinical outcomes. The GRADE approach was used to assess the quality of the body of evidence. Of 9,993 initially-identified studies, ten studies (four of high-quality and six of low-quality) were included. The sample size of the studies included varied from 18 to 205 patients. Four of the six studies (66.7%) reported a significant positive effect of EMF on mean dose adherence levels, whereas a significant positive effect of EMF on mean full adherence levels was found in all of the included studies (100%, five out of five of the studies included). A significant positive effect of EMF on clinical outcomes was reported in one of the seven studies included. The overall effect of EMF on mean dose- and full adherence was positive and the overall effect of EMF on clinical outcomes was inconclusive. Considering the positive effect of EMF on medication adherence, EMF might be a promising intervention to enhance medication adherence. However, the effect of EMF on clinical outcomes was inconclusive. Prior to implementing EMF in clinical practice, future research with high-quality studies (e.g. adequate sample sizes, follow-up periods and no interfering co-interventions) is required to examine the (long-term) efficacy of EMF.

Kentucky geotechnical database.

DOT National Transportation Integrated Search

2005-03-01

Development of a comprehensive dynamic, geotechnical database is described. Computer software selected to program the client/server application in windows environment, components and structure of the geotechnical database, and primary factors cons...

NREL: U.S. Life Cycle Inventory Database - About the LCI Database Project

Science.gov Websites

About the LCI Database Project The U.S. Life Cycle Inventory (LCI) Database is a publicly available data collection and analysis methods. Finding consistent and transparent LCI data for life cycle and maintain the database. The 2009 U.S. Life Cycle Inventory (LCI) Data Stakeholder meeting was an

The EpiSLI Database: A Publicly Available Database on Speech and Language

ERIC Educational Resources Information Center

Tomblin, J. Bruce

2010-01-01

Purpose: This article describes a database that was created in the process of conducting a large-scale epidemiologic study of specific language impairment (SLI). As such, this database will be referred to as the EpiSLI database. Children with SLI have unexpected and unexplained difficulties learning and using spoken language. Although there is no…

Drinking Water Database

NASA Technical Reports Server (NTRS)

Murray, ShaTerea R.

2004-01-01

This summer I had the opportunity to work in the Environmental Management Office (EMO) under the Chemical Sampling and Analysis Team or CS&AT. This team s mission is to support Glenn Research Center (GRC) and EM0 by providing chemical sampling and analysis services and expert consulting. Services include sampling and chemical analysis of water, soil, fbels, oils, paint, insulation materials, etc. One of this team s major projects is the Drinking Water Project. This is a project that is done on Glenn s water coolers and ten percent of its sink every two years. For the past two summers an intern had been putting together a database for this team to record the test they had perform. She had successfully created a database but hadn't worked out all the quirks. So this summer William Wilder (an intern from Cleveland State University) and I worked together to perfect her database. We began be finding out exactly what every member of the team thought about the database and what they would change if any. After collecting this data we both had to take some courses in Microsoft Access in order to fix the problems. Next we began looking at what exactly how the database worked from the outside inward. Then we began trying to change the database but we quickly found out that this would be virtually impossible.

Aviation Safety Issues Database

NASA Technical Reports Server (NTRS)

Morello, Samuel A.; Ricks, Wendell R.

2009-01-01

The aviation safety issues database was instrumental in the refinement and substantiation of the National Aviation Safety Strategic Plan (NASSP). The issues database is a comprehensive set of issues from an extremely broad base of aviation functions, personnel, and vehicle categories, both nationally and internationally. Several aviation safety stakeholders such as the Commercial Aviation Safety Team (CAST) have already used the database. This broader interest was the genesis to making the database publically accessible and writing this report.

BDVC (Bimodal Database of Violent Content): A database of violent audio and video

NASA Astrophysics Data System (ADS)

Rivera Martínez, Jose Luis; Mijes Cruz, Mario Humberto; Rodríguez Vázqu, Manuel Antonio; Rodríguez Espejo, Luis; Montoya Obeso, Abraham; García Vázquez, Mireya Saraí; Ramírez Acosta, Alejandro Álvaro

2017-09-01

Nowadays there is a trend towards the use of unimodal databases for multimedia content description, organization and retrieval applications of a single type of content like text, voice and images, instead bimodal databases allow to associate semantically two different types of content like audio-video, image-text, among others. The generation of a bimodal database of audio-video implies the creation of a connection between the multimedia content through the semantic relation that associates the actions of both types of information. This paper describes in detail the used characteristics and methodology for the creation of the bimodal database of violent content; the semantic relationship is stablished by the proposed concepts that describe the audiovisual information. The use of bimodal databases in applications related to the audiovisual content processing allows an increase in the semantic performance only and only if these applications process both type of content. This bimodal database counts with 580 audiovisual annotated segments, with a duration of 28 minutes, divided in 41 classes. Bimodal databases are a tool in the generation of applications for the semantic web.

FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis.

PubMed

Parente, Eugenio; Cocolin, Luca; De Filippis, Francesca; Zotta, Teresa; Ferrocino, Ilario; O'Sullivan, Orla; Neviani, Erasmo; De Angelis, Maria; Cotter, Paul D; Ercolini, Danilo

2016-02-16

Amplicon targeted high-throughput sequencing has become a popular tool for the culture-independent analysis of microbial communities. Although the data obtained with this approach are portable and the number of sequences available in public databases is increasing, no tool has been developed yet for the analysis and presentation of data obtained in different studies. This work describes an approach for the development of a database for the rapid exploration and analysis of data on food microbial communities. Data from seventeen studies investigating the structure of bacterial communities in dairy, meat, sourdough and fermented vegetable products, obtained by 16S rRNA gene targeted high-throughput sequencing, were collated and analysed using Gephi, a network analysis software. The resulting database, which we named FoodMicrobionet, was used to analyse nodes and network properties and to build an interactive web-based visualisation. The latter allows the visual exploration of the relationships between Operational Taxonomic Units (OTUs) and samples and the identification of core- and sample-specific bacterial communities. It also provides additional search tools and hyperlinks for the rapid selection of food groups and OTUs and for rapid access to external resources (NCBI taxonomy, digital versions of the original articles). Microbial interaction network analysis was carried out using CoNet on datasets extracted from FoodMicrobionet: the complexity of interaction networks was much lower than that found for other bacterial communities (human microbiome, soil and other environments). This may reflect both a bias in the dataset (which was dominated by fermented foods and starter cultures) and the lower complexity of food bacterial communities. Although some technical challenges exist, and are discussed here, the net result is a valuable tool for the exploration of food bacterial communities by the scientific community and food industry. Copyright © 2015. Published by

Analysis of the mobile phone effect on the heart rate variability by using the largest Lyapunov exponent.

PubMed

Yılmaz, Derya; Yıldız, Metin

2010-12-01

In this study, the effects of electromagnetic fields (EMFs) emitted by GSM900 based mobile phones (MPs) on the heart rate variability (HRV) were examined by using nonlinear analysis methods. The largest Lyapunov exponent (LLE) calculation was used to evaluate the effect of MP under various real exposure conditions. Sixteen healthy young volunteers were exposed to EMFs emitted by GSM900 based MP at two levels from a very low EMF (MP at stand-by) to a higher EMF (MP at pre-ring handshaking and ringing). A blind experimental protocol was designed and utilized with consideration to the physiological and psychological factors that may affect HRV. The results showed that the LLE values increased slightly with higher EMF produced by MP (P < 0.05). This change indicates that the degree of chaos in the HRV signals increased at higher EMF compared to low level EMF. Consequently, we have concluded that high level EMF changed the complexity of cardiac system behavior, significantly.

X-ray-induced apoptosis of BEL-7402 cell line enhanced by extremely low frequency electromagnetic field in vitro.

PubMed

Jian, Wen; Wei, Zhao; Zhiqiang, Cheng; Zheng, Fang

2009-02-01

This study was designed to test whether extremely low frequency electromagnetic field (ELF-EMF) could enhance the apoptosis-induction effect of X-ray radiotherapy on liver cancer cell line BEL-7402 in vitro. EMF exposure was performed inside an energized solenoid coil. X-ray irradiation was performed using a linear accelerator. Apoptosis rates of BEL-7402 cells were analyzed using Annexin V-Fit Apoptosis Detection kit. Apoptosis rates of EMF group and sham EMF group were compared when combined with X-ray irradiation. Our results suggested that the apoptosis rate of BEL-7402 cells exposed to low doses of X-ray irradiation could be significantly increased by EMF. More EMF exposures obtain significantly higher apoptosis rates than fewer EMF exposures when combined with 2 Gy X-ray irradiation. These findings suggested that ELF-EMF could augment the cell apoptosis effects of low doses of X-ray irradiation on BEL-7402 cells in a synergistic and cumulative way. Copyright 2008 Wiley-Liss, Inc.

What are the best methodologies for rapid reviews of the research evidence for evidence-informed decision making in health policy and practice: a rapid review.

PubMed

Haby, Michelle M; Chapman, Evelina; Clark, Rachel; Barreto, Jorge; Reveiz, Ludovic; Lavis, John N

2016-11-25

Rapid reviews have the potential to overcome a key barrier to the use of research evidence in decision making, namely that of the lack of timely and relevant research. This rapid review of systematic reviews and primary studies sought to answer the question: What are the best methodologies to enable a rapid review of research evidence for evidence-informed decision making in health policy and practice? This rapid review utilised systematic review methods and was conducted according to a pre-defined protocol including clear inclusion criteria (PROSPERO registration: CRD42015015998). A comprehensive search strategy was used, including published and grey literature, written in English, French, Portuguese or Spanish, from 2004 onwards. Eleven databases and two websites were searched. Two review authors independently applied the eligibility criteria. Data extraction was done by one reviewer and checked by a second. The methodological quality of included studies was assessed independently by two reviewers. A narrative summary of the results is presented. Five systematic reviews and one randomised controlled trial (RCT) that investigated methodologies for rapid reviews met the inclusion criteria. None of the systematic reviews were of sufficient quality to allow firm conclusions to be made. Thus, the findings need to be treated with caution. There is no agreed definition of rapid reviews in the literature and no agreed methodology for conducting rapid reviews. While a wide range of 'shortcuts' are used to make rapid reviews faster than a full systematic review, the included studies found little empirical evidence of their impact on the conclusions of either rapid or systematic reviews. There is some evidence from the included RCT (that had a low risk of bias) that rapid reviews may improve clarity and accessibility of research evidence for decision makers. Greater care needs to be taken in improving the transparency of the methods used in rapid review products. There is

Dose related shifts in the developmental progress of chick embryos exposed to mobile phone induced electromagnetic fields.

PubMed

Zareen, Nusrat; Khan, Muhammad Yunus; Minhas, Liaqat Ali

2009-01-01

The possible adverse effects of Electromagnetic Fields (EMFs) emitted from mobile phones present a major public concern today. Some studies indicate EMFs effects on genes, free radical production, immunological and carcinogenic effects. On the other hand there are studies which do not support the hypothesis of any biological impacts of EMFs. This study was designed to observe the effects of mobile phone induced EMFs on survival and general growth and development of chick embryo, investigating dose-response relationship if any. This was an experimental study in which developing chick embryos were exposed to different doses of mobile phone induced EMFs. For this purpose a mobile phone was placed in the incubator in the centre of fertilised eggs in silent ringing mode and was 'rung' upon from any other line or cell phone. After incubation for 10 or 15 days the eggs were opened and the developmental mile-stones of the surviving embryos were compared with the non exposed subgroup. EMFs exposure significantly decreased the survivability of the chick embryos. The lower doses of EMFs caused growth retardation. However, this effect of growth retardation reallocated to partial growth enhancement on increasing the dose of EMFs and shifted over to definite growth enhancement on further raising the dose. There is an adverse effect of EMFs exposure on embryo survivability. Chick embryos developmental process is influenced by EMFs. However, these effects are variable depending upon the dose of EMFs exposure.

Continuous 900-megahertz electromagnetic field applied in middle and late-adolescence causes qualitative and quantitative changes in the ovarian morphology, tissue and blood biochemistry of the rat.

PubMed

Okatan, Derya Öztürk; Kaya, Haydar; Aliyazıcıoğlu, Yüksel; Demir, Selim; Çolakoğlu, Serdar; Odacı, Ersan

2018-02-01

The purpose of this study was to use histological and biochemical methods in order to evaluate changes taking place in the ovarian of rats exposed to the effect of a 900-megahertz (MHz) electromagnetic field (EMF) in middle and late adolescence. Twenty-four 34-d-old female Sprague-Dawley rats were assigned equally to control, sham and EMF groups. EMF group rats were exposed to the effect of a 900-MHz EMF for 1 h a day, at the same time every day between postnatal days 35 and 59, while inside an EMF cage. Sham group rats were kept inside the EMF cage for the same time between postnatal days 35 and 59 without being exposed to any EMF effect. At the end of the study, rats' ovarian were removed and blood specimens were taken. Right ovarium tissues were subjected to routine histological procedures and stained with hematoxylin and eosin, periodic acid shift and Masson's trichrome. Follicles were counted in ovarian sections stained with hematoxylin and eosin. The TUNEL method was used to evaluate apoptosis. Left ovarian tissue and blood specimens were investigated biochemically. Histopathological examination of EMF group ovarian tissue revealed thinning in the zona granulosa and theca layers, shrinking in granulosa cells, reduced mitotic activity and leukocyte infiltration in the follicles and stroma. Secondary follicle numbers in the EMF group were significantly lower than in the other groups. In terms of biochemistry, EMF and sham group superoxide dismutase, catalase and anti-Mullerian hormone levels and EMF group 3-nitrotyrosine values increased significantly compared to the control group. EMF and sham group serum catalase and 8-hydroxy-deoxiguanosine values increased significantly compared to the control group, and EMF group total oxidant status and oxidative stress index values were significantly higher compared to the sham and control groups. A total of 900-MHz EMF applied in middle and late adolescence may cause changes in the morphology and biochemistry of the

The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences

PubMed Central

Fourment, Mathieu; Gibbs, Mark J

2008-01-01

Background Viruses of the Bunyaviridae have segmented negative-stranded RNA genomes and several of them cause significant disease. Many partial sequences have been obtained from the segments so that GenBank searches give complex results. Sequence databases usually use HTML pages to mediate remote sorting, but this approach can be limiting and may discourage a user from exploring a database. Results The VirusBanker database contains Bunyaviridae sequences and alignments and is presented as two spreadsheets generated by a Java program that interacts with a MySQL database on a server. Sequences are displayed in rows and may be sorted using information that is displayed in columns and includes data relating to the segment, gene, protein, species, strain, sequence length, terminal sequence and date and country of isolation. Bunyaviridae sequences and alignments may be downloaded from the second spreadsheet with titles defined by the user from the columns, or viewed when passed directly to the sequence editor, Jalview. Conclusion VirusBanker allows large datasets of aligned nucleotide and protein sequences from the Bunyaviridae to be compiled and winnowed rapidly using criteria that are formulated heuristically. PMID:18251994

The Danish Testicular Cancer database.

PubMed

Daugaard, Gedske; Kier, Maria Gry Gundgaard; Bandak, Mikkel; Mortensen, Mette Saksø; Larsson, Heidi; Søgaard, Mette; Toft, Birgitte Groenkaer; Engvad, Birte; Agerbæk, Mads; Holm, Niels Vilstrup; Lauritsen, Jakob

2016-01-01

The nationwide Danish Testicular Cancer database consists of a retrospective research database (DaTeCa database) and a prospective clinical database (Danish Multidisciplinary Cancer Group [DMCG] DaTeCa database). The aim is to improve the quality of care for patients with testicular cancer (TC) in Denmark, that is, by identifying risk factors for relapse, toxicity related to treatment, and focusing on late effects. All Danish male patients with a histologically verified germ cell cancer diagnosis in the Danish Pathology Registry are included in the DaTeCa databases. Data collection has been performed from 1984 to 2007 and from 2013 onward, respectively. The retrospective DaTeCa database contains detailed information with more than 300 variables related to histology, stage, treatment, relapses, pathology, tumor markers, kidney function, lung function, etc. A questionnaire related to late effects has been conducted, which includes questions regarding social relationships, life situation, general health status, family background, diseases, symptoms, use of medication, marital status, psychosocial issues, fertility, and sexuality. TC survivors alive on October 2014 were invited to fill in this questionnaire including 160 validated questions. Collection of questionnaires is still ongoing. A biobank including blood/sputum samples for future genetic analyses has been established. Both samples related to DaTeCa and DMCG DaTeCa database are included. The prospective DMCG DaTeCa database includes variables regarding histology, stage, prognostic group, and treatment. The DMCG DaTeCa database has existed since 2013 and is a young clinical database. It is necessary to extend the data collection in the prospective database in order to answer quality-related questions. Data from the retrospective database will be added to the prospective data. This will result in a large and very comprehensive database for future studies on TC patients.

Drinking Water Treatability Database (Database)

EPA Science Inventory

The drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, rec...

Scopus database: a review.

PubMed

Burnham, Judy F

2006-03-08

The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs.

Scopus database: a review

PubMed Central

Burnham, Judy F

2006-01-01

The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs. PMID:16522216

Public variant databases: liability?

PubMed

Thorogood, Adrian; Cook-Deegan, Robert; Knoppers, Bartha Maria

2017-07-01

Public variant databases support the curation, clinical interpretation, and sharing of genomic data, thus reducing harmful errors or delays in diagnosis. As variant databases are increasingly relied on in the clinical context, there is concern that negligent variant interpretation will harm patients and attract liability. This article explores the evolving legal duties of laboratories, public variant databases, and physicians in clinical genomics and recommends a governance framework for databases to promote responsible data sharing.Genet Med advance online publication 15 December 2016.

Wi-Fi is an important threat to human health.

PubMed

Pall, Martin L

2018-07-01

Repeated Wi-Fi studies show that Wi-Fi causes oxidative stress, sperm/testicular damage, neuropsychiatric effects including EEG changes, apoptosis, cellular DNA damage, endocrine changes, and calcium overload. Each of these effects are also caused by exposures to other microwave frequency EMFs, with each such effect being documented in from 10 to 16 reviews. Therefore, each of these seven EMF effects are established effects of Wi-Fi and of other microwave frequency EMFs. Each of these seven is also produced by downstream effects of the main action of such EMFs, voltage-gated calcium channel (VGCC) activation. While VGCC activation via EMF interaction with the VGCC voltage sensor seems to be the predominant mechanism of action of EMFs, other mechanisms appear to have minor roles. Minor roles include activation of other voltage-gated ion channels, calcium cyclotron resonance and the geomagnetic magnetoreception mechanism. Five properties of non-thermal EMF effects are discussed. These are that pulsed EMFs are, in most cases, more active than are non-pulsed EMFs; artificial EMFs are polarized and such polarized EMFs are much more active than non-polarized EMFs; dose-response curves are non-linear and non-monotone; EMF effects are often cumulative; and EMFs may impact young people more than adults. These general findings and data presented earlier on Wi-Fi effects were used to assess the Foster and Moulder (F&M) review of Wi-Fi. The F&M study claimed that there were seven important studies of Wi-Fi that each showed no effect. However, none of these were Wi-Fi studies, with each differing from genuine Wi-Fi in three distinct ways. F&M could, at most conclude that there was no statistically significant evidence of an effect. The tiny numbers studied in each of these seven F&M-linked studies show that each of them lack power to make any substantive conclusions. In conclusion, there are seven repeatedly found Wi-Fi effects which have also been shown to be caused by other

THE ECOTOX DATABASE

EPA Science Inventory

The database provides chemical-specific toxicity information for aquatic life, terrestrial plants, and terrestrial wildlife. ECOTOX is a comprehensive ecotoxicology database and is therefore essential for providing and suppoirting high quality models needed to estimate population...

[Patients' exposure to electromagnetic fields and radon in radon spas].

PubMed

Politański, Piotr; Olszewski, Jerzy; Mamrot, Paweł; Mariańska, Mlagda; Zmyślony, Marek

2014-01-01

Many patients of physiotherapeutic facilities using therapeutic radon are also referred to other treatments involving the use of electromagnetic field (EMF). However, in the light of the theory of EMF influence on free radicals, it is still an open question whether, application of EMF shortly after the radon treatment may alter the biological effects of radon or EMF. The aim of the study was to determine how large is the group of patients exposed to radon and EMF in Poland, and how high is the exposure of these patients to analyzed factors. The results of the study are to be used in the future assessment of the combined effects of radon and EMF in radon spas. Based on the statistical data and interviews held in the major Polish radon spas, the analysis of treatment structure was performed and exposure to radon and EMF was assessed by measuring radon concentrations and characteristic values of exposure to EMF. More than 8000 people per year are subjected to combined exposure to radon and EMF. Significant differences were found between measured radon concentrations (they ranged from approximately 61 kBq/m3 for inhalations with inhaler to only 290 Bq/m3 for graduation towers, p = 0.049) and EMF intensities corresponded to those observed in hazardous and dangerous zones for occupational exposure. The results of the study showed significant differences between radon concentrations during various radon treatments. There is a need to develop clear and universal procedures for the application of radon or radon combined with EMF in radon spas. The effects of patients' exposure to radon, especially combined with EMF need to be further studied.

SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

PubMed

Amigo, Jorge; Salas, Antonio; Phillips, Christopher; Carracedo, Angel

2008-10-10

In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of human diversity, and are widely used as reference sources for population genetics studies. Although many useful conclusions may be extracted by querying databases individually, the lack of flexibility for combining data from within and between each database does not allow the calculation of key population variability statistics. We have developed a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data mart from the most commonly accessed databases of genotypes containing population information: data is mined, summarized into the standard statistical reference indices, and stored into a relational database that currently handles as many as 4 x 10(9) genotypes and that can be easily extended to new database initiatives. We have also built a web interface to the data mart that allows the browsing of underlying data indexed by population and the combining of populations, allowing intuitive and straightforward comparison of population groups. All the information served is optimized for web display, and most of the computations are already pre-processed in the data mart to speed up the data browsing and any computational treatment requested. In practice, SPSmart allows populations to be combined into user-defined groups, while multiple databases can be accessed and compared in a few simple steps from a single query. It performs the queries rapidly and gives straightforward graphical summaries of SNP population variability through visual inspection of allele frequencies outlined in standard pie-chart format. In addition, full numerical description of the data is output in

Phytophthora database 2.0: update and future direction.

PubMed

Park, Bongsoo; Martin, Frank; Geiser, David M; Kim, Hye-Seon; Mansfield, Michele A; Nikolaeva, Ekaterina; Park, Sook-Young; Coffey, Michael D; Russo, Joseph; Kim, Seong H; Balci, Yilmaz; Abad, Gloria; Burgess, Treena; Grünwald, Niklaus J; Cheong, Kyeongchae; Choi, Jaeyoung; Lee, Yong-Hwan; Kang, Seogchan

2013-12-01

The online community resource Phytophthora database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Since its release in 2008, the sequence database has grown to cover 1 to 12 loci for ≈2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PD's future direction.

Ectomycorrhizal diversity and community structure in stands of Quercus oleoides in the seasonally dry tropical forests of Costa Rica

NASA Astrophysics Data System (ADS)

Desai, Nikhilesh S.; Wilson, Andrew W.; Powers, Jennifer S.; Mueller, Gregory M.; Egerton-Warburton, Louise M.

2016-12-01

Most conservation efforts in seasonally dry tropical forests have overlooked less obvious targets for conservation, such as mycorrhizal fungi, that are critical to plant growth and ecosystem structure. We documented the diversity of ectomycorrhizal (EMF) and arbuscular mycorrhizal (AMF) fungal communities in Quercus oleoides (Fagaceae) in Guanacaste province, Costa Rica. Soil cores and sporocarps were collected from regenerating Q. oleoides plots differing in stand age (early vs late regeneration) during the wet season. Sequencing of the nuclear ribosomal ITS region in EMF root tips and sporocarps identified 37 taxa in the Basidiomycota; EMF Ascomycota were uncommon. The EMF community was dominated by one species (Thelephora sp. 1; 70% of soil cores), more than half of all EMF species were found only once in an individual soil core, and there were few conspecific taxa. Most EMF taxa were also restricted to either Early or Late plots. Levels of EMF species richness and diversity, and AMF root colonization were similar between plots. Our results highlight the need for comprehensive spatiotemporal samplings of EMF communities in Q. oleoides to identify and prioritize rare EMF for conservation, and document their genetic and functional diversity.

An integrated high resolution mass spectrometric and informatics approach for the rapid identification of phenolics in plant extract

USDA-ARS?s Scientific Manuscript database

An integrated approach based on high resolution MS analysis (orbitrap), database (db) searching and MS/MS fragmentation prediction for the rapid identification of plant phenols is reported. The approach was firstly validated by using a mixture of phenolic standards (phenolic acids, flavones, flavono...

Public variant databases: liability?

PubMed Central

Thorogood, Adrian; Cook-Deegan, Robert; Knoppers, Bartha Maria

2017-01-01

Public variant databases support the curation, clinical interpretation, and sharing of genomic data, thus reducing harmful errors or delays in diagnosis. As variant databases are increasingly relied on in the clinical context, there is concern that negligent variant interpretation will harm patients and attract liability. This article explores the evolving legal duties of laboratories, public variant databases, and physicians in clinical genomics and recommends a governance framework for databases to promote responsible data sharing. Genet Med advance online publication 15 December 2016 PMID:27977006

Trimetallic nitride template endohedral metallofullerenes: discovery, structural characterization, reactivity, and applications.

PubMed

Zhang, Jianyuan; Stevenson, Steven; Dorn, Harry C

2013-07-16

Shortly after the discovery of the carbon fullerene allotrope, C₆₀, researchers recognized that the hollow spheroidal shape could accommodate metal atoms, or clusters, which quickly led to the discovery of endohedral metallofullerenes (EMFs). In the past 2 decades, the unique features of EMFs have attracted broad interest in many fields, including inorganic chemistry, organic chemistry, materials chemistry, and biomedical chemistry. Some EMFs produce new metallic clusters that do not exist outside of a fullerene cage, and some other EMFs can boost the efficiency of magnetic resonance (MR) imaging 10-50-fold, in comparison with commercial contrast agents. In 1999, the Dorn laboratory discovered the trimetallic nitride template (TNT) EMFs, which consist of a trimetallic nitride cluster and a host fullerene cage. The TNT-EMFs (A₃N@C2n, n = 34-55, A = Sc, Y, or lanthanides) are typically formed in relatively high yields (sometimes only exceeded by empty-cage C₆₀ and C₇₀, but yields may decrease with increasing TNT cluster size), and exhibit high chemical and thermal stability. In this Account, we give an overview of TNT-EMF research, starting with the discovery of these structures and then describing their synthesis and applications. First, we describe our serendipitous discovery of the first member of this class, Sc₃N@Ih-C₈₀. Second, we discuss the methodology for the synthesis of several TNT-EMFs. These results emphasize the importance of chemically adjusting plasma temperature, energy, and reactivity (CAPTEAR) to optimize the type and yield of TNT-EMFs produced. Third, we review the approaches that are used to separate and purify pristine TNT-EMF molecules from their corresponding product mixtures. Although we used high-performance liquid chromatography (HPLC) to separate TNT-EMFs in early studies, we have more recently achieved facile separation based on the reduced chemical reactivity of the TNT-EMFs. These improved production yields and

Database for propagation models

NASA Astrophysics Data System (ADS)

Kantak, Anil V.

1991-07-01

A propagation researcher or a systems engineer who intends to use the results of a propagation experiment is generally faced with various database tasks such as the selection of the computer software, the hardware, and the writing of the programs to pass the data through the models of interest. This task is repeated every time a new experiment is conducted or the same experiment is carried out at a different location generating different data. Thus the users of this data have to spend a considerable portion of their time learning how to implement the computer hardware and the software towards the desired end. This situation may be facilitated considerably if an easily accessible propagation database is created that has all the accepted (standardized) propagation phenomena models approved by the propagation research community. Also, the handling of data will become easier for the user. Such a database construction can only stimulate the growth of the propagation research it if is available to all the researchers, so that the results of the experiment conducted by one researcher can be examined independently by another, without different hardware and software being used. The database may be made flexible so that the researchers need not be confined only to the contents of the database. Another way in which the database may help the researchers is by the fact that they will not have to document the software and hardware tools used in their research since the propagation research community will know the database already. The following sections show a possible database construction, as well as properties of the database for the propagation research.

Comparison of hospital databases on antibiotic consumption in France, for a single management tool.

PubMed

Henard, S; Boussat, S; Demoré, B; Clément, S; Lecompte, T; May, T; Rabaud, C

2014-07-01

The surveillance of antibiotic use in hospitals and of data on resistance is an essential measure for antibiotic stewardship. There are 3 national systems in France to collect data on antibiotic use: DREES, ICATB, and ATB RAISIN. We compared these databases and drafted recommendations for the creation of an optimized database of information on antibiotic use, available to all concerned personnel: healthcare authorities, healthcare facilities, and healthcare professionals. We processed and analyzed the 3 databases (2008 data), and surveyed users. The qualitative analysis demonstrated major discrepancies in terms of objectives, healthcare facilities, participation rate, units of consumption, conditions for collection, consolidation, and control of data, and delay before availability of results. The quantitative analysis revealed that the consumption data for a given healthcare facility differed from one database to another, challenging the reliability of data collection. We specified user expectations: to compare consumption and resistance data, to carry out benchmarking, to obtain data on the prescribing habits in healthcare units, or to help understand results. The study results demonstrated the need for a reliable, single, and automated tool to manage data on antibiotic consumption compared with resistance data on several levels (national, regional, healthcare facility, healthcare units), providing rapid local feedback and educational benchmarking. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions

PubMed Central

Jefferson, Emily R.; Walsh, Thomas P.; Roberts, Timothy J.; Barton, Geoffrey J.

2007-01-01

SNAPPI-DB, a high performance database of Structures, iNterfaces and Alignments of Protein–Protein Interactions, and its associated Java Application Programming Interface (API) is described. SNAPPI-DB contains structural data, down to the level of atom co-ordinates, for each structure in the Protein Data Bank (PDB) together with associated data including SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, Protein Quaternary Structures (PQS) and secondary structure information. Domain–domain interactions are stored for multiple domain definitions and are classified by their Superfamily/Family pair and interaction interface. Each set of classified domain–domain interactions has an associated multiple structure alignment for each partner. The API facilitates data access via PDB entries, domains and domain–domain interactions. Rapid development, fast database access and the ability to perform advanced queries without the requirement for complex SQL statements are provided via an object oriented database and the Java Data Objects (JDO) API. SNAPPI-DB contains many features which are not available in other databases of structural protein–protein interactions. It has been applied in three studies on the properties of protein–protein interactions and is currently being employed to train a protein–protein interaction predictor and a functional residue predictor. The database, API and manual are available for download at: . PMID:17202171

Elevated CO2 and O3 effects on ectomycorrhizal fungal root tip communities in consideration of a post-agricultural soil nutrient gradient legacy

Treesearch

Carrie Andrew; Erik A. Lilleskov

2014-01-01

Despite the critical role of EMF in nutrient and carbon (C) dynamics, combined effects of global atmospheric pollutants on ectomycorrhizal fungi (EMF) are unclear. Here, we present research on EMF root-level community responses to elevated CO2 and O3. We discovered that belowground EMF community richness and similarity were...

Rapid identification and classification of bacteria by 16S rDNA restriction fragment melting curve analyses (RFMCA).

PubMed

Rudi, Knut; Kleiberg, Gro H; Heiberg, Ragnhild; Rosnes, Jan T

2007-08-01

The aim of this work was to evaluate restriction fragment melting curve analyses (RFMCA) as a novel approach for rapid classification of bacteria during food production. RFMCA was evaluated for bacteria isolated from sous vide food products, and raw materials used for sous vide production. We identified four major bacterial groups in the material analysed (cluster I-Streptococcus, cluster II-Carnobacterium/Bacillus, cluster III-Staphylococcus and cluster IV-Actinomycetales). The accuracy of RFMCA was evaluated by comparison with 16S rDNA sequencing. The strains satisfying the RFMCA quality filtering criteria (73%, n=57), with both 16S rDNA sequence information and RFMCA data (n=45) gave identical group assignments with the two methods. RFMCA enabled rapid and accurate classification of bacteria that is database compatible. Potential application of RFMCA in the food or pharmaceutical industry will include development of classification models for the bacteria expected in a given product, and then to build an RFMCA database as a part of the product quality control.

FishTraits Database

USGS Publications Warehouse

Angermeier, Paul L.; Frimpong, Emmanuel A.

2009-01-01

The need for integrated and widely accessible sources of species traits data to facilitate studies of ecology, conservation, and management has motivated development of traits databases for various taxa. In spite of the increasing number of traits-based analyses of freshwater fishes in the United States, no consolidated database of traits of this group exists publicly, and much useful information on these species is documented only in obscure sources. The largely inaccessible and unconsolidated traits information makes large-scale analysis involving many fishes and/or traits particularly challenging. FishTraits is a database of >100 traits for 809 (731 native and 78 exotic) fish species found in freshwaters of the conterminous United States, including 37 native families and 145 native genera. The database contains information on four major categories of traits: (1) trophic ecology, (2) body size and reproductive ecology (life history), (3) habitat associations, and (4) salinity and temperature tolerances. Information on geographic distribution and conservation status is also included. Together, we refer to the traits, distribution, and conservation status information as attributes. Descriptions of attributes are available here. Many sources were consulted to compile attributes, including state and regional species accounts and other databases.

CB Database: A change blindness database for objects in natural indoor scenes.

PubMed

Sareen, Preeti; Ehinger, Krista A; Wolfe, Jeremy M

2016-12-01

Change blindness has been a topic of interest in cognitive sciences for decades. Change detection experiments are frequently used for studying various research topics such as attention and perception. However, creating change detection stimuli is tedious and there is no open repository of such stimuli using natural scenes. We introduce the Change Blindness (CB) Database with object changes in 130 colored images of natural indoor scenes. The size and eccentricity are provided for all the changes as well as reaction time data from a baseline experiment. In addition, we have two specialized satellite databases that are subsets of the 130 images. In one set, changes are seen in rooms or in mirrors in those rooms (Mirror Change Database). In the other, changes occur in a room or out a window (Window Change Database). Both the sets have controlled background, change size, and eccentricity. The CB Database is intended to provide researchers with a stimulus set of natural scenes with defined stimulus parameters that can be used for a wide range of experiments. The CB Database can be found at http://search.bwh.harvard.edu/new/CBDatabase.html .

DNApod: DNA polymorphism annotation database from next-generation sequence read archives.

PubMed

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information.

DNApod: DNA polymorphism annotation database from next-generation sequence read archives

PubMed Central

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information. PMID:28234924

SAM: String-based sequence search algorithm for mitochondrial DNA database queries

PubMed Central

Röck, Alexander; Irwin, Jodi; Dür, Arne; Parsons, Thomas; Parson, Walther

2011-01-01

The analysis of the haploid mitochondrial (mt) genome has numerous applications in forensic and population genetics, as well as in disease studies. Although mtDNA haplotypes are usually determined by sequencing, they are rarely reported as a nucleotide string. Traditionally they are presented in a difference-coded position-based format relative to the corrected version of the first sequenced mtDNA. This convention requires recommendations for standardized sequence alignment that is known to vary between scientific disciplines, even between laboratories. As a consequence, database searches that are vital for the interpretation of mtDNA data can suffer from biased results when query and database haplotypes are annotated differently. In the forensic context that would usually lead to underestimation of the absolute and relative frequencies. To address this issue we introduce SAM, a string-based search algorithm that converts query and database sequences to position-free nucleotide strings and thus eliminates the possibility that identical sequences will be missed in a database query. The mere application of a BLAST algorithm would not be a sufficient remedy as it uses a heuristic approach and does not address properties specific to mtDNA, such as phylogenetically stable but also rapidly evolving insertion and deletion events. The software presented here provides additional flexibility to incorporate phylogenetic data, site-specific mutation rates, and other biologically relevant information that would refine the interpretation of mitochondrial DNA data. The manuscript is accompanied by freeware and example data sets that can be used to evaluate the new software (http://stringvalidation.org). PMID:21056022

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.

PubMed

Fernández-Suárez, Xosé M; Rigden, Daniel J; Galperin, Michael Y

2014-01-01

The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt. There is a strong block of structural databases, which includes, among others, the new RNA Bricks database, updates on PDBe, PDBsum, ArchDB, Gene3D, ModBase, Nucleic Acid Database and the recently revived iPfam database. An update on the NCBI's MMDB describes VAST+, an improved tool for protein structure comparison. Two articles highlight the development of the Structural Classification of Proteins (SCOP) database: one describes SCOPe, which automates assignment of new structures to the existing SCOP hierarchy; the other one describes the first version of SCOP2, with its more flexible approach to classifying protein structures. This issue also includes a collection of articles on bacterial taxonomy and metagenomics, which includes updates on the List of Prokaryotic Names with Standing in Nomenclature (LPSN), Ribosomal Database Project (RDP), the Silva/LTP project and several new metagenomics resources. The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been expanded to 1552 databases. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/).

Antidepressants for depressive disorder in children and adolescents: a database of randomised controlled trials.

PubMed

Zhang, Yuqing; Zhou, Xinyu; Pu, Juncai; Zhang, Hanping; Yang, Lining; Liu, Lanxiang; Zhou, Chanjuan; Yuan, Shuai; Jiang, Xiaofeng; Xie, Peng

2018-05-31

In recent years, whether, when and how to use antidepressants to treat depressive disorder in children and adolescents has been hotly debated. Relevant evidence on this topic has increased rapidly. In this paper, we present the construction and content of a database of randomised controlled trials of antidepressants to treat depressive disorder in children and adolescents. This database can be freely accessed via our website and will be regularly updated. Major bibliographic databases (PubMed, the Cochrane Library, Web of Science, Embase, CINAHL, PsycINFO and LiLACS), international trial registers and regulatory agencies' websites were systematically searched for published and unpublished studies up to April 30, 2017. We included randomised controlled trials in which the efficacy or tolerability of any oral antidepressant was compared with that of a control group or any other treatment. In total, 7377 citations from bibliographical databases and 3289 from international trial registers and regulatory agencies' websites were identified. Of these, 53 trials were eligible for inclusion in the final database. Selected data were extracted from each study, including characteristics of the participants (the study population, setting, diagnostic criteria, type of depression, age, sex, and comorbidity), characteristics of the treatment conditions (the treatment conditions, general information, and detail of pharmacotherapy and psychotherapy) and study characteristics (the sponsor, country, number of sites, blinding method, sample size, treatment duration, depression scales, other scales, and primary outcome measure used, and side-effect monitoring method). Moreover, the risk of bias for each trial were assessed. This database provides information on nearly all randomised controlled trials of antidepressants in children and adolescents. By using this database, researchers can improve research efficiency, avoid inadvertent errors and easily focus on the targeted subgroups in

Designing for Peta-Scale in the LSST Database

NASA Astrophysics Data System (ADS)

Kantor, J.; Axelrod, T.; Becla, J.; Cook, K.; Nikolaev, S.; Gray, J.; Plante, R.; Nieto-Santisteban, M.; Szalay, A.; Thakar, A.

2007-10-01

The Large Synoptic Survey Telescope (LSST), a proposed ground-based 8.4 m telescope with a 10 deg^2 field of view, will generate 15 TB of raw images every observing night. When calibration and processed data are added, the image archive, catalogs, and meta-data will grow 15 PB yr^{-1} on average. The LSST Data Management System (DMS) must capture, process, store, index, replicate, and provide open access to this data. Alerts must be triggered within 30 s of data acquisition. To do this in real-time at these data volumes will require advances in data management, database, and file system techniques. This paper describes the design of the LSST DMS and emphasizes features for peta-scale data. The LSST DMS will employ a combination of distributed database and file systems, with schema, partitioning, and indexing oriented for parallel operations. Image files are stored in a distributed file system with references to, and meta-data from, each file stored in the databases. The schema design supports pipeline processing, rapid ingest, and efficient query. Vertical partitioning reduces disk input/output requirements, horizontal partitioning allows parallel data access using arrays of servers and disks. Indexing is extensive, utilizing both conventional RAM-resident indexes and column-narrow, row-deep tag tables/covering indices that are extracted from tables that contain many more attributes. The DMS Data Access Framework is encapsulated in a middleware framework to provide a uniform service interface to all framework capabilities. This framework will provide the automated work-flow, replication, and data analysis capabilities necessary to make data processing and data quality analysis feasible at this scale.

Retention of seed trees fails to lifeboat ectomycorrhizal fungal diversity in harvested Scots pine forests.

PubMed

Varenius, Kerstin; Lindahl, Björn D; Dahlberg, Anders

2017-09-01

Fennoscandian forestry has in the past decades changed from natural regeneration of forests towards replantation of clear-cuts, which negatively impacts ectomycorrhizal fungal (EMF) diversity. Retention of trees during harvesting enables EMF survival, and we therefore expected EMF communities to be more similar to those in old natural stands after forest regeneration using seed trees compared to full clear-cutting and replanting. We sequenced fungal internal transcribed spacer 2 (ITS2) amplicons to assess EMF communities in 10- to 60-year-old Scots pine stands regenerated either using seed trees or through replanting of clear-cuts with old natural stands as reference. We also investigated local EMF communities around retained old trees. We found that retention of seed trees failed to mitigate the impact of harvesting on EMF community composition and diversity. With increasing stand age, EMF communities became increasingly similar to those in old natural stands and permanently retained trees maintained EMF locally. From our observations, we conclude that EMF communities, at least common species, post-harvest are more influenced by environmental filtering, resulting from environmental changes induced by harvest, than by the continuity of trees. These results suggest that retention of intact forest patches is a more efficient way to conserve EMF diversity than retaining dispersed single trees. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effect of electromagnetic waves from mobile phone on immune status of male rats: possible protective role of vitamin D.

PubMed

El-Gohary, Ola Ahmed; Said, Mona Abdel-Azeem

2017-02-01

There are considerable public concerns about the relationship between mobile phone radiation and human health. The present study assesses the effect of electromagnetic field (EMF) emitted from a mobile phone on the immune system in rats and the possible protective role of vitamin D. Rats were randomly divided into six groups: Group I: control group; Group II: received vitamin D (1000 IU/kg/day) orally; Group III: exposed to EMF 1 h/day; Group IV: exposed to EMF 2 h/day; Group V: exposed to EMF 1 h/day and received vitamin D (1000 IU/kg/day); Group VI: exposed to EMF 2 h/day and received vitamin D (1000 IU/kg/day). After 30 days of exposure time, 1 h/day EMF exposure resulted in significant decrease in immunoglobulin levels (IgA, IgE, IgM, and IgG); total leukocyte, lymphocyte, eosinophil and basophil counts; and a significant increase in neutrophil and monocyte counts. These changes were more increased in the group exposed to 2 h/day EMF. Vitamin D supplementation in EMF-exposed rats reversed these results when compared with EMF-exposed groups. In contrast, 7, 14, and 21 days of EMF exposure produced nonsignificant differences in these parameters among all experimental groups. We concluded that exposure to mobile phone radiation compromises the immune system of rats, and vitamin D appears to have a protective effect.

Effects of electromagnetic field exposure on the heart: a systematic review.

PubMed

Elmas, Onur

2016-01-01

The use of electrical devices has gradually increased throughout the last century, and scientists have suggested that electromagnetic fields (EMF) generated by such devices may have harmful effects on living creatures. This work represents a systematic review of collective scholarly literature examining the effects of EMFs on the heart. Although most works describing effects of EMF exposure have been carried out using city electric frequencies (50-60 Hz), a consensus has not been reached about whether long- or short-term exposure to 50-60 Hz EMF negatively affects the heart. Studies have indicated that EMFs produced at cell-phone frequencies cause no-effect on the heart. Differences between results of studies may be due to a compensatory response developed by the body over time. At greater EMF strengths or shorter exposures, the ability of the body to develop compensation mechanisms is reduced and the potential for heart-related effects increases. It is noteworthy that diseases of heart tissues such as myocardial ischemia can also be successfully treated using EMF. Despite the substantial volume of data that has been collected on heart-related effects of EMFs, additional studies are needed at the cellular and molecular level to fully clarify the subject. Until the effects of EMF on heart tissue are more fully explored, electronic devices generating EMFs should be approached with caution. © The Author(s) 2013.

NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases.

PubMed

Costa, Marta; Manton, James D; Ostrovsky, Aaron D; Prohaska, Steffen; Jefferis, Gregory S X E

2016-07-20

Neural circuit mapping is generating datasets of tens of thousands of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1,052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types, including searching neurons against transgene expression patterns. Finally, we show that NBLAST is effective with data from other invertebrates and zebrafish. VIDEO ABSTRACT. Copyright © 2016 MRC Laboratory of Molecular Biology. Published by Elsevier Inc. All rights reserved.

Structural Ceramics Database

National Institute of Standards and Technology Data Gateway

SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

Mission and Assets Database

NASA Technical Reports Server (NTRS)

Baldwin, John; Zendejas, Silvino; Gutheinz, Sandy; Borden, Chester; Wang, Yeou-Fang

2009-01-01

Mission and Assets Database (MADB) Version 1.0 is an SQL database system with a Web user interface to centralize information. The database stores flight project support resource requirements, view periods, antenna information, schedule, and forecast results for use in mid-range and long-term planning of Deep Space Network (DSN) assets.

Rapid Analysis of Pharmacology for Infectious Diseases

PubMed Central

Hopkins, Andrew L; Bickerton, G. Richard; Carruthers, Ian M; Boyer, Stephen K; Rubin, Harvey; Overington, John P

2011-01-01

Pandemic, epidemic and endemic infectious diseases are united by a common problem: how do we rapidly and cost-effectively identify potential pharmacological interventions to treat infections? Given the large number of emerging and neglected infectious diseases and the fact that they disproportionately afflict the poorest members of the global society, new ways of thinking are required to develop high productivity discovery systems that can be applied to a large number of pathogens. The growing availability of parasite genome data provides the basis for developing methods to prioritize, a priori potential drug targets and analyze the pharmacological landscape of an infectious disease. Thus the overall objective of infectious disease informatics is to enable the rapid generation of plausible, novel medical hypotheses of test-able pharmacological experiments, by uncovering undiscovered relationships in the wealth of biomedical literature and databases that were collected for other purposes. In particular our goal is to identify potential drug targets present in a pathogen genome and prioritize which pharmacological experiments are most likely to discover drug-like lead compounds rapidly against a pathogen (i.e. which specific compounds and drug targets should be screened, in which assays and where they can be sourced). An integral part of the challenge is the development and integration of methods to predict druggability, essentiality, synthetic lethality and polypharmocology in pathogen genomes, while simultaneously integrating the inevitable issues of chemical tractability and the potential for acquired drug resistance from the start. PMID:21401504

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection.

PubMed

Rigden, Daniel J; Fernández, Xosé M

2018-01-04

The 2018 Nucleic Acids Research Database Issue contains 181 papers spanning molecular biology. Among them, 82 are new and 84 are updates describing resources that appeared in the Issue previously. The remaining 15 cover databases most recently published elsewhere. Databases in the area of nucleic acids include 3DIV for visualisation of data on genome 3D structure and RNArchitecture, a hierarchical classification of RNA families. Protein databases include the established SMART, ELM and MEROPS while GPCRdb and the newcomer STCRDab cover families of biomedical interest. In the area of metabolism, HMDB and Reactome both report new features while PULDB appears in NAR for the first time. This issue also contains reports on genomics resources including Ensembl, the UCSC Genome Browser and ENCODE. Update papers from the IUPHAR/BPS Guide to Pharmacology and DrugBank are highlights of the drug and drug target section while a number of proteomics databases including proteomicsDB are also covered. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, reviewing 138 entries, adding 88 new resources and eliminating 47 discontinued URLs, bringing the current total to 1737 databases. It is available at http://www.oxfordjournals.org/nar/database/c/. © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

Extremely Low-Frequency Electromagnetic Fields Promote In Vitro Neuronal Differentiation and Neurite Outgrowth of Embryonic Neural Stem Cells via Up-Regulating TRPC1

PubMed Central

Ma, Qinlong; Chen, Chunhai; Deng, Ping; Zhu, Gang; Lin, Min; Zhang, Lei; Xu, Shangcheng; He, Mindi; Lu, Yonghui; Duan, Weixia; Pi, Huifeng; Cao, Zhengwang; Pei, Liping; Li, Min; Liu, Chuan; Zhang, Yanwen; Zhong, Min; Zhou, Zhou; Yu, Zhengping

2016-01-01

Exposure to extremely low-frequency electromagnetic fields (ELF-EMFs) can enhance hippocampal neurogenesis in adult mice. However, little is focused on the effects of ELF-EMFs on embryonic neurogenesis. Here, we studied the potential effects of ELF-EMFs on embryonic neural stem cells (eNSCs). We exposed eNSCs to ELF-EMF (50 Hz, 1 mT) for 1, 2, and 3 days with 4 hours per day. We found that eNSC proliferation and maintenance were significantly enhanced after ELF-EMF exposure in proliferation medium. ELF-EMF exposure increased the ratio of differentiated neurons and promoted the neurite outgrowth of eNSC-derived neurons without influencing astrocyes differentiation and the cell apoptosis. In addition, the expression of the proneural genes, NeuroD and Ngn1, which are crucial for neuronal differentiation and neurite outgrowth, was increased after ELF-EMF exposure. Moreover, the expression of transient receptor potential canonical 1 (TRPC1) was significantly up-regulated accompanied by increased the peak amplitude of intracellular calcium level induced by ELF-EMF. Furthermore, silencing TRPC1 expression eliminated the up-regulation of the proneural genes and the promotion of neuronal differentiation and neurite outgrowth induced by ELF-EMF. These results suggest that ELF-EMF exposure promotes the neuronal differentiation and neurite outgrowth of eNSCs via up-regulation the expression of TRPC1 and proneural genes (NeuroD and Ngn1). These findings also provide new insights in understanding the effects of ELF-EMF exposure on embryonic brain development. PMID:26950212

OpenFluDB, a database for human and animal influenza virus

PubMed Central

Liechti, Robin; Gleizes, Anne; Kuznetsov, Dmitry; Bougueleret, Lydie; Le Mercier, Philippe; Bairoch, Amos; Xenarios, Ioannis

2010-01-01

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. PMID:20624713

Multi-parameter vital sign database to assist in alarm optimization for general care units.

PubMed

Welch, James; Kanter, Benjamin; Skora, Brooke; McCombie, Scott; Henry, Isaac; McCombie, Devin; Kennedy, Rosemary; Soller, Babs

2016-12-01

Continual vital sign assessment on the general care, medical-surgical floor is expected to provide early indication of patient deterioration and increase the effectiveness of rapid response teams. However, there is concern that continual, multi-parameter vital sign monitoring will produce alarm fatigue. The objective of this study was the development of a methodology to help care teams optimize alarm settings. An on-body wireless monitoring system was used to continually assess heart rate, respiratory rate, SpO 2 and noninvasive blood pressure in the general ward of ten hospitals between April 1, 2014 and January 19, 2015. These data, 94,575 h for 3430 patients are contained in a large database, accessible with cloud computing tools. Simulation scenarios assessed the total alarm rate as a function of threshold and annunciation delay (s). The total alarm rate of ten alarms/patient/day predicted from the cloud-hosted database was the same as the total alarm rate for a 10 day evaluation (1550 h for 36 patients) in an independent hospital. Plots of vital sign distributions in the cloud-hosted database were similar to other large databases published by different authors. The cloud-hosted database can be used to run simulations for various alarm thresholds and annunciation delays to predict the total alarm burden experienced by nursing staff. This methodology might, in the future, be used to help reduce alarm fatigue without sacrificing the ability to continually monitor all vital signs.

Surgical research using national databases

PubMed Central

Leland, Hyuma; Heckmann, Nathanael

2016-01-01

Recent changes in healthcare and advances in technology have increased the use of large-volume national databases in surgical research. These databases have been used to develop perioperative risk stratification tools, assess postoperative complications, calculate costs, and investigate numerous other topics across multiple surgical specialties. The results of these studies contain variable information but are subject to unique limitations. The use of large-volume national databases is increasing in popularity, and thorough understanding of these databases will allow for a more sophisticated and better educated interpretation of studies that utilize such databases. This review will highlight the composition, strengths, and weaknesses of commonly used national databases in surgical research. PMID:27867945

Surgical research using national databases.

PubMed

Alluri, Ram K; Leland, Hyuma; Heckmann, Nathanael

2016-10-01

Recent changes in healthcare and advances in technology have increased the use of large-volume national databases in surgical research. These databases have been used to develop perioperative risk stratification tools, assess postoperative complications, calculate costs, and investigate numerous other topics across multiple surgical specialties. The results of these studies contain variable information but are subject to unique limitations. The use of large-volume national databases is increasing in popularity, and thorough understanding of these databases will allow for a more sophisticated and better educated interpretation of studies that utilize such databases. This review will highlight the composition, strengths, and weaknesses of commonly used national databases in surgical research.

[The database server for the medical bibliography database at Charles University].

PubMed

Vejvalka, J; Rojíková, V; Ulrych, O; Vorísek, M

1998-01-01

In the medical community, bibliographic databases are widely accepted as a most important source of information both for theoretical and clinical disciplines. To improve access to medical bibliographic databases at Charles University, a database server (ERL by Silver Platter) was set up at the 2nd Faculty of Medicine in Prague. The server, accessible by Internet 24 hours/7 days, hosts now 14 years' MEDLINE and 10 years' EMBASE Paediatrics. Two different strategies are available for connecting to the server: a specialized client program that communicates over the Internet (suitable for professional searching) and a web-based access that requires no specialized software (except the WWW browser) on the client side. The server is now offered to academic community to host further databases, possibly subscribed by consortia whose individual members would not subscribe them by themselves.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

PubMed

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. This database will facilitate the analysis of protein-DNA interactions and the development of

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

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

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE PAGES

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the

Exposure to a specific time-varying electromagnetic field inhibits cell proliferation via cAMP and ERK signaling in cancer cells.

PubMed

Buckner, Carly A; Buckner, Alison L; Koren, Stan A; Persinger, Michael A; Lafrenie, Robert M

2018-04-01

Exposure to specific electromagnetic field (EMF) patterns can affect a variety of biological systems. We have shown that exposure to Thomas-EMF, a low-intensity, frequency-modulated (25-6 Hz) EMF pattern, inhibited growth and altered cell signaling in malignant cells. Exposure to Thomas-EMF for 1 h/day inhibited the growth of malignant cells including B16-BL6 mouse melanoma cells, MDA-MB-231, MDA-MB-468, BT-20, and MCF-7 human breast cancer and HeLa cervical cancer cells but did not affect non-malignant cells. The Thomas-EMF-dependent changes in cell proliferation were mediated by adenosine 3',5'-cyclic monophosphate (cAMP) and extracellular-signal-regulated kinase (ERK) signaling pathways. Exposure of malignant cells to Thomas-EMF transiently changed the level of cellular cAMP and promoted ERK phosphorylation. Pharmacologic inhibitors (SQ22536) and activators (forskolin) of cAMP production both blocked the ability of Thomas-EMF to inhibit cell proliferation, and an inhibitor of the MAP kinase pathway (PD98059) was able to partially block Thomas-EMF-dependent inhibition of cell proliferation. Genetic modulation of protein kinase A (PKA) in B16-BL6 cells also altered the effect of Thomas-EMF on cell proliferation. Cells transfected with the constitutively active form of PKA (PKA-CA), which interfered with ERK phosphorylation, also interfered with the Thomas-EMF effect on cell proliferation. The non-malignant cells did not show any EMF-dependent changes in cAMP levels, ERK phosphorylation, or cell growth. These data indicate that exposure to the specific Thomas-EMF pattern can inhibit the growth of malignant cells in a manner dependent on contributions from the cAMP and MAP kinase pathways. Bioelectromagnetics. 39;217-230, 2018. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Effects of extremely low frequency electromagnetic fields on distortion product otoacoustic emissions in rabbits.

PubMed

Budak, Bilgehan; Budak, Gürer G; Oztürk, Göknur Güler; Muluk, Nuray Bayar; Apan, Alpaslan; Seyhan, Nesrin

2009-06-01

Humans are continuously exposed to extremely low frequency (ELF), electromagnetic fields (EMF), transmitted from the common sources like power stations, electric transmission lines, communication and radio-television signal transmission units. The present study aimed to assess the effects of 50 Hz ELF-EMF of 5.068 and 10.182 kV/m electric fields, which refer to the lower and upper intensity limits beyond which hazardous effects can be observed, on the auditory functions of rabbits via Distortion Product Otoacoustic Emission (DPOAE) recordings. The study was performed on 20 healthy adult female New Zealand White rabbits randomly divided into two groups and applied 50 Hz ELF-EMF with either 5.068 kV/m (Group 1) or 10.182 kV/m (Group 2) of electric field for 3h/day during 14 days. DPOAE responses recorded on the 0th day before exposure (B-EMF) and on the 6th (A-EMF-6th) and 14th (A-EMF-14th) days after exposure (AE). Mean stimulus intensity and emission amplitudes at 1.0-8.0 kHz were analyzed. In Group 2 rabbits, on 6th and 14th days, the DPOAE amplitudes were observed as increased at 1.5-4.0 kHz (at 2.0 and 4.0 kHz significantly) than B-EMF values. At 6.0 kHz, A-EMF-14th amplitudes were significantly lower than A-EMF values. These results suggest that ELF EMFs might affect hearing functions by frequency dependent manner. Higher ELF EMFs exposure caused increase of cochlear activity. Ototoxic effect of 10.182 kV/m ELF EMFs may begin at the basal turn of the cochlea by reducing DPOAEs at high frequencies.

Income distribution patterns from a complete social security database

NASA Astrophysics Data System (ADS)

Derzsy, N.; Néda, Z.; Santos, M. A.

2012-11-01

We analyze the income distribution of employees for 9 consecutive years (2001-2009) using a complete social security database for an economically important district of Romania. The database contains detailed information on more than half million taxpayers, including their monthly salaries from all employers where they worked. Besides studying the characteristic distribution functions in the high and low/medium income limits, the database allows us a detailed dynamical study by following the time-evolution of the taxpayers income. To our knowledge, this is the first extensive study of this kind (a previous Japanese taxpayers survey was limited to two years). In the high income limit we prove once again the validity of Pareto’s law, obtaining a perfect scaling on four orders of magnitude in the rank for all the studied years. The obtained Pareto exponents are quite stable with values around α≈2.5, in spite of the fact that during this period the economy developed rapidly and also a financial-economic crisis hit Romania in 2007-2008. For the low and medium income category we confirmed the exponential-type income distribution. Following the income of employees in time, we have found that the top limit of the income distribution is a highly dynamical region with strong fluctuations in the rank. In this region, the observed dynamics is consistent with a multiplicative random growth hypothesis. Contrarily with previous results obtained for the Japanese employees, we find that the logarithmic growth-rate is not independent of the income.

Landslide databases review in the Geological Surveys of Europe

NASA Astrophysics Data System (ADS)

Herrera, Gerardo

2017-04-01

Landslides are one of the most widespread geohazards in Europe, producing significant social and economic damages. Rapid population growth in urban areas throughout many countries in Europe and extreme climatic scenarios can considerably increase landslide risk in the near future. However, many European countries do not include landslide risk into their legislation. Countries lack official methodological assessment guidelines and knowledge about landslide impacts. Although regional and national landslide databases exist in most countries, they are often not integrated because they are owed by different institutions. Hence, a European Landslides Directive, that provides a common legal framework for dealing with landslides, is necessary. With this long-term goal in mind, we present a review of the landslide databases from the Geological Surveys of Europe focusing on their interoperability. The same landslide classification was used for the 849,543 landslide records from the Geological Surveys, from which 36% are slides, 10 % falls, 20% flows, 11% complex slides and 24% remain either unclassified or correspond to another typology. A landslide density map was produced from the available records of the Geological Surveys of 17 countries showing the variable distribution of landslides. There are 0.2 million km2 of landslide prone areas. The comparison of this map with the European landslide susceptibility map ELSUS v1 was successful for 73% of the predictions, and permitted identification of 25% of susceptible areas where landslide records are not available from the Geological Surveys. Taking these results into account the completeness of these landslide databases was evaluated, revealing different landslide hazard management approaches between surveys and countries.

Consolidating emerging evidence surrounding HIVST and HIVSS: a rapid systematic mapping protocol.

PubMed

Witzel, T Charles; Weatherburn, Peter; Burns, Fiona M; Johnson, Cheryl C; Figueroa, Carmen; Rodger, Alison J

2017-04-05

HIV self-testing (HIVST) is becoming popular with policy makers and commissioners globally, with a key aim of expanding access through reducing barriers to testing for individuals at risk of HIV infection. HIV self-sampling (HIVSS) was available previously to self-testing but was confined mainly to the USA and the UK. It remains to be seen whether the momentum behind HIVST will also energise efforts to expand HIVSS. Recent years have seen a rapid growth in the type of evidence related to these interventions as well as several systematic reviews. The vast majority of this evidence relates to acceptability as well as values and preferences, although new types of evidence are emerging. This systematic map aims to consolidate all emerging evidence related to HIVST and HIVSS to respond to this rapidly changing area. We will systematically search databases and the abstracts of five conferences from 2006 to the present date, with monthly-automated database searches. Searches will combine key terms relating to HIV (e.g. HIV, AIDS, human immune-deficiency syndrome) with terms related to self-testing (e.g. home-test, self-test, mail-test, home dried blood spot test). Abstracts will be reviewed against inclusion criteria in duplicate. Data will be manually extracted through a standard form and then entered to an open access relational map (HIVST.org). When new and sufficient evidence emerges which addresses existing knowledge gaps, we will complete a review on a relevant topic. This innovative approach will allow rapid cataloguing, documenting and dissemination of new evidence and key findings as they emerge into the public domain. This protocol has not been registered with PROSPERO as they do not register systematic maps.

The effect of low force chiropractic adjustments on body surface electromagnetic field.

PubMed

Zhang, John; Snyder, Brian J; Vernor, Lori

2004-03-01

The purpose of this study was to investigate the body surface electromagnetic field (EMF) changes using a sensitive magnetometer before and after a specific Toftness chiropractic adjustment in asymptomatic human subjects. Forty-four subjects were randomly assigned into control (20 subjects) and experimental groups (24 subjects) in a pre and post-test design. The Triaxial Fluxgate Magnetometer FGM-5DTAA (Walker Scientific, Worcester, Massachusetts) with five digit display and resolution of 1 nanotesla (nT) was used for EMF detection. The EMF in the research room and on the adjustment table was monitored and recorded. The subjects' body surface (cervical, thoracic, lumbar and sacral areas) EMF was determined in the prone position before and after the chiropractic adjustment. A low force Toftness chiropractic adjustment was applied to the cervical, thoracic, lumbar and sacral areas as determined by the practitioner. The EMF in the research room was recorded as 41611 nT at the Z axis (earth field), 13761 nT at the X axis and 7438 nT at the Y axis. The EMF on the adjusting table changed minimally during the 15 minute observation period. The EMF on the subjects' body surface decreased at 4 spinal locations after chiropractic adjustment. The EMF (mean +/- SD in nT) decreased significantly at the cervical region from 42449 +/- 907 to 41643 +/- 1165 (p < 0.01) and at the sacral regions from 43206 +/- 760 to 42713 +/- 552 (p < 0.01). The EMF at the lumbar and thoracic regions decreased but did not reach a statistically significant level. No significant changes of the body surface EMF were found in the control group. A low force Toftness chiropractic adjustment in the cervical and sacral areas resulted in a significant reduction of the cervical and sacral surface EMF. No significant body surface EMF changes were observed in the lumbar and thoracic regions. The mechanisms of the EMF reduction after chiropractic adjustment are not known.

The effect of low force chiropractic adjustments on body surface electromagnetic field

PubMed Central

Zhang, John; Snyder, Brian J; Vernor, Lori

2004-01-01

Objective The purpose of this study was to investigate the body surface electromagnetic field (EMF) changes using a sensitive magnetometer before and after a specific Toftness chiropractic adjustment in asymptomatic human subjects. Method Forty-four subjects were randomly assigned into control (20 subjects) and experimental groups (24 subjects) in a pre and post-test design. The Triaxial Fluxgate Magnetometer FGM-5DTAA (Walker Scientific, Worcester, Massachusetts) with five digit display and resolution of 1 nanotesla (nT) was used for EMF detection. The EMF in the research room and on the adjustment table was monitored and recorded. The subjects’ body surface (cervical, thoracic, lumbar and sacral areas) EMF was determined in the prone position before and after the chiropractic adjustment. A low force Toftness chiropractic adjustment was applied to the cervical, thoracic, lumbar and sacral areas as determined by the practitioner. Results The EMF in the research room was recorded as 41611 nT at the Z axis (earth field), 13761 nT at the X axis and 7438 nT at the Y axis. The EMF on the adjusting table changed minimally during the 15 minute observation period. The EMF on the subjects’ body surface decreased at 4 spinal locations after chiropractic adjustment. The EMF (mean ± SD in nT) decreased significantly at the cervical region from 42449 ± 907 to 41643 ± 1165 (p < 0.01) and at the sacral regions from 43206 ± 760 to 42713 ± 552 (p < 0.01). The EMF at the lumbar and thoracic regions decreased but did not reach a statistically significant level. No significant changes of the body surface EMF were found in the control group. Conclusion A low force Toftness chiropractic adjustment in the cervical and sacral areas resulted in a significant reduction of the cervical and sacral surface EMF. No significant body surface EMF changes were observed in the lumbar and thoracic regions. The mechanisms of the EMF reduction after chiropractic adjustment are not known. PMID

1950 MHz Electromagnetic Fields Ameliorate Aβ Pathology in Alzheimer’s Disease Mice

PubMed Central

Jeong, Ye Ji; Kang, Ga-Young; Kwon, Jong Hwa; Choi, Hyung-Do; Pack, Jeong-Ki; Kim, Nam; Lee, Yun-Sil; Lee, Hae-June

2015-01-01

The involvement of radiofrequency electromagnetic fields (RF-EMF) in the neurodegenerative disease, especially Alzheimer’s disease (AD), has received wide consideration, however, outcomes from several researches have not shown consistency. In this study, we determined whether RF-EMF influenced AD pathology in vivo using Tg-5xFAD mice as a model of AD-like amyloid β (Aβ) pathology. The transgenic (Tg)-5xFAD and wild type (WT) mice were chronically exposed to RF-EMF for 8 months (1950 MHz, SAR 5W/kg, 2 hrs/day, 5 days/week). Notably, chronic RF-EMF exposure significantly reduced not only Aβ plaques, APP, and APP carboxyl-terminal fragments (CTFs) in whole brain including hippocampus and entorhinal cortex but also the ratio of Aβ42 and Aβ40 peptide in the hippocampus of Tg-5xFAD mice. We also found that parenchymal expression of β-amyloid precursor protein cleaving enzyme 1(BACE1) and neuroinflammation were inhibited by RF-EMF exposure in Tg-5xFAD. In addition, RF-EMF was shown to rescue memory impairment in Tg-5xFAD. Moreover, gene profiling from microarray data using hippocampus of WT and Tg-5xFAD following RF-EMF exposure revealed that 5 genes (Tshz2, Gm12695, St3gal1, Isx and Tll1), which are involved in Aβ, are significantly altered inTg-5xFAD mice, exhibiting different responses to RF-EMF in WT or Tg-5xFAD mice; RF-EMF exposure in WT mice showed similar patterns to control Tg-5xFAD mice, however, RF-EMF exposure in Tg-5xFAD mice showed opposite expression patterns. These findings indicate that chronic RF-EMF exposure directly affects Aβ pathology in AD but not in normal brain. Therefore, RF-EMF has preventive effects against AD-like pathology in advanced AD mice with a high expression of Aβ, which suggests that RF-EMF can have a beneficial influence on AD. PMID:26017559

New perspectives in toxicological information management, and the role of ISSTOX databases in assessing chemical mutagenicity and carcinogenicity.

PubMed

Benigni, Romualdo; Battistelli, Chiara Laura; Bossa, Cecilia; Tcheremenskaia, Olga; Crettaz, Pierre

2013-07-01

Currently, the public has access to a variety of databases containing mutagenicity and carcinogenicity data. These resources are crucial for the toxicologists and regulators involved in the risk assessment of chemicals, which necessitates access to all the relevant literature, and the capability to search across toxicity databases using both biological and chemical criteria. Towards the larger goal of screening chemicals for a wide range of toxicity end points of potential interest, publicly available resources across a large spectrum of biological and chemical data space must be effectively harnessed with current and evolving information technologies (i.e. systematised, integrated and mined), if long-term screening and prediction objectives are to be achieved. A key to rapid progress in the field of chemical toxicity databases is that of combining information technology with the chemical structure as identifier of the molecules. This permits an enormous range of operations (e.g. retrieving chemicals or chemical classes, describing the content of databases, finding similar chemicals, crossing biological and chemical interrogations, etc.) that other more classical databases cannot allow. This article describes the progress in the technology of toxicity databases, including the concepts of Chemical Relational Database and Toxicological Standardized Controlled Vocabularies (Ontology). Then it describes the ISSTOX cluster of toxicological databases at the Istituto Superiore di Sanitá. It consists of freely available databases characterised by the use of modern information technologies and by curation of the quality of the biological data. Finally, this article provides examples of analyses and results made possible by ISSTOX.

The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching

PubMed Central

Howe, Douglas G.; Bradford, Yvonne M.; Eagle, Anne; Fashena, David; Frazer, Ken; Kalita, Patrick; Mani, Prita; Martin, Ryan; Moxon, Sierra Taylor; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruzicka, Leyla; Schaper, Kevin; Shao, Xiang; Singer, Amy; Toro, Sabrina; Van Slyke, Ceri; Westerfield, Monte

2017-01-01

The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for zebrafish (Danio rerio) genetic, genomic, phenotypic and developmental data. ZFIN curators provide expert manual curation and integration of comprehensive data involving zebrafish genes, mutants, transgenic constructs and lines, phenotypes, genotypes, gene expressions, morpholinos, TALENs, CRISPRs, antibodies, anatomical structures, models of human disease and publications. We integrate curated, directly submitted, and collaboratively generated data, making these available to zebrafish research community. Among the vertebrate model organisms, zebrafish are superbly suited for rapid generation of sequence-targeted mutant lines, characterization of phenotypes including gene expression patterns, and generation of human disease models. The recent rapid adoption of zebrafish as human disease models is making management of these data particularly important to both the research and clinical communities. Here, we describe recent enhancements to ZFIN including use of the zebrafish experimental conditions ontology, ‘Fish’ records in the ZFIN database, support for gene expression phenotypes, models of human disease, mutation details at the DNA, RNA and protein levels, and updates to the ZFIN single box search. PMID:27899582

MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data.

PubMed

Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

2015-01-01

The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.jp/) is a comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. Because of the rapid increase in microbial genome data owing to the next-generation sequencing technology, it becomes increasingly challenging to maintain high-quality orthology relationships while allowing the users to incorporate the latest genomic data available into an analysis. Because many of the recently accumulating genomic data are draft genome sequences for which some complete genome sequences of the same or closely related species are available, MBGD now stores draft genome data and allows the users to incorporate them into a user-specific ortholog database using the MyMBGD functionality. In this function, draft genome data are incorporated into an existing ortholog table created only from the complete genome data in an incremental manner to prevent low-quality draft data from affecting clustering results. In addition, to provide high-quality orthology relationships, the standard ortholog table containing all the representative genomes, which is first created by the rapid classification program DomClust, is now refined using DomRefine, a recently developed program for improving domain-level clustering using multiple sequence alignment information. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

A World Wide Web (WWW) server database engine for an organelle database, MitoDat.

PubMed

Lemkin, P F; Chipperfield, M; Merril, C; Zullo, S

1996-03-01

We describe a simple database search engine "dbEngine" which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relationship database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies

PubMed Central

Cserhati, Matyas F.; Pandey, Sanjit; Beaudoin, James J.; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S.

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33 017 407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. Database URL: http://nntc-dcc.unmc.edu PMID:26228431

Morchella MLST database

USDA-ARS?s Scientific Manuscript database

Welcome to the Morchella MLST database. This dedicated database was set up at the CBS-KNAW Biodiversity Center by Vincent Robert in February 2012, using BioloMICS software (Robert et al., 2011), to facilitate DNA sequence-based identifications of Morchella species via the Internet. The current datab...

Dictionary as Database.

ERIC Educational Resources Information Center

Painter, Derrick

1996-01-01

Discussion of dictionaries as databases focuses on the digitizing of The Oxford English dictionary (OED) and the use of Standard Generalized Mark-Up Language (SGML). Topics include the creation of a consortium to digitize the OED, document structure, relational databases, text forms, sequence, and discourse. (LRW)

Freshwater Biological Traits Database (Final Report)

EPA Science Inventory

EPA announced the release of the final report, Freshwater Biological Traits Database. This report discusses the development of a database of freshwater biological traits. The database combines several existing traits databases into an online format. The database is also...

MRPrimerV: a database of PCR primers for RNA virus detection

PubMed Central

Kim, Hyerin; Kang, NaNa; An, KyuHyeon; Kim, Doyun; Koo, JaeHyung; Kim, Min-Soo

2017-01-01

Many infectious diseases are caused by viral infections, and in particular by RNA viruses such as MERS, Ebola and Zika. To understand viral disease, detection and identification of these viruses are essential. Although PCR is widely used for rapid virus identification due to its low cost and high sensitivity and specificity, very few online database resources have compiled PCR primers for RNA viruses. To effectively detect viruses, the MRPrimerV database (http://MRPrimerV.com) contains 152 380 247 PCR primer pairs for detection of 1818 viruses, covering 7144 coding sequences (CDSs), representing 100% of the RNA viruses in the most up-to-date NCBI RefSeq database. Due to rigorous similarity testing against all human and viral sequences, every primer in MRPrimerV is highly target-specific. Because MRPrimerV ranks CDSs by the penalty scores of their best primer, users need only use the first primer pair for a single-phase PCR or the first two primer pairs for two-phase PCR. Moreover, MRPrimerV provides the list of genome neighbors that can be detected using each primer pair, covering 22 192 variants of 532 RefSeq RNA viruses. We believe that the public availability of MRPrimerV will facilitate viral metagenomics studies aimed at evaluating the variability of viruses, as well as other scientific tasks. PMID:27899620

Database-independent Protein Sequencing (DiPS) Enables Full-length de Novo Protein and Antibody Sequence Determination.

PubMed

Savidor, Alon; Barzilay, Rotem; Elinger, Dalia; Yarden, Yosef; Lindzen, Moshit; Gabashvili, Alexandra; Adiv Tal, Ophir; Levin, Yishai

2017-06-01

Traditional "bottom-up" proteomic approaches use proteolytic digestion, LC-MS/MS, and database searching to elucidate peptide identities and their parent proteins. Protein sequences absent from the database cannot be identified, and even if present in the database, complete sequence coverage is rarely achieved even for the most abundant proteins in the sample. Thus, sequencing of unknown proteins such as antibodies or constituents of metaproteomes remains a challenging problem. To date, there is no available method for full-length protein sequencing, independent of a reference database, in high throughput. Here, we present Database-independent Protein Sequencing, a method for unambiguous, rapid, database-independent, full-length protein sequencing. The method is a novel combination of non-enzymatic, semi-random cleavage of the protein, LC-MS/MS analysis, peptide de novo sequencing, extraction of peptide tags, and their assembly into a consensus sequence using an algorithm named "Peptide Tag Assembler." As proof-of-concept, the method was applied to samples of three known proteins representing three size classes and to a previously un-sequenced, clinically relevant monoclonal antibody. Excluding leucine/isoleucine and glutamic acid/deamidated glutamine ambiguities, end-to-end full-length de novo sequencing was achieved with 99-100% accuracy for all benchmarking proteins and the antibody light chain. Accuracy of the sequenced antibody heavy chain, including the entire variable region, was also 100%, but there was a 23-residue gap in the constant region sequence. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Intelligent communication assistant for databases

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

Jakobson, G.; Shaked, V.; Rowley, S.

1983-01-01

An intelligent communication assistant for databases, called FRED (front end for databases) is explored. FRED is designed to facilitate access to database systems by users of varying levels of experience. FRED is a second generation of natural language front-ends for databases and intends to solve two critical interface problems existing between end-users and databases: connectivity and communication problems. The authors report their experiences in developing software for natural language query processing, dialog control, and knowledge representation, as well as the direction of future work. 10 references.

Comparison of the Frontier Distributed Database Caching System to NoSQL Databases

NASA Astrophysics Data System (ADS)

Dykstra, Dave

2012-12-01

One of the main attractions of non-relational “NoSQL” databases is their ability to scale to large numbers of readers, including readers spread over a wide area. The Frontier distributed database caching system, used in production by the Large Hadron Collider CMS and ATLAS detector projects for Conditions data, is based on traditional SQL databases but also adds high scalability and the ability to be distributed over a wide-area for an important subset of applications. This paper compares the major characteristics of the two different approaches and identifies the criteria for choosing which approach to prefer over the other. It also compares in some detail the NoSQL databases used by CMS and ATLAS: MongoDB, CouchDB, HBase, and Cassandra.

The Halophile protein database.

PubMed

Sharma, Naveen; Farooqi, Mohammad Samir; Chaturvedi, Krishna Kumar; Lal, Shashi Bhushan; Grover, Monendra; Rai, Anil; Pandey, Pankaj

2014-01-01

Halophilic archaea/bacteria adapt to different salt concentration, namely extreme, moderate and low. These type of adaptations may occur as a result of modification of protein structure and other changes in different cell organelles. Thus proteins may play an important role in the adaptation of halophilic archaea/bacteria to saline conditions. The Halophile protein database (HProtDB) is a systematic attempt to document the biochemical and biophysical properties of proteins from halophilic archaea/bacteria which may be involved in adaptation of these organisms to saline conditions. In this database, various physicochemical properties such as molecular weight, theoretical pI, amino acid composition, atomic composition, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (Gravy) have been listed. These physicochemical properties play an important role in identifying the protein structure, bonding pattern and function of the specific proteins. This database is comprehensive, manually curated, non-redundant catalogue of proteins. The database currently contains 59 897 proteins properties extracted from 21 different strains of halophilic archaea/bacteria. The database can be accessed through link. Database URL: http://webapp.cabgrid.res.in/protein/ © The Author(s) 2014. Published by Oxford University Press.

A new relational database structure and online interface for the HITRAN database

NASA Astrophysics Data System (ADS)

Hill, Christian; Gordon, Iouli E.; Rothman, Laurence S.; Tennyson, Jonathan

2013-11-01

A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described.

Cross-Border Use of Food Databases: Equivalence of US and Australian Databases for Macronutrients

PubMed Central

Summer, Suzanne S.; Ollberding, Nicholas J.; Guy, Trish; Setchell, Kenneth D. R.; Brown, Nadine; Kalkwarf, Heidi J.

2013-01-01

When estimating dietary intake across multiple countries, the lack of a single comprehensive dietary database may lead researchers to modify one database to analyze intakes for all participants. This approach may yield results different from those using the country-specific database and introduce measurement error. We examined whether nutrient intakes of Australians calculated with a modified US database would be similar to those calculated with an Australian database. We analyzed 3-day food records of 68 Australian adults using the US-based Nutrition Data System for Research, modified to reflect food items consumed in Australia. Modification entailed identifying a substitute food whose energy and macronutrient content were within 10% of the Australian food or by adding a new food to the database. Paired Wilcoxon signed rank tests were used to compare differences in nutrient intakes estimated by both databases, and Pearson and intraclass correlation coefficients measured degree of association and agreement between intake estimates for individuals. Median intakes of energy, carbohydrate, protein, and fiber differed by <5% at the group level. Larger discrepancies were seen for fat (11%; P<0.0001) and most micronutrients. Despite strong correlations, nutrient intakes differed by >10% for an appreciable percentage of participants (35% for energy to 69% for total fat). Adding country-specific food items to an existing database resulted in similar overall macronutrient intake estimates but was insufficient for estimating individual intakes. When analyzing nutrient intakes in multinational studies, greater standardization and modification of databases may be required to more accurately estimate intake of individuals. PMID:23871108

National Transportation Atlas Databases : 1999

DOT National Transportation Integrated Search

1999-01-01

The National Transportation Atlas Databases -- 1999 (NTAD99) is a set of national : geographic databases of transportation facilities. These databases include geospatial : information for transportation modal networks and intermodal terminals, and re...

National Transportation Atlas Databases : 2001

DOT National Transportation Integrated Search

2001-01-01

The National Transportation Atlas Databases-2001 (NTAD-2001) is a set of national geographic databases of transportation facilities. These databases include geospatial information for transportation modal networks and intermodal terminals and related...

National Transportation Atlas Databases : 1996

DOT National Transportation Integrated Search

1996-01-01

The National Transportation Atlas Databases -- 1996 (NTAD96) is a set of national : geographic databases of transportation facilities. These databases include geospatial : information for transportation modal networks and intermodal terminals, and re...

National Transportation Atlas Databases : 2000

DOT National Transportation Integrated Search

2000-01-01

The National Transportation Atlas Databases-2000 (NTAD-2000) is a set of national geographic databases of transportation facilities. These databases include geospatial information for transportation modal networks and intermodal terminals and related...

National Transportation Atlas Databases : 1997

DOT National Transportation Integrated Search

1997-01-01

The National Transportation Atlas Databases -- 1997 (NTAD97) is a set of national : geographic databases of transportation facilities. These databases include geospatial : information for transportation modal networks and intermodal terminals, and re...

FRED, a Front End for Databases.

ERIC Educational Resources Information Center

Crystal, Maurice I.; Jakobson, Gabriel E.

1982-01-01

FRED (a Front End for Databases) was conceived to alleviate data access difficulties posed by the heterogeneous nature of online databases. A hardware/software layer interposed between users and databases, it consists of three subsystems: user-interface, database-interface, and knowledge base. Architectural alternatives for this database machine…

Respiratory cancer database: An open access database of respiratory cancer gene and miRNA.

PubMed

Choubey, Jyotsna; Choudhari, Jyoti Kant; Patel, Ashish; Verma, Mukesh Kumar

2017-01-01

Respiratory cancer database (RespCanDB) is a genomic and proteomic database of cancer of respiratory organ. It also includes the information of medicinal plants used for the treatment of various respiratory cancers with structure of its active constituents as well as pharmacological and chemical information of drug associated with various respiratory cancers. Data in RespCanDB has been manually collected from published research article and from other databases. Data has been integrated using MySQL an object-relational database management system. MySQL manages all data in the back-end and provides commands to retrieve and store the data into the database. The web interface of database has been built in ASP. RespCanDB is expected to contribute to the understanding of scientific community regarding respiratory cancer biology as well as developments of new way of diagnosing and treating respiratory cancer. Currently, the database consist the oncogenomic information of lung cancer, laryngeal cancer, and nasopharyngeal cancer. Data for other cancers, such as oral and tracheal cancers, will be added in the near future. The URL of RespCanDB is http://ridb.subdic-bioinformatics-nitrr.in/.

NASA Records Database

NASA Technical Reports Server (NTRS)

Callac, Christopher; Lunsford, Michelle

2005-01-01

The NASA Records Database, comprising a Web-based application program and a database, is used to administer an archive of paper records at Stennis Space Center. The system begins with an electronic form, into which a user enters information about records that the user is sending to the archive. The form is smart : it provides instructions for entering information correctly and prompts the user to enter all required information. Once complete, the form is digitally signed and submitted to the database. The system determines which storage locations are not in use, assigns the user s boxes of records to some of them, and enters these assignments in the database. Thereafter, the software tracks the boxes and can be used to locate them. By use of search capabilities of the software, specific records can be sought by box storage locations, accession numbers, record dates, submitting organizations, or details of the records themselves. Boxes can be marked with such statuses as checked out, lost, transferred, and destroyed. The system can generate reports showing boxes awaiting destruction or transfer. When boxes are transferred to the National Archives and Records Administration (NARA), the system can automatically fill out NARA records-transfer forms. Currently, several other NASA Centers are considering deploying the NASA Records Database to help automate their records archives.

Rapid COJEC Induction Therapy for High-risk Neuroblastoma Patients - Cochrane Review.

PubMed

Peinemann, F; van Dalen, E C; Berthold, F

2016-04-01

Neuroblastoma is a rare malignant disease and patients with high-risk neuroblastoma have a poor prognosis. Rapid COJEC induction chemotherapy means (almost) the same total doses given within a shorter time period. In theory, rapid COJEC could reduce the risk of drug resistance and it has been considered as a potential candidate for improving the outcome. The objective was to evaluate effects of rapid COJEC compared to standard induction chemotherapy in patients with high-risk neuroblastoma. We searched the databases CENTRAL, MEDLINE, and EMBASE from inception to 11 November 2014 and included randomized controlled trials. We identified one relevant randomized controlled trial with 130 participants receiving rapid COJEC and 132 participants receiving standard OPEC/COJEC induction chemotherapy. There was no statistically significant difference between the treatment groups in complete response (risk ratio 0.99, 95% confidence interval 0.71 to 1.38, P=0.94) and treatment-related mortality (risk ratio 1.21, 95% confidence interval 0.33 to 4.39, P=0.77). A statistically significant difference in favor of the standard treatment arm was identified for the following early toxicities: febrile neutropenia, septicemia, and renal toxicity. The differences in complete response and treatment-related mortality between treatment alternatives were not statistically significantly different. Based on the currently available evidence, we are uncertain about the effects of rapid COJEC induction chemotherapy in patients with high-risk neuroblastoma. © Georg Thieme Verlag KG Stuttgart · New York.

Comparison of the Frontier Distributed Database Caching System to NoSQL Databases

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

Dykstra, Dave

One of the main attractions of non-relational NoSQL databases is their ability to scale to large numbers of readers, including readers spread over a wide area. The Frontier distributed database caching system, used in production by the Large Hadron Collider CMS and ATLAS detector projects for Conditions data, is based on traditional SQL databases but also adds high scalability and the ability to be distributed over a wide-area for an important subset of applications. This paper compares the major characteristics of the two different approaches and identifies the criteria for choosing which approach to prefer over the other. It alsomore » compares in some detail the NoSQL databases used by CMS and ATLAS: MongoDB, CouchDB, HBase, and Cassandra.« less

Solubility Database

National Institute of Standards and Technology Data Gateway

SRD 106 IUPAC-NIST Solubility Database (Web, free access)   These solubilities are compiled from 18 volumes (Click here for List) of the International Union for Pure and Applied Chemistry(IUPAC)-NIST Solubility Data Series. The database includes liquid-liquid, solid-liquid, and gas-liquid systems. Typical solvents and solutes include water, seawater, heavy water, inorganic compounds, and a variety of organic compounds such as hydrocarbons, halogenated hydrocarbons, alcohols, acids, esters and nitrogen compounds. There are over 67,500 solubility measurements and over 1800 references.

University Real Estate Development Database: A Database-Driven Internet Research Tool

ERIC Educational Resources Information Center

Wiewel, Wim; Kunst, Kara

2008-01-01

The University Real Estate Development Database is an Internet resource developed by the University of Baltimore for the Lincoln Institute of Land Policy, containing over six hundred cases of university expansion outside of traditional campus boundaries. The University Real Estate Development database is a searchable collection of real estate…

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.

PubMed