A robust SRAM-PUF key generation scheme based on polar codes

NARCIS (Netherlands)

Chen, Bin; Ignatenko, Tanya; Willems, Frans M.J.; Maes, Roel; van der Sluis, Erik; Selimis, Georgios

2017-01-01

Physical unclonable functions (PUFs) are relatively new security primitives used for device authentication and device-specific secret key generation. In this paper we focus on SRAM- PUFs. The SRAM-PUFs enjoy uniqueness and randomness properties stemming from the intrinsic randomness of SRAM memory

Physicochemical properties and antioxidant capacity of raw, roasted and puffed cacao beans.

Science.gov (United States)

Hu, SuJung; Kim, Byung-Yong; Baik, Moo-Yeol

2016-03-01

The antioxidant capacity and attributable bioactive compounds of puffed cacao beans were investigated. Roasting was carried out at 190°C for 15min and puffing was performed at 4-7kgf/cm(2). Cacao beans puffed at 4kgf/cm(2) showed the highest total polyphenols (23.16mgGAE/gsample) and total flavonoids (10.65mgCE/gsample) (pbeans reflected the total polyphenols and flavonoids measured. The quantities of theobromine, catechin, epicatechin, and procyanidin B2 were higher in cacao beans puffed at 4kgf/cm(2) than in roasted cacao beans. Puffed cacao beans received a good sensory score in flavor, but sourness increased as puffing pressure increased. Thus, these results suggest that, in cacao bean processing, puffing could be an alternative to roasting, which provide a rich taste and high antioxidant capacity. Copyright © 2015 Elsevier Ltd. All rights reserved.

Prescription Drug Profiles PUF

Data.gov (United States)

U.S. Department of Health & Human Services — This release contains the Prescription Drug Profiles Public Use Files (PUFs) drawn from Medicare prescription drug claims for the year of the date on which the...

Neutron and gamma-ray spectra of {sup 239}PuBe and {sup 241}AmBe

Energy Technology Data Exchange (ETDEWEB)

Vega-Carrillo, H.R. E-mail: rvega@cantera.reduaz.mx; Manzanares-Acuna, Eduardo; Becerra-Ferreiro, A.M.; Carrillo-Nunez, Aureliano

2002-08-01

Neutron and gamma-ray spectra of {sup 239}PuBe and {sup 241}AmBe were measured and their dosimetric features were calculated. Neutron spectra were measured using a multisphere neutron spectrometer with a {sup 6}LiI(Eu) scintillator. The {sup 239}PuBe neutron spectrum was measured in an open environment, while the {sup 241}AmBe neutron spectrum was measured in a closed environment. Gamma-ray spectra were measured using a NaI(Tl) scintillator using the same experimental conditions for both sources. The effect of measuring conditions for the {sup 241}AmBe neutron spectrum indicates the presence of epithermal and thermal neutrons. The low-resolution neutron spectra obtained with the multisphere spectrometer allows one to calculate the dosimetric features of neutron sources. At 100 cm both sources produce approximately the same count rate as that of the 4.4 MeV gamma-ray per unit of alpha emitter activity.

Behavior of temperature dependent SRAM-PUFs, and consequences for secret-key capacity

NARCIS (Netherlands)

Kusters, C.J.; Ignatenko, T.; Willems, F.M.J.

2017-01-01

Physical Unclonable Functions (PUFs) are a resource for generating and sharing secret keys. The mutual information between two respective observations of the same PUF gives an upper bound for the achievable secret-key rate of a secret-sharing scheme that relies on this PUF. This mutual information

Role of the PufX protein in photosynthetic growth of Rhodobacter sphaeroides. 2. PufX is required for efficient ubiquinone/ubiquinol exchange between the reaction center QB site and the cytochrome bc1 complex.

Science.gov (United States)

Barz, W P; Verméglio, A; Francia, F; Venturoli, G; Melandri, B A; Oesterhelt, D

1995-11-21

The PufX membrane protein is essential for photosynthetic growth of Rhodobacter sphaeroides because it is required for multiple-turnover electron transfer under anaerobic conditions [see accompanying article; Barz, W. P., Francia, F., Venturoli, G., Melandri, B. A., Verméglio, A., & Oesterhelt, D. (1995) Biochemistry 34, 15235-15247]. In order to understand the molecular role of PufX, light-induced absorption spectroscopy was performed using a pufX- mutant, a pufX+ strain, and two suppressor mutants. We show that the reaction center (RC) requires PufX for its functionality under different redox conditions than the cytochrome bc1 complex: When the kinetics of flash-induced reduction of cytochrome b561 were monitored in chromatophores, we observed a requirement of PufX for turnover of the cytochrome bc1 complex only at high redox potential (Eh > 140 mV), suggesting a function of PufX in lateral ubiquinol transfer from the RC. In contrast, PufX is required for multiple turnover of the RC only under reducing conditions: When the Q pool was partially oxidized in vivo using oxygen or electron acceptors like dimethyl sulfoxide or trimethylamine N-oxide, the deletion of PufX had no effect on light-driven electron flow through the RC. Flash train experiments under anaerobic in vivo conditions revealed that RC photochemistry does not depend on PufX for the first two flash excitations. Following the third and subsequent flashes, however, efficient charge separation requires PufX, indicating an important role of PufX for fast Q/QH2 exchange at the QB site of the RC. We show that the Q/QH2 exchange rate is reduced approximately 500-fold by the deletion of PufX when the Q pool is nearly completely reduced, demonstrating an essential role of PufX for the access of ubiquinone to the QB site. The fast ubiquinone/ubiquinol exchange is partially restored by suppressor mutations altering the macromolecular antenna structure. These results suggest an indirect role of PufX in

Heat damage and in vitro starch digestibility of puffed wheat kernels.

Science.gov (United States)

Cattaneo, Stefano; Hidalgo, Alyssa; Masotti, Fabio; Stuknytė, Milda; Brandolini, Andrea; De Noni, Ivano

2015-12-01

The effect of processing conditions on heat damage, starch digestibility, release of advanced glycation end products (AGEs) and antioxidant capacity of puffed cereals was studied. The determination of several markers arising from Maillard reaction proved pyrraline (PYR) and hydroxymethylfurfural (HMF) as the most reliable indices of heat load applied during puffing. The considerable heat load was evidenced by the high levels of both PYR (57.6-153.4 mg kg(-1) dry matter) and HMF (13-51.2 mg kg(-1) dry matter). For cost and simplicity, HMF looked like the most appropriate index in puffed cereals. Puffing influenced starch in vitro digestibility, being most of the starch (81-93%) hydrolyzed to maltotriose, maltose and glucose whereas only limited amounts of AGEs were released. The relevant antioxidant capacity revealed by digested puffed kernels can be ascribed to both the new formed Maillard reaction products and the conditions adopted during in vitro digestion. Copyright © 2015 Elsevier Ltd. All rights reserved.

Osmosis-Puffing sebagai Suatu Alternatif Proses Pengeringan Buah dan Sayuran

Directory of Open Access Journals (Sweden)

Daniel Saputra

2006-04-01

Full Text Available A new method of drying fruits and vegetables, a combination of the osmotic drying with the CO2 puffing process, was carried out in this study. the fruits were soaked in an osmotic media, continued by puffing the product with CO2 gas and then dried using the fluidized bed dryer wich resulted in a product that resembled the volume and shape of a fresh product. The type of osmotic media and concentration, and the soild gain. Also the sample’s tichness had a significant effect on the water loss and solid gain. The best concentration was 50%, and the best media was sucrose. Osmotic-puffing using sugar solution had no significant effect to the ratio of bulk specific volume (BSV between the osmotic puffing compare to without osmotic. The product treated with the solution of KCI combined with sugar had a lower BSV of puff product compared to the product soaked only with KCI. The concentration of KCI 5% gave the best BSV. The NaCI solution of 5% was also tested for osmotic-puffing dehydration of carrot which resulted in the BSV of 6.8 cm3/g.

A Robust SRAM-PUF Key Generation Scheme Based on Polar Codes

OpenAIRE

Chen, Bin; Ignatenko, Tanya; Willems, Frans M. J.; Maes, Roel; van der Sluis, Erik; Selimis, Georgios

2017-01-01

Physical unclonable functions (PUFs) are relatively new security primitives used for device authentication and device-specific secret key generation. In this paper we focus on SRAM-PUFs. The SRAM-PUFs enjoy uniqueness and randomness properties stemming from the intrinsic randomness of SRAM memory cells, which is a result of manufacturing variations. This randomness can be translated into the cryptographic keys thus avoiding the need to store and manage the device cryptographic keys. Therefore...

MCBS Access to Care PUF

Data.gov (United States)

U.S. Department of Health & Human Services — The MCBS 2013 Access to Care public use file (MCBS PUF) provides the first publically available MCBS file for researchers interested in the health, health care use,...

Puffing, a novel coffee bean processing technique for the enhancement of extract yield and antioxidant capacity.

Science.gov (United States)

Kim, Wooki; Kim, Sang-Youn; Kim, Dae-Ok; Kim, Byung-Yong; Baik, Moo-Yeol

2018-02-01

Puffing of coffee beans, which induces heat- and pressure-derived physicochemical changes, was applied as an alternative to roasting. Roasted or puffed coffee beans with equivalent lightness values were compared. The moisture content was higher while the crude fat and protein compositions were lower in puffed beans than in roasted beans. The pH was lower and the acid content was higher in puffed beans than in roasted beans. The roasted beans exhibited greater specific volumes, while the puffed beans displayed greater extraction yields. The trigonelline and total phenolic contents were greater in puffed beans than in roasted beans resulting in an enhanced antioxidant capacity. Sensory evaluation of roasted and puffed coffee bean brews revealed that puffing did not affect the flavor or overall acceptance. The current study provides evidence that puffing is an alternative to roasting coffee beans with various benefits. Copyright © 2017 Elsevier Ltd. All rights reserved.

Isolation and characterization of a PUF-domain of pumilio gene from ...

African Journals Online (AJOL)

STORAGESEVER

2009-03-20

Mar 20, 2009 ... study, a partial pumilio gene with complete PUF-domain in Bombyx mori has been ... Key words: Bombyx mori, pumilio, PUF-domain, RACE, germline stem cell. .... The first-strand cDNA was synthesized from 2 ug of total. RNA.

Institutional Provider and Beneficiary Summary PUF

Data.gov (United States)

U.S. Department of Health & Human Services — The CMS IPBS PUFs are aggregated files in which each record summarizes information for a particular institutional provider. An institutional provider refers to a...

Security of Quantum-Readout PUFs against quadrature based challenge estimation attacks

NARCIS (Netherlands)

Skoric, B.; Mosk, Allard; Pinkse, Pepijn Willemszoon Harry

2013-01-01

The concept of quantum-secure readout of Physical Unclonable Functions (PUFs) has recently been realized experimentally in an optical PUF system. We analyze the security of this system under the strongest type of classical attack: the challenge estimation attack. The adversary performs a measurement

The active personnel dosimeter---APFEL enterprises superheated drop detector

International Nuclear Information System (INIS)

Ipe, N.E.; Donahue, R.J.; Busick, D.D.

1991-03-01

The Active Personnel Dosimeter (APD) provides a digital readout of events caused by neutrons interacting with superheated liquid droplets. The droplets are suspended in a gel held in a replaceable cartridge. Upon neutron interaction, the superheated droplet vaporizes, forming a bubble. The sound produced in this process is recorded by transducers that sense the accompanying pressure pulse. The APD electronically discriminates against spurious noise and vibration. Studies with the production prototype APDs indicate that the detector response is linear up to about 0.40 mSv, with large variations sometimes from predicted values and between cartridges at higher dose equivalents. The response to standard neutron sources (bare 252 Cf, PuBe, PuB, PuF, PuLi) is reported and compared with the expected response. Unirradiated cartridges self-nucleate when heated to temperatures of 46 degrees C. The APD is insensitive to low-energy photons but responds to high-energy photons and electrons. 8 refs., 2 figs., 3 tabs

Medicare FFS 30 Day Readmission Rate PUF

Data.gov (United States)

U.S. Department of Health & Human Services — The hospital readmission rate PUF presents nation-wide information about inpatient hospital stays that occurred within 30 days of a previous inpatient hospital stay...

Validation of neutron data libraries by backscattered spectra of Pu-Be Neutrons

CERN Document Server

El-Agib, I

1999-01-01

Elastically backscattered spectra of Pu-Be neutrons have been measured for SiO sub 2 , water, graphite, paraffin oil and Al slabs using a proton recoil spectrometer. The results were compared with the calculated spectra obtained by the three-dimensional Monte-Carlo transport code MCNP-4B and point-wise cross sections from the ENDF/B-V, ENDF/B-VI, JENDL-3.1 and BROND-2 data libraries. The good agreement between the measured and calculated results indicates that this procedure can be used for validation of different data libraries. This simple method renders possible the detection of oxygen, carbon and hydrogen in bulk samples. (author)

Changes in puffing behavior among smokers who switched from tobacco to electronic cigarettes.

Science.gov (United States)

Lee, Yong Hee; Gawron, Michal; Goniewicz, Maciej Lukasz

2015-09-01

Nicotine intake from electronic cigarette (e-cigarettes) increases with user's experience. This suggests that smokers who switched from tobacco to electronic cigarettes compensate for nicotine over time to get as much nicotine as they need. One of the mechanisms by which smokers may compensate for nicotine is by modifying their puffing behavior. The aim of the study was to assess the changes in puffing behavior after switching from conventional to electronic cigarettes among regular smokers. Twenty smokers (11 female, aged 31±10, CPD 16±8, FTND 4±3, and exhaled CO 16±17 (mean±SD)) who were naïve to e-cigarettes participated in this study. They were asked to substitute their regular tobacco cigarettes with first generation e-cigarettes (labeled 18mg nicotine) for two weeks. Puffing topography (number of puffs, puff volume, intervals between puffs, and average puff flow rate) was measured at the initial use (baseline), as well as after one and two weeks of product use. We tested changes in puffing topography outcomes using repeated measures ANOVA. We found that after one week of using e-cigarettes, participants significantly increased the average time they puffed on e-cigarettes from 2.2±0.1 (mean±SEM) to 3.1±0.3s (pe-cigarette use (preason for changing puffing behavior is to compensate for less efficient nicotine delivery from e-cigarettes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Investigation of primary cooling water chemistry following the partial meltdown of Pu-Be neutron source in Tehran Research Reactor Core (TRR)

Energy Technology Data Exchange (ETDEWEB)

Aghoyeh, Reza Gholizadeh [School of Research and Development of Nuclear Reactors and Accelerators, Nuclear Science and Technology Research Institute (NSTRI), Atomic Energy Organization of Iran (AEOI), P.O. Box: 14155-1339, Tehran (Iran, Islamic Republic of); Khalafi, Hossein, E-mail: hkhalafi@aeoi.org.i [School of Research and Development of Nuclear Reactors and Accelerators, Nuclear Science and Technology Research Institute (NSTRI), Atomic Energy Organization of Iran (AEOI), P.O. Box: 14155-1339, Tehran (Iran, Islamic Republic of)

2011-03-15

Research highlights: Effect of Pu-Be neutron source meltdown in core on reactor water chemistry. Water chemistry of primary cooling before, during and after of above incident was compared. Training importance. Management of nuclear incident and accident. - Abstract: Effect of Pu-Be neutron source meltdown in core on reactor water chemistry was main aim of this study. Leaving the neutron source in the core after reactor power exceeds a few hundred Watts was the main reason for its partial meltdown. Water chemistry of primary cooling before, during and after of above incident was compared. Activity of some radio-nuclides such as Ba-140, La-140, I-131, I-132, Te-132 and Xe-135 increased. Other radio-nuclides such as Nd-147, Xe-133, Sr-91, I-133 and I-135 are also detected which were not existed before this incident.

Basic Stand Alone Carrier Line Items PUF

Data.gov (United States)

U.S. Department of Health & Human Services — This release contains the Basic Stand Alone (BSA) Carrier Line Items Public Use Files (PUF) with information from Medicare Carrier claims. The CMS BSA Carrier Line...

Security of helper data Schemes for SRAM-PUF in multiple enrollment scenarios

NARCIS (Netherlands)

Kusters, C.J.; Ignatenko, T.; Maes, R.; van der Sluis, E.; Selimis, G.; Willems, F.M.J.

2017-01-01

Fuzzy commitment and syndrome-based schemes are two well-known helper data schemes used to bind and generate, respectively, a secret key to/from SRAM-PUF observations. To allow the decoder to reconstruct this secret key from a new (verification) observation of an SRAM-PUF, an encoder has to generate

An Approach to Function Annotation for Proteins of Unknown Function (PUFs in the Transcriptome of Indian Mulberry.

Directory of Open Access Journals (Sweden)

K H Dhanyalakshmi

Full Text Available The modern sequencing technologies are generating large volumes of information at the transcriptome and genome level. Translation of this information into a biological meaning is far behind the race due to which a significant portion of proteins discovered remain as proteins of unknown function (PUFs. Attempts to uncover the functional significance of PUFs are limited due to lack of easy and high throughput functional annotation tools. Here, we report an approach to assign putative functions to PUFs, identified in the transcriptome of mulberry, a perennial tree commonly cultivated as host of silkworm. We utilized the mulberry PUFs generated from leaf tissues exposed to drought stress at whole plant level. A sequence and structure based computational analysis predicted the probable function of the PUFs. For rapid and easy annotation of PUFs, we developed an automated pipeline by integrating diverse bioinformatics tools, designated as PUFs Annotation Server (PUFAS, which also provides a web service API (Application Programming Interface for a large-scale analysis up to a genome. The expression analysis of three selected PUFs annotated by the pipeline revealed abiotic stress responsiveness of the genes, and hence their potential role in stress acclimation pathways. The automated pipeline developed here could be extended to assign functions to PUFs from any organism in general. PUFAS web server is available at http://caps.ncbs.res.in/pufas/ and the web service is accessible at http://capservices.ncbs.res.in/help/pufas.

Effects of chemical composite, puffing temperature and intermediate moisture content on physical properties of potato and apple slices

Science.gov (United States)

Tabtaing, S.; Paengkanya, S.; Tanthong, P.

2017-09-01

Puffing technique is the process that can improve texture and volumetric of crisp fruit and vegetable. However, the effect of chemical composite in foods on puffing characteristics is still lack of study. Therefore, potato and apple slices were comparative study on their physical properties. Potato and apple were sliced into 2.5 mm thickness and 2.5 cm in diameter. Potato slices were treated by hot water for 2 min while apple slices were not treatment. After that, they were dried in 3 steps. First step, they were dried by hot air at temperature of 90°C until their moisture content reached to 30, 40, and 50 % dry basis. Then they were puffed by hot air at temperature of 130, 150, and 170°C for 2 min. Finally, they were dried again by hot air at temperature of 90°C until their final moisture content reached to 4% dry basis. The experimental results showed that chemical composite of food affected on physical properties of puffed product. Puffed potato had higher volume ratio than those puffed apple because potato slices contains starch. The higher starch content provided more hard texture of potato than those apples. Puffing temperature and moisture content strongly affected on the color, volume ratio, and textural properties of puffed potato slices. In addition, the high drying rate of puffed product observed at high puffing temperature and higher moisture content.

The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization

Directory of Open Access Journals (Sweden)

Tam Michael WC

2010-03-01

Full Text Available Abstract Background Puf proteins have important roles in controlling gene expression at the post-transcriptional level by promoting RNA decay and repressing translation. The Pumilio homology domain (PUM-HD is a conserved region within Puf proteins that binds to RNA with sequence specificity. Although Puf proteins have been well characterized in animal and fungal systems, little is known about the structural and functional characteristics of Puf-like proteins in plants. Results The Arabidopsis and rice genomes code for 26 and 19 Puf-like proteins, respectively, each possessing eight or fewer Puf repeats in their PUM-HD. Key amino acids in the PUM-HD of several of these proteins are conserved with those of animal and fungal homologs, whereas other plant Puf proteins demonstrate extensive variability in these amino acids. Three-dimensional modeling revealed that the predicted structure of this domain in plant Puf proteins provides a suitable surface for binding RNA. Electrophoretic gel mobility shift experiments showed that the Arabidopsis AtPum2 PUM-HD binds with high affinity to BoxB of the Drosophila Nanos Response Element I (NRE1 RNA, whereas a point mutation in the core of the NRE1 resulted in a significant reduction in binding affinity. Transient expression of several of the Arabidopsis Puf proteins as fluorescent protein fusions revealed a dynamic, punctate cytoplasmic pattern of localization for most of these proteins. The presence of predicted nuclear export signals and accumulation of AtPuf proteins in the nucleus after treatment of cells with leptomycin B demonstrated that shuttling of these proteins between the cytosol and nucleus is common among these proteins. In addition to the cytoplasmically enriched AtPum proteins, two AtPum proteins showed nuclear targeting with enrichment in the nucleolus. Conclusions The Puf family of RNA-binding proteins in plants consists of a greater number of members than any other model species studied to

Shared Savings Program Accountable Care Organizations PUF

Data.gov (United States)

U.S. Department of Health & Human Services — SSP ACO PUF - To address the increasing number of requests for SSP ACO data, the Centers for Medicare (CM) has created a standard analytical file that CMS can use to...

Comparison of cigarette smoke exposure atmospheres in different puffing modes

International Nuclear Information System (INIS)

Chen, B.T.; Bechtold, W.E.; Mauderly, J.L.

1988-01-01

Mainstream cigarette smoke generated using different puffing profiles was characterized for particle size distribution, vapor/gas concentration, and chemical composition. Three puffing profiles were compared: (1) a standard, 2-sec, 35 ml puff (SP), once per minute; (2) a puff of double the standard volume (70 mL), once per minute (DP); and (3) a double puff, twice per minute (2-DP). Results from samples collected with a multijet Mercer impactor indicated that the mass median aerodynamic diameter of smoke particles decreased with puff volume. The concentrations of specific chemicals from gas samples (CO, CO 2 , nitrogen oxides, and small molecular weight hydrocarbons), organic vapor samples (acetone, 2-methylfuran, benzene, meta- and para-xylene, ortho-xylene, and limonene), and particulate samples (nicotine, glycerol, hydroquinone, and palmitic acid) showed good agreement among the three puffing profiles. They support a prediction that the health effects of cigarette smoke generated from 2-DP or DP profiles would not be different from those resulting from SP profiles. (author)

Basic Stand Alone Skilled Nursing Facility Beneficiary PUF

Data.gov (United States)

U.S. Department of Health & Human Services — This release contains the Basic Stand Alone (BSA) Skilled Nursing Facility (SNF) Beneficiary Public Use Files (PUF) with information from Medicare SNF claims. The...

Squalene Extraction by Supercritical Fluids from Traditionally Puffed Amaranthus hypochondriacus Seeds

Directory of Open Access Journals (Sweden)

Teresa Rosales-García

2017-01-01

Full Text Available Extraction of squalene, a potent natural antioxidant, from puffed A. hypochondriacus seeds was performed by supercritical fluid extraction (SCFE; besides, to have a blank for comparison, extraction was performed also by Soxhlet method using organic solvents (hexane. Chemical proximal composition and seed morphology were determined in raw, puffed, and SCFE-extracted seeds. Extracts were obtained with a 500 mL capacity commercial supercritical extractor and performed between 10 and 30 MPa at 313, 323, and 333 K under constant CO2 flow of 0.18 kg CO2/h during 8 h. The squalene content was determined and the fatty acids present in the extracts were identified by GC-MS. The extract obtained by SCFE from puffed amaranth seeds reached 460 ± 28.1 g/kg squalene in oily extract at 313 K/20 MPa.

Basic Stand Alone Medicare DME Line Items PUF

Data.gov (United States)

U.S. Department of Health & Human Services — This release contains the Basic Stand Alone (BSA) Durable Medical Equipment (DME) Line Items Public Use Files (PUF) with information from Medicare DME claims. The...

Schmitt-Trigger-based Recycling Sensor and Robust and High-Quality PUFs for Counterfeit IC Detection

OpenAIRE

Lin, Cheng-Wei; Jang, Jae-Won; Ghosh, Swaroop

2015-01-01

We propose Schmitt-Trigger (ST) based recycling sensor that are tailored to amplify the aging mechanisms and detect fine grained recycling (minutes to seconds). We exploit the susceptibility of ST to process variations to realize high-quality arbiter PUF. Conventional SRAM PUF suffer from environmental fluctuation-induced bit flipping. We propose 8T SRAM PUF with a back-to-back PMOS latch to improve robustness by 4X. We also propose a low-power 7T SRAM with embedded Magnetic Tunnel Junction (...

Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center Proteins

Directory of Open Access Journals (Sweden)

Johannes F. Imhoff

2018-01-01

Full Text Available Two different photosystems for performing bacteriochlorophyll-mediated photosynthetic energy conversion are employed in different bacterial phyla. Those bacteria employing a photosystem II type of photosynthetic apparatus include the phototrophic purple bacteria (Proteobacteria, Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction center PufL and PufM are essential components and are common to all bacteria with a type-II photosynthetic apparatus, including the anaerobic as well as the aerobic phototrophic Proteobacteria. Therefore, PufL and PufM proteins and their genes are perfect tools to evaluate the phylogeny of the photosynthetic apparatus and to study the diversity of the bacteria employing this photosystem in nature. Almost complete pufLM gene sequences and the derived protein sequences from 152 type strains and 45 additional strains of phototrophic Proteobacteria employing photosystem II were compared. The results give interesting and comprehensive insights into the phylogeny of the photosynthetic apparatus and clearly define Chromatiales, Rhodobacterales, Sphingomonadales as major groups distinct from other Alphaproteobacteria, from Betaproteobacteria and from Caulobacterales (Brevundimonas subvibrioides. A special relationship exists between the PufLM sequences of those bacteria employing bacteriochlorophyll b instead of bacteriochlorophyll a. A clear phylogenetic association of aerobic phototrophic purple bacteria to anaerobic purple bacteria according to their PufLM sequences is demonstrated indicating multiple evolutionary lines from anaerobic to aerobic phototrophic purple bacteria. The impact of pufLM gene sequences for studies on the environmental diversity of phototrophic bacteria is discussed and the possibility of their identification on the species level in environmental samples is pointed out.

Effect of double false pulses in calibrated neutron coincidence collar during measuring time-correlated neutrons from PuBe neutron sources

Energy Technology Data Exchange (ETDEWEB)

Nguyen, Tam Cong, E-mail: tam.nguyen.cong@energia.mta.hu; Huszti, Jozsef; Nguyen, Quan Van

2015-09-01

Effect of double false pulses of preamplifiers in neutron coincidence collar was investigated to explain non-parallel shape of calibrated D/S–M{sub Pu} curves of two commercial neutron coincidence collars, JCC-31 and JCC-13. Two curves, which were constructed from D/S ratio (doubles and singles count rate), and Pu content M{sub Pu}, of the same set of secondary standard PuBe neutron sources, should be parallel. Non-parallelism rises doubt about usability of the method based on this curve for determination of Pu content in PuBe neutron sources. We have shown in three steps that the problem originates from double false pulses of preamplifiers in JCC-13. First we used a pulse train diagram for analyzing the non-parallel shape, second we used Rossi-Alpha distribution measured by pulse train recorder developed in our institute and finally, we investigated the effect of inserted noise pulses. This implies a new type of QA test option in traditional multiplicity shift registers for excluding presence of double false pulses.

Synthesis of plutonium trifluoride by hydro-fluorination and novel thermodynamic data for the PuF3-LiF system

Science.gov (United States)

Tosolin, A.; Souček, P.; Beneš, O.; Vigier, J.-F.; Luzzi, L.; Konings, R. J. M.

2018-05-01

PuF3 was synthetized by hydro-fluorination of PuO2 and subsequent reduction of the product by hydrogenation. The obtained PuF3 was analysed by X-Ray Diffraction (XRD) and found phase-pure. High purity was also confirmed by the melting point analysis using Differential Scanning Calorimetry (DSC). PuF3 was then used for thermodynamic assessment of the PuF3-LiF system. Phase equilibrium points and enthalpy of fusion of the eutectic composition were measured by DSC. XRD analyses of selected samples after DSC measurement confirm that after solidification from the liquid, the system returns to a mixture of LiF and PuF3.

An Anti-Electromagnetic Attack PUF Based on a Configurable Ring Oscillator for Wireless Sensor Networks.

Science.gov (United States)

Lu, Zhaojun; Li, Dongfang; Liu, Hailong; Gong, Mingyang; Liu, Zhenglin

2017-09-15

Wireless sensor networks (WSNs) are an emerging technology employed in some crucial applications. However, limited resources and physical exposure to attackers make security a challenging issue for a WSN. Ring oscillator-based physical unclonable function (RO PUF) is a potential option to protect the security of sensor nodes because it is able to generate random responses efficiently for a key extraction mechanism, which prevents the non-volatile memory from storing secret keys. In order to deploy RO PUF in a WSN, hardware efficiency, randomness, uniqueness, and reliability should be taken into account. Besides, the resistance to electromagnetic (EM) analysis attack is important to guarantee the security of RO PUF itself. In this paper, we propose a novel architecture of configurable RO PUF based on exclusive-or (XOR) gates. First, it dramatically increases the hardware efficiency compared with other types of RO PUFs. Second, it mitigates the vulnerability to EM analysis attack by placing the adjacent RO arrays in accordance with the cosine wave and sine wave so that the frequency of each RO cannot be detected. We implement our proposal in XINLINX A-7 field programmable gate arrays (FPGAs) and conduct a set of experiments to evaluate the quality of the responses. The results show that responses pass the National Institute of Standards and Technology (NIST) statistical test and have good uniqueness and reliability under different environments. Therefore, the proposed configurable RO PUF is suitable to establish a key extraction mechanism in a WSN.

A novel puf-A gene predicted from evolutionary analysis is involved in the development of eyes and primordial germ-cells.

Directory of Open Access Journals (Sweden)

Ming-Wei Kuo

Full Text Available Although the human genome project has been completed for some time, the issue of the number of transcribed genes with identifiable biological functions remains unresolved. We used zebrafish as a model organism to study the functions of Ka/Ks-predicted novel human exons, which were identified from a comparative evolutionary genomics analysis.In this study, a novel gene, designated as puf-A, was cloned and functionally characterized, and its homologs in zebrafish, mouse, and human were identified as one of the three homolog clusters which were consisted of 14 related proteins with Puf repeats. Computer modeling of human Puf-A structure and a pull-down assay for interactions with RNA targets predicted that it was a RNA-binding protein. Specifically, Puf-A contained a special six Puf-repeat domain, which constituted a unique superhelix half doughnut-shaped Puf domain with a topology similar to, but different from the conventional eight-repeat Pumilio domain. Puf-A transcripts were uniformly distributed in early embryos, but became restricted primarily to eyes and ovaries at a later stage of development. In mice, puf-A expression was detected primarily in retinal ganglion and pigmented cells. Knockdown of puf-A in zebrafish embryos resulted in microphthalmia, a small head, and abnormal primordial germ-cell (PGC migration. The latter was confirmed by microinjecting into embryos puf-A siRNA containing nanos 3' UTR that expressed in PGC only. The importance of Puf-A in the maturation of germline stem cells was also implicated by its unique expression in the most primitive follicles (stage I in adult ovaries, followed by a sharp decline of expression in later stages of folliculogenesis. Taken together, our study shows that puf-A plays an important role not only in eye development, but also in PGC migration and the specification of germ cell lineage. These studies represent an exemplary implementation of a unique platform to uncover unknown function(s of

Development, validation and application of a device to measure e-cigarette users’ puffing topography

Science.gov (United States)

Cunningham, Anthony; Slayford, Sandra; Vas, Carl; Gee, Jodie; Costigan, Sandra; Prasad, Krishna

2016-01-01

With the rapidly rising popularity and substantial evolution of electronic cigarettes (e-cigarettes) in the past 5–6 years, how these devices are used by vapers and consumers’ exposure to aerosol emissions need to be understood. We used puffing topography to measure directly product use. We adapted a cigarette puffing topography device for use with e-cigarettes. We performed validation using air and e-cigarette aerosol under multiple regimes. Consumer puffing topography was measured for 60 vapers provided with rechargeable “cig-a-like” or larger button-activated e-cigarettes, to use ad-libitum in two sessions. Under all regimes, air puff volumes were within 1 mL of the target and aerosol volumes within 5 mL for all device types, serving to validate the device. Vapers’ mean puff durations (2.0 s and 2.2 s) were similar with both types of e-cigarette, but mean puff volumes (52.2 mL and 83.0 mL) and mean inter-puff intervals (23.2 s and 29.3 s) differed significantly. The differing data show that product characteristics influence puffing topography and, therefore, the results obtained from a given e-cigarette might not read across to other products. Understanding the factors that affect puffing topography will be important for standardising testing protocols for e-cigarette emissions. PMID:27721496

Investigating SRAM PUFs in large CPUs and GPUs

NARCIS (Netherlands)

Aubel, Van P.; Bernstein, D.J.; Niederhagen, R.F.

2015-01-01

Physically unclonable functions (PUFs) provide data that can be used for cryptographic purposes: on the one hand randomness for the initialization of random-number generators; on the other hand individual fingerprints for unique identification of specific hardware components. However, today's

Investigating SRAM PUFs in large CPUs and GPUs

NARCIS (Netherlands)

Aubel, Van P.; Bernstein, D.J.; Niederhagen, R.F.; Chakraborty, R.S.; Schwabe, P.; Solworth, J.

2015-01-01

Physically unclonable functions (PUFs) provide data that can be used for cryptographic purposes: on the one hand randomness for the initialization of random-number generators; on the other hand individual fingerprints for unique identification of specific hardware components. However, today’s

Plasma performance improvement with neon gas puffing in HT-7

International Nuclear Information System (INIS)

Gong, X.; Wan, B.; Li, J.; Shi, Y.; Zhang, X.; Zhu, Y.; Wu, Z.; Liu, H.; Qian, J.

2005-01-01

The neon gas puffing for the production of a radiative layer near the plasma edge with the improved energy and particle confinement has been investigated in HT-7 during the 2003 campaign. Plasma characteristics of these discharges in HT-7 are similar to the TEXTOR RI-mode discharges. The peaked electron temperature and the broadened density profiles were formed in these discharges with the combination of LHCD and IBW heating. The central electron temperature was increased by nearly 50%, compared those discharges with the same plasma parameters and injected power without the neon gas puffing. These discharges also exhibited relatively higher plasma inductance. (author)

Low energy neutrons from a sup 2 sup 3 sup 9 PuBe isotopic neutron source inserting in moderating media

CERN Document Server

Vega, H R

2002-01-01

Several neutron applications share a common problem: the neutron source design. In this work MCNP computer code has been used to design a moderated sup 2 sup 3 sup 9 PuBe neutron source to produce low energy neutrons. The design involves the source located at the center of a spherical moderator. Moderator media studied were light water, heavy water and a heterogeneous combination of light water and heavy water. Similar moderating features were found between the 24.5 cm-radius container filled with heavy water (23.0-cm-thick) and that made with light water (3.5-cm-thick) plus heavy water (19.5-cm-thick). A sup 2 sup 3 sup 9 PuBe neutron source inserted in this moderator produces, at 27 cm, a neutron fluence of 1.8 x 10 sup - sup 4 n-cm sup - sup 2 per source neutron, with an average neutron energy of 0.34 MeV, where 47.8 % have an energy <= 0.4 eV. A further study of this moderator was carried out using a reflector medium made of graphite. Thus, 15-cm-thickness reflector improves the neutron field producing...

Study of neutron spectra using sources of {sup 241}AmBE and {sup 238}PuBe moderated in water; Estudo de espectros neutrônicos com fontes de {sup 241}AmBE e {sup 238}PuBe moderados em água

Energy Technology Data Exchange (ETDEWEB)

Gonçalves, Angela S.; Silva, Fellipe S.; Patrão, Karla C.S.; Fonseca, Evaldo S. da; Pereira, Walsan W., E-mail: angela.souzagon@gmail.com [Instituto de Radioprotecao e Dosimetria, (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil). Laboratorio de Metrologia de Neutrons; Fundação Técnico-Educacional Souza Marques (FTESM), Rio de Janeiro, RJ (Brazil)

2017-11-01

Recent works demonstrate the increasing importance of characterizing the spectrum of neutron sources for various energies. The main objective of this study is to make the understanding of the interaction of neutrons as close as possible to the reality in which the workers act, thus allowing to act directly in the area of radioprotection. In this way, neutron fluence determination of the {sup 241}AmBe source of 0.6 TBq (16 Ci) and {sup 238} PuBe 1.8 TBq (50 Ci) free in the air and inserted in aluminium spheres of 16 cm and 20.5 cm filled with distilled water. The measurements were carried out in the low scattering laboratory of the Laboratory of Neutron Metrology, in order to obtain a more realistic spectrum. Spectrum determination is based on measurement using the Bonner multisphere spectrometer containing readings with the ball-free detector and covered with polyethylene spheres having diameters of: 5,08 cm (2″), 7,62 cm (3″), 12,70 cm (5″), 20,32 cm (8″), 25,40 cm (10″) e 30,48 cm (12″). The aim is to characterize a new moderate spectrum in water using the sources of {sup 238}PuBe and {sup 241}AmBe that may represent realistic fields in the radioprotection area useful for testing, calibration and irradiation of individual and area monitors for neutrons.

Parameters' influence estimation on Puf supply and demand in transitional period from LWR to FBR in Japan

International Nuclear Information System (INIS)

Kobayashi, Hiroaki; Ohta, Hirokazu; Inoue, Tadashi

2009-01-01

Plutonium fissile (Puf) amounts to balance supply and demand during transition period were evaluated with different parameters. Estimated total Puf demand in transitional period was sensitive to deployment speed of FBR. Because FBRs will be deployed as replacements of old LWRs for keeping total capacity, deployment history of existing LWRs should be taken into consideration. According to the estimation, LWR fuel burnup and utilized capacity are not big issue. Because certain amount of LWR spent fuel will remain in early phase of transitional period, there is enough time for preparing Puf supply. On the other hand, FBR fuel cycle time (SF cooling time + fuel fabrication time) have large impact on Puf supply. Fuel cycle technologies including transportation for applying to short cooling spent fuels should be developed. (author)

Monomeric RC-LH1 core complexes retard LH2 assembly and intracytoplasmic membrane formation in PufX-minus mutants of Rhodobacter sphaeroides.

Science.gov (United States)

Adams, Peter G; Mothersole, David J; Ng, Irene W; Olsen, John D; Hunter, C Neil

2011-09-01

In the model photosynthetic bacterium Rhodobacter sphaeroides domains of light-harvesting 2 (LH2) complexes surround and interconnect dimeric reaction centre-light-harvesting 1-PufX (RC-LH1-PufX) 'core' complexes, forming extensive networks for energy transfer and trapping. These complexes are housed in spherical intracytoplasmic membranes (ICMs), which are assembled in a stepwise process where biosynthesis of core complexes tends to dominate the early stages of membrane invagination. The kinetics of LH2 assembly were measured in PufX mutants that assemble monomeric core complexes, as a consequence of either a twelve-residue N-terminal truncation of PufX (PufXΔ12) or the complete removal of PufX (PufX(-)). Lower rates of LH2 assembly and retarded maturation of membrane invagination were observed for the larger and less curved ICM from the PufX(-) mutant, consistent with the proposition that local membrane curvature, initiated by arrays of bent RC-LH1-PufX dimers, creates a favourable environment for stable assembly of LH2 complexes. Transmission electron microscopy and high-resolution atomic force microscopy were used to examine ICM morphology and membrane protein organisation in these mutants. Some partitioning of core and LH2 complexes was observed in PufX(-) membranes, resulting in locally ordered clusters of monomeric RC-LH1 complexes. The distribution of core and LH2 complexes in the three types of membrane examined is consistent with previous models of membrane curvature and domain formation (Frese et al., 2008), which demonstrated that a combination of crowding and asymmetries in sizes and shapes of membrane protein complexes drives membrane organisation. 2011 Elsevier B.V. All rights reserved.

Puffing of okara/rice blends using a rice cake machine.

Science.gov (United States)

Xie, M; Huff, H; Hsieh, F; Mustapha, A

2008-10-01

Okara is the insoluble byproduct of soymilk and tofu manufactures. It is cheap, high in nutrients, and possesses great potential to be applied to functional human foods. In this study, a puffed okara/rice cake product was developed with blends of okara pellets and parboiled rice. Consumer preference and acceptance tests were conducted for the product. Okara pellets were prepared by grinding the strands obtained from extruding a mixture of dried okara and rice flour (3:2, w/w) with a twin-screw extruder. Okara pellets and parboiled rice were blended in 4 ratios, 90:10, 70:30, 40:60, and 0:100 (w/w), and tempered to 14% and 17% moisture. The blends were puffed at 221, 232, and 243 degrees C for 4, 5, or 6 s. The okara/rice cakes were evaluated for specific volume (SPV), texture, color, and percent weight loss after tumbling. Overall, the decrease in okara content and increase in moisture, heating temperature and time led to greater specific volume (SPV) and hardness, lighter color, and lower percent weight loss after tumbling. The consumer tests indicated that the okara/rice cake containing 70% okara pellets was preferred and the 90% one was liked the least. The possible drivers of liking for the puffed okara/rice cakes could be the okara content, hardness, SPV, bright color, and percent weight loss after tumbling.

Structure of the dimeric PufX-containing core complex of Rhodobacter blasticus by in situ atomic force microscopy.

Science.gov (United States)

Scheuring, Simon; Busselez, Johan; Lévy, Daniel

2005-01-14

We have studied photosynthetic membranes of wild type Rhodobacter blasticus, a closely related strain to the well studied Rhodobacter sphaeroides, using atomic force microscopy. High-resolution atomic force microscopy topographs of both cytoplasmic and periplasmic surfaces of LH2 and RC-LH1-PufX (RC, reaction center) complexes were acquired in situ. The LH2 is a nonameric ring inserted into the membrane with the 9-fold axis perpendicular to the plane. The core complex is an S-shaped dimer composed of two RCs, each encircled by 13 LH1 alpha/beta-heterodimers, and two PufXs. The LH1 assembly is an open ellipse with a topography-free gap of approximately 25 A. The two PufXs, one of each core, are located at the dimer center. Based on our data, we propose a model of the core complex, which provides explanation for the PufX-induced dimerization of the Rhodobacter core complex. The QB site is located facing a approximately 25-A wide gap within LH1, explaining the PufX-favored quinone passage in and out of the core complex.

Impact of gas puffing location on density control and plasma parameters in TJ-II

International Nuclear Information System (INIS)

Tabares, F.L.; Garcia-Cortes, I.; Estrada, T.; Tafalla, D.; Hidalgo, A.; Ferreira, J.A.; Pastor, I.; Herranz, J.; Ascasibar, E.

2005-01-01

Under pure Electron Cyclotron Resonance Heating (ECRH) conditions in TJ-II plasmas (P<300 kW, 53.2 GHz, 2nd harmonic X-mode, power density < 25 W/m''3), plasma start-up and good density control are obtained only by the proper combination of wall conditions and gas puffing characteristics. Such a control is particularly critical for the optimisation of the NBI power transfer to the target plasmas. The relatively low cut-off limit is easily reached due not only to the unfavourable wall/puffing-fuelling ratio but also due to the steep density profiles developed during the Enhanced Particle Confinement (EPC) modes. These modes are triggered by the gas puffing waveform, and they cannot be achieved for high iota magnetic configurations in TJ-II. Comparative experiments under metallic and boronised wall conditions have shown that the sensitivity of the EPC modes to the puffing rate is at least partially related to the energy balance at the plasma periphery under central heating scenarios. In this work, the impact of gas-fuelling location on the plasma parameters and density control is described. For that purpose, three different fuelling locations have been investigated; broad distribution from a side ports, localized injection from long tubes at different poloidal positions and highly localized injection through a movable limiter. Edge density and temperature profiles from a broad set of diagnostics (atomic beams, reflectometry, Thompson Scattering ECE, etc...) are analysed and compared. It has been found that preventing from transition to the EPC mode is achieved by using slow puffing rates, while neutral penetration into the plasma core can be enhanced for highly localized gas sources. Wall inventory, however, has been found to pl ay a dominant role in the fuelling of the plasma under most conditions. (author)

Characterization of neutron spectra using sources of {sup 241}AmBe, {sup 238}PuBe e {sup 252}Cf moderated in water; Caracterização de espectros neutrônicos com fontes de {sup 241}AmBe, {sup 238}PuBe e {sup 252}Cf moderados em água

Energy Technology Data Exchange (ETDEWEB)

Gonçalves, A.S.; Silva, F.S.; Patrão, K.C.S.; Fonseca, E.S. da; Pereira, W.W., E-mail: angela.souzagon@gmail.com [Instituto de Radioproteção e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil). Laboratório de Metrologia de Nêutrons

2017-07-01

Recent studies have demonstrated the importance of characterizing the spectrum of neutron sources for various energies in order to make the understanding of neutron interaction closer to reality they work with. This work presents the determination of neutron energy flux from the source of {sup 241}AmBe (0.6 TBq), {sup 238}PuBe (1.8 TBq) and {sup 252}Cf (120 μg) free in the air and inserted into spheres of various diameters containing distilled water. The determination of the spectrum is based on the measurement and simulation by the Monte Carlo computational method, using the sources under study, with the Bonner multisphere spectrometer containing readings with the detector without sphere and covered with polyethylene balls of diameters: 5,08 cm (2 ″), 7.62 cm (3″), 12.70 cm (5 ″), 20.32 cm (8 ″), 25.40 cm (10 ″) and 30.48 cm (12 ″). It is sought to characterize a new moderate spectrum in water using the sources of {sup 241}AmBe, {sup 238}PuBe and {sup 252}Cf that may be useful for testing, calibration and irradiation of individual and area monitors for neutrons.

The sensitivity of various thermoluminescent, photoluminescent and photographic detectors to neutrons emitted by a Pu-Be source

International Nuclear Information System (INIS)

Spurny, Frantisek; Marsault, Roger; Medioni, Roger; Portal, Guy.

1975-07-01

A series of experiments were conducted in order to determine the sensitivity of radiothermoluminescent detectors to fast neutrons. Experiments bearing on the determination of the sensitivity to neutrons emitted by a Pu-Be source are related here. The characteristics of the radiation field emitted by the source and especially of the γ-field are analysed as it is essential for the interpretation of results to know the latter, which appears to have been but partly studied so far. The measuring procedures are then described and a study is made of the best experimental procedures liable to eliminate or decrease the effect of external factors. The results are finally analysed [fr

Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane

International Nuclear Information System (INIS)

Hsin, J; Sener, M; Schulten, K; Struempfer, J; Qian, P; Hunter, C N

2010-01-01

Light absorption and the subsequent transfer of excitation energy are the first two steps in the photosynthetic process, carried out by protein-bound pigments, mainly bacteriochlorophylls (BChls), in photosynthetic bacteria. BChls are anchored in light-harvesting (LH) complexes, such as light-harvesting complex I (LH1), which directly associates with the reaction center (RC), forming the RC-LH1 core complex. In Rhodobacter sphaeroides, RC-LH1 core complexes contain an additional protein, PufX, and assemble into dimeric RC-LH1-PufX core complexes. In the absence of LH complex II (LH2), the former complexes can aggregate into a helically ordered tubular photosynthetic membrane. We have examined the excitation transfer dynamics in a single RC-LH1-PufX core complex dimer using the hierarchical equations of motion for dissipative quantum dynamics that accurately, yet in a computationally costly manner, treat the coupling between BChls and their protein environment. A widely employed description, the generalized Foerster (GF) theory, was also used to calculate the transfer rates of the same excitonic system in order to verify the accuracy of this computationally cheap method. Additionally, in light of the structural uncertainties in the Rba. sphaeroides RC-LH1-PufX core complex, geometrical alterations were introduced into the BChl organization. It is shown that the energy transfer dynamics are not affected by the considered changes in the BChl organization and that the GF theory provides accurate transfer rates. An all-atom model for a tubular photosynthetic membrane is then constructed on the basis of electron microscopy data, and the overall energy transfer properties of this membrane are computed.

Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane

Energy Technology Data Exchange (ETDEWEB)

Hsin, J; Sener, M; Schulten, K [Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana (United States); Struempfer, J [Center for Biophysics and Computational Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana (United States); Qian, P; Hunter, C N, E-mail: kschulte@ks.uiuc.ed [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN (United Kingdom)

2010-08-15

Light absorption and the subsequent transfer of excitation energy are the first two steps in the photosynthetic process, carried out by protein-bound pigments, mainly bacteriochlorophylls (BChls), in photosynthetic bacteria. BChls are anchored in light-harvesting (LH) complexes, such as light-harvesting complex I (LH1), which directly associates with the reaction center (RC), forming the RC-LH1 core complex. In Rhodobacter sphaeroides, RC-LH1 core complexes contain an additional protein, PufX, and assemble into dimeric RC-LH1-PufX core complexes. In the absence of LH complex II (LH2), the former complexes can aggregate into a helically ordered tubular photosynthetic membrane. We have examined the excitation transfer dynamics in a single RC-LH1-PufX core complex dimer using the hierarchical equations of motion for dissipative quantum dynamics that accurately, yet in a computationally costly manner, treat the coupling between BChls and their protein environment. A widely employed description, the generalized Foerster (GF) theory, was also used to calculate the transfer rates of the same excitonic system in order to verify the accuracy of this computationally cheap method. Additionally, in light of the structural uncertainties in the Rba. sphaeroides RC-LH1-PufX core complex, geometrical alterations were introduced into the BChl organization. It is shown that the energy transfer dynamics are not affected by the considered changes in the BChl organization and that the GF theory provides accurate transfer rates. An all-atom model for a tubular photosynthetic membrane is then constructed on the basis of electron microscopy data, and the overall energy transfer properties of this membrane are computed.

Increase of hot initial plasma energy content in the end system of AMBAL-M during hydrogen puffing

International Nuclear Information System (INIS)

Akhmetov, Timour; Bekher, Sergei; Davydenko, Vladimir; Krivenko, Aleksander; Muraviev, Maksim; Reva, Vladimir; Sokolov, Vladimir

2001-01-01

At the end system of the completely axisymmetric mirror trap AMBAL-M the experiments on creation and study of a hot initial plasma have been performed. In the experiments a gas-box was used for hydrogen supply into the hot startup plasma in the mirror trap to increase the plasma density. The hot initial plasma in the trap was produced by the trapping of a plasma stream with developed electrostatic turbulence generated by a gas-discharge source located outside the entrance throat. It was found that in addition to the increase in the plasma density by a factor of 2-3, hydrogen puffing resulted in an unexpected nearly twofold diamagnetism increase. The gas puffing did not reduce the electron temperature in the trap. Essential for explanation of the observed effect is the fact that with the gas puffing the measured plasma potential in the trap increased. The increase in the plasma potential enhanced the trapping of the ion flow entering the trap and increased the average energy of the electron flow entering the trap. It was found that with the increasing hydrogen puffing rate plasma parameters in the trap were saturated. (author)

E-cigarette puffing patterns associated with high and low nicotine e-liquid strength: effects on toxicant and carcinogen exposure.

Science.gov (United States)

Cox, Sharon; Kośmider, Leon; McRobbie, Hayden; Goniewicz, Maciej; Kimber, Catherine; Doig, Mira; Dawkins, Lynne

2016-09-20

Contrary to intuition, use of lower strength nicotine e-liquids might not offer reduced health risk if compensatory puffing behaviour occurs. Compensatory puffing (e.g. more frequent, longer puffs) or user behaviour (increasing the wattage) can lead to higher temperatures at which glycerine and propylene glycol (solvents used in e-liquids) undergo decomposition to carbonyl compounds, including the carcinogens formaldehyde and acetaldehyde. This study aims to document puffing patterns and user behaviour associated with using high and low strength nicotine e-liquid and associated toxicant/carcinogen exposure in experienced e-cigarette users (known as vapers herein). A counterbalanced repeated measures design. Non-tobacco smoking vapers; have used an e-cigarette for ≥3 months; currently using nicotine strength e-liquid ≥12mg/mL and a second or third generation device. This study will measure puffing patterns in vapers whilst they use high and low strength nicotine e-liquid under fixed and user-defined settings, each for a week. The 4 counterbalanced conditions are: i) low strength (6mg/mL), fixed settings; ii) low strength user-defined settings; iii) high strength (18mg/mL) fixed settings; iv) high strength user-defined settings. Biomarkers of exposure to toxicants and carcinogens will be measured in urine. In the second phase of this study, toxicant yields will be measured in aerosol generated using a smoking machine operated to replicate the puffing behaviours of each participant. i) Puffing patterns (mean puff number, puff duration, inter-puff interval and mL of liquid consumed) and user behaviour (changes to device settings: voltage and air-flow) associated with using high and low strength nicotine e-liquid. ii) Toxicant/carcinogen exposure associated with the puffing patterns/device settings used by our participants. i) Subjective effects. ii) comparisons with toxicant exposure from tobacco smoke (using documented evidence) and with recommended safety limits

E-cigarette puffing patterns associated with high and low nicotine e-liquid strength: effects on toxicant and carcinogen exposure

Directory of Open Access Journals (Sweden)

Sharon Cox

2016-09-01

Full Text Available Abstract Background Contrary to intuition, use of lower strength nicotine e-liquids might not offer reduced health risk if compensatory puffing behaviour occurs. Compensatory puffing (e.g. more frequent, longer puffs or user behaviour (increasing the wattage can lead to higher temperatures at which glycerine and propylene glycol (solvents used in e-liquids undergo decomposition to carbonyl compounds, including the carcinogens formaldehyde and acetaldehyde. This study aims to document puffing patterns and user behaviour associated with using high and low strength nicotine e-liquid and associated toxicant/carcinogen exposure in experienced e-cigarette users (known as vapers herein. Methods/design A counterbalanced repeated measures design. Participants: Non-tobacco smoking vapers; have used an e-cigarette for ≥3 months; currently using nicotine strength e-liquid ≥12mg/mL and a second or third generation device. Intervention: This study will measure puffing patterns in vapers whilst they use high and low strength nicotine e-liquid under fixed and user-defined settings, each for a week. The 4 counterbalanced conditions are: i low strength (6mg/mL, fixed settings; ii low strength user-defined settings; iii high strength (18mg/mL fixed settings; iv high strength user-defined settings. Biomarkers of exposure to toxicants and carcinogens will be measured in urine. In the second phase of this study, toxicant yields will be measured in aerosol generated using a smoking machine operated to replicate the puffing behaviours of each participant. Primary outcomes: i Puffing patterns (mean puff number, puff duration, inter-puff interval and mL of liquid consumed and user behaviour (changes to device settings: voltage and air-flow associated with using high and low strength nicotine e-liquid. ii Toxicant/carcinogen exposure associated with the puffing patterns/device settings used by our participants. Secondary outcomes: i Subjective effects. ii comparisons

Dietary exposure to aluminium from wheat flour and puffed products of residents in Shanghai, China.

Science.gov (United States)

Guo, Junfei; Peng, Shaojie; Tian, Mingsheng; Wang, Liwei; Chen, Bo; Wu, Min; He, Gengsheng

2015-01-01

A dietary survey of 3431 residents was conducted by a 24-h dietary recall method in Shanghai, China, quarterly from September 2013 to September 2014. A total of 400 food samples were tested for aluminium concentration, including wheat flour and puffed products from 2011 to 2013. Probabilistic analysis was used to estimate the dietary exposure to aluminium from wheat and puffed products. The means of dietary aluminium exposure for children (2-6 years old), juveniles (7-17 years old), adults (18-65 years old) and seniors (over 65 years old) were 1.88, 0.94, 0.44 and 0.42 mg kg(-1) body weight (bw) week(-1) respectively, with a population average of 0.51 mg kg(-1) bw week(-1). The proportions of those who had aluminium exposure from wheat and puffed products lower than the provisional tolerable weekly intake (PTWI) were 77%, 90%, 97%, and 97% respectively from children to seniors. We estimated that the proportions of people at risk would decrease by 13%, 6%, 2% and 2% respectively under the new China National Standards - GB 2760-2014 National Food Safety for Standards for using food additives. The results indicated that aluminium from wheat flour and puffed products is unlikely to cause adverse health effects in the general population in Shanghai; however, children were at a higher risk of excess aluminium exposure. Significant improvements in reducing the dietary exposure to aluminium are expected in the population, especially for children after the implementation of GB 2760-2014.

Container construction for the Pu-Be source at the Atominstitut Wien

International Nuclear Information System (INIS)

Tatlisu Halit

2003-07-01

The aim of this study was to construct a neutron source container as small as possible. For this purpose an aluminum container was ordered to reserve the Pu-Be neutron source of the TRIGA Mark-II research reactor at the Atominstitute of Austrian Universities, Vienna. The important point is the shielding of the neutrons according to the radiation protection policy at ATI. Fast neutrons, which emitted from the source, cannot be shielded directly. They have to be moderated by a suitable moderator material and then they can be absorbed using a strong neutron absorber material. The most effective moderators are elements with low atomic number; therefore hydrogen-containing materials are the major component of neutron shielding. As a moderator and absorber material together we have chosen borated polyethylene among the various materials considering its properties. It contains H and C, which are suitable moderator materials and B for neutron absorption. It is important to quickly moderate the neutron to low energy, where it can be absorbed with boron owing to the high absorption cross section. The constructed shielding, which consists of borated polyethylene, was placed into the ordered A1 container. At the end we measured the emitted radiation dose using a neutron counter at different distances from the container. (author)

Advancing PubMed?

DEFF Research Database (Denmark)

Wildgaard, Lorna Elizabeth; Lund, Haakon

2016-01-01

the efficiency of biomedical literature searches. PubMed remains the primary resource for biomedical literature, and as PubMed makes the Medline data and Entrez PubMed Programming utilities freely available, any developer can produce alternative tools to search the database. The authors question if PubMed still...... provides the superior search interface for systematic searches or if the innovativeness of third-party tools provide alternatives worth considering. The paper aims to discuss these issues. Design/methodology/approach In all, 76 third-party tools that build on PubMed content were identified in a PubMed...... search and in published studies known to the authors. Only tools that provided free access to the broad PubMed content and designed specifically to enhance the search were included, reducing the set to 16 tools. The functionality of each tool within the scenario of a systematic search was compared across...

Effect of apple varieties and irradiation on the quality of explosion puffed apple slices

International Nuclear Information System (INIS)

Bi Jinfeng; Ding Yuanyuan; Wang Pei; Bai Shasha

2009-01-01

Many factors affect the quality of explosion puffed apple slices. Apple varieties of Guoguang, Fuji, Hongxiangjiao and Huangxiangjiao were used as materal, the quality of fresh apple and explosion puffed products were analyzed based on the data of their physical and chemical characteristics and flavor. The results showed that Guoguang apple had the optimal flavor and Huangxiangjiao apple had the optimal product quality. So the Guoguang apple was selected as the material for the following results showed that irradiation could soften apple tissue, improve the pre-drying rate, increase products crispness, and also reduce the products hardness, but the irradiation of 2 and 5 kGy could turn products brown seriously, which reduced the product quality. (authors)

Diversity of pufM genes, involved in aerobic anoxygenic photosynthesis, in the bacterial communities associated with colonial ascidians.

Science.gov (United States)

Martínez-García, Manuel; Díaz-Valdés, Marta; Antón, Josefa

2010-03-01

Ascidians are invertebrate filter feeders widely distributed in benthic marine environments. A total of 14 different ascidian species were collected from the Western Mediterranean and their bacterial communities were analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene. Results showed that ascidian tissues harbored Bacteria belonging to Gamma- and Alphaproteobacteria classes, some of them phylogenetically related to known aerobic anoxygenic phototrophs (AAPs), such as Roseobacter sp. In addition, hierarchical cluster analysis of DGGE patterns showed a large variability in the bacterial diversity among the different ascidians analyzed, which indicates that they would harbor different bacterial communities. Furthermore, pufM genes, involved in aerobic anoxygenic photosynthesis in marine and freshwater systems, were widely detected within the ascidians analyzed, because nine out of 14 species had pufM genes inside their tissues. The pufM gene was only detected in those specimens that inhabited shallow waters (<77 m of depth). Most pufM gene sequences were very closely related to that of uncultured marine bacteria. Thus, our results suggest that the association of ascidians with bacteria related to AAPs could be a general phenomenon and that ascidian-associated microbiota could use the light that penetrates through the tunic tissue as an energy source.

Evaluation of polyurethane foam passive air sampler (PUF) as a tool for occupational PAH measurements.

Science.gov (United States)

Strandberg, Bo; Julander, Anneli; Sjöström, Mattias; Lewné, Marie; Koca Akdeva, Hatice; Bigert, Carolina

2018-01-01

Routine monitoring of workplace exposure to polycyclic aromatic hydrocarbons (PAHs) is performed mainly via active sampling. However, active samplers have several drawbacks and, in some cases, may even be unusable. Polyurethane foam (PUF) as personal passive air samplers constitute good alternatives for PAH monitoring in occupational air (8 h). However, PUFs must be further tested to reliably yield detectable levels of PAHs in short exposure times (1-3 h) and under extreme occupational conditions. Therefore, we compared the personal exposure monitoring performance of a passive PUF sampler with that of an active air sampler and determined the corresponding uptake rates (Rs). These rates were then used to estimate the occupational exposure of firefighters and police forensic specialists to 32 PAHs. The work environments studied were heavily contaminated by PAHs with (for example) benzo(a)pyrene ranging from 0.2 to 56 ng m -3 , as measured via active sampling. We show that, even after short exposure times, PUF can reliably accumulate both gaseous and particle-bound PAHs. The Rs-values are almost independent of variables such as the concentration and the wind speed. Therefore, by using the Rs-values (2.0-20 m 3 day -1 ), the air concentrations can be estimated within a factor of two for gaseous PAHs and a factor of 10 for particulate PAHs. With very short sampling times (1 h), our method can serve as a (i) simple and user-friendly semi-quantitative screening tool for estimating and tracking point sources of PAH in micro-environments and (ii) complement to the traditional active pumping methods. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Field calibration of polyurethane foam (PUF) disk passive air samplers for PCBs and OC pesticides.

Science.gov (United States)

Chaemfa, Chakra; Barber, Jonathan L; Gocht, Tilman; Harner, Tom; Holoubek, Ivan; Klanova, Jana; Jones, Kevin C

2008-12-01

Different passive air sampler (PAS) strategies have been developed for sampling in remote areas and for cost-effective simultaneous spatial mapping of POPs (persistent organic pollutants) over differing geographical scales. The polyurethane foam (PUF) disk-based PAS is probably the most widely used. In a PUF-based PAS, the PUF disk is generally mounted inside two stainless steel bowls to buffer the air flow to the disk and to shield it from precipitation and light. The field study described in this manuscript was conducted to: compare performance of 3 different designs of sampler; to further calibrate the sampler against the conventional active sampler; to derive more information on field-based uptake rates and equilibrium times of the samplers. Samplers were also deployed at different locations across the field site, and at different heights up a meteorological tower, to investigate the possible influence of sampler location. Samplers deployed <5m above ground, and not directly sheltered from the wind gave similar uptake rates. Small differences in dimensions between the 3 designs of passive sampler chamber had no discernable effect on accumulation rates, allowing comparison with previously published data.

Structural model and excitonic properties of the dimeric RC-LH1-PufX complex from Rhodobacter sphaeroides

International Nuclear Information System (INIS)

Sener, Melih; Hsin, Jen; Trabuco, Leonardo G.; Villa, Elizabeth; Qian, Pu; Hunter, C. Neil; Schulten, Klaus

2009-01-01

The light-harvesting apparatus of the purple bacterial photosynthetic unit consists of a pool of peripheral light-harvesting complexes that transfer excitation energy to a reaction center (RC) via the surrounding pigment-protein complex LH1. Recent electron microscopy and atomic force microscopy studies have revealed that RC-LH1 units of Rhodobacter (Rba.) sphaeroides form membrane-bending dimeric complexes together with the polypeptide PufX. We present a structural model for these RC-LH1-PufX dimeric complexes constructed using the molecular dynamics flexible fitting method based on an EM density map. The arrangement of the LH1 BChls displays a distortion near the proposed location of the PufX polypeptide. The resulting atomic model for BChl arrays is used to compute the excitonic properties of the dimeric RC-LH1 complex. A comparison is presented between the structural and excitonic features of the S-shaped dimeric BChl array of Rba. sphaeroides and the circular BChl arrangement found in other purple bacteria

PubMedReco: A Real-Time Recommender System for PubMed Citations.

Science.gov (United States)

Samuel, Hamman W; Zaïane, Osmar R

2017-01-01

We present a recommender system, PubMedReco, for real-time suggestions of medical articles from PubMed, a database of over 23 million medical citations. PubMedReco can recommend medical article citations while users are conversing in a synchronous communication environment such as a chat room. Normally, users would have to leave their chat interface to open a new web browser window, and formulate an appropriate search query to retrieve relevant results. PubMedReco automatically generates the search query and shows relevant citations within the same integrated user interface. PubMedReco analyzes relevant keywords associated with the conversation and uses them to search for relevant citations using the PubMed E-utilities programming interface. Our contributions include improvements to the user experience for searching PubMed from within health forums and chat rooms, and a machine learning model for identifying relevant keywords. We demonstrate the feasibility of PubMedReco using BMJ's Doc2Doc forum discussions.

Literature information in PubChem: associations between PubChem records and scientific articles.

Science.gov (United States)

Kim, Sunghwan; Thiessen, Paul A; Cheng, Tiejun; Yu, Bo; Shoemaker, Benjamin A; Wang, Jiyao; Bolton, Evan E; Wang, Yanli; Bryant, Stephen H

2016-01-01

PubChem is an open archive consisting of a set of three primary public databases (BioAssay, Compound, and Substance). It contains information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically modified) amino acid and nucleic acid sequences (including siRNA and miRNA). Currently (as of Nov. 2015), PubChem contains more than 150 million depositor-provided chemical substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results provided from over 1 million biological assay records. Many PubChem records (substances, compounds, and assays) include depositor-provided cross-references to scientific articles in PubMed. Some PubChem contributors provide bioactivity data extracted from scientific articles. Literature-derived bioactivity data complement high-throughput screening (HTS) data from the concluded NIH Molecular Libraries Program and other HTS projects. Some journals provide PubChem with information on chemicals that appear in their newly published articles, enabling concurrent publication of scientific articles in journals and associated data in public databases. In addition, PubChem links records to PubMed articles indexed with the Medical Subject Heading (MeSH) controlled vocabulary thesaurus. Literature information, both provided by depositors and derived from MeSH annotations, can be accessed using PubChem's web interfaces, enabling users to explore information available in literature related to PubChem records beyond typical web search results. Graphical abstractLiterature information for PubChem records is derived from various sources.

38 CFR 3.953 - Pub. L. 85-56 and Pub. L. 85-857.

Science.gov (United States)

2010-07-01

... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Pub. L. 85-56 and Pub. L... ADJUDICATION Pension, Compensation, and Dependency and Indemnity Compensation Protection § 3.953 Pub. L. 85-56 and Pub. L. 85-857. (a) In receipt of or entitled to receive benefits on December 31, 1958. Any person...

The feasibility study of in-vivo analysis of bone calcium by activation of hand with 5 Ci 238Pu-Be

International Nuclear Information System (INIS)

Sevimli, R.

1985-01-01

An in-vivo partial-body neutron activation technique (IVNAA) was used for evaluaton of the human bone. It was decided to use the hand for studies of osteroporosis. The 48 Ca(n,γ) 49 Ca reaction was employed (f=0.185%, I=900mb) and 5 Ci 238 Pu-Be isotopic neutron source. A sufficient precision was obtained by four 10 min irradiations of the hand phantom tubes, each followed by a 1000 sec counting period. A 5''x5'' NaI (Tl) well-type detector and a 1024 channel multichannel analyser were used for counting gamma rays. The neutron source, covered with 1 cm paraffin wax, is holding during the irradiation in hand

Cleavage of influenza RNA by using a human PUF-based artificial RNA-binding protein–staphylococcal nuclease hybrid

International Nuclear Information System (INIS)

Mori, Tomoaki; Nakamura, Kento; Masaoka, Keisuke; Fujita, Yusuke; Morisada, Ryosuke; Mori, Koichi; Tobimatsu, Takamasa; Sera, Takashi

2016-01-01

Various viruses infect animals and humans and cause a variety of diseases, including cancer. However, effective methodologies to prevent virus infection have not yet been established. Therefore, development of technologies to inactivate viruses is highly desired. We have already demonstrated that cleavage of a DNA virus genome was effective to prevent its replication. Here, we expanded this methodology to RNA viruses. In the present study, we used staphylococcal nuclease (SNase) instead of the PIN domain (PilT N-terminus) of human SMG6 as an RNA-cleavage domain and fused the SNase to a human Pumilio/fem-3 binding factor (PUF)-based artificial RNA-binding protein to construct an artificial RNA restriction enzyme with enhanced RNA-cleavage rates for influenzavirus. The resulting SNase-fusion nuclease cleaved influenza RNA at rates 120-fold greater than the corresponding PIN-fusion nuclease. The cleaving ability of the PIN-fusion nuclease was not improved even though the linker moiety between the PUF and RNA-cleavage domain was changed. Gel shift assays revealed that the RNA-binding properties of the PUF derivative used was not as good as wild type PUF. Improvement of the binding properties or the design method will allow the SNase-fusion nuclease to cleave an RNA target in mammalian animal cells and/or organisms. - Highlights: • A novel RNA restriction enzyme using SNase was developed tor cleave viral RNA. • Our enzyme cleaved influenza RNA with rates >120-fold higher rates a PIN-fusion one. • Our artificial enzyme with the L5 linker showed the highest RNA cleavage rate. • Our artificial enzyme site-selectively cleaved influenza RNA in vitro.

Repression of mitochondrial translation, respiration and a metabolic cycle-regulated gene, SLF1, by the yeast Pumilio-family protein Puf3p.

Directory of Open Access Journals (Sweden)

Marc Chatenay-Lapointe

Full Text Available Synthesis and assembly of the mitochondrial oxidative phosphorylation (OXPHOS system requires genes located both in the nuclear and mitochondrial genomes, but how gene expression is coordinated between these two compartments is not fully understood. One level of control is through regulated expression mitochondrial ribosomal proteins and other factors required for mitochondrial translation and OXPHOS assembly, which are all products of nuclear genes that are subsequently imported into mitochondria. Interestingly, this cadre of genes in budding yeast has in common a 3'-UTR element that is bound by the Pumilio family protein, Puf3p, and is coordinately regulated under many conditions, including during the yeast metabolic cycle. Multiple functions have been assigned to Puf3p, including promoting mRNA degradation, localizing nucleus-encoded mitochondrial transcripts to the outer mitochondrial membrane, and facilitating mitochondria-cytoskeletal interactions and motility. Here we show that Puf3p has a general repressive effect on mitochondrial OXPHOS abundance, translation, and respiration that does not involve changes in overall mitochondrial biogenesis and largely independent of TORC1-mitochondrial signaling. We also identified the cytoplasmic translation factor Slf1p as yeast metabolic cycle-regulated gene that is repressed by Puf3p at the post-transcriptional level and promotes respiration and extension of yeast chronological life span when over-expressed. Altogether, these results should facilitate future studies on which of the many functions of Puf3p is most relevant for regulating mitochondrial gene expression and the role of nuclear-mitochondrial communication in aging and longevity.

High density experiments with gas puffing and ECRH in T-10

International Nuclear Information System (INIS)

Esipchuk, Yu V; Kirneva, N A; Borschegovskij, A A; Chistyakov, V V; Denisov, V Ph; Dremin, M M; Gorbunov, E P; Grashin, S A; Kalupin, D V; Khimchenko, L N; Khramenkov, A V; Kirnev, G S; Krilov, S V; Krupin, V A; Myalton, T B; Pavlov, Yu D; Piterskij, V V; Ploskirev, G N; Poznyak, V I; Roy, I N; Shelukhin, D A; Skosyrev, Yu V; Trukhin, V M; Trukhina, E V; Vershkov, V A; Veschev, E A; Volkov, V V; Zhuravlev, V A

2003-01-01

High density experiments were carried out in T-10 with gas puffing and electron cyclotron resonance heating (with absorbed power value up to 1.4 MW) with oblique and perpendicular power launch. Densities exceeding the Greenwald limit (n Gw ) by up to a factor of 1.8 were achieved in a regime with a high value of the edge safety factor at the current flat-top, q(a)≅8.2. The decrease of q(a) to a value of 3 led to the reduction of the ratio ( n-bar e ) lim /n Gw to 1. Confinement degradation with density increase was not significant up to the density limit. However, the typical T-10 linear increase of energy confinement time with density saturates at n-bar e ≥0.6n Gw . This saturation is the result of the development of an additional transport in the electron heat channel. However, the saturated τ E values exceeded the ITER L-mode scaling predictions by up to a factor of 1.2 and were close to the value predicted by the ITER H-mode scaling. Effect of the strong gas puffing on the plasma confinement and experiments with neon seeding are also discussed in this paper

Analysis of PubMed User Sessions Using a Full-Day PubMed Query Log: A Comparison of Experienced and Nonexperienced PubMed Users

Science.gov (United States)

2015-01-01

Background PubMed is the largest biomedical bibliographic information source on the Internet. PubMed has been considered one of the most important and reliable sources of up-to-date health care evidence. Previous studies examined the effects of domain expertise/knowledge on search performance using PubMed. However, very little is known about PubMed users’ knowledge of information retrieval (IR) functions and their usage in query formulation. Objective The purpose of this study was to shed light on how experienced/nonexperienced PubMed users perform their search queries by analyzing a full-day query log. Our hypotheses were that (1) experienced PubMed users who use system functions quickly retrieve relevant documents and (2) nonexperienced PubMed users who do not use them have longer search sessions than experienced users. Methods To test these hypotheses, we analyzed PubMed query log data containing nearly 3 million queries. User sessions were divided into two categories: experienced and nonexperienced. We compared experienced and nonexperienced users per number of sessions, and experienced and nonexperienced user sessions per session length, with a focus on how fast they completed their sessions. Results To test our hypotheses, we measured how successful information retrieval was (at retrieving relevant documents), represented as the decrease rates of experienced and nonexperienced users from a session length of 1 to 2, 3, 4, and 5. The decrease rate (from a session length of 1 to 2) of the experienced users was significantly larger than that of the nonexperienced groups. Conclusions Experienced PubMed users retrieve relevant documents more quickly than nonexperienced PubMed users in terms of session length. PMID:26139516

Capacity of a dual enrollment system with two keys based on an SRAM-PUF

NARCIS (Netherlands)

Kusters, L.; Willems, F.M.J.

2018-01-01

We investigate the capacity of an SRAM-PUF based secrecy system that produces two secret keys during two consecutive enrollments. We determined the region of secret-key rates that are achievable and show that the total secret-key capacity is larger than for a single enrollment system. In our

A Compact and Low Power RO PUF with High Resilience to the EM Side-Channel Attack and the SVM Modelling Attack of Wireless Sensor Networks.

Science.gov (United States)

Cao, Yuan; Zhao, Xiaojin; Ye, Wenbin; Han, Qingbang; Pan, Xiaofang

2018-01-23

Authentication is a crucial security service for the wireless sensor networks (WSNs) in versatile domains. The deployment of WSN devices in the untrusted open environment and the resource-constrained nature make the on-chip authentication an open challenge. The strong physical unclonable function (PUF) came in handy as light-weight authentication security primitive. In this paper, we present the first ring oscillator (RO) based strong physical unclonable function (PUF) with high resilience to both the electromagnetic (EM) side-channel attack and the support vector machine (SVM) modelling attack. By employing an RO based PUF architecture with the current starved inverter as the delay cell, the oscillation power is significantly reduced to minimize the emitted EM signal, leading to greatly enhanced immunity to the EM side-channel analysis attack. In addition, featuring superior reconfigurability due to the conspicuously simplified circuitries, the proposed implementation is capable of withstanding the SVM modelling attack by generating and comparing a large number of RO frequency pairs. The reported experimental results validate the prototype of a 9-stage RO PUF fabricated using standard 65 nm complementary-metal-oxide-semiconductor (CMOS) process. Operating at the supply voltage of 1.2 V and the frequency of 100 KHz, the fabricated RO PUF occupies a compact silicon area of 250 μ m 2 and consumes a power as low as 5.16 μ W per challenge-response pair (CRP). Furthermore, the uniqueness and the worst-case reliability are measured to be 50.17% and 98.30% for the working temperature range of -40∼120 ∘ C and the supply voltage variation of ±2%, respectively. Thus, the proposed PUF is applicable for the low power, low cost and secure WSN communications.

PubMed-EX: a web browser extension to enhance PubMed search with text mining features.

Science.gov (United States)

Tsai, Richard Tzong-Han; Dai, Hong-Jie; Lai, Po-Ting; Huang, Chi-Hsin

2009-11-15

PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation mark-up, can help researchers to quickly focus on key terms and provide additional information on them. All text processing is performed server-side, freeing up user resources. PubMed-EX is freely available at http://bws.iis.sinica.edu.tw/PubMed-EX and http://iisr.cse.yzu.edu.tw:8000/PubMed-EX/.

Effects of instant controlled pressure drop process on physical and sensory properties of puffed wheat snack.

Science.gov (United States)

Yağcı, Sibel

2017-04-01

In this study, research on the development of a puffed wheat snack using the instant controlled pressure drop (DIC) process was carried out. Snack products were produced by expanding moistened wheat under various DIC processing conditions in order to obtain adequate puffing, followed by drying in a hot air dryer. The effects of operational variables such as wheat initial moisture content (11-23% w/w, wet basis), processing pressure (3-5 × 10 2 kPa) and processing time (3-11 min) on the physical (density, color and textural characteristics) and sensory properties of the product were investigated. The physical properties of the wheat snack were most affected by changes in processing pressure, followed by processing time and wheat moisture content. Increasing processing pressure and time often improved expansion and textural properties but led to darkening of the raw wheat color. The most acceptable snack in terms of physical properties was obtained at the lowest wheat moisture content. Sensory analysis suggested that consumer acceptability was optimal for wheat snacks produced at higher processing pressure, medium processing time and lower moisture content. The most desirable conditions for puffed wheat snack production using the DIC process were determined as 11% (w/w) of wheat moisture content, 5 × 10 2 kPa of processing pressure and 7 min of processing time. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

PubSCIENCE

CERN Document Server

United States. Department of Energy. Office of Scientific and Technical Information

PubSCIENCE, a component of EnergyFiles, indexes 1,000 scientific and technical journals. It contains over one million multi-source journal citations dating back over 25 years from DOE's Energy Science and Technology Database. The focus of PubSCIENCE is on those journals where DOE researchers report their scientific discoveries. Frequency of contributions by DOE-sponsored researchers to scientific journals has been analyzed to prioritize data collection efforts. OSTI partners with participating publishers to provide information that is both relevant and useful to the DOE scientific community as well as information that was developed as the result of government sponsored R&D.

Puffed and bothered: Personality, performance, and the effects of stress on checkered pufferfish.

Science.gov (United States)

Pleizier, Naomi; Wilson, Alexander D M; Shultz, Aaron D; Cooke, Steven J

2015-12-01

Although consistent individual-level differences in behaviour are widespread and potentially important in evolutionary and ecological processes, relatively few studies focus on the physiological mechanisms that might underlie and regulate these individual-level differences in wild populations. We conducted experiments to determine whether checkered pufferfish (Sphoeroides testudineus), which were collected from a dynamic (in terms of depth and water temperature) tidal mangrove creek environment in The Bahamas, have consistent individual-level differences in locomotor activity and the response to a simulated predator threat, as well as swimming performance and puffing in response to stressors. The relationships between personality and performance traits were evaluated to determine whether they represented stress-coping styles or syndromes. Subsequently, a displacement study was conducted to determine how personality and performance in the laboratory compared to movements in the field. In addition, we tested whether a physiological dose of the stress hormone cortisol would alter individual consistency in behavioural and performance traits. We found that pufferfish exhibited consistent individual differences in personality traits over time (e.g., activity and the duration of a response to a threat) and that performance was consistent between the lab and the natural enclosure. Locomotor activity and the duration of startled behaviour were not associated with swimming and puffing performance. Locomotor activity, puffing performance, and swimming performance were not related to whether fish returned to the tidal creek of capture after displacement. Similarly, a cortisol treatment did not modify behaviour or performance in the laboratory. The results reveal that consistent individual-level differences in behaviour and performance were present in a population from a fluctuating and physiologically challenging environment but that such traits are not necessarily correlated

Pub Culture in the U.K.

Institute of Scientific and Technical Information of China (English)

孙鑫

2015-01-01

In the U.K., pubs can be seen everywhere. They play an important role in the British society. How pubs came into being in the U.K.? Why is pub culture formed and what makes it prosperous? What effects does pub culture make on British society both in the past and in the present? Does any British character be shown in pub culture in the U.K.? In this paper, I will give a brief in-troduction of pub culture's history and development in the U.K.. Besides, the above questions will be explored and analyzed one by one.

Adaptação à cultura brasileira dos questionários The O'Leary-Sant e PUF, usados para cistite intersticial Adaptación a la cultura brasileña de los cuestionarios The O'Leary-Sant y Puf, usados para cistitis intersticial Adaptation of the O'Leary-Sant and the PUF for the diagnosis of interstitial cystitis for the Brazilian culture

Directory of Open Access Journals (Sweden)

Marcella Lima Victal

2013-04-01

Full Text Available O objetivo deste estudo foi traduzir e adaptar à cultura brasileira os instrumentos The O'Leary-Sant e PUF, utilizados no diagnóstico de cistite intersticial. Foram realizadas as etapas metodológicas recomendadas pela literatura internacional para a adaptação cultural. As etapas de tradução, síntese das traduções e retrotradução foram realizadas satisfatoriamente, e a avaliação das versões sintéticas pelo comitê de especialistas resultou em algumas alterações, assegurando as equivalências entre as versões originais e traduzidas. O PUF foi pré-testado entre 40 sujeitos e The O'Leary-Sant em uma amostra de 50 indivíduos, devido à necessidade de ajustes em decorrência da baixa escolaridade da população. O processo de tradução e adaptação foi realizado com sucesso e os instrumentos, após as modificações, demonstraram ser de fácil compreensão e rápido preenchimento. Entretanto, este é um estudo que antecede o processo de validação e será premente o emprego do instrumento em novas pesquisas para que sejam avaliadas suas propriedades psicométricas.Se objetivó traducir y adaptar a la cultura brasileña los instrumentos The O'Leary-Sant y PUF, utilizados para diagnosticar cistitis intersticial. Fueron efectuadas las etapas metodológicas recomendadas por la literatura internacional para adaptación cultural. Las etapas de traducción, síntesis de traducciones y retrotraducción se realizaron satisfactoriamente, la evaluación de las versiones sintetizadas por parte del comité de especialistas derivó en algunas alteraciones, asegurando las equivalencias entre versiones originales y traducidas. El PUF fue pre-testeado con 40 sujetos y The O'Leary-Sant en muestra de 50 individuos, por la necesidad de ajustes derivados de la baja escolarización de la población. El proceso de traducción y adaptación se efectuó con suceso y los instrumentos luego de las modificaciones demostraron ser de sencilla comprensión y

Zero-leakage multiple key-binding scenarios for SRAM-PUF systems based on the XOR-method

NARCIS (Netherlands)

Kusters, C.J.; Ignatenko, T.; Willems, F.M.J.

2016-01-01

We show that the XOR-method based on linear error-correcting codes can be applied to achieve the secret-key capacity of binary-symmetric SRAM-PUFs. Then we focus on multiple key-bindings. We prove that no information is leaked by all the helper data about a single secret key both in the case where

Zero-leakage multiple key-binding scenarios for SRAM-PUF systems based on the XOR-Method

NARCIS (Netherlands)

Kusters, C.J.; Ignatenko, T.; Willems, F.M.J.

2016-01-01

We show that the XOR-method based on linear error-correcting codes can be applied to achieve the secret-key capacity of binary-symmetric SRAM-PUFs. Then we focus on multiple key-bindings. We prove that no information is leaked by all the helper data about a single secret key both in the case where

Photochemical removal of NpF6 and PuF6 from UF6 gas streams

International Nuclear Information System (INIS)

Beitz, J.V.; Williams, C.W.

1990-01-01

A novel photochemical method of removing reactive fluorides from UF 6 gas has been discovered. This method reduces generated waste to little more than the volume of the removed impurities, minimizes loss of UF 6 , and can produce a recyclable by-product, fluorine gas. In our new method, impure UF 6 , is exposed to ultraviolet light which dissociates the UF 6 to UF 5 and fluorine atom. Impurities which chemically react with UF 5 are reduced and form solid compounds easily removed from the gas while UF 5 is converted back to UF 6 . Proof-of-concept testing involved UF 6 containing NpF 6 and PuF 6 with CO added as a fluorine atom scavenger. In a single photolysis step, greater than 5000-fold reduction of PuF 6 was demonstrated while reducing NpF 6 by more than 40-fold. This process is likely to remove corrosion and fission product fluorides that are more reactive than UF 6 and has been demonstrated without an added fluorine atom scavenger by periodically removing photogenerated fluorine gas. 44 refs., 3 figs., 2 tabs

Studying the effects of nucleating agents on texture modification of puffed corn-fish snack.

Science.gov (United States)

Shahmohammadi, Hamid Reza; Bakar, Jamilah; Rahman, Russly Abdul; Adzhan, Noranizan Mohd

2014-02-01

To improve textural attributes of puffed corn-fish snack, the effects of 1%, 1.5%, and 2% of calcium carbonate, magnesium silicate (talc), sodium bicarbonate as well as 5% and 10% of wheat bran (as the nucleating materials) on textural attributes were studied. Sensory evaluation, bulk density, expansion ratio, maximum force, and count peaks were measured using the Kramer test. The results showed that all of the additives except bran significantly enhanced the texture. Among them, talc at 0.5% was the best to enhance the density and expansion ratio. Effects of using 0.5% talc on puffed corn-fish snack microstructure were studied using scanning electron microscopy. The average cell diameter of 109 ± 48 μm and cell numbers per square centimeter of 67.4 for talc-treated products were obtained, while for nontalc-treated extrudates, average cell diameter of 798 ± 361 μm and cell numbers per square centimeter of 13.9 were found. Incorporation of 0.5% w/w of magnesium silicate reduced (7-fold) the average cell diameter while increased (4-fold) the cell number. © 2014 Institute of Food Technologists®

PubMed

Data.gov (United States)

U.S. Department of Health & Human Services — PubMed comprises more than 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to...

PubMed

CERN Document Server

PubMed is the National Library of Medicine's search service that provides access to over 10 million citations in MEDLINE, PreMEDLINE, and other related databases, with links to participating online journals.

PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm

Directory of Open Access Journals (Sweden)

Chuong Cheng-Ming

2006-10-01

Full Text Available Abstract Background Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts. Results PubFocus web server automates analysis of MEDLINE/PubMed search queries by enriching them with two widely used human factor-based bibliometric indicators of publication quality: journal impact factor and volume of forward references. In addition to providing basic volumetric statistics, PubFocus also prioritizes citations and evaluates authors' impact on the field of search. PubFocus also analyses presence and occurrence of biomedical key terms within citations by utilizing controlled vocabularies. Conclusion We have developed citations' prioritisation algorithm based on journal impact factor, forward referencing volume, referencing dynamics, and author's contribution level. It can be applied either to the primary set of PubMed search results or to the subsets of these results identified through key terms from controlled biomedical vocabularies and ontologies. NCI (National Cancer Institute thesaurus and MGD (Mouse Genome Database mammalian gene orthology have been implemented for key terms analytics. PubFocus provides a scalable platform for the integration of multiple available ontology databases. PubFocus analytics can be adapted for input sources of biomedical citations other than PubMed.

FK Comae Berenices, King of Spin: The COCOA-PUFS Project

Science.gov (United States)

Ayres, Thomas R.; Kashyap, V.; Saar, S.; Huenemoerder, D.; Korhonen, H.; Drake, J. J.; Testa, P.; Cohen, O.; Garraffo, C.; Granzer, T.; Strassmeier, K.

2016-03-01

COCOA-PUFS is an energy-diverse, time-domain study of the ultra-fast spinning, heavily spotted, yellow giant FK Comae Berenices (FK Com: HD117555; G4 III). This single star is thought to be a recent binary merger, and is exceptionally active by measure of its intense ultraviolet (UV) and X-ray emissions, and proclivity to flare. COCOA-PUFS was carried out with the Hubble Space Telescope in the UV (1200-3000 Å), using mainly its high-performance Cosmic Origins Spectrograph, but also high precision Space Telescope Imaging Spectrograph; Chandra X-ray Observatory in the soft X-rays (0.5-10 keV), utilizing its High-Energy Transmission Grating Spectrometer; together with supporting photometry and spectropolarimetry in the visible from the ground. This is an introductory report on the project. FK Com displayed variability on a wide range of timescales over all wavelengths during the week-long main campaign, including a large X-ray flare; “super-rotational broadening” of the far-ultraviolet “hot lines” (e.g., Si IV 1393 Å 8 × 104 K) together with chromospheric Mg II 2800 Å and C II 1335 Å (1-3 × 104 K); large Doppler swings suggestive of bright regions alternately on advancing and retreating limbs of the star; and substantial redshifts of the epoch-average emission profiles. These behaviors paint a picture of a highly extended, dynamic, hot (˜10 MK) coronal magnetosphere around the star, threaded by cooler structures perhaps analogous to solar prominences and replenished continually by surface activity and flares. Suppression of angular momentum loss by the confining magnetosphere could temporarily postpone the inevitable stellar spindown, thereby lengthening this highly volatile stage of coronal evolution. COordinated Campaign of Observations and Analysis, Photosphere to Upper Atmosphere, of a Fast-rotating Star.

FK COMAE BERENICES, KING OF SPIN: THE COCOA-PUFS PROJECT

Energy Technology Data Exchange (ETDEWEB)

Ayres, Thomas R. [Center for Astrophysics and Space Astronomy, 389 UCB, University of Colorado, Boulder, CO 80309 (United States); Kashyap, V.; Saar, S.; Drake, J. J.; Testa, P.; Cohen, O.; Garraffo, C. [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA (United States); Huenemoerder, D. [Massachusetts Institute of Technology, Cambridge, MA (United States); Korhonen, H. [Finnish Centre for Astronomy with ESO (FINCA), University of Turku, Väisäläntie 20, FI-21500 Piikkiö (Finland); Granzer, T.; Strassmeier, K., E-mail: Thomas.Ayres@Colorado.edu [Leibniz-Institut für Astrophysik Potsdam (AIP), An der Sternwarte 16, D-14482 Potsdam (Germany)

2016-03-15

COCOA-PUFS is an energy-diverse, time-domain study of the ultra-fast spinning, heavily spotted, yellow giant FK Comae Berenices (FK Com: HD117555; G4 III). This single star is thought to be a recent binary merger, and is exceptionally active by measure of its intense ultraviolet (UV) and X-ray emissions, and proclivity to flare. COCOA-PUFS was carried out with the Hubble Space Telescope in the UV (1200–3000 Å), using mainly its high-performance Cosmic Origins Spectrograph, but also high precision Space Telescope Imaging Spectrograph; Chandra X-ray Observatory in the soft X-rays (0.5–10 keV), utilizing its High-Energy Transmission Grating Spectrometer; together with supporting photometry and spectropolarimetry in the visible from the ground. This is an introductory report on the project. FK Com displayed variability on a wide range of timescales over all wavelengths during the week-long main campaign, including a large X-ray flare; “super-rotational broadening” of the far-ultraviolet “hot lines” (e.g., Si iv 1393 Å; 8 × 10{sup 4} K) together with chromospheric Mg ii 2800 Å and C ii 1335 Å (1–3 × 10{sup 4} K); large Doppler swings suggestive of bright regions alternately on advancing and retreating limbs of the star; and substantial redshifts of the epoch-average emission profiles. These behaviors paint a picture of a highly extended, dynamic, hot (∼10 MK) coronal magnetosphere around the star, threaded by cooler structures perhaps analogous to solar prominences and replenished continually by surface activity and flares. Suppression of angular momentum loss by the confining magnetosphere could temporarily postpone the inevitable stellar spindown, thereby lengthening this highly volatile stage of coronal evolution.

FK COMAE BERENICES, KING OF SPIN: THE COCOA-PUFS PROJECT

International Nuclear Information System (INIS)

Ayres, Thomas R.; Kashyap, V.; Saar, S.; Drake, J. J.; Testa, P.; Cohen, O.; Garraffo, C.; Huenemoerder, D.; Korhonen, H.; Granzer, T.; Strassmeier, K.

2016-01-01

COCOA-PUFS is an energy-diverse, time-domain study of the ultra-fast spinning, heavily spotted, yellow giant FK Comae Berenices (FK Com: HD117555; G4 III). This single star is thought to be a recent binary merger, and is exceptionally active by measure of its intense ultraviolet (UV) and X-ray emissions, and proclivity to flare. COCOA-PUFS was carried out with the Hubble Space Telescope in the UV (1200–3000 Å), using mainly its high-performance Cosmic Origins Spectrograph, but also high precision Space Telescope Imaging Spectrograph; Chandra X-ray Observatory in the soft X-rays (0.5–10 keV), utilizing its High-Energy Transmission Grating Spectrometer; together with supporting photometry and spectropolarimetry in the visible from the ground. This is an introductory report on the project. FK Com displayed variability on a wide range of timescales over all wavelengths during the week-long main campaign, including a large X-ray flare; “super-rotational broadening” of the far-ultraviolet “hot lines” (e.g., Si iv 1393 Å; 8 × 10 4 K) together with chromospheric Mg ii 2800 Å and C ii 1335 Å (1–3 × 10 4 K); large Doppler swings suggestive of bright regions alternately on advancing and retreating limbs of the star; and substantial redshifts of the epoch-average emission profiles. These behaviors paint a picture of a highly extended, dynamic, hot (∼10 MK) coronal magnetosphere around the star, threaded by cooler structures perhaps analogous to solar prominences and replenished continually by surface activity and flares. Suppression of angular momentum loss by the confining magnetosphere could temporarily postpone the inevitable stellar spindown, thereby lengthening this highly volatile stage of coronal evolution

Horizontal transfers of two types of puf operons among phototrophic members of the Roseobacter clade

Czech Academy of Sciences Publication Activity Database

Koblížek, Michal; Moulisová, Vladimíra; Muroňová, Markéta; Oborník, Miroslav

2015-01-01

Roč. 60, č. 1 (2015), s. 37-43 ISSN 0015-5632 R&D Projects: GA MŠk ED2.1.00/03.0110; GA ČR GAP501/10/0221; GA ČR GBP501/12/G055 Institutional support: RVO:61388971 Keywords : Rosebacter * horizontal transfer * puf operon s Subject RIV: EE - Microbiology, Virology Impact factor: 1.335, year: 2015

Towards PubMed 2.0.

Science.gov (United States)

Fiorini, Nicolas; Lipman, David J; Lu, Zhiyong

2017-10-30

Staff from the National Center for Biotechnology Information in the US describe recent improvements to the PubMed search engine and outline plans for the future, including a new experimental site called PubMed Labs.

Exploiting PubChem for Virtual Screening.

Science.gov (United States)

Xie, Xiang-Qun

2010-12-01

IMPORTANCE OF THE FIELD: PubChem is a public molecular information repository, a scientific showcase of the NIH Roadmap Initiative. The PubChem database holds over 27 million records of unique chemical structures of compounds (CID) derived from nearly 70 million substance depositions (SID), and contains more than 449,000 bioassay records with over thousands of in vitro biochemical and cell-based screening bioassays established, with targeting more than 7000 proteins and genes linking to over 1.8 million of substances. AREAS COVERED IN THIS REVIEW: This review builds on recent PubChem-related computational chemistry research reported by other authors while providing readers with an overview of the PubChem database, focusing on its increasing role in cheminformatics, virtual screening and toxicity prediction modeling. WHAT THE READER WILL GAIN: These publicly available datasets in PubChem provide great opportunities for scientists to perform cheminformatics and virtual screening research for computer-aided drug design. However, the high volume and complexity of the datasets, in particular the bioassay-associated false positives/negatives and highly imbalanced datasets in PubChem, also creates major challenges. Several approaches regarding the modeling of PubChem datasets and development of virtual screening models for bioactivity and toxicity predictions are also reviewed. TAKE HOME MESSAGE: Novel data-mining cheminformatics tools and virtual screening algorithms are being developed and used to retrieve, annotate and analyze the large-scale and highly complex PubChem biological screening data for drug design.

Praktische handleiding PubMed : hét boek om snel en doeltreffend te zoeken in PubMed

NARCIS (Netherlands)

Etten-Jamaludin, van F.; Deurenberg, H.W.J.

2010-01-01

Praktische handleidng PubMed is de eerste Nederlandstalige gids die op overzichtelijke wijze op de uitgebreide mogelijkheden van PubMed ingaat. PubMed (www.pubmed.gov) biedt gratis toegang tot MEDLINE en is de meest gebruikte medische zoekmachine. In deze geheel herziene derde editie van Praktisch

PuF, an antimetastatic and developmental signaling protein, interacts with the Alzheimer’s amyloid-β precursor protein via a tissue-specific proximal regulatory element (PRE

Directory of Open Access Journals (Sweden)

Lahiri Debomoy K

2013-01-01

Full Text Available Abstract Background Alzheimer’s disease (AD is intimately tied to amyloid-β (Aβ peptide. Extraneuronal brain plaques consisting primarily of Aβ aggregates are a hallmark of AD. Intraneuronal Aβ subunits are strongly implicated in disease progression. Protein sequence mutations of the Aβ precursor protein (APP account for a small proportion of AD cases, suggesting that regulation of the associated gene (APP may play a more important role in AD etiology. The APP promoter possesses a novel 30 nucleotide sequence, or “proximal regulatory element” (PRE, at −76/−47, from the +1 transcription start site that confers cell type specificity. This PRE contains sequences that make it vulnerable to epigenetic modification and may present a viable target for drug studies. We examined PRE-nuclear protein interaction by gel electrophoretic mobility shift assay (EMSA and PRE mutant EMSA. This was followed by functional studies of PRE mutant/reporter gene fusion clones. Results EMSA probed with the PRE showed DNA-protein interaction in multiple nuclear extracts and in human brain tissue nuclear extract in a tissue-type specific manner. We identified transcription factors that are likely to bind the PRE, using competition gel shift and gel supershift: Activator protein 2 (AP2, nm23 nucleoside diphosphate kinase/metastatic inhibitory protein (PuF, and specificity protein 1 (SP1. These sites crossed a known single nucleotide polymorphism (SNP. EMSA with PRE mutants and promoter/reporter clone transfection analysis further implicated PuF in cells and extracts. Functional assays of mutant/reporter clone transfections were evaluated by ELISA of reporter protein levels. EMSA and ELISA results correlated by meta-analysis. Conclusions We propose that PuF may regulate the APP gene promoter and that AD risk may be increased by interference with PuF regulation at the PRE. PuF is targeted by calcium/calmodulin-dependent protein kinase II inhibitor 1, which also

PubMed Informer: Monitoring MEDLINE/PubMed through E-mail Alerts, SMS, PDA downloads and RSS feeds

Science.gov (United States)

Muin, Michael; Fontelo, Paul; Ackerman, Michael

2005-01-01

Summary PubMed Informer is a Web-based monitoring tool for topics of interest from MEDLINE/PubMed primarily designed for healthcare professionals. Five tracking methods are available: Web access, e-mail, Short Message Service (SMS), PDA downloads and RSS feeds. PubMed Informer delivers focused search updates and specific information to users with varying information-seeking practices. PMID:16779344

Sizing of SRAM Cell with Voltage Biasing Techniques for Reliability Enhancement of Memory and PUF Functions

Directory of Open Access Journals (Sweden)

Chip-Hong Chang

2016-08-01

Full Text Available Static Random Access Memory (SRAM has recently been developed into a physical unclonable function (PUF for generating chip-unique signatures for hardware cryptography. The most compelling issue in designing a good SRAM-based PUF (SPUF is that while maximizing the mismatches between the transistors in the cross-coupled inverters improves the quality of the SPUF, this ironically also gives rise to increased memory read/write failures. For this reason, the memory cells of existing SPUFs cannot be reused as storage elements, which increases the overheads of cryptographic system where long signatures and high-density storage are both required. This paper presents a novel design methodology for dual-mode SRAM cell optimization. The design conflicts are resolved by using word-line voltage modulation, dynamic voltage scaling, negative bit-line and adaptive body bias techniques to compensate for reliability degradation due to transistor downsizing. The augmented circuit-level techniques expand the design space to achieve a good solution to fulfill several otherwise contradicting key design qualities for both modes of operation, as evinced by our statistical analysis and simulation results based on complementary metal–oxide–semiconductor (CMOS 45 nm bulk Predictive Technology Model.

Influence of Puffing Parameters and Filter Vent Blocking Condition on Nicotine Fate in a Burning Cigarette - Part 1. Full Flavor Cigarettes

Directory of Open Access Journals (Sweden)

Yu J

2014-12-01

Full Text Available Cigarette testing regulations based on more intensive puffing conditions than standard Federal Trade Commission/International Organisation for Standardization (FTC/ISO conditions, together with intentional filter vent-blocking of cigarettes during testing, are currently required in some countries. Recently, an initial recommendation under the auspices of the Framework Convention on Tobacco Control, has called for international machine-testing of cigarettes with a 55 cc/30 s/2 s puffing regimen after 100% filter vent-blocking. While much is currently known regarding changes in smoke yields with different machine smoking parameters, a more limited understanding of potential changes in smoke composition exists. In the present work, the influence of smoking conditions on nicotine fate in a burning cigarette was studied by gas chromatography with atomic emission detection (GC-AED using core-injected nicotine-d4. Tobacco rods were injected via a syringe to a fixed length with a constant volume of a methanol solution of known concentration of deuterated nicotine. Four different puffing conditions and two different vent-blocking conditions were studied. GC with mass spectrometric detection was used to identify the deuterium-labeled compounds that gave an enhanced deuterium AED-response. A comparison of the distribution of compounds containing deuterium in the mainstream smoke, sidestream smoke, and cigarette remains (butt and ash of a full flavor cigarette brand under the four smoking conditions studied indicated that a greater percentage of labeled nicotine remained intact during the smoking process as the intensity of the puffing regimen increased. As smoking regimen intensity increased, the amounts of nicotine pyrolysis and oxidation products detected in sidestream smoke decreased, while marginal increases in these compounds were observed in mainstream smoke and in the cigarette butt. The sidestream/mainstream nicotine ratio decreased significantly

Predicting clicks of PubMed articles.

Science.gov (United States)

Mao, Yuqing; Lu, Zhiyong

2013-01-01

Predicting the popularity or access usage of an article has the potential to improve the quality of PubMed searches. We can model the click trend of each article as its access changes over time by mining the PubMed query logs, which contain the previous access history for all articles. In this article, we examine the access patterns produced by PubMed users in two years (July 2009 to July 2011). We explore the time series of accesses for each article in the query logs, model the trends with regression approaches, and subsequently use the models for prediction. We show that the click trends of PubMed articles are best fitted with a log-normal regression model. This model allows the number of accesses an article receives and the time since it first becomes available in PubMed to be related via quadratic and logistic functions, with the model parameters to be estimated via maximum likelihood. Our experiments predicting the number of accesses for an article based on its past usage demonstrate that the mean absolute error and mean absolute percentage error of our model are 4.0% and 8.1% lower than the power-law regression model, respectively. The log-normal distribution is also shown to perform significantly better than a previous prediction method based on a human memory theory in cognitive science. This work warrants further investigation on the utility of such a log-normal regression approach towards improving information access in PubMed.

Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

OpenAIRE

Muin, Michael; Fontelo, Paul

2006-01-01

Abstract Background The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhanci...

Investigation of local carbon transport in the ASDEX Upgrade divertor using {sup 13}CH{sub 4} puffing

Energy Technology Data Exchange (ETDEWEB)

Pugno, R. [Max-Planck-Institut fuer Plasmaphysik, IPP-EURATOM Association, Boltzmannstr. 2, D-85748 Garching (Germany)], E-mail: Roberto.Pugno@ipp.mpg.de; Krieger, K. [Max-Planck-Institut fuer Plasmaphysik, IPP-EURATOM Association, Boltzmannstr. 2, D-85748 Garching (Germany); Airila, M.; Aho-Mantila, L. [Helsinki University of Technology, Association EURATOM-Tekes, P.O. Box 4100, FI-02015 TKK (Finland); Kreter, A.; Brezinsek, S. [Institut fuer Plasmaphysik, Forschungzentrum Juelich GmbH, EURATOM Association, Trilateral Euregio Cluster, D-52425 Juelich (Germany); Rohde, V.; Coster, D.; Chankin, A.; Wischmeier, M. [Max-Planck-Institut fuer Plasmaphysik, IPP-EURATOM Association, Boltzmannstr. 2, D-85748 Garching (Germany)

2009-06-15

To investigate the combined effect of re-deposition, re-erosion and local transport, known quantities of {sup 13}CH{sub 4} were puffed at the end of the 2007 experimental campaign in the ASDEX Upgrade outboard divertor. Exposed tiles were carefully removed for analysis. The amount of {sup 13}C locally deposited was measured by nuclear reaction analysis (NRA) and colorimetry. About 100% of injected carbon is deposited within a {+-} 15 cm extension in the toroidal direction. In contrast to H-mode results where re-deposition was exclusively downstream, in L-mode, more than one third of the injected hydrocarbon is found upstream. Colorimetric analysis of images taken with different lighting angles to the surface reveals a strong asymmetry in the carbon deposition pattern with respect to the injection facing/averting side of the surface roughness, with 4x thicker layers on the side facing the puffing location. The deposition pattern deviates clearly from the magnetic trajectories showing the effect of downward and radial drifts. ERO modelling of a similar experiment carried out in 2003 in H-mode background plasma can nicely reproduce the toroidal deposition pattern but drifts are not yet satisfactory described.

Tunable porous structure of carbon nanosheets derived from puffed rice for high energy density supercapacitors

Science.gov (United States)

Hou, Jianhua; Jiang, Kun; Tahir, Muhammad; Wu, Xiaoge; Idrees, Faryal; Shen, Ming; Cao, Chuanbao

2017-12-01

The development of green and clean synthetic techniques to overcome energy requirements have motivated the researchers for the utilization of sustainable biomass. Driven by this desire we choose rice as starting materials source. After the explosion effect, the precursor is converted into puffed rice with a honeycomb-like structures composed of thin sheets. These honeycomb-like macrostructures, effectively prevent the cross-linking tendency towards the adjacent nanosheets during activation process. Furthermore, tuneable micro/mesoporous structures with ultrahigh specific surface areas (SBET) are successfully designed by KOH activation. The highest SBET of 3326 m2 g-1 with optimized proportion of small-mesopores is achieved at 850 °C. The rice-derived porous N-doped carbon nanosheets (NCS-850) are used as the active electrode materials for supercapacitors. It exhibites high specific capacitance specifically of 218 F g-1 at 80 A g-1 in 6 M KOH and a high-energy density of 104 Wh kg-1 (53 Wh L-1) in the ionic liquid electrolytes. These are the highest values among the reported biomass-derived carbon materials for the best of our knowledge. The present work demonstrates that the combination of "puffing effect" and common chemical activation can turn natural products such as rice into functional products with prospective applications in high-performance energy storage devices.

User's manual of self learning gas puffing system for plasma density control

International Nuclear Information System (INIS)

Tanahashi, S.

1989-04-01

Pre-programmed gas puffing is often used to get adequet plasma density wave forms in the pulse operating devices for fusion experiments. This method has a defect that preset values have to be adjusted manually in accordance with changes of out gassing rate in successive shots. In order to remove this defect, a self learning system has been developed so as to keep the plasma density close to a given reference waveform. After a few succesive shots, it accomplishes self learning and is ready to keep up with a gradual change of the wall condition. This manual gives the usage of the system and the program list written in BASIC and ASSEMBLER languages. (author)

OvidSP Medline-to-PubMed search filter translation: a methodology for extending search filter range to include PubMed's unique content.

Science.gov (United States)

Damarell, Raechel A; Tieman, Jennifer J; Sladek, Ruth M

2013-07-02

PubMed translations of OvidSP Medline search filters offer searchers improved ease of access. They may also facilitate access to PubMed's unique content, including citations for the most recently published biomedical evidence. Retrieving this content requires a search strategy comprising natural language terms ('textwords'), rather than Medical Subject Headings (MeSH). We describe a reproducible methodology that uses a validated PubMed search filter translation to create a textword-only strategy to extend retrieval to PubMed's unique heart failure literature. We translated an OvidSP Medline heart failure search filter for PubMed and established version equivalence in terms of indexed literature retrieval. The PubMed version was then run within PubMed to identify citations retrieved by the filter's MeSH terms (Heart failure, Left ventricular dysfunction, and Cardiomyopathy). It was then rerun with the same MeSH terms restricted to searching on title and abstract fields (i.e. as 'textwords'). Citations retrieved by the MeSH search but not the textword search were isolated. Frequency analysis of their titles/abstracts identified natural language alternatives for those MeSH terms that performed less effectively as textwords. These terms were tested in combination to determine the best performing search string for reclaiming this 'lost set'. This string, restricted to searching on PubMed's unique content, was then combined with the validated PubMed translation to extend the filter's performance in this database. The PubMed heart failure filter retrieved 6829 citations. Of these, 834 (12%) failed to be retrieved when MeSH terms were converted to textwords. Frequency analysis of the 834 citations identified five high frequency natural language alternatives that could improve retrieval of this set (cardiac failure, cardiac resynchronization, left ventricular systolic dysfunction, left ventricular diastolic dysfunction, and LV dysfunction). Together these terms reclaimed

A study on PubMed search tag usage pattern: association rule mining of a full-day PubMed query log.

Science.gov (United States)

Mosa, Abu Saleh Mohammad; Yoo, Illhoi

2013-01-09

The practice of evidence-based medicine requires efficient biomedical literature search such as PubMed/MEDLINE. Retrieval performance relies highly on the efficient use of search field tags. The purpose of this study was to analyze PubMed log data in order to understand the usage pattern of search tags by the end user in PubMed/MEDLINE search. A PubMed query log file was obtained from the National Library of Medicine containing anonymous user identification, timestamp, and query text. Inconsistent records were removed from the dataset and the search tags were extracted from the query texts. A total of 2,917,159 queries were selected for this study issued by a total of 613,061 users. The analysis of frequent co-occurrences and usage patterns of the search tags was conducted using an association mining algorithm. The percentage of search tag usage was low (11.38% of the total queries) and only 2.95% of queries contained two or more tags. Three out of four users used no search tag and about two-third of them issued less than four queries. Among the queries containing at least one tagged search term, the average number of search tags was almost half of the number of total search terms. Navigational search tags are more frequently used than informational search tags. While no strong association was observed between informational and navigational tags, six (out of 19) informational tags and six (out of 29) navigational tags showed strong associations in PubMed searches. The low percentage of search tag usage implies that PubMed/MEDLINE users do not utilize the features of PubMed/MEDLINE widely or they are not aware of such features or solely depend on the high recall focused query translation by the PubMed's Automatic Term Mapping. The users need further education and interactive search application for effective use of the search tags in order to fulfill their biomedical information needs from PubMed/MEDLINE.

PubMed searches: overview and strategies for clinicians.

Science.gov (United States)

Lindsey, Wesley T; Olin, Bernie R

2013-04-01

PubMed is a biomedical and life sciences database maintained by a division of the National Library of Medicine known as the National Center for Biotechnology Information (NCBI). It is a large resource with more than 5600 journals indexed and greater than 22 million total citations. Searches conducted in PubMed provide references that are more specific for the intended topic compared with other popular search engines. Effective PubMed searches allow the clinician to remain current on the latest clinical trials, systematic reviews, and practice guidelines. PubMed continues to evolve by allowing users to create a customized experience through the My NCBI portal, new arrangements and options in search filters, and supporting scholarly projects through exportation of citations to reference managing software. Prepackaged search options available in the Clinical Queries feature also allow users to efficiently search for clinical literature. PubMed also provides information regarding the source journals themselves through the Journals in NCBI Databases link. This article provides an overview of the PubMed database's structure and features as well as strategies for conducting an effective search.

Science in the (CERN) Pub!

CERN Multimedia

2001-01-01

The 6th Public Communication of Science and Technology network conference will end on Saturday 3 February with special performances. At 14:30 in the coffee area of restaurant no. 1 (Main Building) all participants and interested CERN members are invited to two events that will address science in an unorthodox and amusing way. Australian scientists will start with Science in the Pub, a fun discussion of topical science in an Australian pub ambiance (free Foster's beer served). Cabaret Pasteur, a French sample of entertainment with a scientific touch will follow.

Assessing levels and seasonal variations of current-use pesticides (CUPs) in the Tuscan atmosphere, Italy, using polyurethane foam disks (PUF) passive air samplers

International Nuclear Information System (INIS)

Estellano, Victor H.; Pozo, Karla; Efstathiou, Christos; Pozo, Katerine; Corsolini, Simonetta; Focardi, Silvano

2015-01-01

Polyurethane foam disks (PUF) passive air samplers (PAS) were deployed over 4 sampling periods of 3–5-months (≥ 1 year) at ten urban and rural locations throughout the Tuscany Region. The purpose was to assess the occurrence and seasonal variations of ten current-use pesticides (CUPs). PUF disk extracts were analyzed using GC–MS. The organophosphates insecticides; chlorpyrifos (3–580 pg m −3 ) and chlorpyrifos-methyl (below detection limit – to 570 pg m −3 ) presented the highest levels in air, and showed seasonal fluctuation coinciding with the growing seasons. The relative proportion urban/(urban + rural) ranged from 0.4 to 0.7 showing no differences between urban and rural concentrations. Air back trajectories analysis showed air masses passing over agricultural fields and potentially enhancing the drift of pesticides into the urban sites. This study represents the first information regarding CUPs in the atmosphere of Tuscany region using PAS-PUF disk. - Highlights: • Current use pesticides (CUPs) were detected in the atmosphere of Tuscany, Italy. • Chlorpyrifos showed the highest concentrations in air with seasonal patterns. • CUPs levels might be influenced by agricultural activities. • No differences were detected between Urban and Rural sites. • Air mass analysis indicated the monitoring sites are influenced by local sources. - Seasonality of CUPs was measured in Tuscany, Italy. Chlorpyrifos showed the highest values. Urban and rural sites showed no differences. Agricultural activities influence CUPs levels in air

Assessing electronic cigarette emissions: linking physico-chemical properties to product brand, e-liquid flavoring additives, operational voltage and user puffing patterns.

Science.gov (United States)

Zhao, Jiayuan; Nelson, Jordan; Dada, Oluwabunmi; Pyrgiotakis, Georgios; Kavouras, Ilias G; Demokritou, Philip

2018-02-01

Users of electronic cigarettes (e-cigs) are exposed to particles and other gaseous pollutants. However, major knowledge gaps on the physico-chemical properties of such exposures and contradictory data in published literature prohibit health risk assessment. Here, the effects of product brand, type, e-liquid flavoring additives, operational voltage, and user puffing patterns on emissions were systematically assessed using a recently developed, versatile, e-cig exposure generation platform and state-of-the-art analytical methods. Parameters of interest in this systematic evaluation included two brands (A and B), three flavors (tobacco, menthol, and fruit), three types of e-cigs (disposable, pre-filled, and refillable tanks), two puffing protocols (4 and 2 s/puff), and four operational voltages (2.2-5.7 V). Particles were generated at a high number concentration (10 6 -10 7 particles/cm 3 ). The particle size distribution was bi-modal (∼200 nm and 1 µm). Furthermore, organic species (humectants propylene glycol and glycerin, nicotine) that were present in e-liquid and trace metals (potassium and sodium) that were present on e-cig heating coil were also released into the emission. In addition, combustion-related byproducts, such as benzene and toluene, were also detected in the range of 100-38,000 ppbv/puff. Parametric analyzes performed in this study show the importance of e-cig brand, type, flavor additives, user puffing pattern (duration and frequency), and voltage on physico-chemical properties of emissions. This observed influence is indicative of the complexity associated with the toxicological screening of emissions from e-cigs and needs to be taken into consideration.

PubData: search engine for bioinformatics databases worldwide

OpenAIRE

Vand, Kasra; Wahlestedt, Thor; Khomtchouk, Kelly; Sayed, Mohammed; Wahlestedt, Claes; Khomtchouk, Bohdan

2016-01-01

We propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence algorithms that can patch into the file transfer protocol servers of any user-specified bioinformatics database, query its contents, retrieve files for download, and adapt to the use...

PubMed Interact: an Interactive Search Application for MEDLINE/PubMed

Science.gov (United States)

Muin, Michael; Fontelo, Paul; Ackerman, Michael

2006-01-01

Online search and retrieval systems are important resources for medical literature research. Progressive Web 2.0 technologies provide opportunities to improve search strategies and user experience. Using PHP, Document Object Model (DOM) manipulation and Asynchronous JavaScript and XML (Ajax), PubMed Interact allows greater functionality so users can refine search parameters with ease and interact with the search results to retrieve and display relevant information and related articles. PMID:17238658

A PUBS Case in a Palliative Care Unit Experience

OpenAIRE

Restuccia, M. R.; Blasi, M.

2014-01-01

Purple urine bag syndrome (PUBS) is a rare condition in which purple discoloration of the collecting bag and its associated tubing occurs. It is considered a benign condition. PUBS is usually associated with urinary tract infection occurring in elderly bedridden women, with chronic urinary catheterization. This syndrome is usually reported to occur in alkaline urine, but here we describe a rare case of PUBS involving acidic urine.

OEDGE modeling of plasma contamination efficiency of Ar puffing from different divertor locations in EAST

Science.gov (United States)

Pengfei, ZHANG; Ling, ZHANG; Zhenwei, WU; Zong, XU; Wei, GAO; Liang, WANG; Qingquan, YANG; Jichan, XU; Jianbin, LIU; Hao, QU; Yong, LIU; Juan, HUANG; Chengrui, WU; Yumei, HOU; Zhao, JIN; J, D. ELDER; Houyang, GUO

2018-04-01

Modeling with OEDGE was carried out to assess the initial and long-term plasma contamination efficiency of Ar puffing from different divertor locations, i.e. the inner divertor, the outer divertor and the dome, in the EAST superconducting tokamak for typical ohmic plasma conditions. It was found that the initial Ar contamination efficiency is dependent on the local plasma conditions at the different gas puff locations. However, it quickly approaches a similar steady state value for Ar recycling efficiency >0.9. OEDGE modeling shows that the final equilibrium Ar contamination efficiency is significantly lower for the more closed lower divertor than that for the upper divertor.

A PUBS Case in a Palliative Care Unit Experience

Directory of Open Access Journals (Sweden)

M. R. Restuccia

2014-01-01

Full Text Available Purple urine bag syndrome (PUBS is a rare condition in which purple discoloration of the collecting bag and its associated tubing occurs. It is considered a benign condition. PUBS is usually associated with urinary tract infection occurring in elderly bedridden women, with chronic urinary catheterization. This syndrome is usually reported to occur in alkaline urine, but here we describe a rare case of PUBS involving acidic urine.

Best, Useful and Objective Precisions for Information Retrieval of Three Search Methods in PubMed and iPubMed

Directory of Open Access Journals (Sweden)

Somayyeh Nadi Ravandi

2016-10-01

Full Text Available MEDLINE is one of the valuable sources of medical information on the Internet. Among the different open access sites of MEDLINE, PubMed is the best-known site. In 2010, iPubMed was established with an interaction-fuzzy search method for MEDLINE access. In the present work, we aimed to compare the precision of the retrieved sources (Best, Useful and Objective precision in the PubMed and iPubMed using two search methods (simple and MeSH search in PubMed and interaction-fuzzy method in iPubmed. During our semi-empirical study period, we held training workshops for 61 students of higher education to teach them Simple Search, MeSH Search, and Fuzzy-Interaction Search methods. Then, the precision of 305 searches for each method prepared by the students was calculated on the basis of Best precision, Useful precision, and Objective precision formulas. Analyses were done in SPSS version 11.5 using the Friedman and Wilcoxon Test, and three precisions obtained with the three precision formulas were studied for the three search methods. The mean precision of the interaction-fuzzy Search method was higher than that of the simple search and MeSH search for all three types of precision, i.e., Best precision, Useful precision, and Objective precision, and the Simple search method was in the next rank, and their mean precisions were significantly different (P < 0.001. The precision of the interaction-fuzzy search method in iPubmed was investigated for the first time. Also for the first time, three types of precision were evaluated in PubMed and iPubmed. The results showed that the Interaction-Fuzzy search method is more precise than using the natural language search (simple search and MeSH search, and users of this method found papers that were more related to their queries; even though search in Pubmed is useful, it is important that users apply new search methods to obtain the best results.

Comparison of PubMed and Google Scholar literature searches.

Science.gov (United States)

Anders, Michael E; Evans, Dennis P

2010-05-01

Literature searches are essential to evidence-based respiratory care. To conduct literature searches, respiratory therapists rely on search engines to retrieve information, but there is a dearth of literature on the comparative efficiencies of search engines for researching clinical questions in respiratory care. To compare PubMed and Google Scholar search results for clinical topics in respiratory care to that of a benchmark. We performed literature searches with PubMed and Google Scholar, on 3 clinical topics. In PubMed we used the Clinical Queries search filter. In Google Scholar we used the search filters in the Advanced Scholar Search option. We used the reference list of a related Cochrane Collaboration evidence-based systematic review as the benchmark for each of the search results. We calculated recall (sensitivity) and precision (positive predictive value) with 2 x 2 contingency tables. We compared the results with the chi-square test of independence and Fisher's exact test. PubMed and Google Scholar had similar recall for both overall search results (71% vs 69%) and full-text results (43% vs 51%). PubMed had better precision than Google Scholar for both overall search results (13% vs 0.07%, P PubMed searches with the Clinical Queries filter are more precise than with the Advanced Scholar Search in Google Scholar for respiratory care topics. PubMed appears to be more practical to conduct efficient, valid searches for informing evidence-based patient-care protocols, for guiding the care of individual patients, and for educational purposes.

PubMed Medical Publications From Libya | Bakoush | Libyan ...

African Journals Online (AJOL)

We also used the same method to obtain data on the PubMed medical publications from Tunisia, Morocco and Yemen. Tunisia had the largest number of PubMed publications among the studied countries: 20.4 publications per million population per year and 7.2 publications per year per one billion US$ GDP. Libya had ...

The Effect of Moisture Content of Maize Grits on Physicochemical Properties of Its Puffed Food Products Properties of Its Puffed Food Products

Directory of Open Access Journals (Sweden)

S. Sharifi

2016-02-01

Full Text Available In this study the effect of different levels of moisture content of maize grits (10, 13, 16 and 19% as an attribute of physicochemical properties of extruder-derived puffed products, was investigated. The results showed that with increasing maize grits' moisture content, water absorption index (WAI and water solubility index (WSI were decreased. Moreover, with changing in feed moisture content from 10 to 16%, the volume and sectional expansion index (SEI increased but further increase of moisture content to 19% caused a reduction in these parameters. The textural tests also revealed that with increase in moisture content, the compression energy (Nmm, maximum force (N and time to achieve the first major peak (s were increased but the number of peaks was decreased. With increase in the moisture content, specific mechanical energy (SME was decreased, due probably to the reduction in the viscosity of melt. With increase in the moisture content the L and b values were increased but the value of the samples were decreased due to the reduction of Maillard reaction rate. Our data confirms that the moisture content of maize grits may play an important role in the quality of produced extruded snacks and a high quality product can be achieved by optimizing this parameter. In this research, the maximum volume of the extruder product was obtained in 16% of moisture level.

MedlinePlus FAQ: MedlinePlus and MEDLINE/PubMed

Science.gov (United States)

... What is the difference between MedlinePlus and MEDLINE/PubMed? To use the sharing features on this page, ... latest health professional articles on your topic. MEDLINE/PubMed: Is a database of professional biomedical literature Is ...

GOClonto: an ontological clustering approach for conceptualizing PubMed abstracts.

Science.gov (United States)

Zheng, Hai-Tao; Borchert, Charles; Kim, Hong-Gee

2010-02-01

Concurrent with progress in biomedical sciences, an overwhelming of textual knowledge is accumulating in the biomedical literature. PubMed is the most comprehensive database collecting and managing biomedical literature. To help researchers easily understand collections of PubMed abstracts, numerous clustering methods have been proposed to group similar abstracts based on their shared features. However, most of these methods do not explore the semantic relationships among groupings of documents, which could help better illuminate the groupings of PubMed abstracts. To address this issue, we proposed an ontological clustering method called GOClonto for conceptualizing PubMed abstracts. GOClonto uses latent semantic analysis (LSA) and gene ontology (GO) to identify key gene-related concepts and their relationships as well as allocate PubMed abstracts based on these key gene-related concepts. Based on two PubMed abstract collections, the experimental results show that GOClonto is able to identify key gene-related concepts and outperforms the STC (suffix tree clustering) algorithm, the Lingo algorithm, the Fuzzy Ants algorithm, and the clustering based TRS (tolerance rough set) algorithm. Moreover, the two ontologies generated by GOClonto show significant informative conceptual structures.

Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filters.

Science.gov (United States)

Lokker, Cynthia; Haynes, R Brian; Wilczynski, Nancy L; McKibbon, K Ann; Walter, Stephen D

2011-01-01

Clinical Queries filters were developed to improve the retrieval of high-quality studies in searches on clinical matters. The study objective was to determine the yield of relevant citations and physician satisfaction while searching for diagnostic and treatment studies using the Clinical Queries page of PubMed compared with searching PubMed without these filters. Forty practicing physicians, presented with standardized treatment and diagnosis questions and one question of their choosing, entered search terms which were processed in a random, blinded fashion through PubMed alone and PubMed Clinical Queries. Participants rated search retrievals for applicability to the question at hand and satisfaction. For treatment, the primary outcome of retrieval of relevant articles was not significantly different between the groups, but a higher proportion of articles from the Clinical Queries searches met methodologic criteria (p=0.049), and more articles were published in core internal medicine journals (p=0.056). For diagnosis, the filtered results returned more relevant articles (p=0.031) and fewer irrelevant articles (overall retrieval less, p=0.023); participants needed to screen fewer articles before arriving at the first relevant citation (p<0.05). Relevance was also influenced by content terms used by participants in searching. Participants varied greatly in their search performance. Clinical Queries filtered searches returned more high-quality studies, though the retrieval of relevant articles was only statistically different between the groups for diagnosis questions. Retrieving clinically important research studies from Medline is a challenging task for physicians. Methodological search filters can improve search retrieval.

Do smoke-free laws affect revenues in pubs and restaurants?

Science.gov (United States)

Melberg, Hans Olav; Lund, Karl E

2012-02-01

In the debate about laws regulating smoking in restaurants and pubs, there has been some controversy as to whether smoke-free laws would reduce revenues in the hospitality industry. Norway presents an interesting case for three reasons. First, it was among the first countries to implement smoke-free laws, so it is possible to assess the long-term effects. Second, it has a cold climate so if there is a negative effect on revenue one would expect to find it in Norway. Third, the data from Norway are detailed enough to distinguish between revenue from pubs and restaurants. Autoregressive integrated moving average (ARIMA) intervention analysis of bi-monthly observations of revenues in restaurants and pubs show that the law did not have a statistically significant long-term effect on revenue in restaurants or on restaurant revenue as a share of personal consumption. Similar analysis for pubs shows that there was no significant long-run effect on pub revenue.

Neutron dosimetry at SLAC: Neutron sources and instrumentation

Energy Technology Data Exchange (ETDEWEB)

Liu, J.C.; Jenkins, T.M.; McCall, R.C.; Ipe, N.E.

1991-10-01

This report summarizes in detail the dosimetric characteristics of the five radioisotopic type neutron sources ({sup 238}PuBe, {sup 252}Cf, {sup 238}PuB, {sup 238}PuF{sub 4}, and {sup 238}PuLi) and the neutron instrumentation (moderated BF{sub 3} detector, Anderson-Braun (AB) detector, AB remmeter, Victoreen 488 Neutron Survey Meter, Beam Shut-Off Ionization Chamber, {sup 12}C plastic scintillator detector, moderated indium foil detector, and moderated and bare TLDs) that are commonly used for neutron dosimetry at the Stanford Linear Accelerator Center (SLAC). 36 refs,. 19 figs.

PubChem Power User Gateway (PUG)

Data.gov (United States)

U.S. Department of Health & Human Services — PUG provides access to PubChem services via a programmatic interface. Users may download data, initiate chemical structure searches, standardize chemical structures...

Removal of crude petroleum hydrocarbons by heterotrophic bacteria ...

African Journals Online (AJOL)

Nitrogenous fertilizer (NPK) plant effluents from NAFCON were used in amending plots of land experimentally polluted with crude oil. Counts of heterotrophic bacteria (THBC) and fungi (TF), and of petroleum utilizing bacteria (PUB) and fungi (PUF) were monitored during an 8 weeks period. Counts obtained showed that ...

Environmental Protection Agency - EPA Pub Central

Data.gov (United States)

U.S. Environmental Protection Agency — PubMed Central (PMC) is a full-text, online archive of journal literature operated by the National Library of Medicine. The EPA is using PMC to permanently preserve...

Puffing and inhalation behaviour in cigarette smoking: Implications for particle diameter and dose

Energy Technology Data Exchange (ETDEWEB)

Dickens, Colin; McGrath, Conor; Warren, Nigel; Biggs, Philip; McAughey, John, E-mail: colin_dickens@bat.co [British American Tobacco, Group R and D Centre, Southampton, SO15 8TL (United Kingdom)

2009-02-01

Inhalation of tobacco smoke aerosol is a two-step process involving puffing followed by inhalation. Measured smoke deposition efficiencies in the lung (20-70%) are greater than expected for smoke particles of diameter 150 - 250 nm CMD. Various mechanisms have been put forward to explain this enhanced deposition pattern, including coagulation, hygroscopic growth, condensation and evaporation, changes in composition, or changes in inhalation behaviour. This paper represents one of a series of studies seeking to better quantify smoke chemistry, inhalation behaviour and cumulative particle growth. The studies have been conducted to better understand smoke dosimetry and links to disease as part of a wider programme defining risk and potential harm reduction. In this study, it was noted that particle deposition increased with increasing inhalation depth, and that smoke inhalation volumes were generally greater than normal tidal breathing volumes. A weak association was observed between particle diameter and puff flow, but no strong association between particle diameter and retention efficiency.

Puffing and inhalation behaviour in cigarette smoking: Implications for particle diameter and dose

International Nuclear Information System (INIS)

Dickens, Colin; McGrath, Conor; Warren, Nigel; Biggs, Philip; McAughey, John

2009-01-01

Inhalation of tobacco smoke aerosol is a two-step process involving puffing followed by inhalation. Measured smoke deposition efficiencies in the lung (20-70%) are greater than expected for smoke particles of diameter 150 - 250 nm CMD. Various mechanisms have been put forward to explain this enhanced deposition pattern, including coagulation, hygroscopic growth, condensation and evaporation, changes in composition, or changes in inhalation behaviour. This paper represents one of a series of studies seeking to better quantify smoke chemistry, inhalation behaviour and cumulative particle growth. The studies have been conducted to better understand smoke dosimetry and links to disease as part of a wider programme defining risk and potential harm reduction. In this study, it was noted that particle deposition increased with increasing inhalation depth, and that smoke inhalation volumes were generally greater than normal tidal breathing volumes. A weak association was observed between particle diameter and puff flow, but no strong association between particle diameter and retention efficiency.

How Complementary and Alternative Medicine Practitioners Use PubMed

Science.gov (United States)

Quint-Rapoport, Mia

2007-01-01

Background PubMed is the largest bibliographic index in the life sciences. It is freely available online and is used by professionals and the public to learn more about medical research. While primarily intended to serve researchers, PubMed provides an array of tools and services that can help a wider readership in the location, comprehension, evaluation, and utilization of medical research. Objective This study sought to establish the potential contributions made by a range of PubMed tools and services to the use of the database by complementary and alternative medicine practitioners. Methods In this study, 10 chiropractors, 7 registered massage therapists, and a homeopath (N = 18), 11 with prior research training and 7 without, were taken through a 2-hour introductory session with PubMed. The 10 PubMed tools and services considered in this study can be divided into three functions: (1) information retrieval (Boolean Search, Limits, Related Articles, Author Links, MeSH), (2) information access (Publisher Link, LinkOut, Bookshelf ), and (3) information management (History, Send To, Email Alert). Participants were introduced to between six and 10 of these tools and services. The participants were asked to provide feedback on the value of each tool or service in terms of their information needs, which was ranked as positive, positive with emphasis, negative, or indifferent. Results The participants in this study expressed an interest in the three types of PubMed tools and services (information retrieval, access, and management), with less well-regarded tools including MeSH Database and Bookshelf. In terms of their comprehension of the research, the tools and services led the participants to reflect on their understanding as well as their critical reading and use of the research. There was universal support among the participants for greater access to complete articles, beyond the approximately 15% that are currently open access. The abstracts provided by PubMed were

Field aligned flows driven by neutral puffing at MAST

Science.gov (United States)

Waters, I.; Frerichs, H.; Silburn, S.; Feng, Y.; Harrison, J.; Kirk, A.; Schmitz, O.

2018-06-01

Neutral deuterium gas puffing at the high field side of the mega ampere spherical tokamak (MAST) is shown to drive carbon impurity flows that are aligned with the trajectory of the magnetic field lines in the plasma scrape-off-layer. These impurity flows were directly imaged with emissions from C2+ ions at MAST by coherence imaging spectroscopy and were qualitatively reproduced in deuterium plasmas by modeling with the EMC3-EIRENE plasma edge fluid and kinetic neutral transport code. A reduced one-dimensional momentum and particle balance shows that a localized increase in the static plasma pressure in front of the neutral gas puff yields an acceleration of the plasma due to local ionization. Perpendicular particle transport yields a decay from which a parallel length scale can be determined. Parameter scans in EMC3-EIRENE were carried out to determine the sensitivity of the deuterium plasma flow phenomena to local fueling and diffusion parameters and it is found that these flows robustly form across a wide variety of plasma conditions. Finally, efforts to couple this behavior in the background plasma directly to the impurity flows observed experimentally in MAST using a trace impurity model are discussed. These results provide insight into the fueling and exhaust features at this pivotal point of the radial and parallel particle flux balance, which is a major part of the plasma fueling and exhaust characteristics in a magnetically confined fusion device.

Time-dependent migration of citations through PubMed and OvidSP subsets: a study on a series of simultaneous PubMed and OvidSP searches.

Science.gov (United States)

Boeker, Martin; Vach, Werner; Motschall, Edith

2013-01-01

To quantitatively describe (1) differences between search results derived at consecutive time points with the PubMed and OvidSP literature search interfaces over a five day interval, and (2) the migration of citations through different subsets to estimate the timeliness of OvidSP. PubMed-Identifiers (PMIDs) of the following subsets were retrieved from PubMed and OvidSP simultaneously (within 8 h) at 11 days in March and April 2010 including 5 consecutive days: as supplied by publisher, in process, PubMed not MEDLINE, and OLDMEDLINE. Search results were compared for difference and intersection sets. The migration of citations on individual level was determined by comparison of corresponding sets over several days. The "in process" set was stable with about 446,000 - 452,000 citations; a small fraction of up to 3 % of the total subsets were in PubMed only and OvidSP only subsets. About 96 % of the ca. 10,500 citations in the OvidSP only subset migrated within 2 days out of the "in process" subset. The database of OvidSP is updated within a period of two days.

Gaps in affiliation indexing in Scopus and PubMed.

Science.gov (United States)

Schmidt, Cynthia M; Cox, Roxanne; Fial, Alissa V; Hartman, Teresa L; Magee, Martha L

2016-04-01

The authors sought to determine whether unexpected gaps existed in Scopus's author affiliation indexing of publications written by the University of Nebraska Medical Center or Nebraska Medicine (UNMC/NM) authors during 2014. First, we compared Scopus affiliation identifier search results to PubMed affiliation keyword search results. Then, we searched Scopus using affiliation keywords (UNMC, etc.) and compared the results to PubMed affiliation keyword and Scopus affiliation identifier searches. We found that Scopus's records for approximately 7% of UNMC/NM authors' publications lacked appropriate UNMC/NM author affiliation identifiers, and many journals' publishers were supplying incomplete author affiliation information to PubMed. Institutions relying on Scopus to track their impact should determine whether Scopus's affiliation identifiers will, in fact, identify all articles published by their authors and investigators.

The inclusion of an online journal in PubMed central - a difficult path.

Science.gov (United States)

Grech, Victor

2016-01-01

The indexing of a journal in a prominent database (such as PubMed) is an important imprimatur. Journals accepted for inclusion in PubMed Central (PMC) are automatically indexed in PubMed but must provide the entire contents of their publications as XML-tagged (Extensible Markup Language) data files compliant with PubMed's document type definition (DTD). This paper describes the various attempts that the journal Images in Paediatric Cardiology made in its efforts to convert the journal contents (including all of the extant backlog) to PMC-compliant XML for archiving and indexing in PubMed after the journal was accepted for inclusion by the database.

CoPub: a literature-based keyword enrichment tool for microarray data analysis.

Science.gov (United States)

Frijters, Raoul; Heupers, Bart; van Beek, Pieter; Bouwhuis, Maurice; van Schaik, René; de Vlieg, Jacob; Polman, Jan; Alkema, Wynand

2008-07-01

Medline is a rich information source, from which links between genes and keywords describing biological processes, pathways, drugs, pathologies and diseases can be extracted. We developed a publicly available tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data. CoPub allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. CoPub is freely accessible at http://services.nbic.nl/cgi-bin/copub/CoPub.pl.

PUB22 and PUB23 U-BOX E3 ligases directly ubiquitinate RPN6, a 26S proteasome lid subunit, for subsequent degradation in Arabidopsis thaliana

DEFF Research Database (Denmark)

Cho, Seok Keun; Bae, Hansol; Ryu, Moonyoung

2015-01-01

and PUB23, two U-box E3 ligase homologs, tether ubiquitins to 19S proteasome regulatory particle (RP) subunit RPN6, leading to its degradation. RPN6 was identified as an interacting substrate of PUB22 by yeast two-hybrid screening, and in vitro pull-down assay confirmed that RPN6 interacts not only......Drought stress strongly affects plant growth and development, directly connected with crop yields, accordingly. However, related to the function of U-BOX E3 ligases, the underlying molecular mechanisms of desiccation stress response in plants are still largely unknown. Here we report that PUB22...

AliBaba: PubMed as a graph.

Science.gov (United States)

Plake, Conrad; Schiemann, Torsten; Pankalla, Marcus; Hakenberg, Jörg; Leser, Ulf

2006-10-01

The biomedical literature contains a wealth of information on associations between many different types of objects, such as protein-protein interactions, gene-disease associations and subcellular locations of proteins. When searching such information using conventional search engines, e.g. PubMed, users see the data only one-abstract at a time and 'hidden' in natural language text. AliBaba is an interactive tool for graphical summarization of search results. It parses the set of abstracts that fit a PubMed query and presents extracted information on biomedical objects and their relationships as a graphical network. AliBaba extracts associations between cells, diseases, drugs, proteins, species and tissues. Several filter options allow for a more focused search. Thus, researchers can grasp complex networks described in various articles at a glance. http://alibaba.informatik.hu-berlin.de/

Health informatics research in Australia: retrospective analysis using PubMed

Directory of Open Access Journals (Sweden)

Kumara Mendis

2007-01-01

Discussion Australian HI publications in PubMed increased consistently throughout the period 1970-2005, which is on a par with world trends in HI publications. In Australia, most HI publications are in general medical journals. Lack of consistency in author names and failure to include the country name and even the state are the main obstacles to PubMed bibliometric analysis.

The PubChem chemical structure sketcher

Directory of Open Access Journals (Sweden)

Ihlenfeldt Wolf D

2009-12-01

Full Text Available Abstract PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects.

Improving accuracy for identifying related PubMed queries by an integrated approach.

Science.gov (United States)

Lu, Zhiyong; Wilbur, W John

2009-10-01

PubMed is the most widely used tool for searching biomedical literature online. As with many other online search tools, a user often types a series of multiple related queries before retrieving satisfactory results to fulfill a single information need. Meanwhile, it is also a common phenomenon to see a user type queries on unrelated topics in a single session. In order to study PubMed users' search strategies, it is necessary to be able to automatically separate unrelated queries and group together related queries. Here, we report a novel approach combining both lexical and contextual analyses for segmenting PubMed query sessions and identifying related queries and compare its performance with the previous approach based solely on concept mapping. We experimented with our integrated approach on sample data consisting of 1539 pairs of consecutive user queries in 351 user sessions. The prediction results of 1396 pairs agreed with the gold-standard annotations, achieving an overall accuracy of 90.7%. This demonstrates that our approach is significantly better than the previously published method. By applying this approach to a one day query log of PubMed, we found that a significant proportion of information needs involved more than one PubMed query, and that most of the consecutive queries for the same information need are lexically related. Finally, the proposed PubMed distance is shown to be an accurate and meaningful measure for determining the contextual similarity between biological terms. The integrated approach can play a critical role in handling real-world PubMed query log data as is demonstrated in our experiments.

PubMed had a higher sensitivity than Ovid-MEDLINE in the search for systematic reviews.

Science.gov (United States)

Katchamart, Wanruchada; Faulkner, Amy; Feldman, Brian; Tomlinson, George; Bombardier, Claire

2011-07-01

To compare the performance of Ovid-MEDLINE vs. PubMed for identifying randomized controlled trials of methotrexate (MTX) in patients with rheumatoid arthritis (RA). We created search strategies for Ovid-MEDLINE and PubMed for a systematic review of MTX in RA. Their performance was evaluated using sensitivity, precision, and number needed to read (NNR). Comparing searches in Ovid-MEDLINE vs. PubMed, PubMed retrieved more citations overall than Ovid-MEDLINE; however, of the 20 citations that met eligibility criteria for the review, Ovid-MEDLINE retrieved 17 and PubMed 18. The sensitivity was 85% for Ovid-MEDLINE vs. 90% for PubMed, whereas the precision and NNR were comparable (precision: 0.881% for Ovid-MEDLINE vs. 0.884% for PubMed and NNR: 114 for Ovid-MEDLINE vs. 113 for PubMed). In systematic reviews of RA, PubMed has higher sensitivity than Ovid-MEDLINE with comparable precision and NNR. This study highlights the importance of well-designed database-specific search strategies. Copyright © 2010 Elsevier Inc. All rights reserved.

An automatic method to generate domain-specific investigator networks using PubMed abstracts

Directory of Open Access Journals (Sweden)

Gwinn Marta

2007-06-01

Full Text Available Abstract Background Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. Results We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8% and from 94.2% of HuGE PubMed records (accuracy 87.0. We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit, indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70–90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. Conclusion We successfully created a

An automatic method to generate domain-specific investigator networks using PubMed abstracts

Science.gov (United States)

Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junfeng; Gwinn, Marta; Khoury, Muin J

2007-01-01

Background Collaboration among investigators has become critical to scientific research. This includes ad hoc collaboration established through personal contacts as well as formal consortia established by funding agencies. Continued growth in online resources for scientific research and communication has promoted the development of highly networked research communities. Extending these networks globally requires identifying additional investigators in a given domain, profiling their research interests, and collecting current contact information. We present a novel strategy for building investigator networks dynamically and producing detailed investigator profiles using data available in PubMed abstracts. Results We developed a novel strategy to obtain detailed investigator information by automatically parsing the affiliation string in PubMed records. We illustrated the results by using a published literature database in human genome epidemiology (HuGE Pub Lit) as a test case. Our parsing strategy extracted country information from 92.1% of the affiliation strings in a random sample of PubMed records and in 97.0% of HuGE records, with accuracies of 94.0% and 91.0%, respectively. Institution information was parsed from 91.3% of the general PubMed records (accuracy 86.8%) and from 94.2% of HuGE PubMed records (accuracy 87.0). We demonstrated the application of our approach to dynamic creation of investigator networks by creating a prototype information system containing a large database of PubMed abstracts relevant to human genome epidemiology (HuGE Pub Lit), indexed using PubMed medical subject headings converted to Unified Medical Language System concepts. Our method was able to identify 70–90% of the investigators/collaborators in three different human genetics fields; it also successfully identified 9 of 10 genetics investigators within the PREBIC network, an existing preterm birth research network. Conclusion We successfully created a web-based prototype

Validation of search filters for identifying pediatric studies in PubMed

NARCIS (Netherlands)

Leclercq, Edith; Leeflang, Mariska M. G.; van Dalen, Elvira C.; Kremer, Leontien C. M.

2013-01-01

To identify and validate PubMed search filters for retrieving studies including children and to develop a new pediatric search filter for PubMed. We developed 2 different datasets of studies to evaluate the performance of the identified pediatric search filters, expressed in terms of sensitivity,

PubMedPortable: A Framework for Supporting the Development of Text Mining Applications.

Science.gov (United States)

Döring, Kersten; Grüning, Björn A; Telukunta, Kiran K; Thomas, Philippe; Günther, Stefan

2016-01-01

Information extraction from biomedical literature is continuously growing in scope and importance. Many tools exist that perform named entity recognition, e.g. of proteins, chemical compounds, and diseases. Furthermore, several approaches deal with the extraction of relations between identified entities. The BioCreative community supports these developments with yearly open challenges, which led to a standardised XML text annotation format called BioC. PubMed provides access to the largest open biomedical literature repository, but there is no unified way of connecting its data to natural language processing tools. Therefore, an appropriate data environment is needed as a basis to combine different software solutions and to develop customised text mining applications. PubMedPortable builds a relational database and a full text index on PubMed citations. It can be applied either to the complete PubMed data set or an arbitrary subset of downloaded PubMed XML files. The software provides the infrastructure to combine stand-alone applications by exporting different data formats, e.g. BioC. The presented workflows show how to use PubMedPortable to retrieve, store, and analyse a disease-specific data set. The provided use cases are well documented in the PubMedPortable wiki. The open-source software library is small, easy to use, and scalable to the user's system requirements. It is freely available for Linux on the web at https://github.com/KerstenDoering/PubMedPortable and for other operating systems as a virtual container. The approach was tested extensively and applied successfully in several projects.

PubChem atom environments.

Science.gov (United States)

Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

2015-01-01

Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many

PubPharm - Der Fachinformationsdienst Pharmazie

Directory of Open Access Journals (Sweden)

Kristof Keßler

2016-09-01

Full Text Available Der Fachinformationsdienst (FID Pharmazie verfolgt das Ziel, die Informationsinfrastruktur und die Literaturversorgung für die pharmazeutische Hochschulforschung nachhaltig zu verbessern. Das Projekt wird seit dem 1. Januar 2015 von der Deutschen Forschungsgemeinschaft gefördert. Eine Besonderheit stellt die Kooperation zwischen der Universitätsbibliothek Braunschweig und dem Institut für Informationssysteme (IfIS der TU Braunschweig dar, wodurch aktuelle Forschung auf dem Gebiet der Informatik in die Implementierung innovativer FID-Dienste mündet. Im Zentrum des Projektes steht der nutzerzentrierte Aufbau einer erweiterbaren und personalisierbaren Informationsinfrastruktur. Das vom FID entwickelte Discovery System „PubPharm“ zur pharmaziespezifischen Recherche basiert, als Weiterentwicklung des beluga-Systems der SUB Hamburg, auf der Open Source Software VuFind. Als Datengrundlage enthält es u.a. die Medline Daten, erweitert durch Normdaten, die unter anderem die Suche nach chemischen Strukturen erlauben. Gleichzeitig werden vom Institut für Informationssysteme innovative Suchmöglichkeiten basierend auf Narrativer Intelligenz untersucht und perspektivisch in das Retrieval des Discovery Systems eingebunden. Im Rahmen von sog. FID-Lizenzen bietet der FID Pharmazie Wissenschaftlern/innen Volltextzugriff auf pharmazeutische Fachzeitschriften. Bestandteil der Lizenzen ist das Recht zur Langzeitarchivierung. Bei deren technischer Umsetzung kooperiert der FID mit der TIB Hannover. Der FID Pharmazie koppelt seine Aktivitäten eng an die pharmazeutische Fachcommunity: unter anderem begleitet ein Fachbeirat die Entwicklungen. Im Rahmen der Öffentlichkeitsarbeit werden Nutzer/innen umfassend über die Angebote informiert, u.a. in Webcasts und im PubPharm Blog. The Specialised Information Service (SIS Pharmacy aims at sustainably improving the information infrastructure and the supply of literature for academic pharmaceutical research in

Enriching PubMed Related Article Search with Sentence Level Co-citations

Science.gov (United States)

Tran, Nam; Alves, Pedro; Ma, Shuangge

2009-01-01

PubMed related article links identify closely related articles and enhance our ability to navigate the biomedical literature. They are derived by calculating the word similarity between two articles, relating articles with overlapping word content. In this paper, we propose to enrich PubMed with a new type of related article link based on citations within a single sentence (i.e. sentence level co-citations or SLCs). Using different similarity metrics, we demonstrated that articles linked by SLCs are highly related. We also showed that only half of SLCs are found among PubMed related article links. Additionally, we discuss how the citing sentence of an SLC explains the connection between two articles. PMID:20351935

Mining PubMed for Biomarker-Disease Associations to Guide Discovery

OpenAIRE

Jessen, Walter; Landschulz, Katherine; Turi, Thomas; Reams, Rachel

2012-01-01

Biomedical knowledge is growing exponentially; however, meta-knowledge around the data is often lacking. PubMed is a database comprising more than 21 million citations for biomedical literature from MEDLINE and additional life science journals dating back to the 1950s. To explore the use and frequency of biomarkers across human disease, we mined PubMed for biomarker-disease associations. We then ranked the top 100 linked diseases by relevance and mapped them to medical subject headings (MeSH)...

PubRunner: A light-weight framework for updating text mining results.

Science.gov (United States)

Anekalla, Kishore R; Courneya, J P; Fiorini, Nicolas; Lever, Jake; Muchow, Michael; Busby, Ben

2017-01-01

Biomedical text mining promises to assist biologists in quickly navigating the combined knowledge in their domain. This would allow improved understanding of the complex interactions within biological systems and faster hypothesis generation. New biomedical research articles are published daily and text mining tools are only as good as the corpus from which they work. Many text mining tools are underused because their results are static and do not reflect the constantly expanding knowledge in the field. In order for biomedical text mining to become an indispensable tool used by researchers, this problem must be addressed. To this end, we present PubRunner, a framework for regularly running text mining tools on the latest publications. PubRunner is lightweight, simple to use, and can be integrated with an existing text mining tool. The workflow involves downloading the latest abstracts from PubMed, executing a user-defined tool, pushing the resulting data to a public FTP or Zenodo dataset, and publicizing the location of these results on the public PubRunner website. We illustrate the use of this tool by re-running the commonly used word2vec tool on the latest PubMed abstracts to generate up-to-date word vector representations for the biomedical domain. This shows a proof of concept that we hope will encourage text mining developers to build tools that truly will aid biologists in exploring the latest publications.

[Use of PubMed to improve evidence-based medicine in routine urological practice].

Science.gov (United States)

Rink, M; Kluth, L A; Shariat, S F; Chun, F K; Fisch, M; Dahm, P

2013-03-01

Applying evidence-based medicine in daily clinical practice is the basis of patient-centered medicine and knowledge of accurate literature acquisition skills is necessary for informed clinical decision-making. PubMed is an easy accessible, free bibliographic database comprising over 21 million citations from the medical field, life-science journals and online books. The article summarizes the effective use of PubMed in routine urological clinical practice based on a common case scenario. This article explains the simple use of PubMed to obtain the best search results with the highest evidence. Accurate knowledge about the use of PubMed in routine clinical practice can improve evidence-based medicine and also patient treatment.

Retrieving clinical evidence: a comparison of PubMed and Google Scholar for quick clinical searches.

Science.gov (United States)

Shariff, Salimah Z; Bejaimal, Shayna Ad; Sontrop, Jessica M; Iansavichus, Arthur V; Haynes, R Brian; Weir, Matthew A; Garg, Amit X

2013-08-15

Physicians frequently search PubMed for information to guide patient care. More recently, Google Scholar has gained popularity as another freely accessible bibliographic database. To compare the performance of searches in PubMed and Google Scholar. We surveyed nephrologists (kidney specialists) and provided each with a unique clinical question derived from 100 renal therapy systematic reviews. Each physician provided the search terms they would type into a bibliographic database to locate evidence to answer the clinical question. We executed each of these searches in PubMed and Google Scholar and compared results for the first 40 records retrieved (equivalent to 2 default search pages in PubMed). We evaluated the recall (proportion of relevant articles found) and precision (ratio of relevant to nonrelevant articles) of the searches performed in PubMed and Google Scholar. Primary studies included in the systematic reviews served as the reference standard for relevant articles. We further documented whether relevant articles were available as free full-texts. Compared with PubMed, the average search in Google Scholar retrieved twice as many relevant articles (PubMed: 11%; Google Scholar: 22%; PGoogle Scholar: 8%; P=.07). Google Scholar provided significantly greater access to free full-text publications (PubMed: 5%; Google Scholar: 14%; PGoogle Scholar returns twice as many relevant articles as PubMed and provides greater access to free full-text articles.

[Systematic literature search in PubMed : A short introduction].

Science.gov (United States)

Blümle, A; Lagrèze, W A; Motschall, E

2018-03-01

In order to identify current (and relevant) evidence for a specific clinical question within the unmanageable amount of information available, solid skills in performing a systematic literature search are essential. An efficient approach is to search a biomedical database containing relevant literature citations of study reports. The best known database is MEDLINE, which is searchable for free via the PubMed interface. In this article, we explain step by step how to perform a systematic literature search via PubMed by means of an example research question in the field of ophthalmology. First, we demonstrate how to translate the clinical problem into a well-framed and searchable research question, how to identify relevant search terms and how to conduct a text word search and a search with keywords in medical subject headings (MeSH) terms. We then show how to limit the number of search results if the search yields too many irrelevant hits and how to increase the number in the case of too few citations. Finally, we summarize all essential principles that guide a literature search via PubMed.

Use of scientific social networking to improve the research strategies of PubMed readers.

Science.gov (United States)

Evdokimov, Pavel; Kudryavtsev, Alexey; Ilgisonis, Ekaterina; Ponomarenko, Elena; Lisitsa, Andrey

2016-02-18

Keeping up with journal articles on a daily basis is an important activity of scientists engaged in biomedical research. Usually, journal articles and papers in the field of biomedicine are accessed through the Medline/PubMed electronic library. In the process of navigating PubMed, researchers unknowingly generate user-specific reading profiles that can be shared within a social networking environment. This paper examines the structure of the social networking environment generated by PubMed users. A web browser plugin was developed to map [in Medical Subject Headings (MeSH) terms] the reading patterns of individual PubMed users. We developed a scientific social network based on the personal research profiles of readers of biomedical articles. A browser plugin is used to record the digital object identifier or PubMed ID of web pages. Recorded items are posted on the activity feed and automatically mapped to PubMed abstract. Within the activity feed a user can trace back previously browsed articles and insert comments. By calculating the frequency with which specific MeSH occur, the research interests of PubMed users can be visually represented with a tag cloud. Finally, research profiles can be searched for matches between network users. A social networking environment was created using MeSH terms to map articles accessed through the Medline/PubMed online library system. In-network social communication is supported by the recommendation of articles and by matching users with similar scientific interests. The system is available at http://bioknol.org/en/.

PubMed Phrases, an open set of coherent phrases for searching biomedical literature

Science.gov (United States)

Kim, Sun; Yeganova, Lana; Comeau, Donald C.; Wilbur, W. John; Lu, Zhiyong

2018-01-01

In biomedicine, key concepts are often expressed by multiple words (e.g., ‘zinc finger protein’). Previous work has shown treating a sequence of words as a meaningful unit, where applicable, is not only important for human understanding but also beneficial for automatic information seeking. Here we present a collection of PubMed® Phrases that are beneficial for information retrieval and human comprehension. We define these phrases as coherent chunks that are logically connected. To collect the phrase set, we apply the hypergeometric test to detect segments of consecutive terms that are likely to appear together in PubMed. These text segments are then filtered using the BM25 ranking function to ensure that they are beneficial from an information retrieval perspective. Thus, we obtain a set of 705,915 PubMed Phrases. We evaluate the quality of the set by investigating PubMed user click data and manually annotating a sample of 500 randomly selected noun phrases. We also analyze and discuss the usage of these PubMed Phrases in literature search. PMID:29893755

Tracking Australian health and medical research expenditure with a PubMed bibliometric method.

Science.gov (United States)

Mendis, Kumara; Bailey, Jannine; McLean, Rick

2015-06-01

To assess Australian health and medical research (HMR) investment returns by measuring the trends in HMR expenditure and PubMed publications by Australian authors. Bibliometric analysis collating Australian HMR expenditure reported by the Australian Institute of Health and Welfare and Australian HMR publications indexed in PubMed. Similar methods were applied to data from the United Kingdom and New Zealand. From financial year 2000/01 through 2011/12, HMR investment increased by 232% from $1.49 to $4.94 billion (current prices adjusted for inflation), while PubMed publications increased by 123% from 10,696 to 23,818. The average HMR investment required for a single PubMed publication rose by 49% from $139,304 in 2000/01 to $207,364 in 2011/12. Quality analyses showed an increase in systematic reviews, cohort studies and clinical trials, and a decrease in publications in PubMed's core clinical journal collection. Comparisons with New Zealand and the United Kingdom showed that Australia has had the greatest overall percentage increase in gross publication numbers and publications per capita. Our analyses confirm that increased HMR expenditure is associated with an increase in HMR publications in PubMed. Tracking HMR investment outcomes using this method could be useful for future policy and funding decisions at a federal and specific institution level. © 2015 Public Health Association of Australia.

Semi-analytical study of the tokamak pedestal density profile in a single-null diverted plasma with puffing-recycling gas sources

Science.gov (United States)

Shi, Bingren

2010-10-01

The tokamak pedestal density structure is generally studied using a diffusion-dominant model. Recent investigations (Stacey and Groebner 2009 Phys. Plasmas 16 102504) from first principle based physics have shown a plausible existence of large inward convection in the pedestal region. The diffusion-convection equation with rapidly varying convection and diffusion coefficients in the near edge region and model puffing-recycling neutral particles is studied in this paper. A peculiar property of its solution for the existence of the large convection case is that the pedestal width of the density profile, qualitatively different from the diffusion-dominant case, depends mainly on the width of the inward convection and only weakly on the neutral penetration length and its injection position.

Semi-analytical study of the tokamak pedestal density profile in a single-null diverted plasma with puffing-recycling gas sources

Energy Technology Data Exchange (ETDEWEB)

Shi Bingren, E-mail: shibr@swip.ac.c [Southwestern Institute of Physics, PO Box 432, Chengdu, Sichuan 610041 (China)

2010-10-15

The tokamak pedestal density structure is generally studied using a diffusion-dominant model. Recent investigations (Stacey and Groebner 2009 Phys. Plasmas 16 102504) from first principle based physics have shown a plausible existence of large inward convection in the pedestal region. The diffusion-convection equation with rapidly varying convection and diffusion coefficients in the near edge region and model puffing-recycling neutral particles is studied in this paper. A peculiar property of its solution for the existence of the large convection case is that the pedestal width of the density profile, qualitatively different from the diffusion-dominant case, depends mainly on the width of the inward convection and only weakly on the neutral penetration length and its injection position.

Quantity and quality assessment of randomized controlled trials on orthodontic practice in PubMed.

Science.gov (United States)

Shimada, Tatsuo; Takayama, Hisako; Nakamura, Yoshiki

2010-07-01

To find current high-quality evidence for orthodontic practice within a reasonable time, we tested the performance of a PubMed search. PubMed was searched using publication type randomized controlled trial and medical subject heading term "orthodontics" for articles published between 2003 and 2007. The PubMed search results were compared with those from a hand search of four orthodontic journals to determine the sensitivity of PubMed search. We evaluated the precision of the PubMed search result and assessed the quality of individual randomized controlled trials using the Jadad scale. Sensitivity and precision were 97.46% and 58.12%, respectively. In PubMed, of the 277 articles retrieved, 161 (58.12%) were randomized controlled trials on orthodontic practice, and 115 of the 161 articles (71.42%) were published in four orthodontic journals: American Journal of Orthodontics and Dentofacial Orthopedics, The Angle Orthodontist, the European Journal of Orthodontics, and the Journal of Orthodontics. Assessment by the Jadad scale revealed 60 high-quality randomized controlled trials on orthodontic practice, of which 45 (75%) were published in these four journals. PubMed is a highly desirable search engine for evidence-based orthodontic practice. To stay current and get high-quality evidence, it is reasonable to look through four orthodontic journals: American Journal of Orthodontics and Dentofacial Orthopedics, The Angle Orthodontist, the European Journal of Orthodontics, and the Journal of Orthodontics.

A search engine to access PubMed monolingual subsets: proof of concept and evaluation in French.

Science.gov (United States)

Griffon, Nicolas; Schuers, Matthieu; Soualmia, Lina Fatima; Grosjean, Julien; Kerdelhué, Gaétan; Kergourlay, Ivan; Dahamna, Badisse; Darmoni, Stéfan Jacques

2014-12-01

PubMed contains numerous articles in languages other than English. However, existing solutions to access these articles in the language in which they were written remain unconvincing. The aim of this study was to propose a practical search engine, called Multilingual PubMed, which will permit access to a PubMed subset in 1 language and to evaluate the precision and coverage for the French version (Multilingual PubMed-French). To create this tool, translations of MeSH were enriched (eg, adding synonyms and translations in French) and integrated into a terminology portal. PubMed subsets in several European languages were also added to our database using a dedicated parser. The response time for the generic semantic search engine was evaluated for simple queries. BabelMeSH, Multilingual PubMed-French, and 3 different PubMed strategies were compared by searching for literature in French. Precision and coverage were measured for 20 randomly selected queries. The results were evaluated as relevant to title and abstract, the evaluator being blind to search strategy. More than 650,000 PubMed citations in French were integrated into the Multilingual PubMed-French information system. The response times were all below the threshold defined for usability (2 seconds). Two search strategies (Multilingual PubMed-French and 1 PubMed strategy) showed high precision (0.93 and 0.97, respectively), but coverage was 4 times higher for Multilingual PubMed-French. It is now possible to freely access biomedical literature using a practical search tool in French. This tool will be of particular interest for health professionals and other end users who do not read or query sufficiently in English. The information system is theoretically well suited to expand the approach to other European languages, such as German, Spanish, Norwegian, and Portuguese.

Searching PubMed for molecular epidemiology studies: the case of chromosome aberrations

DEFF Research Database (Denmark)

Ugolini, Donatella; Neri, Monica; Knudsen, Lisbeth E

2006-01-01

to environmental pollutants. The search, done on the PubMed/MedLine database, was based on a strategy combining descriptors listed in the PubMed Medical Subject Headings (MeSH) Thesaurus and other available tools (free text or phrase search tools). 178 articles were retrieved by searching the period from January 1...

High fusion performance at high T i/T e in JET-ILW baseline plasmas with high NBI heating power and low gas puffing

Science.gov (United States)

Kim, Hyun-Tae; Sips, A. C. C.; Romanelli, M.; Challis, C. D.; Rimini, F.; Garzotti, L.; Lerche, E.; Buchanan, J.; Yuan, X.; Kaye, S.; contributors, JET

2018-03-01

This paper presents the transport analysis of high density baseline discharges in the 2016 experimental campaign of the Joint European Torus with the ITER-Like Wall (JET-ILW), where a significant increase in the deuterium-deuterium (D-D) fusion neutron rate (~2.8  ×  1016 s-1) was achieved with stable high neutral beam injection (NBI) powers of up to 28 MW and low gas puffing. Increase in T i exceeding T e were produced for the first time in baseline discharges despite the high electron density; this enabled a significant increase in the thermal fusion reaction rate. As a result, the new achieved record in fusion performance was much higher than the previous record in the same heating power baseline discharges, where T i  =  T e. In addition to the decreases in collisionality and the increases in ion heating fraction in the discharges with high NBI power, T i  >  T e can also be attributed to positive feedback between the high T i/T e ratio and stabilisation of the turbulent heat flux resulting from the ion temperature gradient driven mode. The high T i/T e ratio was correlated with high rotation frequency. Among the discharges with identical beam heating power, higher rotation frequencies were observed when particle fuelling was provided by low gas puffing and pellet injection. This reveals that particle fuelling played a key role for achieving high T i/T e, and the improved fusion performance.

mirPub: a database for searching microRNA publications.

Science.gov (United States)

Vergoulis, Thanasis; Kanellos, Ilias; Kostoulas, Nikos; Georgakilas, Georgios; Sellis, Timos; Hatzigeorgiou, Artemis; Dalamagas, Theodore

2015-05-01

Identifying, amongst millions of publications available in MEDLINE, those that are relevant to specific microRNAs (miRNAs) of interest based on keyword search faces major obstacles. References to miRNA names in the literature often deviate from standard nomenclature for various reasons, since even the official nomenclature evolves. For instance, a single miRNA name may identify two completely different molecules or two different names may refer to the same molecule. mirPub is a database with a powerful and intuitive interface, which facilitates searching for miRNA literature, addressing the aforementioned issues. To provide effective search services, mirPub applies text mining techniques on MEDLINE, integrates data from several curated databases and exploits data from its user community following a crowdsourcing approach. Other key features include an interactive visualization service that illustrates intuitively the evolution of miRNA data, tag clouds summarizing the relevance of publications to particular diseases, cell types or tissues and access to TarBase 6.0 data to oversee genes related to miRNA publications. mirPub is freely available at http://www.microrna.gr/mirpub/. vergoulis@imis.athena-innovation.gr or dalamag@imis.athena-innovation.gr Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Validation of search filters for identifying pediatric studies in PubMed.

Science.gov (United States)

Leclercq, Edith; Leeflang, Mariska M G; van Dalen, Elvira C; Kremer, Leontien C M

2013-03-01

To identify and validate PubMed search filters for retrieving studies including children and to develop a new pediatric search filter for PubMed. We developed 2 different datasets of studies to evaluate the performance of the identified pediatric search filters, expressed in terms of sensitivity, precision, specificity, accuracy, and number needed to read (NNR). An optimal search filter will have a high sensitivity and high precision with a low NNR. In addition to the PubMed Limits: All Child: 0-18 years filter (in May 2012 renamed to PubMed Filter Child: 0-18 years), 6 search filters for identifying studies including children were identified: 3 developed by Kastner et al, 1 developed by BestBets, one by the Child Health Field, and 1 by the Cochrane Childhood Cancer Group. Three search filters (Cochrane Childhood Cancer Group, Child Health Field, and BestBets) had the highest sensitivity (99.3%, 99.5%, and 99.3%, respectively) but a lower precision (64.5%, 68.4%, and 66.6% respectively) compared with the other search filters. Two Kastner search filters had a high precision (93.0% and 93.7%, respectively) but a low sensitivity (58.5% and 44.8%, respectively). They failed to identify many pediatric studies in our datasets. The search terms responsible for false-positive results in the reference dataset were determined. With these data, we developed a new search filter for identifying studies with children in PubMed with an optimal sensitivity (99.5%) and precision (69.0%). Search filters to identify studies including children either have a low sensitivity or a low precision with a high NNR. A new pediatric search filter with a high sensitivity and a low NNR has been developed. Copyright © 2013 Mosby, Inc. All rights reserved.

Maximizing the number of satisfied subscribers in Pub/Sub systems under capacity constraints

NARCIS (Netherlands)

Setty, V.J.; Kreitz, G; Urdaneta, G; Vitenberg, R; van Steen, M.R.

2014-01-01

Publish/subscribe (pub/sub) is a popular communication paradigm in the design of large-scale distributed systems. A provider of a pub/sub service (whether centralized, peer-assisted, or based on a federated organization of cooperatively managed servers) commonly faces a fundamental challenge: given

Information architecture: study and analysis of data Public Medical base (PubMed

Directory of Open Access Journals (Sweden)

Odete Máyra Mesquita Sales

2016-07-01

Full Text Available Objective. Based on principles proposed by Rosenfeld and Morville (2006, the present study examined the PubMed database interface, since a well-structured information architecture contributes to good usability in any digital environment. Method. The research development occurred through the use of literature techniques and empirical study on the analysis of information architecture based on organization, navigation, recommended labeling and search for Rosenfeld and Morville (2006 for the sake of usability base PubMed. For better understanding and description of these principles, we used the technique of content analysis. Results. The results showed that the database interface meets the criteria established by the elements of Information Architecture, such as organization based on hypertext structure, horizontal menu and local content divided into categories, identifying active links, global navigation , breadcrumb, textual labeling and iconographic and highlight the search engine. Conclusions. This research showed that the PubMed database interface is well structured, friendly and objective, with numerous possibilities of search and information retrieval. However, there is a need to adopt accessibility standards on this website, so that it reaches more efficiently its purpose of facilitating access to information organized and stored in the PubMed database.

Puffing topography and nicotine intake of electronic cigarette users.

Directory of Open Access Journals (Sweden)

Rachel Z Behar

Full Text Available Prior electronic cigarette (EC topography data are based on two video analyses with limited parameters. Alternate methods for measuring topography are needed to understand EC use and nicotine intake.This study evaluated EC topography with a CReSS Pocket device and quantified nicotine intake.Validation tests on pressure drop, flow rate, and volume confirmed reliable performance of the CReSS Pocket device. Twenty participants used Blu Cigs and V2 Cigs for 10 minute intervals with a 10-15 minute break between brands. Brand order was reversed and repeated within 7 days Data were analyzed to determine puff duration, puff count, volume, flow rate, peak flow, and inter-puff interval. Nicotine intake was estimated from cartomizer fluid consumption and topography data.Nine patterns of EC use were identified. The average puff count and inter-puff interval were 32 puffs and 17.9 seconds. All participants, except one, took more than 20 puffs/10 minutes. The averages for puff duration (2.65 seconds/puff, volume/puff (51 ml/puff, total puff volume (1,579 ml, EC fluid consumption (79.6 mg, flow rate (20 ml/s, and peak flow rate (27 ml/s were determined for 10-minute sessions. All parameters except total puff count were significantly different for Blu versus V2 EC. Total volume for Blu versus V2 was four-times higher than for conventional cigarettes. Average nicotine intake for Blu and V2 across both sessions was 1.2 ± 0.5 mg and 1.4 ± 0.7 mg, respectively, which is similar to conventional smokers.EC puffing topography was variable among participants in the study, but often similar within an individual between brands or days. Puff duration, inter-puff interval, and puff volume varied from conventional cigarette standards. Data on total puff volume and nicotine intake are consistent with compensatory usage of EC. These data can contribute to the development of a standard protocol for laboratory testing of EC products.

Puffing Topography and Nicotine Intake of Electronic Cigarette Users

Science.gov (United States)

Behar, Rachel Z.; Hua, My; Talbot, Prue

2015-01-01

Background Prior electronic cigarette (EC) topography data are based on two video analyses with limited parameters. Alternate methods for measuring topography are needed to understand EC use and nicotine intake. Objectives This study evaluated EC topography with a CReSS Pocket device and quantified nicotine intake. Methods Validation tests on pressure drop, flow rate, and volume confirmed reliable performance of the CReSS Pocket device. Twenty participants used Blu Cigs and V2 Cigs for 10 minute intervals with a 10–15 minute break between brands. Brand order was reversed and repeated within 7 days Data were analyzed to determine puff duration, puff count, volume, flow rate, peak flow, and inter-puff interval. Nicotine intake was estimated from cartomizer fluid consumption and topography data. Results Nine patterns of EC use were identified. The average puff count and inter-puff interval were 32 puffs and 17.9 seconds. All participants, except one, took more than 20 puffs/10 minutes. The averages for puff duration (2.65 seconds/puff), volume/puff (51ml/puff), total puff volume (1,579 ml), EC fluid consumption (79.6 mg), flow rate (20 ml/s), and peak flow rate (27 ml/s) were determined for 10-minute sessions. All parameters except total puff count were significantly different for Blu versus V2 EC. Total volume for Blu versus V2 was four-times higher than for conventional cigarettes. Average nicotine intake for Blu and V2 across both sessions was 1.2 ± 0.5 mg and 1.4 ± 0.7 mg, respectively, which is similar to conventional smokers. Conclusions EC puffing topography was variable among participants in the study, but often similar within an individual between brands or days. Puff duration, inter-puff interval, and puff volume varied from conventional cigarette standards. Data on total puff volume and nicotine intake are consistent with compensatory usage of EC. These data can contribute to the development of a standard protocol for laboratory testing of EC products

MET network in PubMed: a text-mined network visualization and curation system.

Science.gov (United States)

Dai, Hong-Jie; Su, Chu-Hsien; Lai, Po-Ting; Huang, Ming-Siang; Jonnagaddala, Jitendra; Rose Jue, Toni; Rao, Shruti; Chou, Hui-Jou; Milacic, Marija; Singh, Onkar; Syed-Abdul, Shabbir; Hsu, Wen-Lian

2016-01-01

Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis requires investigations of the signaling pathways. To this end, we developed a METastasis (MET) network visualization and curation tool to assist metastasis researchers retrieve network information of interest while browsing through the large volume of studies in PubMed. MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in a metastasis network. To facilitate the curation process, MET is developed as a browser extension that allows curators to review and edit concepts and relations related to metastasis directly in PubMed. PubMed users can also view the metastatic networks integrated from the large collection of research papers directly through MET. For the BioCreative 2015 interactive track (IAT), a curation task was proposed to curate metastatic networks among PubMed abstracts. Six curators participated in the proposed task and a post-IAT task, curating 963 unique metastatic relations from 174 PubMed abstracts using MET.Database URL: http://btm.tmu.edu.tw/metastasisway. © The Author(s) 2016. Published by Oxford University Press.

[Limiting a Medline/PubMed query to the "best" articles using the JCR relative impact factor].

Science.gov (United States)

Avillach, P; Kerdelhué, G; Devos, P; Maisonneuve, H; Darmoni, S J

2014-12-01

Medline/PubMed is the most frequently used medical bibliographic research database. The aim of this study was to propose a new generic method to limit any Medline/PubMed query based on the relative impact factor and the A & B categories of the SIGAPS score. The entire PubMed corpus was used for the feasibility study, then ten frequent diseases in terms of PubMed indexing and the citations of four Nobel prize winners. The relative impact factor (RIF) was calculated by medical specialty defined in Journal Citation Reports. The two queries, which included all the journals in category A (or A OR B), were added to any Medline/PubMed query as a central point of the feasibility study. Limitation using the SIGAPS category A was larger than the when using the Core Clinical Journals (CCJ): 15.65% of PubMed corpus vs 8.64% for CCJ. The response time of this limit applied to the entire PubMed corpus was less than two seconds. For five diseases out of ten, limiting the citations with the RIF was more effective than with the CCJ. For the four Nobel prize winners, limiting the citations with the RIF was more effective than the CCJ. The feasibility study to apply a new filter based on the relative impact factor on any Medline/PubMed query was positive. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Multi-lingual search engine to access PubMed monolingual subsets: a feasibility study.

Science.gov (United States)

Darmoni, Stéfan J; Soualmia, Lina F; Griffon, Nicolas; Grosjean, Julien; Kerdelhué, Gaétan; Kergourlay, Ivan; Dahamna, Badisse

2013-01-01

PubMed contains many articles in languages other than English but it is difficult to find them using the English version of the Medical Subject Headings (MeSH) Thesaurus. The aim of this work is to propose a tool allowing access to a PubMed subset in one language, and to evaluate its performance. Translations of MeSH were enriched and gathered in the information system. PubMed subsets in main European languages were also added in our database, using a dedicated parser. The CISMeF generic semantic search engine was evaluated on the response time for simple queries. MeSH descriptors are currently available in 11 languages in the information system. All the 654,000 PubMed citations in French were integrated into CISMeF database. None of the response times exceed the threshold defined for usability (2 seconds). It is now possible to freely access biomedical literature in French using a tool in French; health professionals and lay people with a low English language may find it useful. It will be expended to several European languages: German, Spanish, Norwegian and Portuguese.

Science outreach on tap: insights and practices from three years ofDartmouth Science Pubs.

Science.gov (United States)

Hawley, R. L.; Serrell, N.; Tobery, C. E.; Riordan, S. A.

2015-12-01

The "Cafe Scientifique" (or "Science Cafe") has existed around theworld for decades. In an informal setting, one or more scientistsengage with a lay audience, typically over refreshments of some kind.These Science Cafes have taken many formats and taken place in manyvenues. Some feature a single presenter, some multiple; somecongregate in large venues, some small; some restrict the use of thepowerpoint slides, some do not.Our team at Dartmouth has hosted "Science Pubs" for three years. OurScience Pub takes place in a local pub, from 5-7pm on a weekday once amonth. We choose a theme for a pub and select three presenters. Thecomposition of our panel varies, but we generally have at least onefaculty member and one "less-academic" member, such as a town plannerwhen discussing hurricanes or an organic farmer when discussingpesticides. Often we include a graduate student in the panel. ThePub takes place in three "acts": 1) the presenters each give a briefintroduction to thier take on the topic, usually 10-15 minutes,extemporaneous with no slides, 2) the "wedding reception" phase, whichis a break during which the presenters circulate to the pub tables,answering questions and chatting with the attendees informally, and 3)reconvening for a more 'formal' question and answer period duringwhich the presenters answer questions from the audience.Here, we outline the format that makes up a Dartmouth Science Pub andshare insignts and lessons learned. Among many findings, we havelearned: 1) a group of three presenters makes for a lively discussion,as often presenters 'riff' off one another's points, 2) it is cruicalto have a facilitator, to 'run the show', freeing the sciencepresenters to concentrate on thier audience engagement, and 3) a shortmeeting ahead of time with the presenters is simple and very importantin creating a smooth event, and serves to help the presenters 'codeswitch' and adapt language, in lieu of a formal 'training'.

Using data sources beyond PubMed has a modest impact on the results of systematic reviews of therapeutic interventions.

Science.gov (United States)

Halladay, Christopher W; Trikalinos, Thomas A; Schmid, Ian T; Schmid, Christopher H; Dahabreh, Issa J

2015-09-01

Searching multiple sources when conducting systematic reviews is considered good practice. We aimed to investigate the impact of using sources beyond PubMed in systematic reviews of therapeutic interventions. We randomly selected 50 Cochrane reviews that searched the PubMed (or MEDLINE) and EMBASE databases and included a meta-analysis of ≥10 studies. We checked whether each eligible record in each review (n = 2,700) was retrievable in PubMed and EMBASE. For the first-listed meta-analysis of ≥10 studies in each review, we examined whether excluding studies not found in PubMed affected results. A median of one record per review was indexed in EMBASE but not in PubMed; a median of four records per review was not indexed in PubMed or EMBASE. Meta-analyses included a median of 13.5 studies; a median of zero studies per meta-analysis was indexed in EMBASE but not in PubMed; a median of one study per meta-analysis was not indexed in PubMed or EMBASE. Meta-analysis using only PubMed-indexed vs. all available studies led to a different conclusion in a single case (on the basis of conventional criteria for statistical significance). In meta-regression analyses, effects in PubMed- vs. non-PubMed-indexed studies were statistically significantly different in a single data set. For systematic reviews of the effects of therapeutic interventions, gains from searching sources beyond PubMed, and from searching EMBASE in particular are modest. Copyright © 2015 Elsevier Inc. All rights reserved.

Strategie franchisingového řetězce na příkladu The PUB

OpenAIRE

Šampalík, Martin

2011-01-01

This thesis is focused on an interesting and dynamic form of business, called franchising. For the purpose of explanation of this form of business purely Czech company The PUB Franchising s.r.o. has been selected. This company is the owner of the gastronomic franching concept The PUB Pilsner Unique Bar. This thesis not only illuminates the franchising business as such, but analyzes and proposes a strategy to facilitate the future development of the concept The PUB in the Czech Republic but al...

Impact of PubMed search filters on the retrieval of evidence by physicians.

Science.gov (United States)

Shariff, Salimah Z; Sontrop, Jessica M; Haynes, R Brian; Iansavichus, Arthur V; McKibbon, K Ann; Wilczynski, Nancy L; Weir, Matthew A; Speechley, Mark R; Thind, Amardeep; Garg, Amit X

2012-02-21

Physicians face challenges when searching PubMed for research evidence, and they may miss relevant articles while retrieving too many nonrelevant articles. We investigated whether the use of search filters in PubMed improves searching by physicians. We asked a random sample of Canadian nephrologists to answer unique clinical questions derived from 100 systematic reviews of renal therapy. Physicians provided the search terms that they would type into PubMed to locate articles to answer these questions. We entered the physician-provided search terms into PubMed and applied two types of search filters alone or in combination: a methods-based filter designed to identify high-quality studies about treatment (clinical queries "therapy") and a topic-based filter designed to identify studies with renal content. We evaluated the comprehensiveness (proportion of relevant articles found) and efficiency (ratio of relevant to nonrelevant articles) of the filtered and nonfiltered searches. Primary studies included in the systematic reviews served as the reference standard for relevant articles. The average physician-provided search terms retrieved 46% of the relevant articles, while 6% of the retrieved articles were relevant (corrected) (the ratio of relevant to nonrelevant articles was 1:16). The use of both filters together produced a marked improvement in efficiency, resulting in a ratio of relevant to nonrelevant articles of 1:5 (16 percentage point improvement; 99% confidence interval 9% to 22%; p PubMed search filters improves the efficiency of physician searches. Improved search performance may enhance the transfer of research into practice and improve patient care.

Leaving the Lecture Behind: Putting PubMed Instruction into the Hands of the Students.

Science.gov (United States)

Turner, Rose L; M Ketchum, Andrea; Ratajeski, Melissa A; Wessel, Charles B

2017-01-01

This column describes the development of a one-shot PubMed instruction class for medical students at a health sciences library. Background information on the objective is presented and discussed in the context of educational practice literature. The new course design centers on a guided group method of instruction in order to integrate more active learning. Surveyed students reported that the method was an effective way to learn how to search PubMed and that they preferred it to a traditional lecture. Pros and cons of the method are offered for other health sciences libraries interested in presenting PubMed instruction in a similar manner.

Medical literature searches: a comparison of PubMed and Google Scholar.

Science.gov (United States)

Nourbakhsh, Eva; Nugent, Rebecca; Wang, Helen; Cevik, Cihan; Nugent, Kenneth

2012-09-01

Medical literature searches provide critical information for clinicians. However, the best strategy for identifying relevant high-quality literature is unknown. We compared search results using PubMed and Google Scholar on four clinical questions and analysed these results with respect to article relevance and quality. Abstracts from the first 20 citations for each search were classified into three relevance categories. We used the weighted kappa statistic to analyse reviewer agreement and nonparametric rank tests to compare the number of citations for each article and the corresponding journals' impact factors. Reviewers ranked 67.6% of PubMed articles and 80% of Google Scholar articles as at least possibly relevant (P = 0.116) with high agreement (all kappa P-values PubMed searches and Google Scholar searches often identify different articles. In this study, Google Scholar articles were more likely to be classified as relevant, had higher numbers of citations and were published in higher impact factor journals. The identification of frequently cited articles using Google Scholar for searches probably has value for initial literature searches. © 2012 The authors. Health Information and Libraries Journal © 2012 Health Libraries Group.

Dialysis search filters for PubMed, Ovid MEDLINE, and Embase databases.

Science.gov (United States)

Iansavichus, Arthur V; Haynes, R Brian; Lee, Christopher W C; Wilczynski, Nancy L; McKibbon, Ann; Shariff, Salimah Z; Blake, Peter G; Lindsay, Robert M; Garg, Amit X

2012-10-01

Physicians frequently search bibliographic databases, such as MEDLINE via PubMed, for best evidence for patient care. The objective of this study was to develop and test search filters to help physicians efficiently retrieve literature related to dialysis (hemodialysis or peritoneal dialysis) from all other articles indexed in PubMed, Ovid MEDLINE, and Embase. A diagnostic test assessment framework was used to develop and test robust dialysis filters. The reference standard was a manual review of the full texts of 22,992 articles from 39 journals to determine whether each article contained dialysis information. Next, 1,623,728 unique search filters were developed, and their ability to retrieve relevant articles was evaluated. The high-performance dialysis filters consisted of up to 65 search terms in combination. These terms included the words "dialy" (truncated), "uremic," "catheters," and "renal transplant wait list." These filters reached peak sensitivities of 98.6% and specificities of 98.5%. The filters' performance remained robust in an independent validation subset of articles. These empirically derived and validated high-performance search filters should enable physicians to effectively retrieve dialysis information from PubMed, Ovid MEDLINE, and Embase.

TwiMed: Twitter and PubMed Comparable Corpus of Drugs, Diseases, Symptoms, and Their Relations.

Science.gov (United States)

Alvaro, Nestor; Miyao, Yusuke; Collier, Nigel

2017-05-03

Work on pharmacovigilance systems using texts from PubMed and Twitter typically target at different elements and use different annotation guidelines resulting in a scenario where there is no comparable set of documents from both Twitter and PubMed annotated in the same manner. This study aimed to provide a comparable corpus of texts from PubMed and Twitter that can be used to study drug reports from these two sources of information, allowing researchers in the area of pharmacovigilance using natural language processing (NLP) to perform experiments to better understand the similarities and differences between drug reports in Twitter and PubMed. We produced a corpus comprising 1000 tweets and 1000 PubMed sentences selected using the same strategy and annotated at entity level by the same experts (pharmacists) using the same set of guidelines. The resulting corpus, annotated by two pharmacists, comprises semantically correct annotations for a set of drugs, diseases, and symptoms. This corpus contains the annotations for 3144 entities, 2749 relations, and 5003 attributes. We present a corpus that is unique in its characteristics as this is the first corpus for pharmacovigilance curated from Twitter messages and PubMed sentences using the same data selection and annotation strategies. We believe this corpus will be of particular interest for researchers willing to compare results from pharmacovigilance systems (eg, classifiers and named entity recognition systems) when using data from Twitter and from PubMed. We hope that given the comprehensive set of drug names and the annotated entities and relations, this corpus becomes a standard resource to compare results from different pharmacovigilance studies in the area of NLP. ©Nestor Alvaro, Yusuke Miyao, Nigel Collier. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 03.05.2017.

Supplementary searches of PubMed to improve currency of MEDLINE and MEDLINE In-Process searches via Ovid.

Science.gov (United States)

Duffy, Steven; de Kock, Shelley; Misso, Kate; Noake, Caro; Ross, Janine; Stirk, Lisa

2016-10-01

The research investigated whether conducting a supplementary search of PubMed in addition to the main MEDLINE (Ovid) search for a systematic review is worthwhile and to ascertain whether this PubMed search can be conducted quickly and if it retrieves unique, recently published, and ahead-of-print studies that are subsequently considered for inclusion in the final systematic review. Searches of PubMed were conducted after MEDLINE (Ovid) and MEDLINE In-Process (Ovid) searches had been completed for seven recent reviews. The searches were limited to records not in MEDLINE or MEDLINE In-Process (Ovid). Additional unique records were identified for all of the investigated reviews. Search strategies were adapted quickly to run in PubMed, and reviewer screening of the results was not time consuming. For each of the investigated reviews, studies were ordered for full screening; in six cases, studies retrieved from the supplementary PubMed searches were included in the final systematic review. Supplementary searching of PubMed for studies unavailable elsewhere is worthwhile and improves the currency of the systematic reviews.

Risk factors for bladder cancer: challenges of conducting a literature search using PubMed.

Science.gov (United States)

Joshi, Ashish; Preslan, Elicia

2011-04-01

The objective of this study was to assess the risk factors for bladder cancer using PubMed articles from January 2000 to December 2009. The study also aimed to describe the challenges encountered in the methodology of a literature search for bladder cancer risk factors using PubMed. Twenty-six categories of risk factors for bladder cancer were identified using the National Cancer Institute Web site and the Medical Subject Headings (MeSH) Web site. A total of 1,338 PubMed searches were run using the term "urinary bladder cancer" and a risk factor term (e.g., "cigarette smoking") and were screened to identify 260 articles for final analysis. The search strategy had an overall precision of 3.42 percent, relative recall of 12.64 percent, and an F-measure of 5.39 percent. Although search terms derived from MeSH had the highest overall precision and recall, the differences did not reach significance, which indicates that for generalized, free-text searches of the PubMed database, the searchers' own terms are generally as effective as MeSH terms.

What time-lag for a retraction search on PubMed?

Science.gov (United States)

Decullier, Evelyne; Huot, Laure; Maisonneuve, Hervé

2014-06-25

To investigate fraud and errors, scientists have studied cohorts of retraction notices. These researches have been performed using a PubMed search on publication type "retraction of publication" which retrieves the notices of the retractions. We assessed the stability of the indexation of retraction notices over a 15-month period and what was the time-lag to get stability. A search on notices of retraction issued in 2008 was repeated every 3 months during 15 months from February 2011. The first search resulted in 237 notices of retraction. Throughout the study period, 14 discrepancies with the initial search were observed (6%). We found that the number of retraction notices became stable 35 months after the retraction. The time-lag observed in this study has to be taken into account when performing a PubMed search.

PubMed Central Canada: Beyond an Open Access Repository?

Science.gov (United States)

Nariani, Rajiv

2013-01-01

PubMed Central Canada (PMC Canada) represents a partnership between the Canadian Institutes of Health Research (CIHR), the National Research Council's Canada Institute for Scientific and Technical Information (NRC-CISTI), and the National Library of Medicine of the US. The present study was done to gauge faculty awareness about the CIHR Policy on…

PubMed vs. HighWire Press: a head-to-head comparison of two medical literature search engines.

Science.gov (United States)

Vanhecke, Thomas E; Barnes, Michael A; Zimmerman, Janet; Shoichet, Sandor

2007-09-01

PubMed and HighWire Press are both useful medical literature search engines available for free to anyone on the internet. We measured retrieval accuracy, number of results generated, retrieval speed, features and search tools on HighWire Press and PubMed using the quick search features of each. We found that using HighWire Press resulted in a higher likelihood of retrieving the desired article and higher number of search results than the same search on PubMed. PubMed was faster than HighWire Press in delivering search results regardless of search settings. There are considerable differences in search features between these two search engines.

Data mining a small molecule drug screening representative subset from NIH PubChem.

Science.gov (United States)

Xie, Xiang-Qun; Chen, Jian-Zhong

2008-03-01

PubChem is a scientific showcase of the NIH Roadmap Initiatives. It is a compound repository created to facilitate information exchange and data sharing among the NIH Roadmap-funded Molecular Library Screening Center Network (MLSCN) and the scientific community. However, PubChem has more than 10 million records of compound information. It will be challenging to conduct a drug screening of the whole database of millions of compounds. Thus, the purpose of the present study was to develop a data mining cheminformatics approach in order to construct a representative and structure-diverse sublibrary from the large PubChem database. In this study, a new chemical diverse representative subset, rePubChem, was selected by whole-molecule chemistry-space matrix calculation using the cell-based partition algorithm. The representative subset was generated and was then subjected to evaluations by compound property analyses based on 1D and 2D molecular descriptors. The new subset was also examined and assessed for self-similarity analysis based on 2D molecular fingerprints in comparing with the source compound library. The new subset has a much smaller library size (540K compounds) with minimum similarity and redundancy without loss of the structural diversity and basic molecular properties of its parent library (5.3 million compounds). The new representative subset library generated could be a valuable structure-diverse compound resource for in silico virtual screening and in vitro HTS drug screening. In addition, the established subset generation method of using the combined cell-based chemistry-space partition metrics with pairwised 2D fingerprint-based similarity search approaches will also be important to a broad scientific community interested in acquiring structurally diverse compounds for efficient drug screening, building representative virtual combinatorial chemistry libraries for syntheses, and data mining large compound databases like the PubChem library in general.

PubMed-based quantitative analysis of biomedical publications in the SAARC countries: 1985-2009.

Science.gov (United States)

Azim Majumder, Md Anwarul; Shaban, Sami F; Rahman, Sayeeda; Rahman, Nuzhat; Ahmed, Moslehuddin; Bin Abdulrahman, Khalid A; Islam, Ziauddin

2012-09-01

To conduct a geographical analysis of biomedical publications from the South Asian Association for Regional Cooperation (SAARC) countries over the past 25 years (1985-2009) using the PubMed database. A qualitative study. Web-based search during September 2010. A data extraction program, developed by one of the authors (SFS), was used to extract the raw publication counts from the downloaded PubMed data. A search of PubMed was performed for all journals indexed by selecting the advanced search option and entering the country name in the 'affiliation' field. The publications were normalized by total population, adult illiteracy rate, gross domestic product (GDP), secondary school enrollment ratio and Internet usage rate. The number of PubMed-listed papers published by the SAARC countries over the last 25 years totalled 141,783, which is 1.1% of the total papers indexed by PubMed in the same period. India alone produced 90.5% of total publications generated by SAARC countries. The average number of papers published per year from 1985 to 2009 was 5671 and number of publication increased approximately 242-fold. Normalizing by the population (per million) and GDP (per billion), India (133, 27.6%) and Nepal (323, 37.3%) had the highest publications respectively. There was a marked imbalance among the SAARC countries in terms of biomedical research and publication. Because of huge population and the high disease burden, biomedical research and publication output should receive special attention to formulate health policies, re-orient medical education curricula, and alleviate diseases and poverty.

Discrepancies among Scopus, Web of Science, and PubMed coverage of funding information in medical journal articles.

Science.gov (United States)

Kokol, Peter; Vošner, Helena Blažun

2018-01-01

The overall aim of the present study was to compare the coverage of existing research funding information for articles indexed in Scopus, Web of Science, and PubMed databases. The numbers of articles with funding information published in 2015 were identified in the three selected databases and compared using bibliometric analysis of a sample of twenty-eight prestigious medical journals. Frequency analysis of the number of articles with funding information showed statistically significant differences between Scopus, Web of Science, and PubMed databases. The largest proportion of articles with funding information was found in Web of Science (29.0%), followed by PubMed (14.6%) and Scopus (7.7%). The results show that coverage of funding information differs significantly among Scopus, Web of Science, and PubMed databases in a sample of the same medical journals. Moreover, we found that, currently, funding data in PubMed is more difficult to obtain and analyze compared with that in the other two databases.

Characterization of the mechanism of drug-drug interactions from PubMed using MeSH terms.

Science.gov (United States)

Lu, Yin; Figler, Bryan; Huang, Hong; Tu, Yi-Cheng; Wang, Ju; Cheng, Feng

2017-01-01

Identifying drug-drug interaction (DDI) is an important topic for the development of safe pharmaceutical drugs and for the optimization of multidrug regimens for complex diseases such as cancer and HIV. There have been about 150,000 publications on DDIs in PubMed, which is a great resource for DDI studies. In this paper, we introduced an automatic computational method for the systematic analysis of the mechanism of DDIs using MeSH (Medical Subject Headings) terms from PubMed literature. MeSH term is a controlled vocabulary thesaurus developed by the National Library of Medicine for indexing and annotating articles. Our method can effectively identify DDI-relevant MeSH terms such as drugs, proteins and phenomena with high accuracy. The connections among these MeSH terms were investigated by using co-occurrence heatmaps and social network analysis. Our approach can be used to visualize relationships of DDI terms, which has the potential to help users better understand DDIs. As the volume of PubMed records increases, our method for automatic analysis of DDIs from the PubMed database will become more accurate.

Do language fluency and other socioeconomic factors influence the use of PubMed and MedlinePlus?

Science.gov (United States)

Sheets, L; Gavino, A; Callaghan, F; Fontelo, P

2013-01-01

Increased usage of MedlinePlus by Spanish-speakers was observed after introduction of MedlinePlus in Spanish. This probably reflects increased usage of MEDLINE and PubMed by those with greater fluency in the language in which it is presented; but this has never been demonstrated in English speakers. Evidence that lack of English fluency deters international healthcare personnel from using PubMed could support the use of multi-language search tools like Babel-MeSH. This study aims to measure the effects of language fluency and other socioeconomic factors on PubMed MEDLINE and MedlinePlus access by international users. We retrospectively reviewed server pageviews of PubMed and MedlinePlus from various periods of time, and analyzed them against country statistics on language fluency, GDP, literacy rate, Internet usage, medical schools, and physicians per capita, to determine whether they were associated. We found fluency in English to be positively associated with pageviews of PubMed and MedlinePlus in countries with high literacy rates. Spanish was generally found to be positively associated with pageviews of MedlinePlus en Español. The other parameters also showed varying degrees of association with pageviews. After adjusting for the other factors investigated in this study, language fluency was a consistently significant predictor of the use of PubMed, MedlinePlus English and MedlinePlus en Español. This study may support the need for multi-language search tools and may increase access of health information resources from non-English speaking countries.

Student drinking patterns and blood alcohol concentration on commercially organised pub crawls in the UK.

Science.gov (United States)

Quigg, Zara; Hughes, Karen; Bellis, Mark A

2013-12-01

Commercial student pub crawls are associated with high levels of alcohol consumption, and are of growing concern amongst public health and student bodies. However, little is currently known about drinking behaviours whilst participating in these events. A questionnaire was implemented amongst 227 students attending commercial pub crawls across three UK events. Questions established alcohol consumption patterns up to the point of interview and throughout the remaining night out, and pub crawl experience. Breathalyser tests were used to measure breath alcohol concentration (converted to blood alcohol concentration [BAC]) at interview. Analyses used chi squared, Mann-Whitney U, Kruskal-Wallis and logistic regression. 94.3% of participants had consumed alcohol, 90.9% of whom reported preloading. Drinkers reported consuming a median of 10.0 alcohol units (80g of pure alcohol) up to the point of interview (range one-40.6), with estimated total consumption over the evening exceeding 16units (range three-70.6). Median BAC of drinkers at the time of interview was 0.10%BAC (range 0.00-0.27). High BAC (>0.08%; at interview) was associated with having not eaten food in the four hours prior (AOR 4.8, palcohol consumption before and during commercial pub crawls should aim to alter drinking behaviours such as preloading and rapid and excessive drinking. Organisers, local authorities, universities and students should all be involved in ensuring the effective management of pub crawls, including implementation of harm prevention measures. © 2013.

Use of scientific social networking to improve the research strategies of PubMed readers

OpenAIRE

Evdokimov, Pavel; Kudryavtsev, Alexey; Ilgisonis, Ekaterina; Ponomarenko, Elena; Lisitsa, Andrey

2016-01-01

Background Keeping up with journal articles on a daily basis is an important activity of scientists engaged in biomedical research. Usually, journal articles and papers in the field of biomedicine are accessed through the Medline/PubMed electronic library. In the process of navigating PubMed, researchers unknowingly generate user-specific reading profiles that can be shared within a social networking environment. This paper examines the structure of the social networking environment generated...

Comparison between gas puffing and supersonic molecular beam injection in plasma density feedback experiments in EAST

International Nuclear Information System (INIS)

Zheng, Xingwei; Li, Jiangang; Hu, Jiansheng; Li, Jiahong; Ding, Rui; Cao, Bin; Wu, Jinhua

2013-01-01

To achieve desirable plasma density control, a supersonic molecular beam injection (SMBI) feedback control system has been developed recently for the EAST tokamak. The performance of the SMBI and gas puffing (GP) feedback systems were used and compared. The performance of pulse width mode is better than that of pulse amplitude mode when GP was used for density feedback control. During one-day experiments, the variation of gas input and wall retention can be clarified into two stages. In the first stage the retention ratio is as high as 80–90%, and the gas input is about an order of 10 22 D 2 . However, in the second stage, the retention ratio is at a range of 50–70%. The gas input of a single discharge is small and the net wall retention grows slowly. The results of the SMBI feedback control experiment was analyzed. The shorter delay time of SMBI makes it faster at feeding back control the plasma density. The result showed that, compared with GP, the gas input of SMBI was decreased ∼30% and the wall retention was reduced ∼40%. This shows SMBI's advantage for the long pulse high density discharges in EAST. (paper)

Searching PubMed during a pandemic.

Directory of Open Access Journals (Sweden)

Ole Norgaard

Full Text Available BACKGROUND: The 2009 influenza A(H1N1 pandemic has generated thousands of articles and news items. However, finding relevant scientific articles in such rapidly developing health crises is a major challenge which, in turn, can affect decision-makers' ability to utilise up-to-date findings and ultimately shape public health interventions. This study set out to show the impact that the inconsistent naming of the pandemic can have on retrieving relevant scientific articles in PubMed/MEDLINE. METHODOLOGY: We first formulated a PubMed search algorithm covering different names of the influenza pandemic and simulated the results that it would have retrieved from weekly searches for relevant new records during the first 10 weeks of the pandemic. To assess the impact of failing to include every term in this search, we then conducted the same searches but omitted in turn "h1n1," "swine," "influenza" and "flu" from the search string, and compared the results to those for the full string. PRINCIPAL FINDINGS: On average, our core search string identified 44.3 potentially relevant new records at the end of each week. Of these, we determined that an average of 27.8 records were relevant. When we excluded one term from the string, the percentage of records missed out of the total number of relevant records averaged 18.7% for omitting "h1n1," 13.6% for "swine," 17.5% for "influenza," and 20.6% for "flu." CONCLUSIONS: Due to inconsistent naming, while searching for scientific material about rapidly evolving situations such as the influenza A(H1N1 pandemic, there is a risk that one will miss relevant articles. To address this problem, the international scientific community should agree on nomenclature and the specific name to be used earlier, and the National Library of Medicine in the US could index potentially relevant materials faster and allow publishers to add alert tags to such materials.

Characterization of the mechanism of drug-drug interactions from PubMed using MeSH terms.

Directory of Open Access Journals (Sweden)

Yin Lu

Full Text Available Identifying drug-drug interaction (DDI is an important topic for the development of safe pharmaceutical drugs and for the optimization of multidrug regimens for complex diseases such as cancer and HIV. There have been about 150,000 publications on DDIs in PubMed, which is a great resource for DDI studies. In this paper, we introduced an automatic computational method for the systematic analysis of the mechanism of DDIs using MeSH (Medical Subject Headings terms from PubMed literature. MeSH term is a controlled vocabulary thesaurus developed by the National Library of Medicine for indexing and annotating articles. Our method can effectively identify DDI-relevant MeSH terms such as drugs, proteins and phenomena with high accuracy. The connections among these MeSH terms were investigated by using co-occurrence heatmaps and social network analysis. Our approach can be used to visualize relationships of DDI terms, which has the potential to help users better understand DDIs. As the volume of PubMed records increases, our method for automatic analysis of DDIs from the PubMed database will become more accurate.

Why does ‘PubPeer’ not acknowledge ‘Retraction Watch’ as a media source?

Directory of Open Access Journals (Sweden)

Jaime A. Teixeira da Silva

2017-05-01

Full Text Available Retraction Watch is a social media organization that relies on a blog to transmit information primarily about retractions in the scientific literature. One of the Retraction Watch co-founders, Ivan Oransky, is in fact a “Distinguished Writer in Residence at New York University’s Carter Journalism Institute” and the vice president of the Association of Health Care Journalists. Sharing a common funder, a philanthropic organization, the Laura and John Arnold Foundation, Retraction Watch regularly coordinates with a whistle-blower website that refers to itself as an “online journal club”, PubPeer. Retraction Watch regularly cites and refers to PubPeer, and vice versa. It is therefore surprising that PubPeer does not list Retraction Watch on its “Press” and media coverage page. This potentially deliberate omission may be equivalent to a hidden conflict of interest, undermining the ethical fortitude and image of these science watchdogs, and fortifying the fake news era.

How to improve your PubMed/MEDLINE searches: 3. advanced searching, MeSH and My NCBI.

Science.gov (United States)

Fatehi, Farhad; Gray, Leonard C; Wootton, Richard

2014-03-01

Although the basic PubMed search is often helpful, the results may sometimes be non-specific. For more control over the search process you can use the Advanced Search Builder interface. This allows a targeted search in specific fields, with the convenience of being able to select the intended search field from a list. It also provides a history of your previous searches. The search history is useful to develop a complex search query by combining several previous searches using Boolean operators. For indexing the articles in MEDLINE, the NLM uses a controlled vocabulary system called MeSH. This standardised vocabulary solves the problem of authors, researchers and librarians who may use different terms for the same concept. To be efficient in a PubMed search, you should start by identifying the most appropriate MeSH terms and use them in your search where possible. My NCBI is a personal workspace facility available through PubMed and makes it possible to customise the PubMed interface. It provides various capabilities that can enhance your search performance.

Study of sorption behavior, shelf life and colour kinetics of vacuum puffed honey powder at accelerated storage conditions.

Science.gov (United States)

Devi, K Deepika; Paul, Sanjib Kr; Sahu, Jatindra K

2016-05-01

In the study, the storage life of vacuum puffed honey powder at accelerated storage environment (90 % relative humidity and 36 °C) was computed by determining the sticky-point moisture content as the critical parameter of the honey powder. The value of monolayer moisture content in the GAB model was calculated to be 0.081 kg water/kg dry solids by fitting water activity and moisture sorption data. Shelf life of the honey powder was predicted to be 222 days when the powder was packaged in aluminum foil-laminated polyethylene pouches with permeability value of 5.427X10(-8) kg/m(2)//day/Pa. Actual shelf life of honey powder was experimentally determined as 189 days and analysis of mean relative percent derivation modulus (Rd) and root mean square (RMS) established the accuracy and acceptability of the technique for the prediction of shelf life of honey powder. Overall colour deviation pattern followed first order reaction kinetics with rate constant (k1) as 0.037 day(-1). This study revealed overall colour difference of 18.1 till the end of shelf life with drastic change during initial storage period.

Comparison of optical spectra recorded during DPF-1000U plasma experiments with gas-puffing

Directory of Open Access Journals (Sweden)

Zaloga Dobromil R.

2015-06-01

Full Text Available The results are presented of the optical spectra measurements for free plasma streams generated with the use of the modified DPF-1000U machine. This facility was recently equipped with a gas injection system (the so-called gas-puff placed on the symmetry axis behind the central opening in the inner electrode. The DPF-1000U experimental chamber was filled up with pure deuterium at the initial pressure of 1.6 or 2.4 mbar. Additionally, when the use was made of the gas-puff system about 1 cm3 of pure deuterium was injected at the pressure of 2 bars. The gas injection was initiated 1.5 or 2 ms before the triggering of the main discharge. The investigated plasma discharges were powered from a condenser bank charged initially to 23 kV (corresponding to the energy of 352 kJ, and the maximum discharge current amounted to about 1.8 MA. In order to investigate properties of a dense plasma column formed during DPF-1000U discharges the use was made of the optical emission spectroscopy. The optical spectra were recorded along the line of sight perpendicular to the vacuum chamber, using a Mechelle®900 spectrometer. The recent analysis of all the recorded spectra made it possible to compare the temporal changes in the electron density of a freely propagating plasma stream for discharges without and with the gas-puffing. Using this data an appropriate mode of operation of the DPF-1000U facility could be determined.

Diagnosis checking of statistical analysis in RCTs indexed in PubMed.

Science.gov (United States)

Lee, Paul H; Tse, Andy C Y

2017-11-01

Statistical analysis is essential for reporting of the results of randomized controlled trials (RCTs), as well as evaluating their effectiveness. However, the validity of a statistical analysis also depends on whether the assumptions of that analysis are valid. To review all RCTs published in journals indexed in PubMed during December 2014 to provide a complete picture of how RCTs handle assumptions of statistical analysis. We reviewed all RCTs published in December 2014 that appeared in journals indexed in PubMed using the Cochrane highly sensitive search strategy. The 2014 impact factors of the journals were used as proxies for their quality. The type of statistical analysis used and whether the assumptions of the analysis were tested were reviewed. In total, 451 papers were included. Of the 278 papers that reported a crude analysis for the primary outcomes, 31 (27·2%) reported whether the outcome was normally distributed. Of the 172 papers that reported an adjusted analysis for the primary outcomes, diagnosis checking was rarely conducted, with only 20%, 8·6% and 7% checked for generalized linear model, Cox proportional hazard model and multilevel model, respectively. Study characteristics (study type, drug trial, funding sources, journal type and endorsement of CONSORT guidelines) were not associated with the reporting of diagnosis checking. The diagnosis of statistical analyses in RCTs published in PubMed-indexed journals was usually absent. Journals should provide guidelines about the reporting of a diagnosis of assumptions. © 2017 Stichting European Society for Clinical Investigation Journal Foundation.

Public accessibility of biomedical articles from PubMed Central reduces journal readership--retrospective cohort analysis.

Science.gov (United States)

Davis, Philip M

2013-07-01

Does PubMed Central--a government-run digital archive of biomedical articles--compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers.

PubMed search filters for the study of putative outdoor air pollution determinants of disease

OpenAIRE

Curti, Stefania; Gori, Davide; Di Gregori, Valentina; Farioli, Andrea; Baldasseroni, Alberto; Fantini, Maria Pia; Christiani, David C; Violante, Francesco S; Mattioli, Stefano

2016-01-01

Objectives: Several PubMed search filters have been developed in contexts other than environmental. We aimed at identifying efficient PubMed search filters for the study of environmental determinants of diseases related to outdoor air pollution. Methods: We compiled a list of Medical Subject Headings (MeSH) and non-MeSH terms seeming pertinent to outdoor air pollutants exposure as determinants of diseases in the general population. We estimated proportions of potentially pertinent articles to...

Skapandet av en handbok för ett franchiseföretag : Case: Pub Niska

OpenAIRE

Juvonen, Jenni

2017-01-01

Syftet med detta examensarbete är att skapa en franchisehandbok för franchiserestaurangen Pub Niska. En franchisehandbok innehåller mer detaljerad information om ett företag, dess riktlinjer och vardagliga rutiner. En franchisehandboks viktigaste uppgift är att säkra kvaliteten i ett koncept. Franchisehandboken för Pub Niska innehåller information om företaget i allmänhet och beskriver hur företaget är uppbyggt samt presenterar riktlinjer för marknadsföring, inredning och ekonomi. Dessuto...

Quality and storage stability of extruded puffed corn-fish snacks during 6-month storage at ambient temperature.

Science.gov (United States)

Shaviklo, Gholam Reza; Thorkelsson, Gudjon; Rafipour, Fereidon; Sigurgisladottir, Sjofn

2011-03-30

Cereal-based snacks are usually low in protein and other nutrients. Increased health awareness of consumers has led the food industry to develop fortified snacks with functional ingredients. Three types of extruded corn-fish snacks, containing 150 g kg(-1) carp mince and 150 g kg(-1) trout mince, 30 g kg(-1) freeze-dried saithe protein and a regular corn snack (control). were produced to study quality changes and storage stability of the products during 6-month storage at 27±2 °C. All products had the same level of water activity and proximate composition except for protein. Fortified snacks had a protein content of 93-98 g kg(-1) , compared with 65 g kg(-1) in the control. A significant increase was observed for peroxide value during storage (0.0 to 2.8 meq kg(-1)). Scores for attributes describing oxidation and off odors and flavors increased after 5-6 months' storage but attributes describing puffed corn snack odor and flavor did not change during storage of any of the products. Extrusion of corn grits with fish flesh/fish protein can be used to produce high-protein products that would be an option to provide nutrient snacks for consumers and to increase fish consumption. Copyright © 2011 Society of Chemical Industry.

Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses.

Science.gov (United States)

Falagas, Matthew E; Pitsouni, Eleni I; Malietzis, George A; Pappas, Georgios

2008-02-01

The evolution of the electronic age has led to the development of numerous medical databases on the World Wide Web, offering search facilities on a particular subject and the ability to perform citation analysis. We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar. The official Web pages of the databases were used to extract information on the range of journals covered, search facilities and restrictions, and update frequency. We used the example of a keyword search to evaluate the usefulness of these databases in biomedical information retrieval and a specific published article to evaluate their utility in performing citation analysis. All databases were practical in use and offered numerous search facilities. PubMed and Google Scholar are accessed for free. The keyword search with PubMed offers optimal update frequency and includes online early articles; other databases can rate articles by number of citations, as an index of importance. For citation analysis, Scopus offers about 20% more coverage than Web of Science, whereas Google Scholar offers results of inconsistent accuracy. PubMed remains an optimal tool in biomedical electronic research. Scopus covers a wider journal range, of help both in keyword searching and citation analysis, but it is currently limited to recent articles (published after 1995) compared with Web of Science. Google Scholar, as for the Web in general, can help in the retrieval of even the most obscure information but its use is marred by inadequate, less often updated, citation information.

Identifying nurse staffing research in Medline: development and testing of empirically derived search strategies with the PubMed interface.

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Simon, Michael; Hausner, Elke; Klaus, Susan F; Dunton, Nancy E

2010-08-23

The identification of health services research in databases such as PubMed/Medline is a cumbersome task. This task becomes even more difficult if the field of interest involves the use of diverse methods and data sources, as is the case with nurse staffing research. This type of research investigates the association between nurse staffing parameters and nursing and patient outcomes. A comprehensively developed search strategy may help identify nurse staffing research in PubMed/Medline. A set of relevant references in PubMed/Medline was identified by means of three systematic reviews. This development set was used to detect candidate free-text and MeSH terms. The frequency of these terms was compared to a random sample from PubMed/Medline in order to identify terms specific to nurse staffing research, which were then used to develop a sensitive, precise and balanced search strategy. To determine their precision, the newly developed search strategies were tested against a) the pool of relevant references extracted from the systematic reviews, b) a reference set identified from an electronic journal screening, and c) a sample from PubMed/Medline. Finally, all newly developed strategies were compared to PubMed's Health Services Research Queries (PubMed's HSR Queries). The sensitivities of the newly developed search strategies were almost 100% in all of the three test sets applied; precision ranged from 6.1% to 32.0%. PubMed's HSR queries were less sensitive (83.3% to 88.2%) than the new search strategies. Only minor differences in precision were found (5.0% to 32.0%). As with other literature on health services research, nurse staffing studies are difficult to identify in PubMed/Medline. Depending on the purpose of the search, researchers can choose between high sensitivity and retrieval of a large number of references or high precision, i.e. and an increased risk of missing relevant references, respectively. More standardized terminology (e.g. by consistent use of the

Abstract databases in nuclear medicine; New database for articles not indexed in PubMed

International Nuclear Information System (INIS)

Ugrinska, A.; Mustafa, B.

2004-01-01

Full text: Abstract databases available on Internet free of charge were searched for nuclear medicine contents. The only comprehensive database found was PubMed. Analysis of nuclear medicine journals included in PubMed was performed. PubMed contains 25 medical journals that contain the phrase 'nuclear medicine' in different languages in their title. Searching the Internet with the search engine 'Google' we have found four more peer-reviewed journals with the phrase 'nuclear medicine' in their title. In addition, we are fully aware that many articles related to nuclear medicine are published in national medical journals devoted to general medicine. For example in year 2000 colleagues from Institute of Pathophysiology and Nuclear Medicine, Skopje, Macedonia have published 10 articles out of which none could be found on PubMed. This suggested that a big amount of research work is not accessible for the people professionally involved in nuclear medicine. Therefore, we have created a database framework for abstracts that couldn't be found in PubMed. The database is organized in user-friendly manner. There are two main sections: 'post an abstract' and 'search for abstracts'. Authors of the articles are expected to submit their work in the section 'post an abstract'. During the submission process authors should fill the separate boxes with the Title in English, Title in original language, Country of origin, Journal name, Volume, Issue and Pages. Authors should choose up to five keywords from a drop-down menu. Authors are encouraged if the abstract is not published in English to translate it. The section 'search for abstract' is searchable according to Author, Keywords, and words and phrases incorporated in the English title. The abstract database currently resides on an MS Access back-end, with a front-end in ASP (Active Server Pages). In the future, we plan to migrate the database on a MS SQL Server, which should provide a faster and more reliable framework for hosting a

Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS.

Science.gov (United States)

Yu, Hwanjo; Kim, Taehoon; Oh, Jinoh; Ko, Ilhwan; Kim, Sungchul; Han, Wook-Shin

2010-04-16

Finding relevant articles from PubMed is challenging because it is hard to express the user's specific intention in the given query interface, and a keyword query typically retrieves a large number of results. Researchers have applied machine learning techniques to find relevant articles by ranking the articles according to the learned relevance function. However, the process of learning and ranking is usually done offline without integrated with the keyword queries, and the users have to provide a large amount of training documents to get a reasonable learning accuracy. This paper proposes a novel multi-level relevance feedback system for PubMed, called RefMed, which supports both ad-hoc keyword queries and a multi-level relevance feedback in real time on PubMed. RefMed supports a multi-level relevance feedback by using the RankSVM as the learning method, and thus it achieves higher accuracy with less feedback. RefMed "tightly" integrates the RankSVM into RDBMS to support both keyword queries and the multi-level relevance feedback in real time; the tight coupling of the RankSVM and DBMS substantially improves the processing time. An efficient parameter selection method for the RankSVM is also proposed, which tunes the RankSVM parameter without performing validation. Thereby, RefMed achieves a high learning accuracy in real time without performing a validation process. RefMed is accessible at http://dm.postech.ac.kr/refmed. RefMed is the first multi-level relevance feedback system for PubMed, which achieves a high accuracy with less feedback. It effectively learns an accurate relevance function from the user's feedback and efficiently processes the function to return relevant articles in real time.

PIE the search: searching PubMed literature for protein interaction information.

Science.gov (United States)

Kim, Sun; Kwon, Dongseop; Shin, Soo-Yong; Wilbur, W John

2012-02-15

Finding protein-protein interaction (PPI) information from literature is challenging but an important issue. However, keyword search in PubMed(®) is often time consuming because it requires a series of actions that refine keywords and browse search results until it reaches a goal. Due to the rapid growth of biomedical literature, it has become more difficult for biologists and curators to locate PPI information quickly. Therefore, a tool for prioritizing PPI informative articles can be a useful assistant for finding this PPI-relevant information. PIE (Protein Interaction information Extraction) the search is a web service implementing a competition-winning approach utilizing word and syntactic analyses by machine learning techniques. For easy user access, PIE the search provides a PubMed-like search environment, but the output is the list of articles prioritized by PPI confidence scores. By obtaining PPI-related articles at high rank, researchers can more easily find the up-to-date PPI information, which cannot be found in manually curated PPI databases. http://www.ncbi.nlm.nih.gov/IRET/PIE/.

Aging and social networks in Spain: the importance of pubs and churches.

Science.gov (United States)

Buz, José; Sanchez, Marta; Levenson, Michael R; Aldwin, Carolyn M

2014-01-01

We examined whether the social convoy model and socioemotional selectivity theory apply in collectivistic cultures by examining the contextual factors which are hypothesized to mediate age-related differences in social support in a collectivist European country. Five hundred Spanish community-dwelling older adults (Mean age = 74.78, SD = 7.76, range = 60-93) were interviewed to examine structural aspects of their social networks. We found that age showed highly complex relationships with network size and frequency of interaction, depending on the network circle and the mediation of cultural factors. Family structure was important for social relations in the inner circle, while pubs and churches were important for peripheral relations. Surprisingly, pub attendance was the most important variable for maintenance of social support of peripheral network members. In general, the results support the applicability of the social convoy and socioemotional selectivity constructs to social support among Spanish older adults.

Sensitivity and predictive value of 15 PubMed search strategies to answer clinical questions rated against full systematic reviews.

Science.gov (United States)

Agoritsas, Thomas; Merglen, Arnaud; Courvoisier, Delphine S; Combescure, Christophe; Garin, Nicolas; Perrier, Arnaud; Perneger, Thomas V

2012-06-12

Clinicians perform searches in PubMed daily, but retrieving relevant studies is challenging due to the rapid expansion of medical knowledge. Little is known about the performance of search strategies when they are applied to answer specific clinical questions. To compare the performance of 15 PubMed search strategies in retrieving relevant clinical trials on therapeutic interventions. We used Cochrane systematic reviews to identify relevant trials for 30 clinical questions. Search terms were extracted from the abstract using a predefined procedure based on the population, interventions, comparison, outcomes (PICO) framework and combined into queries. We tested 15 search strategies that varied in their query (PIC or PICO), use of PubMed's Clinical Queries therapeutic filters (broad or narrow), search limits, and PubMed links to related articles. We assessed sensitivity (recall) and positive predictive value (precision) of each strategy on the first 2 PubMed pages (40 articles) and on the complete search output. The performance of the search strategies varied widely according to the clinical question. Unfiltered searches and those using the broad filter of Clinical Queries produced large outputs and retrieved few relevant articles within the first 2 pages, resulting in a median sensitivity of only 10%-25%. In contrast, all searches using the narrow filter performed significantly better, with a median sensitivity of about 50% (all P PubMed pages. These results can help clinicians apply effective strategies to answer their questions at the point of care.

GeneView: a comprehensive semantic search engine for PubMed.

Science.gov (United States)

Thomas, Philippe; Starlinger, Johannes; Vowinkel, Alexander; Arzt, Sebastian; Leser, Ulf

2012-07-01

Research results are primarily published in scientific literature and curation efforts cannot keep up with the rapid growth of published literature. The plethora of knowledge remains hidden in large text repositories like MEDLINE. Consequently, life scientists have to spend a great amount of time searching for specific information. The enormous ambiguity among most names of biomedical objects such as genes, chemicals and diseases often produces too large and unspecific search results. We present GeneView, a semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured representation of biomedical texts enables a number of features extending classical search engines. For instance, users may search for entities using unique database identifiers or they may rank documents by the number of specific mentions they contain. Annotation is performed by a multitude of state-of-the-art text-mining tools for recognizing mentions from 10 entity classes and for identifying protein-protein interactions. GeneView currently contains annotations for >194 million entities from 10 classes for ∼21 million citations with 271,000 full text bodies. GeneView can be searched at http://bc3.informatik.hu-berlin.de/.

Enhancing search efficiency by means of a search filter for finding all studies on animal experimentation in PubMed.

Science.gov (United States)

Hooijmans, Carlijn R; Tillema, Alice; Leenaars, Marlies; Ritskes-Hoitinga, Merel

2010-07-01

Collecting and analysing all available literature before starting an animal experiment is important and it is indispensable when writing a systematic review (SR) of animal research. Writing such review prevents unnecessary duplication of animal studies and thus unnecessary animal use (Reduction). One of the factors currently impeding the production of 'high-quality' SRs in laboratory animal science is the fact that searching for all available literature concerning animal experimentation is rather difficult. In order to diminish these difficulties, we developed a search filter for PubMed to detect all publications concerning animal studies. This filter was compared with the method most frequently used, the PubMed Limit: Animals, and validated further by performing two PubMed topic searches. Our filter performs much better than the PubMed limit: it retrieves, on average, 7% more records. Other important advantages of our filter are that it also finds the most recent records and that it is easy to use. All in all, by using our search filter in PubMed, all available literature concerning animal studies on a specific topic can easily be found and assessed, which will help in increasing the scientific quality and thereby the ethical validity of animal experiments.

Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.

Science.gov (United States)

Huang, Chung-Chi; Lu, Zhiyong

2016-01-01

Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as 'CHEMICAL-1 compared to CHEMICAL-2' With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical-disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked order

Virtuous suffering and the predicament of being handicapped. Towards a theology of the ‘disabled God puffing in a wheelchair’

Directory of Open Access Journals (Sweden)

Daniel J. Louw

2014-04-01

Full Text Available The reality of disablement, being handicapped and physical disfigurement, opens up anew the theological debate regarding God-images in human suffering. It is argued that the Hellenistic understanding of the power of God, God as a pantokrator [Almighty], presupposes the immutability of an apathetic God. In terms of the logic of a cause-effect paradigm, God becomes the deterministic principle behind human suffering. With reference to a theologia crucis [theology of the Cross], the paradigm of theopaschitic theology proposes a pathetic understanding of God. Weakness and vulnerability (astheneia describes an authentic identification of God with human suffering. Forsakenness (derelictio reframes power as compassionate weakness or vulnerability and divine disability. The disabled God is, in terms of the New Testament a connection between divine compassion and human predicament (ta splanchna, the passionate God. Bowel categories make it possible to speak of the ‘puffing God in the wheelchair’. A theology of the cross should be supplemented by a theology of ability (theologia resurrectionis. The resurrection introduces the spiritual ability parrhesia− the transformation of the weakness of suffering into the fortigenitics of hope.

Analysis of queries sent to PubMed at the point of care: Observation of search behaviour in a medical teaching hospital

Science.gov (United States)

Hoogendam, Arjen; Stalenhoef, Anton FH; Robbé, Pieter F de Vries; Overbeke, A John PM

2008-01-01

Background The use of PubMed to answer daily medical care questions is limited because it is challenging to retrieve a small set of relevant articles and time is restricted. Knowing what aspects of queries are likely to retrieve relevant articles can increase the effectiveness of PubMed searches. The objectives of our study were to identify queries that are likely to retrieve relevant articles by relating PubMed search techniques and tools to the number of articles retrieved and the selection of articles for further reading. Methods This was a prospective observational study of queries regarding patient-related problems sent to PubMed by residents and internists in internal medicine working in an Academic Medical Centre. We analyzed queries, search results, query tools (Mesh, Limits, wildcards, operators), selection of abstract and full-text for further reading, using a portal that mimics PubMed. Results PubMed was used to solve 1121 patient-related problems, resulting in 3205 distinct queries. Abstracts were viewed in 999 (31%) of these queries, and in 126 (39%) of 321 queries using query tools. The average term count per query was 2.5. Abstracts were selected in more than 40% of queries using four or five terms, increasing to 63% if the use of four or five terms yielded 2–161 articles. Conclusion Queries sent to PubMed by physicians at our hospital during daily medical care contain fewer than three terms. Queries using four to five terms, retrieving less than 161 article titles, are most likely to result in abstract viewing. PubMed search tools are used infrequently by our population and are less effective than the use of four or five terms. Methods to facilitate the formulation of precise queries, using more relevant terms, should be the focus of education and research. PMID:18816391

PubMed and beyond: a survey of web tools for searching biomedical literature

Science.gov (United States)

Lu, Zhiyong

2011-01-01

The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search PMID:21245076

PubMed and beyond: a survey of web tools for searching biomedical literature.

Science.gov (United States)

Lu, Zhiyong

2011-01-01

The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search.

Utilization of bar and izakaya-pub establishments among middle-aged and elderly Japanese men to mitigate stress

Directory of Open Access Journals (Sweden)

Ohnishi Mayumi

2012-06-01

Full Text Available Abstract Japanese suicide rate is one of the highest among industrialized nations, especially following the economic crisis of the 1990s, with more than 30000 suicides every year since 1998. Previous studies have pointed out to relationships between overwork and/or job stress, and death and other health risks, and suggested several possible avenues for releasing stress and emotional burden, including suicidal ideation, through talking with intimate friends, family, and specialists, such as counselors and physicians. The present study was performed to explore the potential role of owners and managers of bars and izakaya-pub establishments in mitigating stress of middle-aged and elderly Japanese men by having informal conversations with them. A self-administered questionnaire was posted to all bars and izakaya-pubs registered in Ohmura-city, Nagasaki prefecture, in December 2009. Among 260 bars and izakaya-pubs, a total of 103 owners and managers completed the questionnaire. More than half of the respondents experienced engaging in conversations with their customers regarding customers’ various personal and private issues. The most frequently talked about problem was that regarding work (56.3%. Regardless of sex and age of the respondents, those with longer working experience in bar and izakaya-pub establishments were more likely to have had customers confiding in them financial problems including debts/loans (adjusted odds ratio: 5.48, p = 0.033. Owners and managers of bars and izakaya-pubs may be in a position to act as “listeners”, to whom middle-aged and elderly men can talk about their personal problems casually and without having to worry about conflict of interests, and direct those in need to professional counseling.

Utilization of bar and izakaya-pub establishments among middle-aged and elderly Japanese men to mitigate stress.

Science.gov (United States)

Ohnishi, Mayumi; Nakao, Rieko; Kawasaki, Ryokko; Nitta, Akiko; Hamada, Yukari; Nakane, Hideyuki

2012-06-18

Japanese suicide rate is one of the highest among industrialized nations, especially following the economic crisis of the 1990s, with more than 30000 suicides every year since 1998. Previous studies have pointed out to relationships between overwork and/or job stress, and death and other health risks, and suggested several possible avenues for releasing stress and emotional burden, including suicidal ideation, through talking with intimate friends, family, and specialists, such as counselors and physicians. The present study was performed to explore the potential role of owners and managers of bars and izakaya-pub establishments in mitigating stress of middle-aged and elderly Japanese men by having informal conversations with them. A self-administered questionnaire was posted to all bars and izakaya-pubs registered in Ohmura-city, Nagasaki prefecture, in December 2009. Among 260 bars and izakaya-pubs, a total of 103 owners and managers completed the questionnaire. More than half of the respondents experienced engaging in conversations with their customers regarding customers' various personal and private issues. The most frequently talked about problem was that regarding work (56.3%). Regardless of sex and age of the respondents, those with longer working experience in bar and izakaya-pub establishments were more likely to have had customers confiding in them financial problems including debts/loans (adjusted odds ratio: 5.48, p = 0.033). Owners and managers of bars and izakaya-pubs may be in a position to act as "listeners", to whom middle-aged and elderly men can talk about their personal problems casually and without having to worry about conflict of interests, and direct those in need to professional counseling.

Combining PubMed knowledge and EHR data to develop a weighted bayesian network for pancreatic cancer prediction.

Science.gov (United States)

Zhao, Di; Weng, Chunhua

2011-10-01

In this paper, we propose a novel method that combines PubMed knowledge and Electronic Health Records to develop a weighted Bayesian Network Inference (BNI) model for pancreatic cancer prediction. We selected 20 common risk factors associated with pancreatic cancer and used PubMed knowledge to weigh the risk factors. A keyword-based algorithm was developed to extract and classify PubMed abstracts into three categories that represented positive, negative, or neutral associations between each risk factor and pancreatic cancer. Then we designed a weighted BNI model by adding the normalized weights into a conventional BNI model. We used this model to extract the EHR values for patients with or without pancreatic cancer, which then enabled us to calculate the prior probabilities for the 20 risk factors in the BNI. The software iDiagnosis was designed to use this weighted BNI model for predicting pancreatic cancer. In an evaluation using a case-control dataset, the weighted BNI model significantly outperformed the conventional BNI and two other classifiers (k-Nearest Neighbor and Support Vector Machine). We conclude that the weighted BNI using PubMed knowledge and EHR data shows remarkable accuracy improvement over existing representative methods for pancreatic cancer prediction. Copyright © 2011 Elsevier Inc. All rights reserved.

A bibliometric analysis of Australian general practice publications from 1980 to 2007 using PubMed.

Science.gov (United States)

Mendis, Kumara; Kidd, Michael R; Schattner, Peter; Canalese, Joseph

2010-01-01

We analysed Australian general practice (GP) publications in PubMed from 1980 to 2007 to determine journals, authors, publication types, national health priority areas (NHPA) and compared the results with those from three specialties (public health, cardiology and medical informatics) and two countries (the UK and New Zealand). Australian GP publications were downloaded in MEDLINE format using PubMed queries and were written to a Microsoft Access database using a software application. Search Query Language and online PubMed queries were used for further analysis. There were 4777 publications from 1980 to 2007. Australian Family Physician (38.1%) and the Medical Journal of Australia (17.6%) contributed 55.7% of publications. Reviews (12.7%), letters (6.6%), clinical trials (6.5%) and systematic reviews (5%) were the main PubMed publication types. Thirty five percent of publications addressed National Health Priority Areas with material on mental health (13.7%), neoplasms (6.5%) and cardiovascular conditions (5.9%). The comparable numbers of publications for the three specialties were: public health - 80 911, cardiology - 15 130 and medical informatics - 3338; total country GP comparisons were: UK - 14 658 and New Zealand - 1111. Australian GP publications have shown an impressive growth from 1980 to 2007 with a 15-fold increase. This increase may be due in part to the actions of the Australian government over the past decade to financially support research in primary care, as well as the maturing of academic general practice. This analysis can assist governments, researchers, policy makers and others to target resources so that further developments can be encouraged, supported and monitored.

The potential effect of differential ambient and deployment chamber temperatures on PRC derived sampling rates with polyurethane foam (PUF) passive air samplers

Energy Technology Data Exchange (ETDEWEB)

Kennedy, Karen, E-mail: k.kennedy@uq.edu.a [University of Queensland, EnTox (National Research Centre for Environmental Toxicology), 39 Kessels Rd., Coopers Plains QLD 4108 (Australia); Hawker, Darryl W. [Griffith University, School of Environment, Nathan QLD 4111 (Australia); Bartkow, Michael E. [University of Queensland, EnTox (National Research Centre for Environmental Toxicology), 39 Kessels Rd., Coopers Plains QLD 4108 (Australia); Carter, Steve [Queensland Health Forensic and Scientific Services, Coopers Plains QLD 4108 (Australia); Ishikawa, Yukari; Mueller, Jochen F. [University of Queensland, EnTox (National Research Centre for Environmental Toxicology), 39 Kessels Rd., Coopers Plains QLD 4108 (Australia)

2010-01-15

Performance reference compound (PRC) derived sampling rates were determined for polyurethane foam (PUF) passive air samplers in both sub-tropical and temperate locations across Australia. These estimates were on average a factor of 2.7 times higher in summer than winter. The known effects of wind speed and temperature on mass transfer coefficients could not account for this observation. Sampling rates are often derived using ambient temperatures, not the actual temperatures within deployment chambers. If deployment chamber temperatures are in fact higher than ambient temperatures, estimated sampler-air partition coefficients would be greater than actual partition coefficients resulting in an overestimation of PRC derived sampling rates. Sampling rates determined under measured ambient temperatures and estimated deployment chamber temperatures in summer ranged from 7.1 to 10 m{sup 3} day{sup -1} and 2.2-6.8 m{sup 3} day{sup -1} respectively. These results suggest that potential differences between ambient and deployment chamber temperatures should be considered when deriving PRC-based sampling rates. - Internal deployment chamber temperatures rather than ambient temperatures may be required to accurately estimate PRC-based sampling rates.

Key steps in developing a cognitive vaccine against traumatic flashbacks: visuospatial Tetris versus verbal Pub Quiz.

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Holmes, Emily A; James, Ella L; Kilford, Emma J; Deeprose, Catherine

2010-11-10

Flashbacks (intrusive memories of a traumatic event) are the hallmark feature of Post Traumatic Stress Disorder, however preventative interventions are lacking. Tetris may offer a 'cognitive vaccine' [1] against flashback development after trauma exposure. We previously reported that playing the computer game Tetris soon after viewing traumatic material reduced flashbacks compared to no-task [1]. However, two criticisms need to be addressed for clinical translation: (1) Would all games have this effect via distraction/enjoyment, or might some games even be harmful? (2) Would effects be found if administered several hours post-trauma? Accordingly, we tested Tetris versus an alternative computer game--Pub Quiz--which we hypothesized not to be helpful (Experiments 1 and 2), and extended the intervention interval to 4 hours (Experiment 2). The trauma film paradigm was used as an experimental analog for flashback development in healthy volunteers. In both experiments, participants viewed traumatic film footage of death and injury before completing one of the following: (1) no-task control condition (2) Tetris or (3) Pub Quiz. Flashbacks were monitored for 1 week. Experiment 1: 30 min after the traumatic film, playing Tetris led to a significant reduction in flashbacks compared to no-task control, whereas Pub Quiz led to a significant increase in flashbacks. Experiment 2: 4 hours post-film, playing Tetris led to a significant reduction in flashbacks compared to no-task control, whereas Pub Quiz did not. First, computer games can have differential effects post-trauma, as predicted by a cognitive science formulation of trauma memory. In both Experiments, playing Tetris post-trauma film reduced flashbacks. Pub Quiz did not have this effect, even increasing flashbacks in Experiment 1. Thus not all computer games are beneficial or merely distracting post-trauma - some may be harmful. Second, the beneficial effects of Tetris are retained at 4 hours post-trauma. Clinically

Key steps in developing a cognitive vaccine against traumatic flashbacks: visuospatial Tetris versus verbal Pub Quiz.

Directory of Open Access Journals (Sweden)

Emily A Holmes

2010-11-01

Full Text Available Flashbacks (intrusive memories of a traumatic event are the hallmark feature of Post Traumatic Stress Disorder, however preventative interventions are lacking. Tetris may offer a 'cognitive vaccine' [1] against flashback development after trauma exposure. We previously reported that playing the computer game Tetris soon after viewing traumatic material reduced flashbacks compared to no-task [1]. However, two criticisms need to be addressed for clinical translation: (1 Would all games have this effect via distraction/enjoyment, or might some games even be harmful? (2 Would effects be found if administered several hours post-trauma? Accordingly, we tested Tetris versus an alternative computer game--Pub Quiz--which we hypothesized not to be helpful (Experiments 1 and 2, and extended the intervention interval to 4 hours (Experiment 2.The trauma film paradigm was used as an experimental analog for flashback development in healthy volunteers. In both experiments, participants viewed traumatic film footage of death and injury before completing one of the following: (1 no-task control condition (2 Tetris or (3 Pub Quiz. Flashbacks were monitored for 1 week. Experiment 1: 30 min after the traumatic film, playing Tetris led to a significant reduction in flashbacks compared to no-task control, whereas Pub Quiz led to a significant increase in flashbacks. Experiment 2: 4 hours post-film, playing Tetris led to a significant reduction in flashbacks compared to no-task control, whereas Pub Quiz did not.First, computer games can have differential effects post-trauma, as predicted by a cognitive science formulation of trauma memory. In both Experiments, playing Tetris post-trauma film reduced flashbacks. Pub Quiz did not have this effect, even increasing flashbacks in Experiment 1. Thus not all computer games are beneficial or merely distracting post-trauma - some may be harmful. Second, the beneficial effects of Tetris are retained at 4 hours post

77 FR 37445 - Notice of Permit Modification Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

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2012-06-21

... Conservation Act of 1978 (Pub. L. 95-541) AGENCY: National Science Foundation. ACTION: Notice of Permit... directed by the Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science... feathers removed to confirm gender of the penguin, and have GPS/TDR tags attached and later removed. The...

How to improve your PubMed/MEDLINE searches: 2. display settings, complex search queries and topic searching.

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Fatehi, Farhad; Gray, Leonard C; Wootton, Richard

2014-01-01

The way that PubMed results are displayed can be changed using the Display Settings drop-down menu in the result screen. There are three groups of options: Format, Items per page and Sort by, which allow a good deal of control. The results from several searches can be temporarily stored on the Clipboard. Records of interest can be selected on the results page using check boxes and can then be combined, for example to form a reference list. The Related Citations is a valuable feature of PubMed that can provide a set of similar articles when you have identified a record of interest among the results. You can easily search for RCTs or reviews using the appropriate filters or field tags. If you are interested in clinical articles, rather than basic science or health service research, then the Clinical Queries tool on the PubMed home page can be used to retrieve them.

The development of PubMed search strategies for patient preferences for treatment outcomes.

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van Hoorn, Ralph; Kievit, Wietske; Booth, Andrew; Mozygemba, Kati; Lysdahl, Kristin Bakke; Refolo, Pietro; Sacchini, Dario; Gerhardus, Ansgar; van der Wilt, Gert Jan; Tummers, Marcia

2016-07-29

The importance of respecting patients' preferences when making treatment decisions is increasingly recognized. Efficiently retrieving papers from the scientific literature reporting on the presence and nature of such preferences can help to achieve this goal. The objective of this study was to create a search filter for PubMed to help retrieve evidence on patient preferences for treatment outcomes. A total of 27 journals were hand-searched for articles on patient preferences for treatment outcomes published in 2011. Selected articles served as a reference set. To develop optimal search strategies to retrieve this set, all articles in the reference set were randomly split into a development and a validation set. MeSH-terms and keywords retrieved using PubReMiner were tested individually and as combinations in PubMed and evaluated for retrieval performance (e.g. sensitivity (Se) and specificity (Sp)). Of 8238 articles, 22 were considered to report empirical evidence on patient preferences for specific treatment outcomes. The best search filters reached Se of 100 % [95 % CI 100-100] with Sp of 95 % [94-95 %] and Sp of 97 % [97-98 %] with 75 % Se [74-76 %]. In the validation set these queries reached values of Se of 90 % [89-91 %] with Sp 94 % [93-95 %] and Se of 80 % [79-81 %] with Sp of 97 % [96-96 %], respectively. Narrow and broad search queries were developed which can help in retrieving literature on patient preferences for treatment outcomes. Identifying such evidence may in turn enhance the incorporation of patient preferences in clinical decision making and health technology assessment.

Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks.

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Deeter, Anthony; Dalman, Mark; Haddad, Joseph; Duan, Zhong-Hui

2017-01-01

The PubMed database offers an extensive set of publication data that can be useful, yet inherently complex to use without automated computational techniques. Data repositories such as the Genomic Data Commons (GDC) and the Gene Expression Omnibus (GEO) offer experimental data storage and retrieval as well as curated gene expression profiles. Genetic interaction databases, including Reactome and Ingenuity Pathway Analysis, offer pathway and experiment data analysis using data curated from these publications and data repositories. We have created a method to generate and analyze consensus networks, inferring potential gene interactions, using large numbers of Bayesian networks generated by data mining publications in the PubMed database. Through the concept of network resolution, these consensus networks can be tailored to represent possible genetic interactions. We designed a set of experiments to confirm that our method is stable across variation in both sample and topological input sizes. Using gene product interactions from the KEGG pathway database and data mining PubMed publication abstracts, we verify that regardless of the network resolution or the inferred consensus network, our method is capable of inferring meaningful gene interactions through consensus Bayesian network generation with multiple, randomized topological orderings. Our method can not only confirm the existence of currently accepted interactions, but has the potential to hypothesize new ones as well. We show our method confirms the existence of known gene interactions such as JAK-STAT-PI3K-AKT-mTOR, infers novel gene interactions such as RAS- Bcl-2 and RAS-AKT, and found significant pathway-pathway interactions between the JAK-STAT signaling and Cardiac Muscle Contraction KEGG pathways.

The Tomato U-Box Type E3 Ligase PUB13 Acts With Group III Ubiquitin E2 Enzymes to Modulate FLS2-Mediated Immune Signaling

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Bangjun Zhou

2018-05-01

Full Text Available In Arabidopsis and rice, the ubiquitin ligase PUB13-mediated protein degradation plays a significant role in plant pattern-triggered immunity (PTI and flowering time control. The Arabidopsis PUB13 has been shown to attenuate the pattern recognition receptor FLS2-mediated immune signaling by ubiquitinating FLS2 and consequently promoting its degradation by the 26S proteasome. Nevertheless, the cognate ubiquitin-conjugating enzymes (E2 with which PUB13 acts to modulate FLS2-mediated PTI are unknown. To address this question, we investigate here the tomato (Solanum lycopersicum homolog of PUB13, SlPUB13 by utilizing the recently characterized complete set of tomato E2s. Of the 13 groups of tomato E2s, only members in group III are found to interact and act with SlPUB13. Knocking-down of the group III E2 genes enhances callose deposition and induction of the RbohB gene in the immunity-associated, early oxidative burst after flg22 treatment. The group III E2s are also found to work with SlPUB13 to ubiquitinate FLS2 in vitro and are required for PUB13-mediated degradation of FLS2 in vivo upon flg22 treatment, suggesting an essential role for group III E2s in the modulation of FLS2-mediated immune signaling by PUB13. Additionally, another immunity-associated E3, NtCMPG1 is shown to also work specifically with members of group III E2 in the in vitro ubiquitination assay, which implies the group III E2 enzymes may cooperate with many E3 ligases to regulate different aspects of PTI. Taken together, these data corroborate the notion that group III E2 enzymes play an important role in PTI and build a foundation for further functional and mechanistic characterization of tomato PUB13.

Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database

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Mariusz Butkiewicz

2013-01-01

Full Text Available With the rapidly increasing availability of High-Throughput Screening (HTS data in the public domain, such as the PubChem database, methods for ligand-based computer-aided drug discovery (LB-CADD have the potential to accelerate and reduce the cost of probe development and drug discovery efforts in academia. We assemble nine data sets from realistic HTS campaigns representing major families of drug target proteins for benchmarking LB-CADD methods. Each data set is public domain through PubChem and carefully collated through confirmation screens validating active compounds. These data sets provide the foundation for benchmarking a new cheminformatics framework BCL::ChemInfo, which is freely available for non-commercial use. Quantitative structure activity relationship (QSAR models are built using Artificial Neural Networks (ANNs, Support Vector Machines (SVMs, Decision Trees (DTs, and Kohonen networks (KNs. Problem-specific descriptor optimization protocols are assessed including Sequential Feature Forward Selection (SFFS and various information content measures. Measures of predictive power and confidence are evaluated through cross-validation, and a consensus prediction scheme is tested that combines orthogonal machine learning algorithms into a single predictor. Enrichments ranging from 15 to 101 for a TPR cutoff of 25% are observed.

Searching PubMed for a broad subject area: how effective are palliative care clinicians in finding the evidence in their field?

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Damarell, Raechel A; Tieman, Jennifer J

2016-03-01

Health professionals must be able to search competently for evidence to support practice. We sought to understand how palliative care clinicians construct searches for palliative care literature in PubMed, to quantify search efficacy in retrieving a set of relevant articles and to compare performance against a Palliative CareSearch Filter (PCSF). Included studies from palliative care systematic reviews formed a test set. Palliative care clinicians (n = 37) completed a search task using PubMed. Individual clinician searches were reconstructed in PubMed and combined with the test set to calculate retrieval sensitivity. PCSF performance in the test set was also determined. Many clinicians struggled to create useful searches. Twelve used a single search term, 17 narrowed the search inappropriately and 8 confused Boolean operators. The mean number of test set citations (n = 663) retrieved was 166 (SD = 188), or 25% although 76% of clinicians believed they would find more than 50% of the articles. Only 8 participants (22%) achieved this. Correlations between retrieval and PubMed confidence (r = 0.13) or frequency of use (r = -0.18) were weak. Many palliative care clinicians search PubMed ineffectively. Targeted skills training and PCSF promotion may improve evidence retrieval. © 2015 Health Libraries Group.

Worldwide access to evidence-based mental health literature: how useful is PubMed in Anglo-Saxon and non-Anglo-Saxon countries?

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Morlino, Massimo; Polese, Daniela; Bruni, Andrea; Renato, Bellinello

2005-10-01

The aim of this study was to verify the presence of cultural variety among the psychiatric journals available on PubMed, the major online tool for accessing literature. Data for analysis were taken from a survey of the world psychiatric journals indexed in Index Medicus 1999 (IM), the alphabetical list used by PubMed, and from the mean impact factor (IF) values of the journals. Approximately 80% of international psychiatric literature available on PubMed is published in Anglo-Saxon countries, especially in the USA (59.8% of the total). The widespread use of the English language (94.9% of all the journals) further stresses the dominance of the Anglo-Saxon cultural model, as do the mean IF values of Anglo-Saxon journals compared to non-Anglo-Saxon publications (3.252 vs. 1.693; P=0.0079). The under-representation of non-Anglo-Saxon cultural models on PubMed plays a negative role for bringing about a truly multicultural literature in psychiatry.

The development of PubMed search strategies for patient preferences for treatment outcomes

Directory of Open Access Journals (Sweden)

Ralph van Hoorn

2016-07-01

Full Text Available Abstract Background The importance of respecting patients’ preferences when making treatment decisions is increasingly recognized. Efficiently retrieving papers from the scientific literature reporting on the presence and nature of such preferences can help to achieve this goal. The objective of this study was to create a search filter for PubMed to help retrieve evidence on patient preferences for treatment outcomes. Methods A total of 27 journals were hand-searched for articles on patient preferences for treatment outcomes published in 2011. Selected articles served as a reference set. To develop optimal search strategies to retrieve this set, all articles in the reference set were randomly split into a development and a validation set. MeSH-terms and keywords retrieved using PubReMiner were tested individually and as combinations in PubMed and evaluated for retrieval performance (e.g. sensitivity (Se and specificity (Sp. Results Of 8238 articles, 22 were considered to report empirical evidence on patient preferences for specific treatment outcomes. The best search filters reached Se of 100 % [95 % CI 100-100] with Sp of 95 % [94–95 %] and Sp of 97 % [97–98 %] with 75 % Se [74–76 %]. In the validation set these queries reached values of Se of 90 % [89–91 %] with Sp 94 % [93–95 %] and Se of 80 % [79–81 %] with Sp of 97 % [96–96 %], respectively. Conclusions Narrow and broad search queries were developed which can help in retrieving literature on patient preferences for treatment outcomes. Identifying such evidence may in turn enhance the incorporation of patient preferences in clinical decision making and health technology assessment.

Using PubMed search strings for efficient retrieval of manual therapy research literature.

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Pillastrini, Paolo; Vanti, Carla; Curti, Stefania; Mattioli, Stefano; Ferrari, Silvano; Violante, Francesco Saverio; Guccione, Andrew

2015-02-01

The aim of this study was to construct PubMed search strings that could efficiently retrieve studies on manual therapy (MT), especially for time-constrained clinicians. Our experts chose 11 Medical Subject Heading terms describing MT along with 84 additional potential terms. For each term that was able to retrieve more than 100 abstracts, we systematically extracted a sample of abstracts from which we estimated the proportion of studies potentially relevant to MT. We then constructed 2 search strings: 1 narrow (threshold of pertinent articles ≥40%) and 1 expanded (including all terms for which a proportion had been calculated). We tested these search strings against articles on 2 conditions relevant to MT (thoracic and temporomandibular pain). We calculated the number of abstracts needed to read (NNR) to identify 1 potentially pertinent article in the context of these conditions. Finally, we evaluated the efficiency of the proposed PubMed search strings to identify relevant articles included in a systematic review on spinal manipulative therapy for chronic low back pain. Fifty-five search terms were able to extract more than 100 citations. The NNR to find 1 potentially pertinent article using the narrow string was 1.2 for thoracic pain and 1.3 for temporomandibular pain, and the NNR for the expanded string was 1.9 and 1.6, respectively. The narrow search strategy retrieved all the randomized controlled trials included in the systematic review selected for comparison. The proposed PubMed search strings may help health care professionals locate potentially pertinent articles and review a large number of MT studies efficiently to better implement evidence-based practice. Copyright © 2015 National University of Health Sciences. Published by Elsevier Inc. All rights reserved.

High-performance information search filters for CKD content in PubMed, Ovid MEDLINE, and EMBASE.

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Iansavichus, Arthur V; Hildebrand, Ainslie M; Haynes, R Brian; Wilczynski, Nancy L; Levin, Adeera; Hemmelgarn, Brenda R; Tu, Karen; Nesrallah, Gihad E; Nash, Danielle M; Garg, Amit X

2015-01-01

Finding relevant articles in large bibliographic databases such as PubMed, Ovid MEDLINE, and EMBASE to inform care and future research is challenging. Articles relevant to chronic kidney disease (CKD) are particularly difficult to find because they are often published under different terminology and are found across a wide range of journal types. We used computer automation within a diagnostic test assessment framework to develop and validate information search filters to identify CKD articles in large bibliographic databases. 22,992 full-text articles in PubMed, Ovid MEDLINE, or EMBASE. 1,374,148 unique search filters. We established the reference standard of article relevance to CKD by manual review of all full-text articles using prespecified criteria to determine whether each article contained CKD content or not. We then assessed filter performance by calculating sensitivity, specificity, and positive predictive value for the retrieval of CKD articles. Filters with high sensitivity and specificity for the identification of CKD articles in the development phase (two-thirds of the sample) were then retested in the validation phase (remaining one-third of the sample). We developed and validated high-performance CKD search filters for each bibliographic database. Filters optimized for sensitivity reached at least 99% sensitivity, and filters optimized for specificity reached at least 97% specificity. The filters were complex; for example, one PubMed filter included more than 89 terms used in combination, including "chronic kidney disease," "renal insufficiency," and "renal fibrosis." In proof-of-concept searches, physicians found more articles relevant to the topic of CKD with the use of these filters. As knowledge of the pathogenesis of CKD grows and definitions change, these filters will need to be updated to incorporate new terminology used to index relevant articles. PubMed, Ovid MEDLINE, and EMBASE can be filtered reliably for articles relevant to CKD. These

The trend of indexed papers in PubMed covering different aspects of self-immolation.

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Rezaeian, Mohsen

2014-01-01

Self-immolation is a fatal and devastating method of committing suicide used around the world. The chief aim of the present article is to look at the trend of indexed papers in PubMed covering different aspects of self-immolation. PubMed search engine (http://www.ncbi.nlm.nih.gov) was searched by using six keywords i.e. "self-immolation", "self-inflicted burn", "self-burning", "self-incineration", "suicidal burns" and "suicide by burning". These keywords should appear either in the title or the abstract of the articles. The time frame was set as to retrieve papers expanding from early indexing time up to end of the year 2011. Based on the search strategy 132 papers were retrieved from these total numbers; 12 (9%) were categorized as review papers; 24 (18%) as case reports and the rest 96 (73%) were original studies. It seems that the number of papers increased during the years of investigations and the highest indexed papers i.e. 14 (10.6%) belonged to the year 2011. While most journals, published only one article the highest indexed papers i.e. 35 (26.5%) belonged to Burns. There was an increasing trend in the number of self-immolation articles indexed in PubMed since 1965. Three journals i.e. Burns, Journal of Burn Care and Rehabilitation and Journal of Forensic Sciences hosted for more than 37% of all those indexed articles. However, given the increasing trend of self-immolation still more studies are needed to shed light on the diverse aspects of this appalling human behavior.

Answers to questions posed during daily patient care are more likely to be answered by UpToDate than PubMed.

NARCIS (Netherlands)

Hoogendam, A.; Stalenhoef, A.F.H.; Vries Robbe, P.F. de; Overbeke, A.J.P.M.

2008-01-01

BACKGROUND: UpToDate and PubMed are popular sources for medical information. Data regarding the efficiency of PubMed and UpToDate in daily medical care are lacking. OBJECTIVE: The purpose of this observational study was to describe the percentage of answers retrieved by these information sources,

Analysis of queries sent to PubMed at the point of care: observation of search behaviour in a medical teaching hospital.

NARCIS (Netherlands)

Hoogendam, A.; Stalenhoef, A.F.H.; Vries Robbe, P.F. de; Overbeke, A.J.P.M.

2008-01-01

BACKGROUND: The use of PubMed to answer daily medical care questions is limited because it is challenging to retrieve a small set of relevant articles and time is restricted. Knowing what aspects of queries are likely to retrieve relevant articles can increase the effectiveness of PubMed searches.

Astronomy on Tap: science engagement in the pub

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Livermore, Rachael C.; Silverman, Jeffrey Michael

2015-08-01

Astronomy on Tap is a series of free lectures by astronomers in the pub, aimed at disseminating the latest research to the public in an informal setting. Started in New York City in 2013, Astronomy on Tap has now expanded to seven cities across North and South America. Organized by local astronomers, each event features talks by astronomers from local institutions or visitors, or others whose professions or hobbies intersect with astronomy, along with games and opportunities for the public to interact with professional astronomers. The largest Astronomy on Tap events are in Austin, Texas, attracting over 150 people each month, which consists of populations outside of the self-selected groups that might be reached by more formal EPO activities. The organisers of Astronomy on Tap in Austin (AoTATX) will discuss the impact of and feedback from all of the locations, and present information on setting up new satellite locations.

Physical Unclonable Function with Multiplexing Units and its Evaluation

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Yoshikawa, Masaya; Asai, Toshiya; Shiozaki, Mitsuru; Fujino, Takeshi

Recently, semiconductor counterfeiting has become an increasingly serious problem. Therefore, techniques to prevent the counterfeit by using random characteristic patterns that are difficult to control artificially have attracted attention. The physical unclonable function (PUF) is one of the techniques. It is a method to derive ID information peculiar to a device by detecting random physical features that cannot be controlled during the device's manufacture. Because information such as the ID information is difficult to replicate, PUF is used as a technique to prevent counterfeiting. Several studies have been reported on PUF. Arbiter PUF, which utilizes the difference in signal propagation delay between selectors, is the typical method of composing PUF using delay characteristics. This paper proposed a new PUF which is based on the arbiter PUF. The proposed PUF introduces new multiplexing selector units. It attempts to generate an effective response using the orders of three signal arrivals. Experiments using FPGAs verify the validity of the proposed PUF. Although Uniqueness is deteriorated, Correctness, Steadiness, Randomness and Resistance against the machine learning attacks are improved in comparison with conventional one.

[A statistical analysis and perspective of headache-related papers covered in 2011 PubMed].

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Zhang, Ming-jie; Yu, Sheng-yuan; Chu, Bing-qian; Dai, Wei

2013-01-01

To investigate the distribution and hot spots of literatures on headache by bibliometric analysis in order to provide reference for further study. Literatures that contained headache or migraine in text words published in 2011 in PubMed databases (www.ncbi.nlm.nih.gov/Pubmed) were searched. Journals, countries and subjects were bibliometrically analysed. There were 3683 papers involved to headache published in PubMed in 2011, of which 1527 papers were on headache research. The number of papers on headache research published by USA was the most followed by Italy and Germany (USA 23.25%, Italy 10.74%, Germany 5.83%). The mainly studied subjects were therapy (29.60%), pathophysiology (18.66%) and etiology (16.31%). 14.86% papers published in Cephalalgia, which is one of the most important journals, reported negative results. The emphasis of headache research was on migraine. Therapy, pathophysiology and etiology were the hot spot. Literatures with negative result attracted authors to give the more attention.

Physical Unclonable Functions in Theory and Practice

CERN Document Server

Böhm, Christoph

2013-01-01

In Physical Unclonable Functions in Theory and Practice, the authors present an in-depth overview of various topics concerning PUFs, providing theoretical background and application details. This book concentrates on the practical issues of PUF hardware design, focusing on dedicated microelectronic PUF circuits. Additionally, the authors discuss the whole process of circuit design, layout and chip verification. The book also offers coverage of: Different published approaches focusing on dedicated microelectronic PUF circuits Specification of PUF circuits and different error rate reducing pre-selection techniques General design issues and minimizing error rate from the circuit’s perspective Transistor modeling issues of Montecarlo mismatch simulation and solutions Examples of PUF circuits including an accurate description of the circuits and testing/measurement results  This monograph gives insight into PUFs in general and provides knowledge in the field of PUF circuit design and implementation. It coul...

Bibliometric and content analysis of medical articles in the PubMed database published by North Korean authors from 1997 to July 2017

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Geum Hee Jeong

2017-08-01

Full Text Available This study aimed at analyzing the bibliometric characteristics and content of medical articles from North Korea in PubMed and characterizing the patterns of international cooperation of medical researchers in North Korea. We hypothesized that the number of publications from North Korea in PubMed has increased recently as a result of active cooperation with foreign researchers. PubMed was searched on July 19, 2017 using the search term “(North Korea [Affiliation] OR Democratic People’s Republic of Korea [Affiliation] OR DPRK [Affiliation].” The content of medical articles was analyzed and cooperative work with foreign researchers was noted. The number of medical articles in PubMed through July 2017 was 16, of which 2 were by North Korean authors only. From the content of these articles, it was found that researchers in top-notch institutions, including Kim Il Sung University, can access the internet, and that a dental caries prevention program supported by Finland has been in place for more than 10 years. The number of publications from North Korea in PubMed has increased recently, although the amount is still very small. Providing internet access to North Korean researchers will accelerate their submissions to international journals.

GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique

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Khoury Muin J

2008-04-01

Full Text Available Abstract Background Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a substantial proportion of the abstracts in PubMed, identifying them with standard queries is not always accurate or efficient. Further automating the literature-screening process can reduce the burden of a labor-intensive and time-consuming traditional literature search. The Support Vector Machine (SVM, a well-established machine learning technique, has been successful in classifying text, including biomedical literature. The GAPscreener, a free SVM-based software tool, can be used to assist in screening PubMed abstracts for human genetic association studies. Results The data source for this research was the HuGE Navigator, formerly known as the HuGE Pub Lit database. Weighted SVM feature selection based on a keyword list obtained by the two-way z score method demonstrated the best screening performance, achieving 97.5% recall, 98.3% specificity and 31.9% precision in performance testing. Compared with the traditional screening process based on a complex PubMed query, the SVM tool reduced by about 90% the number of abstracts requiring individual review by the database curator. The tool also ascertained 47 articles that were missed by the traditional literature screening process during the 4-week test period. We examined the literature on genetic associations with preterm birth as an example. Compared with the traditional, manual process, the GAPscreener both reduced effort and improved accuracy. Conclusion GAPscreener is the first free SVM-based application available for screening the human genetic association literature in PubMed with high recall and specificity. The user-friendly graphical user interface makes this a practical, stand-alone application. The software can be downloaded at no charge.

25 CFR 1000.84 - Does a Tribe/Consortium have the right to include provisions of Title I of Pub. L. 93-638 in an AFA?

Science.gov (United States)

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false Does a Tribe/Consortium have the right to include.../Consortium have the right to include provisions of Title I of Pub. L. 93-638 in an AFA? Yes, under Pub. L. 104-109, a Tribe/Consortium has the right to include any provision of Title I of Pub. L. 93-638 in an...

Automatic identification of high impact articles in PubMed to support clinical decision making.

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Bian, Jiantao; Morid, Mohammad Amin; Jonnalagadda, Siddhartha; Luo, Gang; Del Fiol, Guilherme

2017-09-01

The practice of evidence-based medicine involves integrating the latest best available evidence into patient care decisions. Yet, critical barriers exist for clinicians' retrieval of evidence that is relevant for a particular patient from primary sources such as randomized controlled trials and meta-analyses. To help address those barriers, we investigated machine learning algorithms that find clinical studies with high clinical impact from PubMed®. Our machine learning algorithms use a variety of features including bibliometric features (e.g., citation count), social media attention, journal impact factors, and citation metadata. The algorithms were developed and evaluated with a gold standard composed of 502 high impact clinical studies that are referenced in 11 clinical evidence-based guidelines on the treatment of various diseases. We tested the following hypotheses: (1) our high impact classifier outperforms a state-of-the-art classifier based on citation metadata and citation terms, and PubMed's® relevance sort algorithm; and (2) the performance of our high impact classifier does not decrease significantly after removing proprietary features such as citation count. The mean top 20 precision of our high impact classifier was 34% versus 11% for the state-of-the-art classifier and 4% for PubMed's® relevance sort (p=0.009); and the performance of our high impact classifier did not decrease significantly after removing proprietary features (mean top 20 precision=34% vs. 36%; p=0.085). The high impact classifier, using features such as bibliometrics, social media attention and MEDLINE® metadata, outperformed previous approaches and is a promising alternative to identifying high impact studies for clinical decision support. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification of risk conditions for the development of adrenal disorders: how optimized PubMed search strategies makes the difference.

Science.gov (United States)

Guaraldi, Federica; Parasiliti-Caprino, Mirko; Goggi, Riccardo; Beccuti, Guglielmo; Grottoli, Silvia; Arvat, Emanuela; Ghizzoni, Lucia; Ghigo, Ezio; Giordano, Roberta; Gori, Davide

2014-12-01

The exponential growth of scientific literature available through electronic databases (namely PubMed) has increased the chance of finding interesting articles. At the same time, search has become more complicated, time consuming, and at risk of missing important information. Therefore, optimized strategies have to be adopted to maximize searching impact. The aim of this study was to formulate efficient strings to search PubMed for etiologic associations between adrenal disorders (ADs) and other conditions. A comprehensive list of terms identifying endogenous conditions primarily affecting adrenals was compiled. An ad hoc analysis was performed to find the best way to express each term in order to find the highest number of potentially pertinent articles in PubMed. A predefined number of retrieved abstracts were read to assess their association with ADs' etiology. A more sensitive (providing the largest literature coverage) and a more specific (including only those terms retrieving >40 % of potentially pertinent articles) string were formulated. Various researches were performed to assess strings' ability to identify articles of interest in comparison with non-optimized literature searches. We formulated optimized, ready applicable tools for the identification of the literature assessing etiologic associations in the field of ADs using PubMed, and demonstrated the advantages deriving from their application. Detailed description of the methodological process is also provided, so that this work can easily be translated to other fields of practice.

PubChemQC Project: A Large-Scale First-Principles Electronic Structure Database for Data-Driven Chemistry.

Science.gov (United States)

Nakata, Maho; Shimazaki, Tomomi

2017-06-26

Large-scale molecular databases play an essential role in the investigation of various subjects such as the development of organic materials, in silico drug design, and data-driven studies with machine learning. We have developed a large-scale quantum chemistry database based on first-principles methods. Our database currently contains the ground-state electronic structures of 3 million molecules based on density functional theory (DFT) at the B3LYP/6-31G* level, and we successively calculated 10 low-lying excited states of over 2 million molecules via time-dependent DFT with the B3LYP functional and the 6-31+G* basis set. To select the molecules calculated in our project, we referred to the PubChem Project, which was used as the source of the molecular structures in short strings using the InChI and SMILES representations. Accordingly, we have named our quantum chemistry database project "PubChemQC" ( http://pubchemqc.riken.jp/ ) and placed it in the public domain. In this paper, we show the fundamental features of the PubChemQC database and discuss the techniques used to construct the data set for large-scale quantum chemistry calculations. We also present a machine learning approach to predict the electronic structure of molecules as an example to demonstrate the suitability of the large-scale quantum chemistry database.

Architecture and dynamics of overlapped RNA regulatory networks.

Science.gov (United States)

Lapointe, Christopher P; Preston, Melanie A; Wilinski, Daniel; Saunders, Harriet A J; Campbell, Zachary T; Wickens, Marvin

2017-11-01

A single protein can bind and regulate many mRNAs. Multiple proteins with similar specificities often bind and control overlapping sets of mRNAs. Yet little is known about the architecture or dynamics of overlapped networks. We focused on three proteins with similar structures and related RNA-binding specificities-Puf3p, Puf4p, and Puf5p of S. cerevisiae Using RNA Tagging, we identified a "super-network" comprised of four subnetworks: Puf3p, Puf4p, and Puf5p subnetworks, and one controlled by both Puf4p and Puf5p. The architecture of individual subnetworks, and thus the super-network, is determined by competition among particular PUF proteins to bind mRNAs, their affinities for binding elements, and the abundances of the proteins. The super-network responds dramatically: The remaining network can either expand or contract. These strikingly opposite outcomes are determined by an interplay between the relative abundance of the RNAs and proteins, and their affinities for one another. The diverse interplay between overlapping RNA-protein networks provides versatile opportunities for regulation and evolution. © 2017 Lapointe et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Searching for observational studies: what does citation tracking add to PubMed? A case study in depression and coronary heart disease

Directory of Open Access Journals (Sweden)

Hemingway Harry

2006-02-01

Full Text Available Abstract Background PubMed is the most widely used method for searches of the medical literature, but fails to identify many relevant articles. Electronic citation tracking offers an alternative search method. Methods Articles investigating the role of depression in the aetiology and prognosis of coronary heart disease were sought through two methods: a PubMed, and b citation tracking where Science Citation Index was searched for all articles which cited ("forward citation tracking" or were cited by ("backward citation tracking" any of the articles in an index review. The number and quality of eligible articles identified by the two methods were compared. Results 50 articles that were not already included in the index review met our inclusion criteria; 11 were identified through Science Citation Index alone, 8 through PubMed alone, and 31 through both methods. Articles identified by Science Citation Index alone were published in higher impact factor journals, were larger and were less likely to show a positive association. Conclusion Science Citation Index identified more eligible articles than PubMed, and these differed qualitatively. Failing to use citation tracking in a systematic review of observational studies may result in bias.

Validation of a search strategy to identify nutrition trials in PubMed using the relative recall method.

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Durão, Solange; Kredo, Tamara; Volmink, Jimmy

2015-06-01

To develop, assess, and maximize the sensitivity of a search strategy to identify diet and nutrition trials in PubMed using relative recall. We developed a search strategy to identify diet and nutrition trials in PubMed. We then constructed a gold standard reference set to validate the identified trials using the relative recall method. Relative recall was calculated by dividing the number of references from the gold standard our search strategy identified by the total number of references in the gold standard. Our gold standard comprised 298 trials, derived from 16 included systematic reviews. The initial search strategy identified 242 of 298 references, with a relative recall of 81.2% [95% confidence interval (CI): 76.3%, 85.5%]. We analyzed titles and abstracts of the 56 missed references for possible additional terms. We then modified the search strategy accordingly. The relative recall of the final search strategy was 88.6% (95% CI: 84.4%, 91.9%). We developed a search strategy to identify diet and nutrition trials in PubMed with a high relative recall (sensitivity). This could be useful for establishing a nutrition trials register to support the conduct of future research, including systematic reviews. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed.

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Capuzzi, Stephen J; Thornton, Thomas E; Liu, Kammy; Baker, Nancy; Lam, Wai In; O'Banion, Colin P; Muratov, Eugene N; Pozefsky, Diane; Tropsha, Alexander

2018-02-26

Elucidation of the mechanistic relationships between drugs, their targets, and diseases is at the core of modern drug discovery research. Thousands of studies relevant to the drug-target-disease (DTD) triangle have been published and annotated in the Medline/PubMed database. Mining this database affords rapid identification of all published studies that confirm connections between vertices of this triangle or enable new inferences of such connections. To this end, we describe the development of Chemotext, a publicly available Web server that mines the entire compendium of published literature in PubMed annotated by Medline Subject Heading (MeSH) terms. The goal of Chemotext is to identify all known DTD relationships and infer missing links between vertices of the DTD triangle. As a proof-of-concept, we show that Chemotext could be instrumental in generating new drug repurposing hypotheses or annotating clinical outcomes pathways for known drugs. The Chemotext Web server is freely available at http://chemotext.mml.unc.edu .

Plasma confinement modification and convective transport suppression in the scrape-off layer using additional gas puffing in the STOR-M tokamak

International Nuclear Information System (INIS)

Dreval, M; Hubeny, M; Ding, Y; Onchi, T; Liu, Y; Hthu, K; Elgriw, S; Xiao, C; Hirose, A

2013-01-01

The influence of short gas puffing (GP) pulses on the scrape-off layer (SOL) transport is studied. Similar responses of ion saturation current and floating potential measured near the GP injection valve and in the 90° toroidally separated cross-section suggest that the GP influence on the SOL region should be global. A drop in plasma temperature and a decrease in the rotational velocity of the plasma are observed in the SOL region immediately after the GP pulse; however, an unexpected increase in electron and ion temperatures is observed in the second stage of the plasma response. The decrease in floating potential fluctuations indicates that the turbulent transport is dumped immediately after the GP pulse. The GP-induced modification of turbulence properties in the SOL points to a convective transport suppression in the STOR-M tokamak. A substantial decrease in the skewness and kurtosis of ion saturation current fluctuations is observed in the SOL region resulting in the probability distribution function (PDF) getting closer to the Gaussian distribution. The plasma potential reduction, the change in plasma rotation and the suppression of turbulent transport in the SOL region indicate that the plasma confinement is modified after the GP injection. Some features of the H-mode-like confinement in the plasma bulk also accompany the SOL observations after application of the additional sharp GP pulse. (paper)

Levels of second hand smoke in pubs and bars by deprivation and food-serving status: a cross-sectional study from North West England

Directory of Open Access Journals (Sweden)

Hart Judy

2006-02-01

Full Text Available Abstract Background The UK government proposed introducing partial smokefree legislation for England with exemptions for pubs and bars that do not prepare and serve food. We set out to test the hypothesis that pubs from more deprived areas and non food-serving pubs have higher levels of particulate air pollution. Methods We conducted a cross sectional study in four mainly urban areas of the North West of England. We recruited a stratified random sample of 64 pubs divided into four groups based on whether their local population was affluent or deprived (using a UK area based deprivation measure, and whether or not they served food. The timing of air quality monitoring stratified to ensure similar distribution of monitoring by day of the week and time of evening between groups. We used a portable air quality monitor to collect fine particle (PM2.5 levels over a minimum of 30 minutes in areas where smoking was allowed,, and calculated mean time-time weighted average PM2.5 levels. Results Mean PM2.5 was 285.5 μg/m3 (95% CI 212.7 to 358.3. Mean levels in the four groups were: affluent food-serving pubs (n = 16 188.1 μg/m3 (95%CI 128.1 to 248.1; affluent non food-serving (n = 16 186.8 μg/m3 (95%CI 118.9 to 254.3; deprived food-serving (n = 17 399.4 μg/m3 (95%CI 177.7 to 621.2; and deprived non food-serving (n = 15 365.7 μg/m3 (195.6 to 535.7. Levels were higher in pubs in deprived communities: mean 383.6 μg/m3 (95% CI 249.2 to 518.0 vs 187.4 μg/m3 (144.8 to 229.9; geometric mean 245.2 μg/m3 vs 151.2 μg/m3 (p = 0.03. There was little difference in particulate levels between food and non food-serving pubs. Conclusion This study adds to the evidence that the UK government’s proposals for partial smokefree legislation in England would offer the least protection to the most heavily exposed group - bar workers and customers in non food-serving pubs in deprived areas. The results suggest these proposals would work against the UK government�

Hardware device to physical structure binding and authentication

Science.gov (United States)

Hamlet, Jason R.; Stein, David J.; Bauer, Todd M.

2013-08-20

Detection and deterrence of device tampering and subversion may be achieved by including a cryptographic fingerprint unit within a hardware device for authenticating a binding of the hardware device and a physical structure. The cryptographic fingerprint unit includes an internal physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generate an internal PUF value. Binding logic is coupled to receive the internal PUF value, as well as an external PUF value associated with the physical structure, and generates a binding PUF value, which represents the binding of the hardware device and the physical structure. The cryptographic fingerprint unit also includes a cryptographic unit that uses the binding PUF value to allow a challenger to authenticate the binding.

Bibliometric assessment of publication output of child and adolescent psychiatric/psychological affiliations between 2005 and 2010 based on the databases PubMed and Scopus.

Science.gov (United States)

Albayrak, Ozgür; Föcker, Manuel; Wibker, Katrin; Hebebrand, Johannes

2012-06-01

We aimed to determine the quantitative scientific publication output of child and adolescent psychiatric/psychological affiliations during 2005-2010 by country based on both, "PubMed" and "Scopus" and performed a bibliometric qualitative evaluation for 2009 using "PubMed". We performed our search by affiliation related to child and adolescent psychiatric/psychological institutions using "PubMed". For the quantitative analysis for 2005-2010, we counted the number of abstracts. For the qualitative analysis for 2009 we derived the impact factor of each abstract's journal from "Journal Citation Reports". We related total impact factor scores to the gross domestic product (GDP) and population size of each country. Additionally, we used "Scopus" to determine the number of abstracts for each country that was identified via "PubMed" for 2009 and compared the ranking of countries between the two databases. 61 % of the publications between 2005 and 2010 originated from European countries and 26 % from the USA. After adjustment for GDP and population size, the ranking positions changed in favor of smaller European countries with a population size of less than 20 million inhabitants. The ranking of countries for the count of articles in 2009 as derived from "Scopus" was similar to that identified via the "PubMed" search. The performed search revealed only minor differences between "Scopus" and "PubMed" related to the ranking of countries. Our data indicate a sharp difference between countries with a high versus low GDP with regard to scientific publication output in child and adolescent psychiatry/psychology.

Recurrent rewiring and emergence of RNA regulatory networks.

Science.gov (United States)

Wilinski, Daniel; Buter, Natascha; Klocko, Andrew D; Lapointe, Christopher P; Selker, Eric U; Gasch, Audrey P; Wickens, Marvin

2017-04-04

Alterations in regulatory networks contribute to evolutionary change. Transcriptional networks are reconfigured by changes in the binding specificity of transcription factors and their cognate sites. The evolution of RNA-protein regulatory networks is far less understood. The PUF (Pumilio and FBF) family of RNA regulatory proteins controls the translation, stability, and movements of hundreds of mRNAs in a single species. We probe the evolution of PUF-RNA networks by direct identification of the mRNAs bound to PUF proteins in budding and filamentous fungi and by computational analyses of orthologous RNAs from 62 fungal species. Our findings reveal that PUF proteins gain and lose mRNAs with related and emergent biological functions during evolution. We demonstrate at least two independent rewiring events for PUF3 orthologs, independent but convergent evolution of PUF4/5 binding specificity and the rewiring of the PUF4/5 regulons in different fungal lineages. These findings demonstrate plasticity in RNA regulatory networks and suggest ways in which their rewiring occurs.

Beyond PubMed: Searching the "Grey Literature" for Clinical Trial Results.

Science.gov (United States)

Citrome, Leslie

2014-07-01

Clinical trial results have been traditionally communicated through the publication of scholarly reports and reviews in biomedical journals. However, this dissemination of information can be delayed or incomplete, making it difficult to appraise new treatments, or in the case of missing data, evaluate older interventions. Going beyond the routine search of PubMed, it is possible to discover additional information in the "grey literature." Examples of the grey literature include clinical trial registries, patent databases, company and industrywide repositories, regulatory agency digital archives, abstracts of paper and poster presentations on meeting/congress websites, industry investor reports and press releases, and institutional and personal websites.

The proportion of cancer-related entries in PubMed has increased considerably; is cancer truly "The Emperor of All Maladies"?

Science.gov (United States)

Reyes-Aldasoro, Constantino Carlos

2017-01-01

In this work, the public database of biomedical literature PubMed was mined using queries with combinations of keywords and year restrictions. It was found that the proportion of Cancer-related entries per year in PubMed has risen from around 6% in 1950 to more than 16% in 2016. This increase is not shared by other conditions such as AIDS, Malaria, Tuberculosis, Diabetes, Cardiovascular, Stroke and Infection some of which have, on the contrary, decreased as a proportion of the total entries per year. Organ-related queries were performed to analyse the variation of some specific cancers. A series of queries related to incidence, funding, and relationship with DNA, Computing and Mathematics, were performed to test correlation between the keywords, with the hope of elucidating the cause behind the rise of Cancer in PubMed. Interestingly, the proportion of Cancer-related entries that contain "DNA", "Computational" or "Mathematical" have increased, which suggests that the impact of these scientific advances on Cancer has been stronger than in other conditions. It is important to highlight that the results obtained with the data mining approach here presented are limited to the presence or absence of the keywords on a single, yet extensive, database. Therefore, results should be observed with caution. All the data used for this work is publicly available through PubMed and the UK's Office for National Statistics. All queries and figures were generated with the software platform Matlab and the files are available as supplementary material.

Development of a PubMed Based Search Tool for Identifying Sex and Gender Specific Health Literature.

Science.gov (United States)

Song, Michael M; Simonsen, Cheryl K; Wilson, Joanna D; Jenkins, Marjorie R

2016-02-01

An effective literature search strategy is critical to achieving the aims of Sex and Gender Specific Health (SGSH): to understand sex and gender differences through research and to effectively incorporate the new knowledge into the clinical decision making process to benefit both male and female patients. The goal of this project was to develop and validate an SGSH literature search tool that is readily and freely available to clinical researchers and practitioners. PubMed, a freely available search engine for the Medline database, was selected as the platform to build the SGSH literature search tool. Combinations of Medical Subject Heading terms, text words, and title words were evaluated for optimal specificity and sensitivity. The search tool was then validated against reference bases compiled for two disease states, diabetes and stroke. Key sex and gender terms and limits were bundled to create a search tool to facilitate PubMed SGSH literature searches. During validation, the search tool retrieved 50 of 94 (53.2%) stroke and 62 of 95 (65.3%) diabetes reference articles selected for validation. A general keyword search of stroke or diabetes combined with sex difference retrieved 33 of 94 (35.1%) stroke and 22 of 95 (23.2%) diabetes reference base articles, with lower sensitivity and specificity for SGSH content. The Texas Tech University Health Sciences Center SGSH PubMed Search Tool provides higher sensitivity and specificity to sex and gender specific health literature. The tool will facilitate research, clinical decision-making, and guideline development relevant to SGSH.

PubstractHelper: A Web-based Text-Mining Tool for Marking Sentences in Abstracts from PubMed Using Multiple User-Defined Keywords.

Science.gov (United States)

Chen, Chou-Cheng; Ho, Chung-Liang

2014-01-01

While a huge amount of information about biological literature can be obtained by searching the PubMed database, reading through all the titles and abstracts resulting from such a search for useful information is inefficient. Text mining makes it possible to increase this efficiency. Some websites use text mining to gather information from the PubMed database; however, they are database-oriented, using pre-defined search keywords while lacking a query interface for user-defined search inputs. We present the PubMed Abstract Reading Helper (PubstractHelper) website which combines text mining and reading assistance for an efficient PubMed search. PubstractHelper can accept a maximum of ten groups of keywords, within each group containing up to ten keywords. The principle behind the text-mining function of PubstractHelper is that keywords contained in the same sentence are likely to be related. PubstractHelper highlights sentences with co-occurring keywords in different colors. The user can download the PMID and the abstracts with color markings to be reviewed later. The PubstractHelper website can help users to identify relevant publications based on the presence of related keywords, which should be a handy tool for their research. http://bio.yungyun.com.tw/ATM/PubstractHelper.aspx and http://holab.med.ncku.edu.tw/ATM/PubstractHelper.aspx.

A Bibliometric Analysis of PubMed Literature on Middle East Respiratory Syndrome.

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Wang, Zhengting; Chen, Yongdi; Cai, Gaofeng; Jiang, Zhenggang; Liu, Kui; Chen, Bin; Jiang, Jianmin; Gu, Hua

2016-06-13

Middle East Respiratory Syndrome (MERS), a pandemic threat to human beings, has aroused huge concern worldwide, but no bibliometric studies have been conducted on MERS research. The aim of this study was to map research productivity on the disease based on the articles indexed in PubMed. The articles related to MERS dated from 2012 to 2015 were retrieved from PubMed. The articles were classified into three categories according to their focus. Publication outputs were assessed and frequently used terms were mapped using the VOS viewer software. A total of 443 articles were included for analysis. They were published in 162 journals, with Journal of Virology being the most productive (44 articles; 9.9%) and by six types of organizations, with universities being the most productive (276 articles; 62.4%).The largest proportion of the articles focused on basic medical sciences and clinical studies (47.2%) and those on prevention and control ranked third (26.2%), with those on other focuses coming in between (26.6%). The articles on prevention and control had the highest mean rank for impact factor (IF) (226.34), followed by those on basic medical sciences and clinical studies (180.23) and those on other focuses (168.03). The mean rank differences were statistically significant (p = 0.000). Besides, "conronavirus", "case", "transmission" and "detection" were found to be the most frequently used terms. The findings of this first bibliometric study on MERS suggest that the prevention and control of the disease has become a big concern and related research should be strengthened.

The interest of Romanian consumers in using QR codes in restaurants and pubs

OpenAIRE

Marius BĂLĂŞESCU; Lavinia DOVLEAC

2017-01-01

The fast development of smartphone technology has created an opportunity to use QR code, considered a popular way of mobile tagging due to its ease of use. Various types of hospitality units, such as accommodations or restaurants and bars have found in QR codes an excellent marketing tool. This paper presents the results of a marketing research study conducted in Brasov city from Romania regarding the consumers’ interest in using QR codes in restaurants and pubs. The results show that mostly ...

Measurement of polyurethane foam - air partition coefficients for semivolatile organic compounds as a function of temperature: Application to passive air sampler monitoring.

Science.gov (United States)

Francisco, Ana Paula; Harner, Tom; Eng, Anita

2017-05-01

Polyurethane foam - air partition coefficients (K PUF-air ) for 9 polycyclic aromatic hydrocarbons (PAHs), 10 alkyl-substituted PAHs, 4 organochlorine pesticides (OCPs) and dibenzothiophene were measured as a function of temperature over the range 5 °C-35 °C, using a generator column approach. Enthalpies of PUF-to-air transfer (ΔH PUF-air , kJ/mol) were determined from the slopes of log K PUF-air versus 1000/T (K), and have an average value of 81.2 ± 7.03 kJ/mol. The log K PUF-air values at 22 °C ranged from 4.99 to 7.25. A relationship for log K PUF-air versus log K OA was shown to agree with a previous relationship based on only polychlorinated biphenyls (PCBs) and derived from long-term indoor uptake study experiments. The results also confirm that the existing K OA -based model for predicting log K PUF-air values is accurate. This new information is important in the derivation of uptake profiles and effective air sampling volumes for PUF disk samplers so that results can be reported in units of concentration in air. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

BTB-BACK Domain Protein POB1 Suppresses Immune Cell Death by Targeting Ubiquitin E3 ligase PUB17 for Degradation.

Directory of Open Access Journals (Sweden)

Beatriz Orosa

2017-01-01

Full Text Available Hypersensitive response programmed cell death (HR-PCD is a critical feature in plant immunity required for pathogen restriction and prevention of disease development. The precise control of this process is paramount to cell survival and an effective immune response. The discovery of new components that function to suppress HR-PCD will be instrumental in understanding the regulation of this fundamental mechanism. Here we report the identification and characterisation of a BTB domain E3 ligase protein, POB1, that functions to suppress HR-PCD triggered by evolutionarily diverse pathogens. Nicotiana benthamiana and tobacco plants with reduced POB1 activity show accelerated HR-PCD whilst those with increased POB1 levels show attenuated HR-PCD. We demonstrate that POB1 dimerization and nuclear localization are vital for its function in HR-PCD suppression. Using protein-protein interaction assays, we identify the Plant U-Box E3 ligase PUB17, a well established positive regulator of plant innate immunity, as a target for POB1-mediated proteasomal degradation. Using confocal imaging and in planta immunoprecipitation assays we show that POB1 interacts with PUB17 in the nucleus and stimulates its degradation. Mutated versions of POB1 that show reduced interaction with PUB17 fail to suppress HR-PCD, indicating that POB1-mediated degradation of PUB17 U-box E3 ligase is an important step for negative regulation of specific immune pathways in plants. Our data reveals a new mechanism for BTB domain proteins in suppressing HR-PCD in plant innate immune responses.

Global visibility for global health: Is it time for a new descriptor in Medical Subject Heading (MeSH of MEDLINE/PubMed?

Directory of Open Access Journals (Sweden)

Ana Marušic´

2013-06-01

Full Text Available Despite a large body of research in global health (almost 9000 articles published in PubMed until 2012, the term “global health” is not included in the Medical Subject Headings (MeSH of the NLM – its controlled vocabulary thesaurus which NLM uses to index articles in MEDL INE. There are only 6 journals currently covered by PubMed which specialize in global health, including Journal of Global Health.

A framework to enhance security of physically unclonable functions using chaotic circuits

Science.gov (United States)

Chen, Lanxiang

2018-05-01

As a new technique for authentication and key generation, physically unclonable function (PUF) has attracted considerable attentions, with extensive research results achieved already. To resist the popular machine learning modeling attacks, a framework to enhance the security of PUFs is proposed. The basic idea is to combine PUFs with a chaotic system of which the response is highly sensitive to initial conditions. For this framework, a specific construction which combines the common arbiter PUF circuit, a converter, and the Chua's circuit is given to implement a more secure PUF. Simulation experiments are presented to further validate the framework. Finally, some practical suggestions for the framework and specific construction are also discussed.

On the Support of Scientific Workflows over Pub/Sub Brokers

Directory of Open Access Journals (Sweden)

Edwin Cedeño

2013-08-01

Full Text Available The execution of scientific workflows is gaining importance as more computing resources are available in the form of grid environments. The Publish/Subscribe paradigm offers well-proven solutions for sustaining distributed scenarios while maintaining the high level of task decoupling required by scientific workflows. In this paper, we propose a new model for supporting scientific workflows that improves the dissemination of control events. The proposed solution is based on the mapping of workflow tasks to the underlying Pub/Sub event layer, and the definition of interfaces and procedures for execution on brokers. In this paper we also analyze the strengths and weaknesses of current solutions that are based on existing message exchange models for scientific workflows. Finally, we explain how our model improves the information dissemination, event filtering, task decoupling and the monitoring of scientific workflows.

On the support of scientific workflows over Pub/Sub brokers.

Science.gov (United States)

Morales, Augusto; Robles, Tomas; Alcarria, Ramon; Cedeño, Edwin

2013-08-20

The execution of scientific workflows is gaining importance as more computing resources are available in the form of grid environments. The Publish/Subscribe paradigm offers well-proven solutions for sustaining distributed scenarios while maintaining the high level of task decoupling required by scientific workflows. In this paper, we propose a new model for supporting scientific workflows that improves the dissemination of control events. The proposed solution is based on the mapping of workflow tasks to the underlying Pub/Sub event layer, and the definition of interfaces and procedures for execution on brokers. In this paper we also analyze the strengths and weaknesses of current solutions that are based on existing message exchange models for scientific workflows. Finally, we explain how our model improves the information dissemination, event filtering, task decoupling and the monitoring of scientific workflows.

Comparison of the time-to-indexing in PubMed between biomedical journals according to impact factor, discipline, and focus.

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Irwin, Adriane N; Rackham, Daniel

Practicing evidence-based medicine requires health care professionals to efficiently retrieve relevant and current literature. The purpose of this study was to compare the time interval between PubMed entry and indexing with Medical Subject Headings (MeSH) between biomedical journals with varying impact factors, focus areas, and health care discipline representation. This was a cross-sectional study of articles entered into PubMed database between January 1 and December 31, 2012. The primary endpoint was the number of days between PubMed entry and indexing with MeSH terms. A total of 7906 articles were reviewed across 18 journals. In the first comparison, the time-to-indexing was 177 ± 100 days, 111 ± 69 days, and 23 ± 40 days for articles published in journals with impact factors of 2.0-2.5, 4.5-6.5, and >25, respectively (P ≤ 0.001). In the second comparison, the time-to-indexing was 111 ± 69 days for general medicine versus 170 ± 74 days for specialty journals (P ≤ 0.001). In the third comparison, the overall time-to-indexing was 177 ± 100 days, 234 ± 107 days, and 163 ± 58 days for medicine, nursing, and pharmacy journals, respectively (P ≤ 0.001). Study results identified a significant delay between entry of articles into the PubMed database and time-to-indexing with MeSH terms across journals of varying impact factor, discipline, and focus. Results suggest that there may be factors that influence the priority by which articles are indexed with MeSH terms. Future research should focus on determining those journal characteristics and any impact of this delay on clinical practice. Copyright © 2016 Elsevier Inc. All rights reserved.

48 CFR 32.405 - Applying Pub. L. 85-804 to advance payments under sealed bid contracts.

Science.gov (United States)

2010-10-01

... advance payments under sealed bid contracts. 32.405 Section 32.405 Federal Acquisition Regulations System... Non-Commercial Items 32.405 Applying Pub. L. 85-804 to advance payments under sealed bid contracts. (a... provisions of law relating to contracts, as explained in 50.101-1(a), also include making advance payments...

Past and future trends in cancer and biomedical research: a comparison between Egypt and the world using PubMed-indexed publications.

Science.gov (United States)

Zeeneldin, Ahmed Abdelmabood; Taha, Fatma Mohamed; Moneer, Manar

2012-07-10

PubMed is a free web literature search service that contains almost 21 millions of abstracts and publications with almost 5 million user queries daily. The purposes of the study were to compare trends in PubMed-indexed cancer and biomedical publications from Egypt to that of the world and to predict future publication volumes. The PubMed was searched for the biomedical publications between 1991 and 2010 (publications dates). Affiliation was then limited to Egypt. Further limitation was applied to cancer, human and animal publications. Poisson regression model was used for prediction of future number of publications between 2011 and 2020. Cancer publications contributed 23% to biomedical publications both for Egypt and the world. Egyptian biomedical and cancer publications contributed about 0.13% to their world counterparts. This contribution was more than doubled over the study period. Egyptian and world's publications increased from year to year with rapid rise starting the year 2003. Egyptian as well as world's human cancer publications showed the highest increases. Egyptian publications had some peculiarities; they showed some drop at the years 1994 and 2002 and apart from the decline in the animal: human ratio with time, all Egyptian publications in the period 1991-2000 were significantly more than those in 2001-2010 (P PubMed publications, respectively. The Egyptian contribution to world's biomedical and cancer publications needs significant improvements through research strategic planning, setting national research priorities, adequate funding and researchers' training.

Long-term reliable physically unclonable function based on oxide tunnel barrier breakdown on two-transistors two-magnetic-tunnel-junctions cell-based embedded spin transfer torque magnetoresistive random access memory

Science.gov (United States)

Takaya, Satoshi; Tanamoto, Tetsufumi; Noguchi, Hiroki; Ikegami, Kazutaka; Abe, Keiko; Fujita, Shinobu

2017-04-01

Among the diverse applications of spintronics, security for internet-of-things (IoT) devices is one of the most important. A physically unclonable function (PUF) with a spin device (spin transfer torque magnetoresistive random access memory, STT-MRAM) is presented. Oxide tunnel barrier breakdown is used to realize long-term stability for PUFs. A secure PUF has been confirmed by evaluating the Hamming distance of a 32-bit STT-MRAM-PUF fabricated using 65 nm CMOS technology.

Ultra-lightweight and Reconfigurable Tristate Inverter Based Physical Unclonable Function Design

OpenAIRE

Cui, Yijun; Gu, Chongyan; Wang, Chenghua; O'Neill, Maire; Liu, Weiqiang

2018-01-01

A physical unclonable function (PUF) is a promising security primitive which utilizes the manufacturing process variations to generate a unique unclonable digital fingerprint for a chip. It is especially suitable for resource constrained security applications, e.g. internet of things (IoT) devices. The ring oscillator (RO) PUF and the static RAM (SRAM) PUF are two of the most extensively studied PUFdesigns. However, previous RO PUF designs require a lot of hardware resources for ROs to be rob...

Performance evaluation of unified medical language system®'s synonyms expansion to query PubMed

Directory of Open Access Journals (Sweden)

Griffon Nicolas

2012-02-01

Full Text Available Abstract Background PubMed is the main access to medical literature on the Internet. In order to enhance the performance of its information retrieval tools, primarily non-indexed citations, the authors propose a method: expanding users' queries using Unified Medical Language System' (UMLS synonyms i.e. all the terms gathered under one unique Concept Unique Identifier. Methods This method was evaluated using queries constructed to emphasize the differences between this new method and the current PubMed automatic term mapping. Four experts assessed citation relevance. Results Using UMLS, we were able to retrieve new citations in 45.5% of queries, which implies a small increase in recall. The new strategy led to a heterogeneous 23.7% mean increase in non-indexed citation retrieved. Of these, 82% have been published less than 4 months earlier. The overall mean precision was 48.4% but differed according to the evaluators, ranging from 36.7% to 88.1% (Inter rater agreement was poor: kappa = 0.34. Conclusions This study highlights the need for specific search tools for each type of user and use-cases. The proposed strategy may be useful to retrieve recent scientific advancement.

High-performance information search filters for acute kidney injury content in PubMed, Ovid Medline and Embase.

Science.gov (United States)

Hildebrand, Ainslie M; Iansavichus, Arthur V; Haynes, R Brian; Wilczynski, Nancy L; Mehta, Ravindra L; Parikh, Chirag R; Garg, Amit X

2014-04-01

We frequently fail to identify articles relevant to the subject of acute kidney injury (AKI) when searching the large bibliographic databases such as PubMed, Ovid Medline or Embase. To address this issue, we used computer automation to create information search filters to better identify articles relevant to AKI in these databases. We first manually reviewed a sample of 22 992 full-text articles and used prespecified criteria to determine whether each article contained AKI content or not. In the development phase (two-thirds of the sample), we developed and tested the performance of >1.3-million unique filters. Filters with high sensitivity and high specificity for the identification of AKI articles were then retested in the validation phase (remaining third of the sample). We succeeded in developing and validating high-performance AKI search filters for each bibliographic database with sensitivities and specificities in excess of 90%. Filters optimized for sensitivity reached at least 97.2% sensitivity, and filters optimized for specificity reached at least 99.5% specificity. The filters were complex; for example one PubMed filter included >140 terms used in combination, including 'acute kidney injury', 'tubular necrosis', 'azotemia' and 'ischemic injury'. In proof-of-concept searches, physicians found more articles relevant to topics in AKI with the use of the filters. PubMed, Ovid Medline and Embase can be filtered for articles relevant to AKI in a reliable manner. These high-performance information filters are now available online and can be used to better identify AKI content in large bibliographic databases.

Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed.

Science.gov (United States)

Eisinger, Daniel; Tsatsaronis, George; Bundschus, Markus; Wieneke, Ulrich; Schroeder, Michael

2013-04-15

Document search on PubMed, the pre-eminent database for biomedical literature, relies on the annotation of its documents with relevant terms from the Medical Subject Headings ontology (MeSH) for improving recall through query expansion. Patent documents are another important information source, though they are considerably less accessible. One option to expand patent search beyond pure keywords is the inclusion of classification information: Since every patent is assigned at least one class code, it should be possible for these assignments to be automatically used in a similar way as the MeSH annotations in PubMed. In order to develop a system for this task, it is necessary to have a good understanding of the properties of both classification systems. This report describes our comparative analysis of MeSH and the main patent classification system, the International Patent Classification (IPC). We investigate the hierarchical structures as well as the properties of the terms/classes respectively, and we compare the assignment of IPC codes to patents with the annotation of PubMed documents with MeSH terms.Our analysis shows a strong structural similarity of the hierarchies, but significant differences of terms and annotations. The low number of IPC class assignments and the lack of occurrences of class labels in patent texts imply that current patent search is severely limited. To overcome these limits, we evaluate a method for the automated assignment of additional classes to patent documents, and we propose a system for guided patent search based on the use of class co-occurrence information and external resources.

Pictorial Menus as a Wall-Space Design Strategy for Izakaya, Japanese-Style Pubs

OpenAIRE

小島, 茂

1993-01-01

In izakaya, Japanese - style pubs, menus can play an important role in wall-space design and merchandising, because, unlike those of an American restaurant or bar, they are much bigger in size and hang on the wall. In general, however, they are not artistic in quality and hence do not function as an effective means of spatial design, even though they occupy much of the wall. Moreover, since they are written only in Japanese and have no pictures, the menus are not sufficient as a source of inf...

Use of positive and negative words in scientific PubMed abstracts between 1974 and 2014 : retrospective analysis

NARCIS (Netherlands)

Vinkers, Christiaan H|info:eu-repo/dai/nl/304824755; Tijdink, Joeri K; Otte, Willem M

2015-01-01

OBJECTIVE: To investigate whether language used in science abstracts can skew towards the use of strikingly positive and negative words over time. DESIGN: Retrospective analysis of all scientific abstracts in PubMed between 1974 and 2014. METHODS: The yearly frequencies of positive, negative, and

The quality of the reported sample size calculations in randomized controlled trials indexed in PubMed.

Science.gov (United States)

Lee, Paul H; Tse, Andy C Y

2017-05-01

There are limited data on the quality of reporting of information essential for replication of the calculation as well as the accuracy of the sample size calculation. We examine the current quality of reporting of the sample size calculation in randomized controlled trials (RCTs) published in PubMed and to examine the variation in reporting across study design, study characteristics, and journal impact factor. We also reviewed the targeted sample size reported in trial registries. We reviewed and analyzed all RCTs published in December 2014 with journals indexed in PubMed. The 2014 Impact Factors for the journals were used as proxies for their quality. Of the 451 analyzed papers, 58.1% reported an a priori sample size calculation. Nearly all papers provided the level of significance (97.7%) and desired power (96.6%), and most of the papers reported the minimum clinically important effect size (73.3%). The median (inter-quartile range) of the percentage difference of the reported and calculated sample size calculation was 0.0% (IQR -4.6%;3.0%). The accuracy of the reported sample size was better for studies published in journals that endorsed the CONSORT statement and journals with an impact factor. A total of 98 papers had provided targeted sample size on trial registries and about two-third of these papers (n=62) reported sample size calculation, but only 25 (40.3%) had no discrepancy with the reported number in the trial registries. The reporting of the sample size calculation in RCTs published in PubMed-indexed journals and trial registries were poor. The CONSORT statement should be more widely endorsed. Copyright © 2016 European Federation of Internal Medicine. Published by Elsevier B.V. All rights reserved.

PubMed-supported clinical term weighting approach for improving inter-patient similarity measure in diagnosis prediction.

Science.gov (United States)

Chan, Lawrence Wc; Liu, Ying; Chan, Tao; Law, Helen Kw; Wong, S C Cesar; Yeung, Andy Ph; Lo, K F; Yeung, S W; Kwok, K Y; Chan, William Yl; Lau, Thomas Yh; Shyu, Chi-Ren

2015-06-02

Similarity-based retrieval of Electronic Health Records (EHRs) from large clinical information systems provides physicians the evidence support in making diagnoses or referring examinations for the suspected cases. Clinical Terms in EHRs represent high-level conceptual information and the similarity measure established based on these terms reflects the chance of inter-patient disease co-occurrence. The assumption that clinical terms are equally relevant to a disease is unrealistic, reducing the prediction accuracy. Here we propose a term weighting approach supported by PubMed search engine to address this issue. We collected and studied 112 abdominal computed tomography imaging examination reports from four hospitals in Hong Kong. Clinical terms, which are the image findings related to hepatocellular carcinoma (HCC), were extracted from the reports. Through two systematic PubMed search methods, the generic and specific term weightings were established by estimating the conditional probabilities of clinical terms given HCC. Each report was characterized by an ontological feature vector and there were totally 6216 vector pairs. We optimized the modified direction cosine (mDC) with respect to a regularization constant embedded into the feature vector. Equal, generic and specific term weighting approaches were applied to measure the similarity of each pair and their performances for predicting inter-patient co-occurrence of HCC diagnoses were compared by using Receiver Operating Characteristics (ROC) analysis. The Areas under the curves (AUROCs) of similarity scores based on equal, generic and specific term weighting approaches were 0.735, 0.728 and 0.743 respectively (p PubMed. Our findings suggest that the optimized similarity measure with specific term weighting to EHRs can improve significantly the accuracy for predicting the inter-patient co-occurrence of diagnosis when compared with equal and generic term weighting approaches.

Electronic Cigarette Topography in the Natural Environment.

Science.gov (United States)

Robinson, R J; Hensel, E C; Morabito, P N; Roundtree, K A

2015-01-01

This paper presents the results of a clinical, observational, descriptive study to quantify the use patterns of electronic cigarette users in their natural environment. Previously published work regarding puff topography has been widely indirect in nature, and qualitative rather than quantitative, with the exception of three studies conducted in a laboratory environment for limited amounts of time. The current study quantifies the variation in puffing behaviors among users as well as the variation for a given user throughout the course of a day. Puff topography characteristics computed for each puffing session by each subject include the number of subject puffs per puffing session, the mean puff duration per session, the mean puff flow rate per session, the mean puff volume per session, and the cumulative puff volume per session. The same puff topography characteristics are computed across all puffing sessions by each single subject and across all subjects in the study cohort. Results indicate significant inter-subject variability with regard to puffing topography, suggesting that a range of representative puffing topography patterns should be used to drive machine-puffed electronic cigarette aerosol evaluation systems.

75 FR 53723 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2010-09-01

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and...-depth sensing equipment is available, however positioning such devices near seabird and pinniped...

Lost in translation? A multilingual Query Builder improves the quality of PubMed queries: a randomised controlled trial.

Science.gov (United States)

Schuers, Matthieu; Joulakian, Mher; Kerdelhué, Gaetan; Segas, Léa; Grosjean, Julien; Darmoni, Stéfan J; Griffon, Nicolas

2017-07-03

MEDLINE is the most widely used medical bibliographic database in the world. Most of its citations are in English and this can be an obstacle for some researchers to access the information the database contains. We created a multilingual query builder to facilitate access to the PubMed subset using a language other than English. The aim of our study was to assess the impact of this multilingual query builder on the quality of PubMed queries for non-native English speaking physicians and medical researchers. A randomised controlled study was conducted among French speaking general practice residents. We designed a multi-lingual query builder to facilitate information retrieval, based on available MeSH translations and providing users with both an interface and a controlled vocabulary in their own language. Participating residents were randomly allocated either the French or the English version of the query builder. They were asked to translate 12 short medical questions into MeSH queries. The main outcome was the quality of the query. Two librarians blind to the arm independently evaluated each query, using a modified published classification that differentiated eight types of errors. Twenty residents used the French version of the query builder and 22 used the English version. 492 queries were analysed. There were significantly more perfect queries in the French group vs. the English group (respectively 37.9% vs. 17.9%; p PubMed queries in particular for researchers whose first language is not English.

The proportion of cancer-related entries in PubMed has increased considerably; is cancer truly “The Emperor of All Maladies”?

Science.gov (United States)

2017-01-01

In this work, the public database of biomedical literature PubMed was mined using queries with combinations of keywords and year restrictions. It was found that the proportion of Cancer-related entries per year in PubMed has risen from around 6% in 1950 to more than 16% in 2016. This increase is not shared by other conditions such as AIDS, Malaria, Tuberculosis, Diabetes, Cardiovascular, Stroke and Infection some of which have, on the contrary, decreased as a proportion of the total entries per year. Organ-related queries were performed to analyse the variation of some specific cancers. A series of queries related to incidence, funding, and relationship with DNA, Computing and Mathematics, were performed to test correlation between the keywords, with the hope of elucidating the cause behind the rise of Cancer in PubMed. Interestingly, the proportion of Cancer-related entries that contain “DNA”, “Computational” or “Mathematical” have increased, which suggests that the impact of these scientific advances on Cancer has been stronger than in other conditions. It is important to highlight that the results obtained with the data mining approach here presented are limited to the presence or absence of the keywords on a single, yet extensive, database. Therefore, results should be observed with caution. All the data used for this work is publicly available through PubMed and the UK’s Office for National Statistics. All queries and figures were generated with the software platform Matlab and the files are available as supplementary material. PMID:28282418

Author Disambiguation in PubMed: Evidence on the Precision and Recall of Author-ity among NIH-Funded Scientists.

Science.gov (United States)

Lerchenmueller, Marc J; Sorenson, Olav

2016-01-01

We examined the usefulness (precision) and completeness (recall) of the Author-ity author disambiguation for PubMed articles by associating articles with scientists funded by the National Institutes of Health (NIH). In doing so, we exploited established unique identifiers-Principal Investigator (PI) IDs-that the NIH assigns to funded scientists. Analyzing a set of 36,987 NIH scientists who received their first R01 grant between 1985 and 2009, we identified 355,921 articles appearing in PubMed that would allow us to evaluate the precision and recall of the Author-ity disambiguation. We found that Author-ity identified the NIH scientists with 99.51% precision across the articles. It had a corresponding recall of 99.64%. Precision and recall, moreover, appeared stable across common and uncommon last names, across ethnic backgrounds, and across levels of scientist productivity.

Toroidally symmetric/asymmetric effect on the divertor flux due to neon/nitrogen seeding in LHD

Directory of Open Access Journals (Sweden)

H. Tanaka

2017-08-01

Full Text Available Toroidal distributions of divertor particle flux during neon (Ne and nitrogen (N2 seeded discharges were investigated in the Large Helical Device (LHD. By using 14 toroidally distributed divertor probe arrays, which were positioned at radially inner side where the divertor flux concentrates in the inward-shifted magnetic axis configuration, it is found that Ne puffing leads to toroidally quasi-uniform reduction of divertor particle fluxes; whereas toroidally localized reductions were observed with N2 puffing. The toroidally asymmetric reduction pattern with N2 puffing is strongly related to the magnetic field structure around the N2 puffing port. Assuming that nitrogen particles do not recycle, EMC3-EIRENE simulation shows similar reduction pattern with the experiment around the N2 puffing port.

75 FR 42462 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2010-07-21

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and... Promontory to collect ground control point with highly precise GPS equipment. Activity would include hiking...

75 FR 68830 - Notice of permit applications received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2010-11-09

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and... impacts initial CO\\2\\ sequestration and how it impacts the composition of the phytoplankton community...

77 FR 22004 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2012-04-12

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and... educational purposes. Location Palmer Station area, Marguerite Bay including ASPA 107-Dion Islands, ASPA 113...

Developing topic-specific search filters for PubMed with click-through data.

Science.gov (United States)

Li, J; Lu, Z

2013-01-01

Search filters have been developed and demonstrated for better information access to the immense and ever-growing body of publications in the biomedical domain. However, to date the number of filters remains quite limited because the current filter development methods require significant human efforts in manual document review and filter term selection. In this regard, we aim to investigate automatic methods for generating search filters. We present an automated method to develop topic-specific filters on the basis of users' search logs in PubMed. Specifically, for a given topic, we first detect its relevant user queries and then include their corresponding clicked articles to serve as the topic-relevant document set accordingly. Next, we statistically identify informative terms that best represent the topic-relevant document set using a background set composed of topic irrelevant articles. Lastly, the selected representative terms are combined with Boolean operators and evaluated on benchmark datasets to derive the final filter with the best performance. We applied our method to develop filters for four clinical topics: nephrology, diabetes, pregnancy, and depression. For the nephrology filter, our method obtained performance comparable to the state of the art (sensitivity of 91.3%, specificity of 98.7%, precision of 94.6%, and accuracy of 97.2%). Similarly, high-performing results (over 90% in all measures) were obtained for the other three search filters. Based on PubMed click-through data, we successfully developed a high-performance method for generating topic-specific search filters that is significantly more efficient than existing manual methods. All data sets (topic-relevant and irrelevant document sets) used in this study and a demonstration system are publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/downloads/CQ_filter/

75 FR 57299 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2010-09-20

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and... spatial scales of various types of disturbances in and around McMurdo Station, Antarctica. The sampling...

76 FR 61117 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2011-10-03

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and... and spatial scales of various types of disturbances in and around McMurdo Station. The sampling...

76 FR 20721 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2011-04-13

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and... imaging (MRI) scans. The study, to be conducted in collaboration with the University of California San...

[Google and PubMed for physicians: how to find information without getting lost].

Science.gov (United States)

Muñoz Núñez, C F; Sendra Portero, F

2013-06-01

Searching on Internet looking for clinically relevant medical information, used as a clinical decision aid tool, for self-learning or for research, is currently a common practice in Radiology. This task has been strengthened by the technological environment where radiologists work with direct access to information sources from the Workstation. The aim of this paper is to review the basic features of information searching tools in order to understand their functions and to optimize medical information searching on Internet. Google, Google Scholar and PubMed are reviewed as models for that purpose. Copyright © 2012 SERAM. Published by Elsevier Espana. All rights reserved.

78 FR 33115 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2013-06-03

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and... pregnancy and future parturition rates; and (3) To what extent might changes in food availability during the...

In-situ strain monitoring in liquid containers of LNG transporting carriers

Science.gov (United States)

Oh, Min-Cheol; Seo, Jun-Kyu; Kim, Kyung-Jo; Lee, Sang-Min; Kim, Myung-Hyun

2008-08-01

Liquefied natural gas (LNG) transport carriers are exposed to a risk by the repeated bump in the LNG container during the vessel traveling over the wave in ocean. The liquid inside the container, especially when it was not fully contained, make a strong bump onto the insulation panel of the tank wall. The insulation panel consists of several layers of thick polyurethane foam (PUF) to maintain the LNG below the cryogenic temperature, -162°C. Due to the repeated shock on the PUF, a crack could be developed on the tank wall causing a tremendous disaster for LNG carriers. To prevent the accidental crack on the tank, a continuous monitoring of the strain imposed on the PUF is recommended. In this work, a fiber-optic Bragg grating was imbedded inside the PUF for monitoring the strain parallel to the impact direction. The optical fiber sensor with a small diameter of 125 μm was suitable to be inserted in the PUF through a small hole drilled after the PUF was cured. In-situ monitoring of the strain producing the change of Bragg reflection wavelength, a high speed wavelength interrogation method was employed by using an arrayed waveguide grating. By dropping a heavy mass on the PUF, we measured the strain imposed on the insulation panel.

77 FR 32701 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2012-06-01

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and... overriding incentives is to know how best to conserve this great natural resource of the bird, the food...

78 FR 3920 - Notice of Permit Applications Received; Under the Antarctic Conservation Act of 1978 (Pub. L. 95...

Science.gov (United States)

2013-01-17

... Conservation Act of 1978 (Pub. L. 95-541) AGENCY: National Science Foundation. ACTION: Notice of Permit... explore for, discover, and collect vertebrate fossils (primarily those of fishes, marine reptiles, non... be shed on the evolution, faunal dynamics, and/or paleobiogeography of such important vertebrate...

An exploratory analysis of PubMed's free full-text limit on citation retrieval for clinical questions.

Science.gov (United States)

Krieger, Mary M; Richter, Randy R; Austin, Tricia M

2008-10-01

The research sought to determine (1) how use of the PubMed free full-text (FFT) limit affects citation retrieval and (2) how use of the FFT limit impacts the types of articles and levels of evidence retrieved. Four clinical questions based on a research agenda for physical therapy were searched in PubMed both with and without the use of the FFT limit. Retrieved citations were examined for relevancy to each question. Abstracts of relevant citations were reviewed to determine the types of articles and levels of evidence. Descriptive analysis was used to compare the total number of citations, number of relevant citations, types of articles, and levels of evidence both with and without the use of the FFT limit. Across all 4 questions, the FFT limit reduced the number of citations to 11.1% of the total number of citations retrieved without the FFT limit. Additionally, high-quality evidence such as systematic reviews and randomized controlled trials were missed when the FFT limit was used. Health sciences librarians play a key role in educating users about the potential impact the FFT limit has on the number of citations, types of articles, and levels of evidence retrieved.

Repeated batch cultivation of the hydrocarbon-degrading, micro-algal strain Prototheca zopfii RND16 immobilized in polyurethane foam.

Science.gov (United States)

Ueno, Ryohei; Wada, Shun; Urano, Naoto

2008-01-01

This study reports on the stability of the cells of a heterotrophic green micro-algal strain Prototheca zopfii RND16 immobilized in polyurethane foam (PUF) cubes during degradation of mixed hydrocarbon substrate, which was composed of n-alkanes and polycyclic aromatic hydrocarbons (PAHs), in 5 successive cycles of repeated batch cultivation at 30 degrees C. Both RND16 cells and mixed hydrocarbon substrate components had been entrapped in PUF cubes through cultivation. PUF-immobilized RND16 degraded n-alkanes almost completely, whereas the strain hardly degraded PAHs in PUFs, rather they accumulated in the matrices. It is noteworthy that this result is strikingly different from that of the free-living cell culture, where RND16 reduced concentrations of both n-alkanes and PAHs. However, PAHs accumulation in the PUFs did not impair the performance of the immobilized alga to utilize n-alkanes. These results suggest that the PUFs harboring RND16 cells could be used repeatedly for selective retrieval of PAHs from oil-polluted waters after preferential biodegradation of n-alkanes by algae.

Anisotropy of neutrons sources of the Neutron Metrology Laboratory

International Nuclear Information System (INIS)

Silva, A.C.F.; Silva, F.S.; Creazolla, P.G.; Patrão, K.C.S.; Fonseca, E.S. da; Pereira, W.W.

2017-01-01

The anisotropy measurements have as main objective to define the emission of the radiation by different angles of an encapsulated neutron source. Measurements were performed using a Precision Long Counter (PLC) detector in the Laboratório de Baixo Espalhamento of the LNMRI / IRD. In this study were used an 241 AmBe (α,n) 5.92 GBq and a 238 PuBe (α,n) 1.85 TBq. The anisotropy factor was 8.65% to 241 AmBe and 4.36% to 238 PuBe, due to variations in the source encapsulation. The results in this work will focus mainly on the area of radiation protection and studies that will improve the process of routine measurements in laboratories and instrument calibrations. (author)

Anisotropy of neutrons sources of the Neutron Metrology Laboratory; Anisotropia de fontes de nêutrons do Laboratório de Metrologia de Nêutrons

Energy Technology Data Exchange (ETDEWEB)

Silva, A.C.F., E-mail: alexander.camargo@oi.com.br [Fundação Técnico Educacional Souza Marques, Rio de Janeiro, RJ (Brazil); Silva, F.S.; Creazolla, P.G.; Patrão, K.C.S.; Fonseca, E.S. da; Pereira, W.W. [Instituto de Radioproteção e Dosimetria (LNMRI/IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil). Laboratório Nacional de Metrologia das Radiações Ionizantes

2017-07-01

The anisotropy measurements have as main objective to define the emission of the radiation by different angles of an encapsulated neutron source. Measurements were performed using a Precision Long Counter (PLC) detector in the Laboratório de Baixo Espalhamento of the LNMRI / IRD. In this study were used an {sup 241}AmBe (α,n) 5.92 GBq and a {sup 238}PuBe (α,n) 1.85 TBq. The anisotropy factor was 8.65% to {sup 241}AmBe and 4.36% to {sup 238}PuBe, due to variations in the source encapsulation. The results in this work will focus mainly on the area of radiation protection and studies that will improve the process of routine measurements in laboratories and instrument calibrations. (author)

The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews.

Science.gov (United States)

Bramer, Wichor M; Giustini, Dean; Kramer, Bianca Mr; Anderson, Pf

2013-12-23

The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. GS' overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be

77 FR 71842 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2012-12-04

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and..., as well as 500 grams of Artemia salina cysts as food for krill. They plan to measure how fast DNA is...

The interest of Romanian consumers in using QR codes in restaurants and pubs

Directory of Open Access Journals (Sweden)

Marius BĂLĂŞESCU

2017-07-01

Full Text Available The fast development of smartphone technology has created an opportunity to use QR code, considered a popular way of mobile tagging due to its ease of use. Various types of hospitality units, such as accommodations or restaurants and bars have found in QR codes an excellent marketing tool. This paper presents the results of a marketing research study conducted in Brasov city from Romania regarding the consumers’ interest in using QR codes in restaurants and pubs. The results show that mostly the young generation of consumers is aware of QR codes existence because they have smartphones and they are always interested in testing the latest technologies.

Meshable: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms.

Science.gov (United States)

Kim, Sun; Yeganova, Lana; Wilbur, W John

2016-10-01

Medical Subject Headings (MeSH(®)) is a controlled vocabulary for indexing and searching biomedical literature. MeSH terms and subheadings are organized in a hierarchical structure and are used to indicate the topics of an article. Biologists can use either MeSH terms as queries or the MeSH interface provided in PubMed(®) for searching PubMed abstracts. However, these are rarely used, and there is no convenient way to link standardized MeSH terms to user queries. Here, we introduce a web interface which allows users to enter queries to find MeSH terms closely related to the queries. Our method relies on co-occurrence of text words and MeSH terms to find keywords that are related to each MeSH term. A query is then matched with the keywords for MeSH terms, and candidate MeSH terms are ranked based on their relatedness to the query. The experimental results show that our method achieves the best performance among several term extraction approaches in terms of topic coherence. Moreover, the interface can be effectively used to find full names of abbreviations and to disambiguate user queries. https://www.ncbi.nlm.nih.gov/IRET/MESHABLE/ CONTACT: sun.kim@nih.gov Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

77 FR 51831 - Notice of Permit Applications Received; Under the Antarctic Conservation Act of 1978 (Pub. L. 95...

Science.gov (United States)

2012-08-27

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and... applicant plans to enter ASPA 130-Tramway Ridge, Mt. Erebus to measure soil temperatures and sample gases... in the soil. Location ASPA 130-Tramway Ridge, Mt. Erebus, Ross Island. Dates December 1, 2012 to...

Testing search strategies for systematic reviews in the Medline literature database through PubMed.

Science.gov (United States)

Volpato, Enilze S N; Betini, Marluci; El Dib, Regina

2014-04-01

A high-quality electronic search is essential in ensuring accuracy and completeness in retrieved records for the conducting of a systematic review. We analysed the available sample of search strategies to identify the best method for searching in Medline through PubMed, considering the use or not of parenthesis, double quotation marks, truncation and use of a simple search or search history. In our cross-sectional study of search strategies, we selected and analysed the available searches performed during evidence-based medicine classes and in systematic reviews conducted in the Botucatu Medical School, UNESP, Brazil. We analysed 120 search strategies. With regard to the use of phrase searches with parenthesis, there was no difference between the results with and without parenthesis and simple searches or search history tools in 100% of the sample analysed (P = 1.0). The number of results retrieved by the searches analysed was smaller using double quotations marks and using truncation compared with the standard strategy (P = 0.04 and P = 0.08, respectively). There is no need to use phrase-searching parenthesis to retrieve studies; however, we recommend the use of double quotation marks when an investigator attempts to retrieve articles in which a term appears to be exactly the same as what was proposed in the search form. Furthermore, we do not recommend the use of truncation in search strategies in the Medline via PubMed. Although the results of simple searches or search history tools were the same, we recommend using the latter.

Deterrence of device counterfeiting, cloning, and subversion by substitution using hardware fingerprinting

Science.gov (United States)

Hamlet, Jason R; Bauer, Todd M; Pierson, Lyndon G

2014-09-30

Deterrence of device subversion by substitution may be achieved by including a cryptographic fingerprint unit within a computing device for authenticating a hardware platform of the computing device. The cryptographic fingerprint unit includes a physically unclonable function ("PUF") circuit disposed in or on the hardware platform. The PUF circuit is used to generate a PUF value. A key generator is coupled to generate a private key and a public key based on the PUF value while a decryptor is coupled to receive an authentication challenge posed to the computing device and encrypted with the public key and coupled to output a response to the authentication challenge decrypted with the private key.

Preparation and characterization of new biologically active polyurethane foams.

Science.gov (United States)

Savelyev, Yuri; Veselov, Vitali; Markovskaya, Ludmila; Savelyeva, Olga; Akhranovich, Elena; Galatenko, Natalya; Robota, Ludmila; Travinskaya, Tamara

2014-12-01

Biologically active polyurethane foams are the fast-developed alternative to many applications of biomedical materials. Due to the polyurethane structure features and foam technology it is possible to incorporate into their structure the biologically active compounds of target purpose via structural-chemical modification of macromolecule. A series of new biologically active polyurethane foams (PUFs) was synthesized with polyethers (MM 2500-5000), polyesters MM (500-2200), 2,4(2,6) toluene diisocyanate, water as a foaming agent, catalysts, foam stabilizers and functional compounds. Different functional compounds: 1,4-di-N-oxy-2,3-bis-(oxymethyl)-quinoxaline (DOMQ), partial sodium salt of poly(acrylic acid) and 2,6-dimethyl-N,N-diethyl aminoacetatanilide hydrochloride were incorporated into the polymer structure/composition due to the chemical and/or physical bonding. Structural peculiarities of PUFs were studied by FTIR spectroscopy and X-ray scattering. Self-adhesion properties of PUFs were estimated by measuring of tensile strength at break of adhesive junction. The optical microscopy method was performed for the PUF morphology studies. Toxicological estimation of the PUFs was carried out in vitro and in vivo. The antibacterial action towards the Gram-positive and Gram-negative bacteria (Escherichia coli ATC 25922, E. coli ATC 2150, Klebsiella pneumoniae 6447, Staphylococcus aureus 180, Pseudomonas aeruginosa 8180, Proteus mirabilis F 403, P. mirabilis 6054, and Proteus vulgaris 8718) was studied by the disc method on the solid nutrient. Physic-chemical properties of the PUFs (density, tensile strength and elongation at break, water absorption and vapor permeability) showed that all studied PUFs are within the operational requirements for such materials and represent fine-cellular foams. Spectral studies confirmed the incorporation of DOMQ into the PUF's macrochain. PUFs are characterized by microheterogeneous structure. They are antibacterially active, non

76 FR 39905 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2011-07-07

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and... ASPA 134--Cierva Point and Offshore islands, Danco Coast, Antarctica, to install boreholes and a soil... occurrence and properties, and soil properties along a latitudinal gradient on the western Antarctic...

Interactions between the S-domain receptor kinases and AtPUB-ARM E3 ubiquitin ligases suggest a conserved signaling pathway in Arabidopsis.

Science.gov (United States)

Samuel, Marcus A; Mudgil, Yashwanti; Salt, Jennifer N; Delmas, Frédéric; Ramachandran, Shaliny; Chilelli, Andrea; Goring, Daphne R

2008-08-01

The Arabidopsis (Arabidopsis thaliana) genome encompasses multiple receptor kinase families with highly variable extracellular domains. Despite their large numbers, the various ligands and the downstream interacting partners for these kinases have been deciphered only for a few members. One such member, the S-receptor kinase, is known to mediate the self-incompatibility (SI) response in Brassica. S-receptor kinase has been shown to interact and phosphorylate a U-box/ARM-repeat-containing E3 ligase, ARC1, which, in turn, acts as a positive regulator of the SI response. In an effort to identify conserved signaling pathways in Arabidopsis, we performed yeast two-hybrid analyses of various S-domain receptor kinase family members with representative Arabidopsis plant U-box/ARM-repeat (AtPUB-ARM) E3 ligases. The kinase domains from S-domain receptor kinases were found to interact with ARM-repeat domains from AtPUB-ARM proteins. These kinase domains, along with M-locus protein kinase, a positive regulator of SI response, were also able to phosphorylate the ARM-repeat domains in in vitro phosphorylation assays. Subcellular localization patterns were investigated using transient expression assays in tobacco (Nicotiana tabacum) BY-2 cells and changes were detected in the presence of interacting kinases. Finally, potential links to the involvement of these interacting modules to the hormone abscisic acid (ABA) were investigated. Interestingly, AtPUB9 displayed redistribution to the plasma membrane of BY-2 cells when either treated with ABA or coexpressed with the active kinase domain of ARK1. As well, T-DNA insertion mutants for ARK1 and AtPUB9 lines were altered in their ABA sensitivity during germination and acted at or upstream of ABI3, indicating potential involvement of these proteins in ABA responses.

Relative Citation Ratio of Top Twenty Macedonian Biomedical Scientists in PubMed: A New Metric that Uses Citation Rates to Measure Influence at the Article Level.

Science.gov (United States)

Spiroski, Mirko

2016-06-15

The aim of this study was to analyze relative citation ratio (RCR) of top twenty Macedonian biomedical scientists with a new metric that uses citation rates to measure influence at the article level. Top twenty Macedonian biomedical scientists were identified by GoPubMed on the base of the number of deposited abstracts in PubMed, corrected with the data from previously published paper, and completed with the Macedonian biomedical scientists working in countries outside the Republic of Macedonia, but born or previously worked in the country. iCite was used as a tool to access a dashboard of bibliometrics for papers associated with a portfolio. The biggest number of top twenty Macedonian biomedical scientists has RCR lower than one. Only four Macedonian biomedical scientists have bigger RCR in comparison with those in PubMed. The most prominent RCR of 2.29 has Rosoklija G. RCR of the most influenced individual papers deposited in PubMed has shown the biggest value for the paper of Efremov D (35.19). This paper has the biggest number of authors (860). It is necessary to accept top twenty Macedonian biomedical scientists as an example of new metric that uses citation rates to measure influence at the article level, rather than qualification of the best Macedonian biomedical scientists.

Quatre espèces nouvelles d’Élatérides de l’ile de Sumatra

NARCIS (Netherlands)

Candèze, E.

1887-01-01

Piceus, pube fulva subsericea dense obductus; antennis articulo tertio quarto breviore; prothorace latitudine longiore, creberrime punctato, medio longitrorsum et late elevato, angulis posticis tenuibus, valde divaricatis, apice acutis; elytris tenuiter punctato-seriatis, apice breviter emarginatis.

To compare PubMed Clinical Queries and UpToDate in teaching information mastery to clinical residents: a crossover randomized controlled trial.

Science.gov (United States)

Sayyah Ensan, Ladan; Faghankhani, Masoomeh; Javanbakht, Anna; Ahmadi, Seyed-Foad; Baradaran, Hamid Reza

2011-01-01

To compare PubMed Clinical Queries and UpToDate regarding the amount and speed of information retrieval and users' satisfaction. A cross-over randomized trial was conducted in February 2009 in Tehran University of Medical Sciences that included 44 year-one or two residents who participated in an information mastery workshop. A one-hour lecture on the principles of information mastery was organized followed by self learning slide shows before using each database. Subsequently, participants were randomly assigned to answer 2 clinical scenarios using either UpToDate or PubMed Clinical Queries then crossed to use the other database to answer 2 different clinical scenarios. The proportion of relevantly answered clinical scenarios, time to answer retrieval, and users' satisfaction were measured in each database. Based on intention-to-treat analysis, participants retrieved the answer of 67 (76%) questions using UpToDate and 38 (43%) questions using PubMed Clinical Queries (PPubMed Clinical Queries (PPubMed Clinical Queries users (PPubmed Clinical Queries can lead to not only a higher proportion of relevant answer retrieval within a shorter time, but also a higher users' satisfaction. So, addition of tutoring pre-appraised sources such as UpToDate to the information mastery curricula seems to be highly efficient.

Application of polyurethane foam as a sorbent for trace metal pre-concentration — A review

Science.gov (United States)

Lemos, V. A.; Santos, M. S.; Santos, E. S.; Santos, M. J. S.; dos Santos, W. N. L.; Souza, A. S.; de Jesus, D. S.; das Virgens, C. F.; Carvalho, M. S.; Oleszczuk, N.; Vale, M. G. R.; Welz, B.; Ferreira, S. L. C.

2007-01-01

The first publication on the use of polyurethane foam (PUF) for sorption processes dates back to 1970, and soon after the material was applied for separation processes. The application of PUF as a sorbent for solid phase extraction of inorganic analytes for separation and pre-concentration purposes is reviewed. The physical and chemical characteristics of PUF (polyether and polyester type) are discussed and an introduction to the characterization of these sorption processes using different types of isotherms is given. Separation and pre-concentration methods using unloaded and loaded PUF in batch and on-line procedures with continuous flow and flow injection systems are presented. Methods for the direct solid sampling analysis of the PUF after pre-concentration are discussed as well as approaches for speciation analysis. Thermodynamic proprieties of some extraction processes are evaluated and the interpretation of determined parameters, such as enthalpy, entropy and Gibbs free energy in light of the physico-chemical processes is explained.

Optimization of HTST process parameters for production of ready-to-eat potato-soy snack.

Science.gov (United States)

Nath, A; Chattopadhyay, P K; Majumdar, G C

2012-08-01

Ready-to-eat (RTE) potato-soy snacks were developed using high temperature short time (HTST) air puffing process and the process was found to be very useful for production of highly porous and light texture snack. The process parameters considered viz. puffing temperature (185-255 °C) and puffing time (20-60 s) with constant initial moisture content of 36.74% and air velocity of 3.99 m.s(-1) for potato-soy blend with varying soy flour content from 5% to 25% were investigated using response surface methodology following central composite rotatable design (CCRD). The optimum product in terms of minimum moisture content (11.03% db), maximum expansion ratio (3.71), minimum hardness (2,749.4 g), minimum ascorbic acid loss (9.24% db) and maximum overall acceptability (7.35) were obtained with 10.0% soy flour blend in potato flour at the process conditions of puffing temperature (231.0 °C) and puffing time (25.0 s).

Integration of two RAB5 groups during endosomal transport in plants

Science.gov (United States)

Ebine, Kazuo; Choi, Seung-won; Ichinose, Sakura; Uemura, Tomohiro; Nakano, Akihiko

2018-01-01

RAB5 is a key regulator of endosomal functions in eukaryotic cells. Plants possess two different RAB5 groups, canonical and plant-unique types, which act via unknown counteracting mechanisms. Here, we identified an effector molecule of the plant-unique RAB5 in Arabidopsis thaliana, ARA6, which we designated PLANT-UNIQUE RAB5 EFFECTOR 2 (PUF2). Preferential colocalization with canonical RAB5 on endosomes and genetic interaction analysis indicated that PUF2 coordinates vacuolar transport with canonical RAB5, although PUF2 was identified as an effector of ARA6. Competitive binding of PUF2 with GTP-bound ARA6 and GDP-bound canonical RAB5, together interacting with the shared activating factor VPS9a, showed that ARA6 negatively regulates canonical RAB5-mediated vacuolar transport by titrating PUF2 and VPS9a. These results suggest a unique and unprecedented function for a RAB effector involving the integration of two RAB groups to orchestrate endosomal trafficking in plant cells. PMID:29749929

Polyurethane foam impregnated with lignin as a filler for the removal of crude oil from contaminated water

Energy Technology Data Exchange (ETDEWEB)

Santos, O.S.H. [Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31.270-901 (Brazil); Coelho da Silva, Mercês [Engenharia de Materiais, Universidade Federal de Itajubá—UNIFEI, Campus Universitário de Itabira. Itabira, Minas Gerais, CEP: 35.903-087 (Brazil); Silva, V.R.; Mussel, W.N. [Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31.270-901 (Brazil); Yoshida, M.I., E-mail: mirene@ufmg.br [Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP: 31.270-901 (Brazil)

2017-02-15

Highlights: • The presence of lignin in polyurethane foams increased oil sorption capacity. • The presence of lignin resulted in a decrease in the hydrophobicity of the foams. • Langmuir isotherm predicted a maximum oil adsorption of 28.9 g g{sup −1} by the PUF-10. • ΔG° (−4.4 kJ mol{sup −1}) indicated that adsorption process by PUF-10 was spontaneous. • The recyclability of the foam showed efficiency greater than 95% after five cycles. - Abstract: The present study describes the influence of the concentration of lignin when used as a filler in polyurethane foam for crude oil sorption. The foams (lignin 0–20 wt%) were characterized by Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), thermogravimetric analysis, contact angle and density. The FTIR analysis confirmed urethane linkage formation, showing that the chemical structure of the polymer was preserved, despite the addition of different lignin concentrations. Thermogravimetric analysis showed that the presence of lignin has altered the onset temperature (T{sub onset}) of the foams, decreasing as the concentration of lignin is increased. The contact angle analysis showed a decrease in the hydrophobicity of the foams with increasing lignin concentration. All modified foams showed an improvement in the oil sorption capacity in a PUF/oil/water system, and the PUF-10 showed an improvement of about 35.5% compared to the PUF-blank. The Langmuir isotherm showed a better fit to the data and predicted a maximum oil adsorption of 28.9 g g{sup −1} by the PUF-10. The ΔG° value of −4.4 kJ mol{sup −1} indicated that crude oil adsorption process by PUF-10 was spontaneous. The results of reuse of the PUF-10 showed that oil removal efficiency remained greater than 95% after five consecutive cycles.

Trend Analysis of Studies on Water Fluoridation Related to Dental Caries in PubMed.

Science.gov (United States)

Oh, Hyo-Jung; Choi, Hyeon-Mi; Kim, Chonghyuck; Jeon, Jae-Gyu

2018-04-04

Water fluoridation has been cited as one of the top 10 public health achievements of the 20th century. Herein, we analyzed water fluoridation articles related to dental caries published in PubMed between 1950 and 2016 using informetrics and linguistic methods to investigate trends in the studies. To this aim, queries such as "dental caries and (water fluoridation or fluoridated water)," "dental caries and (fluoride or fluoridation)," and "dental caries" were submitted to PubMed to retrieve information about articles on water fluoridation within the area of dental caries and fluoride - their titles, abstracts, publication dates, author affiliations, and publication journals. This article information was then collected by an automatic web crawler and examined through informetrics and linguistic analyses. It was found that the number of articles concerned with water fluoridation and dental caries was 3,381 and declined over time after 1970. The articles were published by 750 journals - most notably, Community Dentistry and Oral Epidemiology and Caries Research. With regard to the geographic distribution of the authors, Europe and North America, especially the USA and UK, accounted for 59.9% of the articles published during the years 1987 to 2015, though there was a sharp increase in the number of authors in Oceania and Asia in recent years. In the titles and abstracts of the articles, "community" and "fluorosis" were mentioned more frequently than the other key terms selected in this study, regardless of the period examined. Our findings may allow one to assess how the research on water fluoridation has evolved over the past several decades. © 2018 S. Karger AG, Basel.

Reporting characteristics and risk of bias in randomised controlled trials of acupuncture analgesia published in PubMed-listed journals.

Science.gov (United States)

Li, Xiuxia; Wang, Rong; Shi, Xiue; Chen, Zehao; Pan, Yuanqing; Li, Xusheng; Yang, Kehu

2017-08-01

Acupuncture analgesia has been evaluated by a number of randomised controlled trials (RCTs); however, a systematic summary of reporting quality of RCTs in this specific field is lacking. To examine the reporting characteristics and risk of bias of RCTs of acupuncture analgesia indexed in the PubMed database. A PubMed search of RCTs of acupuncture analgesia was conducted through November 2015. The Cochrane Collaboration Risk of Bias Tool was used to assess the risk of bias of each trial. 206 articles were identified across 59 journals (impact factor 0.4-20), of which 56% of articles and 86% of journals were Science Citation Index (SCI)-indexed. Nearly half of the articles were published in China. The next most represented countries of origin were the UK (22%) and USA (21%). Of the included trials, postoperative pain was the most prevalent phenotype, and manual acupuncture was the most frequently applied type of stimulation (46%). A total of 12% of articles reported on analgesic mechanisms. The most frequently used acupuncture points were LI4, ST36, PC6, SP6 and Shenmen . The overwhelming majority of trials were considered to be at high risk of bias (84%). Furthermore, 79% of trials enrolled PubMed journals generally exhibited poor reporting of methodological and treatment details. Future studies should provide more information regarding clinical trial registration, blinding of participants (including sham procedures where applicable) and outcome assessors, as well as the training and qualification of acupuncturists. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Hardware device binding and mutual authentication

Science.gov (United States)

Hamlet, Jason R; Pierson, Lyndon G

2014-03-04

Detection and deterrence of device tampering and subversion by substitution may be achieved by including a cryptographic unit within a computing device for binding multiple hardware devices and mutually authenticating the devices. The cryptographic unit includes a physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generates a binding PUF value. The cryptographic unit uses the binding PUF value during an enrollment phase and subsequent authentication phases. During a subsequent authentication phase, the cryptographic unit uses the binding PUF values of the multiple hardware devices to generate a challenge to send to the other device, and to verify a challenge received from the other device to mutually authenticate the hardware devices.

A Case Study on Sepsis Using PubMed and Deep Learning for Ontology Learning.

Science.gov (United States)

Arguello Casteleiro, Mercedes; Maseda Fernandez, Diego; Demetriou, George; Read, Warren; Fernandez Prieto, Maria Jesus; Des Diz, Julio; Nenadic, Goran; Keane, John; Stevens, Robert

2017-01-01

We investigate the application of distributional semantics models for facilitating unsupervised extraction of biomedical terms from unannotated corpora. Term extraction is used as the first step of an ontology learning process that aims to (semi-)automatic annotation of biomedical concepts and relations from more than 300K PubMed titles and abstracts. We experimented with both traditional distributional semantics methods such as Latent Semantic Analysis (LSA) and Latent Dirichlet Allocation (LDA) as well as the neural language models CBOW and Skip-gram from Deep Learning. The evaluation conducted concentrates on sepsis, a major life-threatening condition, and shows that Deep Learning models outperform LSA and LDA with much higher precision.

77 FR 6826 - Notice of Permit Applications Received Under the Antarctic Conservation Act of 1978 (Pub. L. 95-541)

Science.gov (United States)

2012-02-09

... Antarctic Conservation Act of 1978 (Pub. L. 95-541), as amended by the Antarctic Science, Tourism and... transport soil samples to isolate soil microorganisms. Location: Palmer Station vicinity, Anders Island... applicant will use Escherichia coli strain BL21DE3 for the production of \\35\\S-labeled proteins to be used...

Magnetically-tunable rebound property for variable elastic devices made of magnetic elastomer and polyurethane foam

Science.gov (United States)

Oguro, Tsubasa; Endo, Hiroyuki; Kawai, Mika; Mitsumata, Tetsu

2017-12-01

A device consisting of a phase of magnetic elastomer, a phase of polyurethane foam (PUF), and permanent magnet was fabricated and the stress-strain curves for the two-phase magnetic elastomer were measured by a uniaxial compression measurement. A disk of magnetic elastomer was adhered on a disk of PUF by an adhesive agent. The PUF thickness was varied from 1 mm to 5 mm while the thickness of magnetic elastomers was constant at 5 mm. The stress at a strain of 0.15 for the two-phase magnetic elastomers was evaluated in the absence and in the presence of a magnetic field of 410 mT. The stress at 0 mT decreased remarkably with the PUF thickness due to the deformation of the PUF phase. On the other hand, the stress at 410 mT slightly decreased with the thickness; however, it kept high values even at high thickness. When the PUF thickness was 5 mm, the maximum stress increment with 45 times to the off-field stress was observed. An experiment using ping-pong balls demonstrated that the coefficient of restitution for the two-phase magnetic elastomers can be dramatically altered by the magnetic field.

26 CFR 1.9004 - Statutory provisions; the Act of September 26, 1961 (Pub. L. 87-312, 75 Stat. 674).

Science.gov (United States)

2010-04-01

... 26 Internal Revenue 13 2010-04-01 2010-04-01 false Statutory provisions; the Act of September 26, 1961 (Pub. L. 87-312, 75 Stat. 674). 1.9004 Section 1.9004 Internal Revenue INTERNAL REVENUE SERVICE..., flower pots, and kindred products (without regard to the applicable rate of percentage depletion), if an...

Connecting the dots between PubMed abstracts.

Directory of Open Access Journals (Sweden)

M Shahriar Hossain

Full Text Available BACKGROUND: There are now a multitude of articles published in a diversity of journals providing information about genes, proteins, pathways, and diseases. Each article investigates subsets of a biological process, but to gain insight into the functioning of a system as a whole, we must integrate information from multiple publications. Particularly, unraveling relationships between extra-cellular inputs and downstream molecular response mechanisms requires integrating conclusions from diverse publications. METHODOLOGY: We present an automated approach to biological knowledge discovery from PubMed abstracts, suitable for "connecting the dots" across the literature. We describe a storytelling algorithm that, given a start and end publication, typically with little or no overlap in content, identifies a chain of intermediate publications from one to the other, such that neighboring publications have significant content similarity. The quality of discovered stories is measured using local criteria such as the size of supporting neighborhoods for each link and the strength of individual links connecting publications, as well as global metrics of dispersion. To ensure that the story stays coherent as it meanders from one publication to another, we demonstrate the design of novel coherence and overlap filters for use as post-processing steps. CONCLUSIONS: WE DEMONSTRATE THE APPLICATION OF OUR STORYTELLING ALGORITHM TO THREE CASE STUDIES: i a many-one study exploring relationships between multiple cellular inputs and a molecule responsible for cell-fate decisions, ii a many-many study exploring the relationships between multiple cytokines and multiple downstream transcription factors, and iii a one-to-one study to showcase the ability to recover a cancer related association, viz. the Warburg effect, from past literature. The storytelling pipeline helps narrow down a scientist's focus from several hundreds of thousands of relevant documents to only

Connecting the Dots between PubMed Abstracts

Science.gov (United States)

Hossain, M. Shahriar; Gresock, Joseph; Edmonds, Yvette; Helm, Richard; Potts, Malcolm; Ramakrishnan, Naren

2012-01-01

Background There are now a multitude of articles published in a diversity of journals providing information about genes, proteins, pathways, and diseases. Each article investigates subsets of a biological process, but to gain insight into the functioning of a system as a whole, we must integrate information from multiple publications. Particularly, unraveling relationships between extra-cellular inputs and downstream molecular response mechanisms requires integrating conclusions from diverse publications. Methodology We present an automated approach to biological knowledge discovery from PubMed abstracts, suitable for “connecting the dots” across the literature. We describe a storytelling algorithm that, given a start and end publication, typically with little or no overlap in content, identifies a chain of intermediate publications from one to the other, such that neighboring publications have significant content similarity. The quality of discovered stories is measured using local criteria such as the size of supporting neighborhoods for each link and the strength of individual links connecting publications, as well as global metrics of dispersion. To ensure that the story stays coherent as it meanders from one publication to another, we demonstrate the design of novel coherence and overlap filters for use as post-processing steps. Conclusions We demonstrate the application of our storytelling algorithm to three case studies: i) a many-one study exploring relationships between multiple cellular inputs and a molecule responsible for cell-fate decisions, ii) a many-many study exploring the relationships between multiple cytokines and multiple downstream transcription factors, and iii) a one-to-one study to showcase the ability to recover a cancer related association, viz. the Warburg effect, from past literature. The storytelling pipeline helps narrow down a scientist's focus from several hundreds of thousands of relevant documents to only around a hundred

What is covered by "cancer rehabilitation" in PubMed? A review of randomized controlled trials 1990-2011.

Science.gov (United States)

Gudbergsson, Sævar Berg; Dahl, Alv A; Loge, Jon Håvard; Thorsen, Lene; Oldervoll, Line M; Grov, Ellen K

2015-02-01

This focused review examines randomized controlled studies included by the term "cancer rehabilitation" in PubMed. The research questions concern the type of interventions performed and their methodological quality. Using the Medical Subject Headings (MeSH) terms: neoplasm AND rehabilitation, all articles with randomized controlled studies that included adult cancer patients, written in English, were extracted from PubMed. Papers covering physical exercise, psychiatric/psychological treatment or social support only were excluded as they had been reviewed recently. Abstracts and papers were assessed by 3 pairs of reviewers, and descriptive information was extracted systematically. Methodological quality was rated on a 10-item index scale, and the cut-off for acceptable quality was set at ≥ 8. A total of 132 (19%) of the 683 identified papers met the eligibility criteria and were assessed in detail. The papers were grouped into 5 thematic categories: 44 physical; 15 art and expressive; 47 psycho-educative; 21 emotionally supportive; and 5 others. Good quality of design was observed in 32 studies, 18 of them uni-dimensional and 14 multi-dimensional. Published randomized controlled studies on cancer rehabilitation are heterogeneous in terms of content and samples, and are mostly characterized by suboptimal design quality. Future studies should be more specific and well-designed with sufficient statistical strength.

Past and future trends in cancer and biomedical research: a comparison between Egypt and the World using PubMed-indexed publications

Directory of Open Access Journals (Sweden)

Zeeneldin Ahmed Abdelmabood

2012-07-01

Full Text Available Abstract Background PubMed is a free web literature search service that contains almost 21 millions of abstracts and publications with almost 5 million user queries daily. The purposes of the study were to compare trends in PubMed-indexed cancer and biomedical publications from Egypt to that of the world and to predict future publication volumes. Methods The PubMed was searched for the biomedical publications between 1991 and 2010 (publications dates. Affiliation was then limited to Egypt. Further limitation was applied to cancer, human and animal publications. Poisson regression model was used for prediction of future number of publications between 2011 and 2020. Results Cancer publications contributed 23% to biomedical publications both for Egypt and the world. Egyptian biomedical and cancer publications contributed about 0.13% to their world counterparts. This contribution was more than doubled over the study period. Egyptian and world’s publications increased from year to year with rapid rise starting the year 2003. Egyptian as well as world’s human cancer publications showed the highest increases. Egyptian publications had some peculiarities; they showed some drop at the years 1994 and 2002 and apart from the decline in the animal: human ratio with time, all Egyptian publications in the period 1991-2000 were significantly more than those in 2001-2010 (P  Conclusions The Egyptian contribution to world’s biomedical and cancer publications needs significant improvements through research strategic planning, setting national research priorities, adequate funding and researchers’ training.

Information management and complementary alternative medicine: the anatomy of information about CAMs through PubMed.

Science.gov (United States)

Corrao, Salvatore; Argano, Christiano; Colomba, Daniela; Ippolito, Calogero; Gargano, Vincenzo; Arcoraci, Vincenzo; Licata, Giuseppe

2013-10-01

In recent years, there has been a growing interest about complementary and alternative medicine (CAM), and the use of CAM interventions has become more common among people. For these reasons, health professionals must be able to effectively manage information in this field of knowledge according to an evidence-based point of view. This study assessed the anatomy of the available information about CAMs using PubMed, to give practical instructions to manage information in this field. We also analyzed the anatomy of information according to each alternative medicine branch, narrow and broad search methods, subset filters for indexed-for-Medline and non-indexed citations, and different publication types including randomized controlled trials (RCTs) and meta-analyses. Our results demonstrated that the use of CAMs subset (supplied by PubMed search engine) leads to a great number of citations determining an information overload. Our data reveal that it would be more useful to search for the CAM separately, identifying specific items and study design. Moreover, we found the largest number of randomized clinical trials and meta-analyses related to herbal medicine and acupuncture, neither RCTs nor meta-analyses were available for bach and flower remedies, auriculoacupuncture, iridology, and pranotherapy. For the first time, our study gives a comprehensive view of the anatomy of information regarding CAMs and each branch of them. We suggest a methodological approach to face with searching information about this emerging issue from an evidence-based point of view. Finally, our data pointed out some "grey zones" since neither RCTs nor meta-analyses were available for some CAMs.

Use of positive and negative words in scientific PubMed abstracts between 1974 and 2014 : retrospective analysis

OpenAIRE

Vinkers, Christiaan H; Tijdink, Joeri K; Otte, Willem M

2015-01-01

OBJECTIVE: To investigate whether language used in science abstracts can skew towards the use of strikingly positive and negative words over time. DESIGN: Retrospective analysis of all scientific abstracts in PubMed between 1974 and 2014. METHODS: The yearly frequencies of positive, negative, and neutral words (25 preselected words in each category), plus 100 randomly selected words were normalised for the total number of abstracts. Subanalyses included pattern quantification of individual wo...

Bibliometrics analysis of the PubMed literatures on low-dose CT

International Nuclear Information System (INIS)

Wang Qian; Xia Guanghui; Ma Xiaohong; Zhao Xinming

2012-01-01

Objective: The purposes of this study were to evaluate the developmental rule and feature in low-dose CT examinations and to provide useful references for study in the future. Materials and Methods: The journal articles on PubMed from 2002 to 2011 were processed by Thomson Data Analyzer and five aspects were analysed: time, authors, institutions, journals, countries, and keywords. Results: The number of journal articles in low-dose CT examinations were 6 433, 3165 were from US (49.2%), 112 from China (1.4%); 3664 authors (80.42%) published only one article, the famous authors published more than 4 articles; there were 9 core journals in this area. In the last decade, the number and quality of the journal articles in low -dose CT have been dramatically increased. Conclusion: The interest on the low -dose CT examination has been steadily increasing, and world famous research teams have been established. The research in low-dose CT is a multi-discipline involving medicine, medical physics, and mathematics. Cooperation between multiple scientific domains is needed for the future studies. (authors)

Extraction of plutonium from lean residues by room temperature fluoride volatility

International Nuclear Information System (INIS)

Campbell, G.M.; Foropoulos, J.; Kennedy, R.C.; Dye, B.A.; Behrens, R.G.

1989-01-01

The use of dioxygen difluoride (FOOF) and KrF 2 for the recovery of Pu from lean residues by conversion to gaseous PuF 6 is being investigated. The greater stability of PuF 6 at room temperature allows much more extensive removal of Pu from contaminated wastes, when compared to the high temperature fluoride volatility process. The process also requires fewer additive chemicals than aqueous processes, thus minimizing the amount of material that must be disposed of as radioactive waste. The transportability of gaseous PuF 6 allows much of the process to be automated, reducing operator exposure to radiation. Removal of PuF 6 decomposition product is easily facilitated by the use of these fluorinating agents. 9 refs., 8 figs

Recent trends in hardware security exploiting hybrid CMOS-resistive memory circuits

Science.gov (United States)

Sahay, Shubham; Suri, Manan

2017-12-01

This paper provides a comprehensive review and insight of recent trends in the field of random number generator (RNG) and physically unclonable function (PUF) circuits implemented using different types of emerging resistive non-volatile (NVM) memory devices. We present a detailed review of hybrid RNG/PUF implementations based on the use of (i) Spin-Transfer Torque (STT-MRAM), and (ii) metal-oxide based (OxRAM), NVM devices. Various approaches on Hybrid CMOS-NVM RNG/PUF circuits are considered, followed by a discussion on different nanoscale device phenomena. Certain nanoscale device phenomena (variability/stochasticity etc), which are otherwise undesirable for reliable memory and storage applications, form the basis for low power and highly scalable RNG/PUF circuits. Detailed qualitative comparison and benchmarking of all implementations is performed.

76 FR 7862 - Implementation of the James Zadroga 9/11 Health and Compensation Act of 2010 (Pub. L. 111-347)

Science.gov (United States)

2011-02-11

... brief introduction by Federal officials, followed by presentations from attendees who register to speak...), Department of Health and Human Services (HHS) announces a public meeting for receiving comments from the public on implementing the provisions of the James Zadroga 9/11 Health and Compensation Act of 2010 (Pub...

Shifting Sands: Science Researchers on Google Scholar, Web of Science, and PubMed, with Implications for Library Collections Budgets

Science.gov (United States)

Hightower, Christy; Caldwell, Christy

2010-01-01

Science researchers at the University of California Santa Cruz were surveyed about their article database use and preferences in order to inform collection budget choices. Web of Science was the single most used database, selected by 41.6%. Statistically there was no difference between PubMed (21.5%) and Google Scholar (18.7%) as the second most…

Methane penetration in DIII-D ELMing H-mode plasmas

International Nuclear Information System (INIS)

West, W.P.; Lasnier, C.J.; Whyte, D.G.; Isler, R.C.; Evans, T.E.; Jackson, G.L.; Rudakov, D.; Wade, M.R.; Strachan, J.

2003-01-01

Carbon penetration into the core plasma during midplane and divertor methane puffing has been measured for DIII-D ELMing H-mode plasmas. The methane puffs are adjusted to a measurable signal, but global plasma parameters are only weakly affected (line average density, e > increases by E , drops by 6+ density profiles in the core measured as a function of time using charge exchange recombination spectroscopy. The methane penetration factor is defined as the difference in the core content with the puff on and puff off, divided by the carbon confinement time and the methane puffing rate. In ELMing H-mode discharges with ion ∇B drift direction into the X-point, increasing the line averaged density from 5 to 8x10 19 m -3 dropped the penetration factor from 6.6% to 4.6% for main chamber puffing. The penetration factor for divertor puffing was below the detection limit (<1%). Changing the ion ∇B drift to away from the X-point decreased the penetration factor by more than a factor of five for main chamber puffing

Engineered photoproteins that give rise to photosynthetically-incompetent bacteria are effective as photovoltaic materials for biohybrid photoelectrochemical cells.

Science.gov (United States)

Liu, Juntai; Friebe, Vincent M; Swainsbury, David J K; Crouch, Lucy I; Szabo, David A; Frese, Raoul N; Jones, Michael R

2018-04-17

Reaction centre/light harvesting proteins such as the RCLH1X complex from Rhodobacter sphaeroides carry out highly quantum-efficient conversion of solar energy through ultrafast energy transfer and charge separation, and these pigment-proteins have been incorporated into biohybrid photoelectrochemical cells for a variety of applications. In this work we demonstrate that, despite not being able to support normal photosynthetic growth of Rhodobacter sphaeroides, an engineered variant of this RCLH1X complex lacking the PufX protein and with an enlarged light harvesting antenna is unimpaired in its capacity for photocurrent generation in two types of bio-photoelectrochemical cells. Removal of PufX also did not impair the ability of the RCLH1 complex to act as an acceptor of energy from synthetic light harvesting quantum dots. Unexpectedly, the removal of PufX led to a marked improvement in the overall stability of the RCLH1 complex under heat stress. We conclude that PufX-deficient RCLH1 complexes are fully functional in solar energy conversion in a device setting and that their enhanced structural stability could make them a preferred choice over their native PufX-containing counterpart. Our findings on the competence of RCLH1 complexes for light energy conversion in vitro are discussed with reference to the reason why these PufX-deficient proteins are not capable of light energy conversion in vivo.

Analysis of divertor asymmetry using a simple five-point model

International Nuclear Information System (INIS)

Hayashi, Nobuhiko; Takizuka, Tomonori; Hatayama, Akiyoshi; Ogasawara, Masatada.

1997-03-01

A simple five-point model of the scrape-off layer (SOL) plasma outside the separatrix of a diverted tokamak has been developed to study the inside/outside divertor asymmetry. The SOL current, gas pumping/puffing in the divertor region, and divertor plate biasing are included in this model. Gas pumping/puffing and biasing are shown to control divertor asymmetry. In addition, the SOL current is found to form asymmetric solutions without external controls of gas pumping/puffing and biasing. (author)

Transparency in ovarian cancer clinical trial results: ClinicalTrials.gov versus PubMed, Embase and Google scholar.

Science.gov (United States)

Roberto, Anna; Radrezza, Silvia; Mosconi, Paola

2018-04-10

In recent years the question of the lack of transparency in clinical research has been debated by clinicians, researchers, citizens and their representatives, authors and publishers. This is particularly important for infrequent cancers such as ovarian cancer, where treatment still gives disappointing results in the majority of cases. Our aim was to assess the availability to the public of results in ClinicalTrials.gov, and the frequency of non-publication of results in ClinicalTrials.gov and in PubMed, Embase and Google Scholar. We collected all trials on ovarian cancer identified as "completed status" in the ClinicalTrials.gov registry on 17 January 2017. We checked the availability of the results in ClinicalTrials.gov and systematically identified published manuscripts on results. Out of 2725 trials on ovarian cancer identified, 752 were classified as "completed status". In those closed between 2008 and 2015, excluding phase I, the frequency of results in ClinicalTrials.gov was 35%. Of the 752 completed studies the frequency of published results in PubMed, Embase or Google Scholar ranged from 57.9% to 69.7% in the last years. These findings show a lack of transparency and credibility of research. Citizens or patients' representatives, with the medical community, should continuously support initiatives to improve the publication and dissemination of clinical study results.

Design Impedance Mismatch Physical Unclonable Functions for IoT Security

Directory of Open Access Journals (Sweden)

Xiaomin Zheng

2017-01-01

Full Text Available We propose a new design, Physical Unclonable Function (PUF scheme, for the Internet of Things (IoT, which has been suffering from multiple-level security threats. As more and more objects interconnect on IoT networks, the identity of each thing is very important. To authenticate each object, we design an impedance mismatch PUF, which exploits random physical factors of the transmission line to generate a security unique private key. The characteristic impedance of the transmission line and signal transmission theory of the printed circuit board (PCB are also analyzed in detail. To improve the reliability, current feedback amplifier (CFA method is applied on the PUF. Finally, the proposed scheme is implemented and tested. The measure results show that impedance mismatch PUF provides better unpredictability and randomness.

Clinicians' perceptions of usefulness of the PubMed4Hh mobile device application for clinical decision making at the point of care: a pilot study.

Science.gov (United States)

Gartrell, Kyungsook; Brennan, Caitlin W; Wallen, Gwenyth R; Liu, Fang; Smith, Karen G; Fontelo, Paul

2018-05-08

Although evidence-based practice in healthcare has been facilitated by Internet access through wireless mobile devices, research on the effectiveness of clinical decision support for clinicians at the point of care is lacking. This study examined how evidence as abstracts and the bottom-line summaries, accessed with PubMed4Hh mobile devices, affected clinicians' decision making at the point of care. Three iterative steps were taken to evaluate the usefulness of PubMed4Hh tools at the NIH Clinical Center. First, feasibility testing was conducted using data collected from a librarian. Next, usability testing was carried out by a postdoctoral research fellow shadowing clinicians during rounds for one month in the inpatient setting. Then, a pilot study was conducted from February, 2016 to January, 2017, with clinicians using a mobile version of PubMed4Hh. Invitations were sent via e-mail lists to clinicians (physicians, physician assistants and nurse practitioners) along with periodic reminders. Participants rated the usefulness of retrieved bottom-line summaries and abstracts and indicated their usefulness on a 7-point Likert scale. They also indicated location of use (office, rounds, etc.). Of the 166 responses collected in the feasibility phase, more than half of questions (57%, n = 94) were answerable by both the librarian using various resources and by the postdoctoral research fellow using PubMed4Hh. Sixty-six questions were collected during usability testing. More than half of questions (60.6%) were related to information about medication or treatment, while 21% were questions regarding diagnosis, and 12% were specific to disease entities. During the pilot study, participants reviewed 34 abstracts and 40 bottom-line summaries. The abstracts' usefulness mean scores were higher (95% CI [6.12, 6.64) than the scores of the bottom-line summaries (95% CI [5.25, 6.10]). The most frequent reason given was that it confirmed current or tentative diagnostic or

Interactive text mining with Pipeline Pilot: a bibliographic web-based tool for PubMed.

Science.gov (United States)

Vellay, S G P; Latimer, N E Miller; Paillard, G

2009-06-01

Text mining has become an integral part of all research in the medical field. Many text analysis software platforms support particular use cases and only those. We show an example of a bibliographic tool that can be used to support virtually any use case in an agile manner. Here we focus on a Pipeline Pilot web-based application that interactively analyzes and reports on PubMed search results. This will be of interest to any scientist to help identify the most relevant papers in a topical area more quickly and to evaluate the results of query refinement. Links with Entrez databases help both the biologist and the chemist alike. We illustrate this application with Leishmaniasis, a neglected tropical disease, as a case study.

Nursing identity and patient-centredness in scholarly health services research: a computational text analysis of PubMed abstracts 1986-2013.

Science.gov (United States)

Bell, Erica; Campbell, Steve; Goldberg, Lynette R

2015-01-22

The most important and contested element of nursing identity may be the patient-centredness of nursing, though this concept is not well-treated in the nursing identity literature. More conceptually-based mapping of nursing identity constructs are needed to help nurses shape their identity. The field of computational text analytics offers new opportunities to scrutinise how growing disciplines such as health services research construct nursing identity. This paper maps the conceptual content of scholarly health services research in PubMed as it relates to the patient-centeredness of nursing. Computational text analytics software was used to analyse all health services abstracts in the database PubMed since 1986. Abstracts were treated as indicative of the content of health services research. The database PubMed was searched for all research papers using the term "service" or "services" in the abstract or keywords for the period 01/01/1986 to 30/06/2013. A total of 234,926 abstracts were obtained. Leximancer software was used in 1) mapping of 4,144,458 instances of 107 concepts; 2) analysis of 106 paired concept co-occurrences for the nursing concept; and 3) sentiment analysis of the nursing concept versus patient, family and community concepts, and clinical concepts. Nursing is constructed within quality assurance or service implementation or workforce development concepts. It is relatively disconnected from patient, family or community care concepts. For those who agree that patient-centredness should be a part of nursing identity in practice, this study suggests that there is a need for development of health services research into both the nature of the caring construct in nursing identity and its expression in practice. More fundamentally, the study raises questions about whether health services research cultures even value the politically popular idea of nurses as patient-centred caregivers and whether they should.

Reclamation of greater than Class C sealed sources at the Los Alamos National Laboratory

International Nuclear Information System (INIS)

Behrens, R.G.; Jones, S.W.

1995-01-01

One of the important overriding themes of the Los Alamos National Laboratory as a world-class scientific institution is to utilize its expertise in enhancing the long-term welfare of society by minimizing negative side effects of nuclear technology over the past five decades. The Los Alamos National Laboratory is therefore committed to the use of its technical competencies and nuclear facilities, developed through programs in the areas of defense and civilian nuclear research, to support activities which will benefit the United States as a whole. As such, this paper discusses the organizational details and requirements of the Neutron Source Reclamation Program at Los Alamos. This program has as its mission the retrieval, interim storage, and chemical reprocessing of 238 PuBe, 239 PuBe and 24l AmBe neutron sources residing in the hands of private companies and industries, academic institutions, and various state and Federal government agencies

Cupping Therapy May be Harmful for Eczema: A PubMed Search

Science.gov (United States)

Hon, Kam Lun E.; Luk, David Chi Kong; Leong, Kin Fon; Leung, Alexander K. C.

2013-01-01

Eczema is a common childhood atopic condition and treatment is with emollients, topical corticosteroids, and avoidance of possible triggers. S. aureus colonization is a common complication. As there is no immediate cure, many parents seek alternative therapies that claim unproven therapeutic efficacy. We report a girl with long history of treatment noncompliance. After practicing a long period of dietary avoidance and supplementation, the grandparents took her to an alternative medicine practitioner. Following cupping therapy and acupuncture, the child developed blistering and oozing over her back the next day, which rapidly evolved to two large irregular-edge deep ulcers. She was treated with intravenous antibiotics and received multidisciplinary supportive intervention. Using search words of  “cupping,” “eczema,” and “atopic dermatitis,” only two reports were found on PubMed. Therapeutic efficacy was claimed but not scientifically documented in these reports. Childhood eczema is an eminently treatable atopic disease. Extreme alternative therapy seems not to be efficacious and may even be associated with serious undesirable sequelae. Physicians should be aware of various alternative treatment modalities and be prepared to offer evidence-based advice to the patients with eczema and their families. PMID:24282650

Cupping Therapy May be Harmful for Eczema: A PubMed Search

Directory of Open Access Journals (Sweden)

Kam Lun E. Hon

2013-01-01

Full Text Available Eczema is a common childhood atopic condition and treatment is with emollients, topical corticosteroids, and avoidance of possible triggers. S. aureus colonization is a common complication. As there is no immediate cure, many parents seek alternative therapies that claim unproven therapeutic efficacy. We report a girl with long history of treatment noncompliance. After practicing a long period of dietary avoidance and supplementation, the grandparents took her to an alternative medicine practitioner. Following cupping therapy and acupuncture, the child developed blistering and oozing over her back the next day, which rapidly evolved to two large irregular-edge deep ulcers. She was treated with intravenous antibiotics and received multidisciplinary supportive intervention. Using search words of  “cupping,” “eczema,” and “atopic dermatitis,” only two reports were found on PubMed. Therapeutic efficacy was claimed but not scientifically documented in these reports. Childhood eczema is an eminently treatable atopic disease. Extreme alternative therapy seems not to be efficacious and may even be associated with serious undesirable sequelae. Physicians should be aware of various alternative treatment modalities and be prepared to offer evidence-based advice to the patients with eczema and their families.

Systematic identification of latent disease-gene associations from PubMed articles.

Science.gov (United States)

Zhang, Yuji; Shen, Feichen; Mojarad, Majid Rastegar; Li, Dingcheng; Liu, Sijia; Tao, Cui; Yu, Yue; Liu, Hongfang

2018-01-01

Recent scientific advances have accumulated a tremendous amount of biomedical knowledge providing novel insights into the relationship between molecular and cellular processes and diseases. Literature mining is one of the commonly used methods to retrieve and extract information from scientific publications for understanding these associations. However, due to large data volume and complicated associations with noises, the interpretability of such association data for semantic knowledge discovery is challenging. In this study, we describe an integrative computational framework aiming to expedite the discovery of latent disease mechanisms by dissecting 146,245 disease-gene associations from over 25 million of PubMed indexed articles. We take advantage of both Latent Dirichlet Allocation (LDA) modeling and network-based analysis for their capabilities of detecting latent associations and reducing noises for large volume data respectively. Our results demonstrate that (1) the LDA-based modeling is able to group similar diseases into disease topics; (2) the disease-specific association networks follow the scale-free network property; (3) certain subnetwork patterns were enriched in the disease-specific association networks; and (4) genes were enriched in topic-specific biological processes. Our approach offers promising opportunities for latent disease-gene knowledge discovery in biomedical research.

Omavalvontasuunnitelma lähiöpubiin : Omavalvontasuunnitelman uusiminen ja kehittäminen Pub Nattarin Yläbaariin

OpenAIRE

Muurimäki, Marja

2010-01-01

Työn tarkoituksena oli laatia uusi omavalvontasuunnitelma Pub Nattarin Yläbaariin. Omavalvonta on ollut lakisääteistä vuodesta 1995 lähtien, jolloin Suomen liityttyä Euroopan unioniin elintarvikehygieniadirektiivin määräys omavalvonnasta sisällytettiin lainsäädäntöön. Laki edellyttää, että omavalvontasuunnitelma tulee löytyä kirjallisena omavalvontasuunnitelmana, jossa elinkeinonharjoittaja on selvittänyt tuotteidensa käsittelyyn liittyvät riskikohdat ja sen, miten ne saadaan mahdollisimman p...

Radioactive source recovery program responses to neutron source emergencies

International Nuclear Information System (INIS)

Dinehart, S.M.; Hatler, V.A.; Gray, D.W.; Guillen, A.D.

1997-01-01

Recovery of neutron sources containing Pu 239 and Be is currently taking place at Los Alamos National Laboratory. The program was initiated in 1979 by the Department of Energy (DOE) to dismantle and recover sources owned primarily by universities and the Department of Defense. Since the inception of this program, Los Alamos has dismantled and recovered more than 1000 sources. The dismantlement and recovery process involves the removal of source cladding and the chemical separation of the source materials to eliminate neutron emissions. While this program continues for the disposal of 239 Pu/Be sources, there is currently no avenue for the disposition of any sources other than those containing Pu 239 . Increasingly, there have been demands from agencies both inside and outside the Federal Government and from the public to dispose of unwanted sources containing 238 Pu/Be and 241 Am/Be. DOE is attempting to establish a formal program to recover these sources and is working closely with the Nuclear Regulatory Commission (NRC) on a proposed Memorandum of Understanding to formalize an Acceptance Program. In the absence of a formal program to handle 238 Pu/Be and 241 Am/Be neutron sources, Los Alamos has responded to several emergency requests to receive and recover sources that have been determined to be a threat to public health and safety. This presentation will: (1) review the established 239 Pu neutron source recovery program at Los Alamos, (2) detail plans for a more extensive neutron source disposal program, and (3) focus on recent emergency responses

Polyurethane foam loaded with SDS for the adsorption of cationic dyes from aqueous medium: Multivariate optimization of the loading process.

Science.gov (United States)

Robaina, Nicolle F; Soriano, Silvio; Cassella, Ricardo J

2009-08-15

This paper reports the development of a new procedure for the adsorption of four cationic dyes (Rhodamine B, Methylene Blue, Crystal Violet and Malachite Green) from aqueous medium employing polyurethane foam (PUF) loaded with sodium dodecylsulfate (SDS) as solid phase. PUF loading process was based on the stirring of 200mg PUF cylinders with acidic solutions containing SDS. The conditions for loading were optimized by response surface methodology (RSM) using a Doehlert design with three variables that were SDS and HCl concentrations and stirring time. Results obtained in the optimization process showed that the stirring time is not a relevant parameter in the PUF loading, evidencing that the transport of SDS from solution to PUF surface is fast. On the other hand, both SDS and HCl concentrations were important parameters causing significant variation in the efficiency of the resulting solid phase for the removal of dyes from solution. At optimized conditions, SDS and HCl concentrations were 4.0 x 10(-4) and 0.90 mol L(-1), respectively. The influence of stirring time was evaluated by univariate methodology. A 20 min stirring time was established in order to make the PUF loading process fast and robust without losing efficiency. The procedure was tested for the removal of the four cationic dyes from aqueous solutions and removal efficiencies always better than 90% were achieved for the two concentrations tested (2.0 x 10(-5) and 1.0 x 10(-4)mol L(-1)).

Defluoridation technology for drinking water and tea by green synthesized Fe3O4/Al2O3 nanoparticles coated polyurethane foams for rural communities.

Science.gov (United States)

Kumari, Sonu; Khan, Suphiya

2017-08-14

Fluoride (F) contaminated ground water poses a serious public health concern to rural population with unaffordable purification technologies. Therefore, development of a cost-effective, portable, environment and user-friendly defluoridation technique is imperative. In the present study, we report on the development of a green and cost-effective method that utilizes Fe 3 O 4 and Al 2 O 3 nanoparticles (NPs) that were synthesized using jojoba defatted meal. These NPs were impregnated on to polyurethane foam (PUF) and made into tea infusion bags. The Al 2 O 3 NPs-PUF displayed a higher water defluoridation capacity of 43.47 mg g -1 of F as compared to 34.48 mg g -1 of F with Fe 3 O 4 NPs-PUF. The synthesized Al 2 O 3 -PUF infusion bags removed the F that was under the permissible limit of 1.5 mg L -1 . The sorption experiments were conducted to verify the effect of different parameters such as pH, contact time, size of PUF and initial F concentration. The different properties of adsorbent were characterized using a combination of FESEM, EDX, XRD and FTIR techniques, respectively. The calculated total cost per NPs-PUF pouch developed is as low as US $0.05, which makes the technology most suitable for rural communities. This paper will be beneficial for researchers working toward further improvement in water purification technologies.

Synthesis and Structure Characterization of Phenol-Urea-Formaldehyde Resins in the Presence of Magnesium Oxide as Catalyst

Directory of Open Access Journals (Sweden)

Dong-Bin Fan

2014-08-01

Full Text Available The objective of this research was to provide a useful approach of polymer synthesis for accelerating the fast cure of phenol-urea-formaldehyde (PUF resin as wood adhesive by optimizing its structure and composition. The PUF resins containing high contents of very reactive groups such as para-methylol groups were synthesized by reacting methylolurea, phenol, and formaldehyde in the presence of magnesium oxide (MgO as catalyst. The effects of synthesis parameters including F/(P + U, OH/P, and MgO/P mole ratios on the structure, composition, curing characteristics, and their relationships of PUF resins were investigated. The results indicated that MgO seemed to be an efficacious catalyst for PUF resin synthesis and promote its faster cure. The increase in the F/(P + U mole ratio or/and OH/P mole ratio appeared to be beneficial for the formation of para-methylol groups and cocondensed methylene linkages between phenolic methylol groups and urea units, and for the removal of unreacted urea. In case of Catalyst/P mole ratio, an appropriate dosage of added metal-ion was very important for synthesizing the high-content reactive groups of PUF resins, otherwise leading to the reverse effects.

On Improving Reliability of SRAM-Based Physically Unclonable Functions

Directory of Open Access Journals (Sweden)

Arunkumar Vijayakumar

2017-01-01

Full Text Available Physically unclonable functions (PUFs have been touted for their inherent resistance to invasive attacks and low cost in providing a hardware root of trust for various security applications. SRAM PUFs in particular are popular in industry for key/ID generation. Due to intrinsic process variations, SRAM cells, ideally, tend to have the same start-up behavior. SRAM PUFs exploit this start-up behavior. Unfortunately, not all SRAM cells exhibit reliable start-up behavior due to noise susceptibility. Hence, design enhancements are needed for improving reliability. Some of the proposed enhancements in literature include fuzzy extraction, error-correcting codes and voting mechanisms. All enhancements involve a trade-off between area/power/performance overhead and PUF reliability. This paper presents a design enhancement technique for reliability that improves upon previous solutions. We present simulation results to quantify improvement in SRAM PUF reliability and efficiency. The proposed technique is shown to generate a 128-bit key in ≤0.2 μ s at an area estimate of 4538 μ m 2 with error rate as low as 10 − 6 for intrinsic error probability of 15%.

PubMed search filters for the study of putative outdoor air pollution determinants of disease

Science.gov (United States)

Curti, Stefania; Gori, Davide; Di Gregori, Valentina; Farioli, Andrea; Baldasseroni, Alberto; Fantini, Maria Pia; Christiani, David C; Violante, Francesco S; Mattioli, Stefano

2016-01-01

Objectives Several PubMed search filters have been developed in contexts other than environmental. We aimed at identifying efficient PubMed search filters for the study of environmental determinants of diseases related to outdoor air pollution. Methods We compiled a list of Medical Subject Headings (MeSH) and non-MeSH terms seeming pertinent to outdoor air pollutants exposure as determinants of diseases in the general population. We estimated proportions of potentially pertinent articles to formulate two filters (one ‘more specific’, one ‘more sensitive’). Their overall performance was evaluated as compared with our gold standard derived from systematic reviews on diseases potentially related to outdoor air pollution. We tested these filters in the study of three diseases potentially associated with outdoor air pollution and calculated the number of needed to read (NNR) abstracts to identify one potentially pertinent article in the context of these diseases. Last searches were run in January 2016. Results The ‘more specific’ filter was based on the combination of terms that yielded a threshold of potentially pertinent articles ≥40%. The ‘more sensitive’ filter was based on the combination of all search terms under study. When compared with the gold standard, the ‘more specific’ filter reported the highest specificity (67.4%; with a sensitivity of 82.5%), while the ‘more sensitive’ one reported the highest sensitivity (98.5%; with a specificity of 47.9%). The NNR to find one potentially pertinent article was 1.9 for the ‘more specific’ filter and 3.3 for the ‘more sensitive’ one. Conclusions The proposed search filters could help healthcare professionals investigate environmental determinants of medical conditions that could be potentially related to outdoor air pollution. PMID:28003291

PubMed search filters for the study of putative outdoor air pollution determinants of disease.

Science.gov (United States)

Curti, Stefania; Gori, Davide; Di Gregori, Valentina; Farioli, Andrea; Baldasseroni, Alberto; Fantini, Maria Pia; Christiani, David C; Violante, Francesco S; Mattioli, Stefano

2016-12-21

Several PubMed search filters have been developed in contexts other than environmental. We aimed at identifying efficient PubMed search filters for the study of environmental determinants of diseases related to outdoor air pollution. We compiled a list of Medical Subject Headings (MeSH) and non-MeSH terms seeming pertinent to outdoor air pollutants exposure as determinants of diseases in the general population. We estimated proportions of potentially pertinent articles to formulate two filters (one 'more specific', one 'more sensitive'). Their overall performance was evaluated as compared with our gold standard derived from systematic reviews on diseases potentially related to outdoor air pollution. We tested these filters in the study of three diseases potentially associated with outdoor air pollution and calculated the number of needed to read (NNR) abstracts to identify one potentially pertinent article in the context of these diseases. Last searches were run in January 2016. The 'more specific' filter was based on the combination of terms that yielded a threshold of potentially pertinent articles ≥40%. The 'more sensitive' filter was based on the combination of all search terms under study. When compared with the gold standard, the 'more specific' filter reported the highest specificity (67.4%; with a sensitivity of 82.5%), while the 'more sensitive' one reported the highest sensitivity (98.5%; with a specificity of 47.9%). The NNR to find one potentially pertinent article was 1.9 for the 'more specific' filter and 3.3 for the 'more sensitive' one. The proposed search filters could help healthcare professionals investigate environmental determinants of medical conditions that could be potentially related to outdoor air pollution. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Multi-factor authentication

Science.gov (United States)

Hamlet, Jason R; Pierson, Lyndon G

2014-10-21

Detection and deterrence of spoofing of user authentication may be achieved by including a cryptographic fingerprint unit within a hardware device for authenticating a user of the hardware device. The cryptographic fingerprint unit includes an internal physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generates a PUF value. Combining logic is coupled to receive the PUF value, combines the PUF value with one or more other authentication factors to generate a multi-factor authentication value. A key generator is coupled to generate a private key and a public key based on the multi-factor authentication value while a decryptor is coupled to receive an authentication challenge posed to the hardware device and encrypted with the public key and coupled to output a response to the authentication challenge decrypted with the private key.

Investigation of the ageing effects on phenol-urea-formaldehyde binder and alkanol amine-acid anhydride binder coated mineral fibres

DEFF Research Database (Denmark)

Zafar, Ashar; Schjødt-Thomsen, Jan; Sodhi, R.

2013-01-01

-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were employed to identify the chemical changes occurring in the PUF binder coated mineral fibres and alkanol amine-acid anhydride binder coated mineral fibres during that ageing. The samples were aged in a climate......Phenol-Urea-Formaldehyde (PUF) binder coated mineral fibres' mechanical properties have been observed to degrade during ageing at elevated temperatures and humidity, while alkanol amine-acid anhydride binder based mineral fibres exhibited better ageing properties for same duration of ageing. X...... chamber for 7 days at 70 °C and 95% relative humidity. In the case of the PUF binder coated fibres, quantitative XPS measurements showed some significant changes in the atomic composition of the PUF binder coated mineral fibres after ageing, including decreased urea and carbonyl groups concentrations...

Interactions between the S-Domain Receptor Kinases and AtPUB-ARM E3 Ubiquitin Ligases Suggest a Conserved Signaling Pathway in Arabidopsis1[W][OA

Science.gov (United States)

Samuel, Marcus A.; Mudgil, Yashwanti; Salt, Jennifer N.; Delmas, Frédéric; Ramachandran, Shaliny; Chilelli, Andrea; Goring, Daphne R.

2008-01-01

The Arabidopsis (Arabidopsis thaliana) genome encompasses multiple receptor kinase families with highly variable extracellular domains. Despite their large numbers, the various ligands and the downstream interacting partners for these kinases have been deciphered only for a few members. One such member, the S-receptor kinase, is known to mediate the self-incompatibility (SI) response in Brassica. S-receptor kinase has been shown to interact and phosphorylate a U-box/ARM-repeat-containing E3 ligase, ARC1, which, in turn, acts as a positive regulator of the SI response. In an effort to identify conserved signaling pathways in Arabidopsis, we performed yeast two-hybrid analyses of various S-domain receptor kinase family members with representative Arabidopsis plant U-box/ARM-repeat (AtPUB-ARM) E3 ligases. The kinase domains from S-domain receptor kinases were found to interact with ARM-repeat domains from AtPUB-ARM proteins. These kinase domains, along with M-locus protein kinase, a positive regulator of SI response, were also able to phosphorylate the ARM-repeat domains in in vitro phosphorylation assays. Subcellular localization patterns were investigated using transient expression assays in tobacco (Nicotiana tabacum) BY-2 cells and changes were detected in the presence of interacting kinases. Finally, potential links to the involvement of these interacting modules to the hormone abscisic acid (ABA) were investigated. Interestingly, AtPUB9 displayed redistribution to the plasma membrane of BY-2 cells when either treated with ABA or coexpressed with the active kinase domain of ARK1. As well, T-DNA insertion mutants for ARK1 and AtPUB9 lines were altered in their ABA sensitivity during germination and acted at or upstream of ABI3, indicating potential involvement of these proteins in ABA responses. PMID:18552232

CHRISTMAS 2015 : THE PUBLICATION GAME Use of positive and negative words in scientific PubMed abstracts between 1974 and 2014: retrospective analysis

NARCIS (Netherlands)

Vinkers, Christiaan H.; Tijdink, Joeri K.; Otte, Wim

2015-01-01

Objective To investigate whether language used in science abstracts can skew towards the use of strikingly positive and negative words over time. Design Retrospective analysis of all scientific abstracts in PubMed between 1974 and 2014. Methods The yearly frequencies of positive, negative, and

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.

Science.gov (United States)

Kim, Sun; Kim, Won; Wei, Chih-Hsuan; Lu, Zhiyong; Wilbur, W John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical-gene interactions, chemical-disease relationships and gene-disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein-protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team.

CMS 2008-2010 Data Entrepreneurs Synthetic Public Use File

Data.gov (United States)

U.S. Department of Health & Human Services — The DE SynPUF is built from a 5 percent random sample of Medicare beneficiaries in 2008 and their claims from 2008 through 2010. The DE SynPUF contains five types of...

Reproducibility of artificial multiple scattering media

NARCIS (Netherlands)

Marakis, Evangelos; van Harten, Wouter; Uppu, Ravitej; Pinkse, Pepijn Willemszoon Harry

2016-01-01

State of the art authentication systems depend on physical unclonable functions (PUF) [1], physical keys that are assumed unclonable due to technological constraints. Random scattering media, dielectric materials with rapid and random refractive index variations, are considered as ideal optical PUFs

Neutron producing reactions in PuBe neutron sources

Energy Technology Data Exchange (ETDEWEB)

Bagi, János [European Commission, Joint Research Centre (JRC), Institute for Transuranium Elements (ITU) (Germany); Lakosi, László; Nguyen, Cong Tam [Centre for Energy Research, Hungarian Academy of Sciences, Budapest (Hungary)

2016-01-01

There are a plenty of out-of-use plutonium–beryllium neutron sources in Eastern Europe presenting both nuclear safeguards and security issues. Typically, their actual Pu content is not known. In the last couple of years different non-destructive methods were developed for their characterization. For such methods detailed knowledge of the nuclear reactions taking place within the source is necessary. In this paper we investigate the role of the neutron producing reactions, their contribution to the neutron yield and their dependence on the properties of the source.

Towards hydrochemical PUB - stable vs. heterogeneous NO3 and COD signatures across hydrographic structure and size

Science.gov (United States)

Ecrepont, Stephane; Cudennec, Christophe; Jaffrezic, Anne; de Lavenne, Alban

2017-04-01

Towards hydrochemical PUB - stable vs. heterogeneous NO3 and DOC signatures across hydrographic structure and size Ecrepont, S.1Cudennec, C.1 Jaffrézic, A.1 de Lavenne, A.2 1UMR SAS, Agrocampus Ouest, Rennes, France 2 HBAN, Irstea, Antony, France Intensive agriculture is a major disturbing factor for water quality in Brittany, France. Observations of chemical data from 350 catchments over a 15 year period show that the high variability of hydrochemical dynamics between catchments in relation to geographic characteristics and farming practices, decreases with an increase in the catchment size. A stable signature of nitrate and DOC dynamics does emerge for bigger catchments, and was evidenced statistically. We adapted a modified version of the standard deviation formula to calculate an index on mean inter-annual winter nitrate and dissolved organic carbon concentrations to characterize each catchment. The method was applied to the whole sample of catchments, some of them nested, to investigate variation of our new index across scales and regions. Results show an increasing and non-linear relationship between the criterion and the surface, with threshold effects. The stability of the thresholds across river basins in Brittany, and across seasons and years is explored. This emergence relates to the progressive connection of streams with heterogeneous characteristic chemical signatures into a mixing dominant effect. The better assessment of this relationship opens two major perspectives: i) to define a geomorphology-based PUB (Prediction in Ungauged Basins) approach for hydrochemistry; ii) to identify the most critical sub-catchments for mitigating actions in terms of farming and landscape practices towards water quality recovery.

Level of evidence, sponsorship, conflict of interest policy and commercial impact of PubMed-listed clinical urolithiasis-related trials in 2014.

Science.gov (United States)

Schoenthaler, Martin; Miernik, Arkadiusz; Wilhelm, Konrad; Schlager, Daniel; Schoeb, Dominik Stefan; Adams, Fabian; Dahm, Philipp; Hein, Simon

2016-05-01

To evaluate published trials on urolithiasis regarding level of evidence, type of sponsorship and declared conflicts of interest (COIs), and to elucidate a potential commercial impact. We performed a systematic PubMed(®) literature search using a predefined Boolean search term to identify PubMed-listed clinical research studies on urolithiasis in 2014 (fourth quarter). All authors screened the results for eligibility criteria and two independent reviewers evaluated and performed data extraction of predefined endpoints, including level of evidence, declaration of COI and sponsorship/funding (as indicated in the published print version), and commercial impact. A total of 110 clinical trials in urolithiasis listed in PubMed met the inclusion criteria. Levels of evidence 1, 2, 3 and 4 were found in 15%, 14%, 21% and 51% of trials, respectively. A COI was indicated in a total of 90% of publications, 93% of which declared no existing conflict of interest. Sponsorship was indicated in 36% of publications, 55% of which stated public funding, 33% institutional funding, 10% industrial funding and 2% both public and industrial funding. A total of 11% of the published trials were rated as having a high commercial impact. The present study provides evidence of increasing levels of evidence for published clinical trials on urolithiasis in 2014 (as compared with earlier data). Ninety percent of publications indicated conflicts of interest, whereas sponsoring of studies was declared only by one-third. A considerable number of trials involved issues of high commercial impact. Recently established legal programmes and voluntary acts on self-reporting of financial relationships will enhance transparency in the future; however, increased public funding will be needed to further promote the quality of trials on urolithiasis. © 2015 The Authors BJU International © 2015 BJU International Published by John Wiley & Sons Ltd.

Endocrine profiles during attainment of puberty may predict reproductive longevity in heifers

Science.gov (United States)

We hypothesized that attainment of puberty through initiation and continuation of cyclic activity may be a predictor of reproductive longevity in heifers. Blood plasma was collected from 379 spring born heifers over four years from weaning to prior to breeding (October-June) in 2012-2015. Four pube...

Laboratory-scale catalysis studies of uranium and plutonium fluorination reactions by solid metal-fluorides

International Nuclear Information System (INIS)

Hochel, R.C.

1984-03-01

Various catalysts were evaluated for their effect on the rate of fluorination of the tetrafluorides of uranium and plutonium to produce the hexafluorides. Results of this work show that CoF 3 and AgF 2 are more effective than NiF 2 for UF 4 fluorination, producing rate increases in the range of 150 to 300 compared to UF 4 and fluorine alone. The use of these three catalysts was also found effective in the fluorinations of PuO 2 /PuF 4 and pure PuF 4 . However, enhancements were less. NiF 2 produced the best increases which were 8.1 for PuO 2 /PuF 4 and 3.6 for PuF 4 . Experiments were conducted in a simple flow-loop. Even larger enhancements might be obtained with fluidized beds. Details of the apparatus, experiments, methods, and a discussion of results are presented

An automatic evaluation system for NTA film neutron dosimeters

CERN Document Server

Müller, R

1999-01-01

At CERN, neutron personal monitoring for over 4000 collaborators is performed with Kodak NTA films, which have been shown to be the most suitable neutron dosimeter in the radiation environment around high-energy accelerators. To overcome the lengthy and strenuous manual scanning process with an optical microscope, an automatic analysis system has been developed. We report on the successful automatic scanning of NTA films irradiated with sup 2 sup 3 sup 8 Pu-Be source neutrons, which results in densely ionised recoil tracks, as well as on the extension of the method to higher energy neutrons causing sparse and fragmentary tracks. The application of the method in routine personal monitoring is discussed. $9 overcome the lengthy and strenuous manual scanning process with an optical microscope, an automatic analysis system has been developed. We report on the successful automatic scanning of NTA films irradiated with /sup 238/Pu-Be source $9 discussed. (10 refs).

Different spectra with the same neutron source

International Nuclear Information System (INIS)

Vega C, H. R.; Ortiz R, J. M.; Hernandez D, V. M.; Martinez B, M. R.; Hernandez A, B.; Ortiz H, A. A.; Mercado, G. A.

2010-01-01

Using as source term the spectrum of a 239 Pu-Be source several neutron spectra have been calculated using Monte Carlo methods. The source term was located in the centre of spherical moderators made of light water, heavy water and polyethylene of different diameters. Also a 239 Pu-Be source was used to measure its neutron spectrum, bare and moderated by water. The neutron spectra were measured at 100 cm with a Bonner spheres spectrometer. Monte Carlo calculations were used to calculate the neutron spectra of bare and water-moderated spectra that were compared with those measured with the spectrometer. Resulting spectra are similar to those found in power plants with PWR, BWR and Candu nuclear reactors. Beside the spectra the dosimetric features were determined. Using moderators and a single neutron source can be produced neutron spectra alike those found in workplaces, this neutron fields can be utilized to calibrate neutron dosimeters and area monitors. (Author)

Bibliometric analysis of the Korean Journal of Parasitology: measured from SCI, PubMed, Scopus, and Synapse databases.

Science.gov (United States)

Lee, Choon Shil

2009-10-01

The Korean Journal of Parasitology (KJP) is the official journal of the Korean Society for Parasitology which is celebrating its 50th anniversary in 2009. To assess the contributions and achievements of the KJP, bibliometric analysis was conducted based on the citation data retrieved from 4 major databases; SCI, PubMed, Synapse, and Scopus. It was found that the KJP articles were constantly cited by the articles published in major international journals represented in these databases. More than 60% of 1,370 articles published in the KJP from 1963 to June 2009 were cited at least once by SCI articles. The overall average times cited by SCI articles are 2.6. The rate is almost 3 times higher for the articles published in the last 10 years compared to 1.0 for the articles of the 1960s. The SCI journal impact factor for 2008 is calculated as 0.871. It is increasing and it is expected to increase further with the introduction of the KJP in the database in 2008. The more realistic h-indices were measured from the study data set covering all the citations to the KJP; 17 for SCI, 6 for PubMed, 19 for Synapse, and 17 for Scopus. Synapse extensively picked up the citations to the earlier papers not retrievable from the other 3 databases. It identified many papers published in the 1960s and in the 1980s which have been cited heavily, proving the central role of the KJP in the dissemination of the important research findings over the last 5 decades.

Leveraging Distributions in Physical Unclonable Functions

Directory of Open Access Journals (Sweden)

Wenjie Che

2017-10-01

Full Text Available A special class of Physical Unclonable Functions (PUFs referred to as strong PUFs can be used in novel hardware-based authentication protocols. Strong PUFs are required for authentication because the bit strings and helper data are transmitted openly by the token to the verifier, and therefore are revealed to the adversary. This enables the adversary to carry out attacks against the token by systematically applying challenges and obtaining responses in an attempt to machine learn, and later predict, the token’s response to an arbitrary challenge. Therefore, strong PUFs must both provide an exponentially large challenge space and be resistant to machine-learning attacks in order to be considered secure. We investigate a transformation called temperature–voltage compensation (TVCOMP, which is used within the Hardware-Embedded Delay PUF (HELP bit string generation algorithm. TVCOMP increases the diversity and unpredictability of the challenge–response space, and therefore increases resistance to model-building attacks. HELP leverages within-die variations in path delays as a source of random information. TVCOMP is a linear transformation designed specifically for dealing with changes in delay introduced by adverse temperature–voltage (environmental variations. In this paper, we show that TVCOMP also increases entropy and expands the challenge–response space dramatically.

Spent nuclear fuel recycling with plasma reduction and etching

Science.gov (United States)

Kim, Yong Ho

2012-06-05

A method of extracting uranium from spent nuclear fuel (SNF) particles is disclosed. Spent nuclear fuel (SNF) (containing oxides of uranium, oxides of fission products (FP) and oxides of transuranic (TRU) elements (including plutonium)) are subjected to a hydrogen plasma and a fluorine plasma. The hydrogen plasma reduces the uranium and plutonium oxides from their oxide state. The fluorine plasma etches the SNF metals to form UF6 and PuF4. During subjection of the SNF particles to the fluorine plasma, the temperature is maintained in the range of 1200-2000 deg K to: a) allow any PuF6 (gas) that is formed to decompose back to PuF4 (solid), and b) to maintain stability of the UF6. Uranium (in the form of gaseous UF6) is easily extracted and separated from the plutonium (in the form of solid PuF4). The use of plasmas instead of high temperature reactors or flames mitigates the high temperature corrosive atmosphere and the production of PuF6 (as a final product). Use of plasmas provide faster reaction rates, greater control over the individual electron and ion temperatures, and allow the use of CF4 or NF3 as the fluorine sources instead of F2 or HF.

Residents and Medical Students Correctly Answer Clinical Questions More Often with Google and UpToDate than With PubMed or Ovid MEDLINE. A Review of: Thiele, R. H., Poiro, N. C., Scalzo, D. C., & Nemergut, E. C. (2010. Speed, accuracy, and confidence in Google, Ovid, PubMed, and UpToDate: Results of a randomised trial. Postgraduate Medical Journal, 86(1018, 459-465. doi:10.1136/pgmj.2010.098053

Directory of Open Access Journals (Sweden)

Theresa Arndt

2011-06-01

Full Text Available Objective – To determine which search tool (Google, UpToDate, PubMed or Ovid-MEDLINE produces more accurate answers for residents, medical students, and attending physicians searching on clinical questions in anesthesiology and critical care. Searcher confidence in the answers and speed with which answers were found were also examined.Design – Randomized study without a control group.Setting – Large university medical center.Subjects –Subjects included 15 fourth year medical students (third and fourth year, 35 residents, and 4 attending physicians volunteered and completed the study. One additional attending withdrew halfway through the study. The authors were unsuccessful in recruiting an equal number of subjects from each group.Methods – A set of eight anesthesia and critical care questions was developed, based on their commonality and importance in clinical practice and their answerability. Four search tools were employed: Google, UpToDate, PubMed, and Ovid MEDLINE. In part I, subjects were given a random set of four of the questions to answer with the search tool(s of their choice, but could use only one search tool per question. In part II, several weeks later, the same subjects were randomly assigned a search tool with which to answer all 8 questions. The authors state that “for data analysis, PubMed was arbitrarily chosen to be the “reference standard.”” Statistical analysis was used to identify significant differences between PubMed and the other search tools.Main Results – Part I: Subjects choosing a search tool were more likely to find a correct answer with Google or UpToDate. There were no statistically significant differences in confidence with answers between any of the search tools and PubMed.Part II: Though subjects were assigned a search tool, some questions were repeated from part I. For repeated questions, Ovid users (compared to PubMed users were significantly less likely to find the correct answer for

How Twitter Is Studied in the Medical Professions: A Classification of Twitter Papers Indexed in PubMed.

Science.gov (United States)

Williams, Shirley Ann; Terras, Melissa; Warwick, Claire

2013-01-01

Since their inception, Twitter and related microblogging systems have provided a rich source of information for researchers and have attracted interest in their affordances and use. Since 2009 PubMed has included 123 journal articles on medicine and Twitter, but no overview exists as to how the field uses Twitter in research. This paper aims to identify published work relating to Twitter within the fields indexed by PubMed, and then to classify it. This classification will provide a framework in which future researchers will be able to position their work, and to provide an understanding of the current reach of research using Twitter in medical disciplines. Papers on Twitter and related topics were identified and reviewed. The papers were then qualitatively classified based on the paper's title and abstract to determine their focus. The work that was Twitter focused was studied in detail to determine what data, if any, it was based on, and from this a categorization of the data set size used in the studies was developed. Using open coded content analysis additional important categories were also identified, relating to the primary methodology, domain, and aspect. As of 2012, PubMed comprises more than 21 million citations from biomedical literature, and from these a corpus of 134 potentially Twitter related papers were identified, eleven of which were subsequently found not to be relevant. There were no papers prior to 2009 relating to microblogging, a term first used in 2006. Of the remaining 123 papers which mentioned Twitter, thirty were focused on Twitter (the others referring to it tangentially). The early Twitter focused papers introduced the topic and highlighted the potential, not carrying out any form of data analysis. The majority of published papers used analytic techniques to sort through thousands, if not millions, of individual tweets, often depending on automated tools to do so. Our analysis demonstrates that researchers are starting to use knowledge

How Twitter Is Studied in the Medical Professions: A Classification of Twitter Papers Indexed in PubMed

Science.gov (United States)

2013-01-01

Background Since their inception, Twitter and related microblogging systems have provided a rich source of information for researchers and have attracted interest in their affordances and use. Since 2009 PubMed has included 123 journal articles on medicine and Twitter, but no overview exists as to how the field uses Twitter in research. Objective This paper aims to identify published work relating to Twitter within the fields indexed by PubMed, and then to classify it. This classification will provide a framework in which future researchers will be able to position their work, and to provide an understanding of the current reach of research using Twitter in medical disciplines. Methods Papers on Twitter and related topics were identified and reviewed. The papers were then qualitatively classified based on the paper’s title and abstract to determine their focus. The work that was Twitter focused was studied in detail to determine what data, if any, it was based on, and from this a categorization of the data set size used in the studies was developed. Using open coded content analysis additional important categories were also identified, relating to the primary methodology, domain, and aspect. Results As of 2012, PubMed comprises more than 21 million citations from biomedical literature, and from these a corpus of 134 potentially Twitter related papers were identified, eleven of which were subsequently found not to be relevant. There were no papers prior to 2009 relating to microblogging, a term first used in 2006. Of the remaining 123 papers which mentioned Twitter, thirty were focused on Twitter (the others referring to it tangentially). The early Twitter focused papers introduced the topic and highlighted the potential, not carrying out any form of data analysis. The majority of published papers used analytic techniques to sort through thousands, if not millions, of individual tweets, often depending on automated tools to do so. Our analysis demonstrates that

Impact of curing time on ageing and degradation of phenol-urea-formaldehyde binder

DEFF Research Database (Denmark)

Okhrimenko, D. V.; Thomsen, A. B.; Ceccato, M.

2018-01-01

Phenol-urea-formaldehyde (PUF) resin is one of the most important thermosetting polymers. It is widely used in many industrial and construction applications as an organic coating and adhesive. For example, in production of mineral wool for insulation, PUF is used together with the coupling agent (3...

Generel populationsscreening af mentalt helbred hos småbørn

DEFF Research Database (Denmark)

Ammitzbøll, Janni; Skovgaard, Anne Mette; Kreiner, Svend

Psykiske vanskeligheder rammer mere end 10 % af børnepopulationen, og udgør de hyppigste årsager til sociale og helbredsmæssige problemer hos børn og unge. De fleste former for psykiske forstyrrelser opstår tidligt i livet, og intervention i førskolealderen vil kunne begrænse udviklingen af...... autismetilstande, adfærdsforstyrrelser og ADHD. Resultater fra det danske forløbsstudie CCC2000 har vist at mentale helbredsproblemer kan opspores ved sundhedsplejerskernes hjemmebesøg. Forudsætningen er, at der foreligger valide screeningsmetoder, hvilket der ikke gør i dag. Der findes således ikke validerede...... hyppighed i normalbefolkningen. Undersøgelsen viser at validiteten er høj og at PUF er egnet til populationsscreening. Analyser af den prædiktive validitet af PUF er i gang, og der er planlagt udvikling af en interventionsmetode, der kan kobles til PUF screeningen. Såfremt tidlig intervention baseret på PUF...

A Theoretical Analysis: Physical Unclonable Functions and The Software Protection Problem

Energy Technology Data Exchange (ETDEWEB)

Nithyanand, Rishab [Stony Brook Univ., NY (United States); Solis, John H. [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

2011-09-01

Physical Unclonable Functions (PUFs) or Physical One Way Functions (P-OWFs) are physical systems whose responses to input stimuli (i.e., challenges) are easy to measure (within reasonable error bounds) but hard to clone. This property of unclonability is due to the accepted hardness of replicating the multitude of uncontrollable manufacturing characteristics and makes PUFs useful in solving problems such as device authentication, software protection, licensing, and certified execution. In this paper, we focus on the effectiveness of PUFs for software protection and show that traditional non-computational (black-box) PUFs cannot solve the problem against real world adversaries in offline settings. Our contributions are the following: We provide two real world adversary models (weak and strong variants) and present definitions for security against the adversaries. We continue by proposing schemes secure against the weak adversary and show that no scheme is secure against a strong adversary without the use of trusted hardware. Finally, we present a protection scheme secure against strong adversaries based on trusted hardware.

National smokefree law in New Zealand improves air quality inside bars, pubs and restaurants

Directory of Open Access Journals (Sweden)

Näthe Jenny

2007-05-01

Full Text Available Abstract Background: We aimed to: (i assess compliance with a new smokefree law in a range of hospitality settings; and (ii to assess the impact of the new law by measuring air quality and making comparisons with air quality in outdoor smoking areas and with international data from hospitality settings. Methods: We included 34 pubs, restaurants and bars, 10 transportation settings, nine other indoor settings, six outdoor smoking areas of bars and restaurants, and six other outdoor settings. These were selected using a mix of random, convenience and purposeful sampling. The number of lit cigarettes among occupants at defined time points in each venue was observed and a portable real-time aerosol monitor was used to measure fine particulate levels (PM2.5. Results: No smoking was observed during the data collection periods among over 3785 people present in the indoor venues, nor in any of the transportation settings. The levels of fine particulates were relatively low inside the bars, pubs and restaurants in the urban and rural settings (mean 30-minute level = 16 μg/m3 for 34 venues; range of mean levels for each category: 13 μg/m3 to 22 μg/m3. The results for other smokefree indoor settings (shops, offices etc and for smokefree transportation settings (eg, buses, trains, etc were even lower. However, some "outdoor" smoking areas attached to bars/restaurants had high levels of fine particulates, especially those that were partly enclosed (eg, up to a 30-minute mean value of 182 μg/m3 and a peak of maximum value of 284 μg/m3. The latter are far above WHO guideline levels for 24-hour exposure (ie, 25μg/m3. Conclusion: There was very high compliance with the new national smokefree law and this was also reflected by the relatively good indoor air quality in hospitality settings (compared to the "outdoor" smoking areas and the comparable settings in countries that permit indoor smoking. Nevertheless, adopting enhanced regulations (as used in

National smokefree law in New Zealand improves air quality inside bars, pubs and restaurants.

Science.gov (United States)

Wilson, Nick; Edwards, Richard; Maher, Anthony; Näthe, Jenny; Jalali, Rafed

2007-05-18

We aimed to: (i) assess compliance with a new smokefree law in a range of hospitality settings; and (ii) to assess the impact of the new law by measuring air quality and making comparisons with air quality in outdoor smoking areas and with international data from hospitality settings. We included 34 pubs, restaurants and bars, 10 transportation settings, nine other indoor settings, six outdoor smoking areas of bars and restaurants, and six other outdoor settings. These were selected using a mix of random, convenience and purposeful sampling. The number of lit cigarettes among occupants at defined time points in each venue was observed and a portable real-time aerosol monitor was used to measure fine particulate levels (PM2.5). No smoking was observed during the data collection periods among over 3785 people present in the indoor venues, nor in any of the transportation settings. The levels of fine particulates were relatively low inside the bars, pubs and restaurants in the urban and rural settings (mean 30-minute level = 16 microg/m3 for 34 venues; range of mean levels for each category: 13 microg/m3 to 22 microg/m3). The results for other smokefree indoor settings (shops, offices etc) and for smokefree transportation settings (eg, buses, trains, etc) were even lower. However, some "outdoor" smoking areas attached to bars/restaurants had high levels of fine particulates, especially those that were partly enclosed (eg, up to a 30-minute mean value of 182 microg/m3 and a peak of maximum value of 284 microg/m3). The latter are far above WHO guideline levels for 24-hour exposure (ie, 25 microg/m3). There was very high compliance with the new national smokefree law and this was also reflected by the relatively good indoor air quality in hospitality settings (compared to the "outdoor" smoking areas and the comparable settings in countries that permit indoor smoking). Nevertheless, adopting enhanced regulations (as used in various US and Canadian jurisdictions) may be

Comparison of the efficacy of three PubMed search filters in finding randomized controlled trials to answer clinical questions.

Science.gov (United States)

Yousefi-Nooraie, Reza; Irani, Shirin; Mortaz-Hedjri, Soroush; Shakiba, Behnam

2013-10-01

The aim of this study was to compare the performance of three search methods in the retrieval of relevant clinical trials from PubMed to answer specific clinical questions. Included studies of a sample of 100 Cochrane reviews which recorded in PubMed were considered as the reference standard. The search queries were formulated based on the systematic review titles. Precision, recall and number of retrieved records for limiting the results to clinical trial publication type, and using sensitive and specific clinical queries filters were compared. The number of keywords, presence of specific names of intervention and syndrome in the search keywords were used in a model to predict the recalls and precisions. The Clinical queries-sensitive search strategy retrieved the largest number of records (33) and had the highest recall (41.6%) and lowest precision (4.8%). The presence of specific intervention name was the only significant predictor of all recalls and precisions (P = 0.016). The recall and precision of combination of simple clinical search queries and methodological search filters to find clinical trials in various subjects were considerably low. The limit field strategy yielded in higher precision and fewer retrieved records and approximately similar recall, compared with the clinical queries-sensitive strategy. Presence of specific intervention name in the search keywords increased both recall and precision. © 2010 John Wiley & Sons Ltd.

PucC and LhaA direct efficient assembly of the light-harvesting complexes in Rhodobacter sphaeroides

DEFF Research Database (Denmark)

Mothersole, David; Jackson, Philip J.; Vasilev, Cvetelin

2016-01-01

. Here we investigate the assembly of light-harvesting LH2 and reaction centre-light-harvesting1-PufX (RC-LH1-PufX) photosystem complexes using spectroscopy, pull-downs, native gel electrophoresis, quantitative mass spectrometry and fluorescence lifetime microscopy to characterise a series of lha......A and pucC mutants. LhaA and PucC are important for specific assembly of LH1 or LH2 complexes, respectively, but they are not essential; the few LH1 subunits found in ΔlhaA mutants assemble to form normal RC-LH1-PufX core complexes showing that, once initiated, LH1 assembly round the RC is cooperative...

Nominal ISOMERs (Incorrect Spellings Of Medicines Eluding Researchers)-variants in the spellings of drug names in PubMed: a database review.

Science.gov (United States)

Ferner, Robin E; Aronson, Jeffrey K

2016-12-14

 To examine how misspellings of drug names could impede searches for published literature.  Database review.  PubMed.  The study included 30 drug names that are commonly misspelt on prescription charts in hospitals in Birmingham, UK (test set), and 30 control names randomly chosen from a hospital formulary (control set). The following definitions were used: standard names-the international non-proprietary names, variant names-deviations in spelling from standard names that are not themselves standard names in English language nomenclature, and hidden reference variants-variant spellings that identified publications in textword (tw) searches of PubMed or other databases, and which were not identified by textword searches for the standard names. Variant names were generated from standard names by applying letter substitutions, omissions, additions, transpositions, duplications, deduplications, and combinations of these. Searches were carried out in PubMed (30 June 2016) for "standard name[tw]" and "variant name[tw] NOT standard name[tw]."  The 30 standard names of drugs in the test set gave 325 979 hits in total, and 160 hidden reference variants gave 3872 hits (1.17%). The standard names of the control set gave 470 064 hits, and 79 hidden reference variants gave 766 hits (0.16%). Letter substitutions (particularly i to y and vice versa) and omissions together accounted for 2924 (74%) of the variants. Amitriptyline (8530 hits) yielded 18 hidden reference variants (179 (2.1%) hits). Names ending in "in," "ine," or "micin" were commonly misspelt. Failing to search for hidden reference variants of "gentamicin," "amitriptyline," "mirtazapine," and "trazodone" would miss at least 19 systematic reviews. A hidden reference variant related to Christmas, "No-el", was rare; variants of "X-miss" were rarer.  When performing searches, researchers should include misspellings of drug names among their search terms. Published by the BMJ Publishing Group Limited. For

PubMed search strategies for the identification of etiologic associations between hypothalamic-pituitary disorders and other medical conditions.

Science.gov (United States)

Guaraldi, Federica; Grottoli, Silvia; Arvat, Emanuela; Mattioli, Stefano; Ghigo, Ezio; Gori, Davide

2013-12-01

Biomedical literature has enormously grown in the last decades and become broadly available through online databases. Ad-hoc search methods, created on the basis of research field and goals, are required to enhance the quality of searching. Aim of this study was to formulate efficient, evidence-based PubMed search strategies to retrieve articles assessing etiologic associations between a condition of interest and hypothalamic-pituitary disorders (HPD). Based on expert knowledge, 17 MeSH (Medical Subjects Headings) and 79 free terms related to HPD were identified to search PubMed. Using random samples of abstracts retrieved by each term, we estimated the proportion of articles containing pertinent information and formulated two strings (one more specific, one more sensitive) for the detection of articles focusing on the etiology of HPD, that were then applied to retrieve articles identifying possible etiologic associations between HPD and three diseases (malaria, LHON and celiac disease) considered not associated to HPD, and define the number of abstracts needed to read (NNR) to find one potentially pertinent article. We propose two strings: one sensitive string derived from the combination of articles providing the largest literature coverage in the field and one specific including combined terms retrieving ≥40% of potentially pertinent articles. NNR were 2.1 and 1.6 for malaria, 3.36 and 2.29 for celiac disease, 2.8 and 2.2 for LHON, respectively. For the first time, two reliable, readily applicable strings are proposed for the retrieval of medical literature assessing putative etiologic associations between HPD and other medical conditions of interest.

Producción científica española en obesidad a través de PubMed (1988-2007 Spanish scientific production in obesity research published in PubMed (1988-2007

Directory of Open Access Journals (Sweden)

Jesús Vioque

2010-06-01

Full Text Available Objetivo: Analizar la producción científica española sobre obesidad en PubMed durante dos décadas (1988-2007 y contextualizarla en el marco de la Unión Europea. Métodos: Se realizó un estudio bibliométrico a través de la base de datos MEDLINE en PubMed mediante la búsqueda de «obesity» en MeSH, estimando las tendencias del número de publicaciones anuales mediante análisis de regresión. Resultados: Se recopilaron 50.120 documentos sobre obesidad, y 1.407 (2,8% de la producción mundial eran de autores españoles. España fue el quinto país con más documentos de la Unión Europea (8,1%. El 69,1% (n=932 estaban publicados en inglés. El crecimiento medio anual fue del 15%, pasando de 91 documentos en el primer quinquenio a 702 en el último. La especialidad más frecuente del primer firmante fue endocrinología, con 279 (22,8% documentos, seguida de fisiología-nutrición-bromatología con 203 (16,6% y bioquímica con 161 (13,2%. Medicina Clínica con 83 (6,1%, Obesity Surgery con 79 (5,8%, International Journal of Obesity con 73 (5,3% y Nutrición Hospitalaria con 59 (4,3% fueron las revistas con mayor número de documentos. Las comunidades autónomas más productoras fueron Cataluña (n=338; 24,9%, Madrid (n=286; 20,6% y Navarra (n=159; 11,7%. Las instituciones más productivas fueron los hospitales, con 708 (52,1% documentos, y las universidades, con 521 (38,5% documentos. Conclusiones: La investigación sobre obesidad en España ha crecido en los últimos 20 años y ha supuesto una aportación importante en el conjunto de la Unión Europea. La mitad de las publicaciones españolas se hicieron en revistas extranjeras y procedían predominantemente de hospitales y universidades.Objective: To analyse Spanish scientific research output related to obesity during a 20-year period from 1988 to 2007 into context with the European Union productivity Methods: The bibliometric study was based on research of the MEDLINE database in Pub

Quantum readout of physical unclonable functions

NARCIS (Netherlands)

Skoric, B.

2012-01-01

Physical unclonable functions (PUFs) are physical structures that are hard to clone and have a unique challenge-response behavior. The term PUF was coined by Pappu et al. in 2001. That work triggered a lot of interest, and since then a substantial number of papers has been written about the use of a

A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records

DEFF Research Database (Denmark)

Jiang, Li; Edwards, Stefan M.; Thomsen, Bo

2014-01-01

from PubMed abstracts, OMIM, and GeneRIF records. We also investigated the validity of several vocabulary filters and different likelihood thresholds for predicted protein-protein interactions in terms of their effect on the network-based gene-prioritization approach, which relies on text...

Error free physically unclonable function with programmed resistive random access memory using reliable resistance states by specific identification-generation method

Science.gov (United States)

Tseng, Po-Hao; Hsu, Kai-Chieh; Lin, Yu-Yu; Lee, Feng-Min; Lee, Ming-Hsiu; Lung, Hsiang-Lan; Hsieh, Kuang-Yeu; Chung Wang, Keh; Lu, Chih-Yuan

2018-04-01

A high performance physically unclonable function (PUF) implemented with WO3 resistive random access memory (ReRAM) is presented in this paper. This robust ReRAM-PUF can eliminated bit flipping problem at very high temperature (up to 250 °C) due to plentiful read margin by using initial resistance state and set resistance state. It is also promised 10 years retention at the temperature range of 210 °C. These two stable resistance states enable stable operation at automotive environments from -40 to 125 °C without need of temperature compensation circuit. The high uniqueness of PUF can be achieved by implementing a proposed identification (ID)-generation method. Optimized forming condition can move 50% of the cells to low resistance state and the remaining 50% remain at initial high resistance state. The inter- and intra-PUF evaluations with unlimited separation of hamming distance (HD) are successfully demonstrated even under the corner condition. The number of reproduction was measured to exceed 107 times with 0% bit error rate (BER) at read voltage from 0.4 to 0.7 V.

Preconcentration and determination of uranium on to polyurethane foam functionalized with salicylate

International Nuclear Information System (INIS)

Sousa, Alvaro S.F. de; Ferreira, Elizabeth de M.M.; Cassella, Ricardo J.

2009-01-01

Salicylate was covalently linking with a commercial polyurethane foam (PUF) through -N=N-group generating a stable chelating sorbent (PUFS). The synthesized sorbent was characterized by Infrared Spectrometry (IR) measurement. Good stability towards various solvents was noticed. The pH influence and equilibration shaking time adsorption onto foam functionalized was studied as factors influencing the extraction process of the uranium ion solution. Extraction of uranium was accomplished in 10 minutes. Uranium at ppb level was absorbed as the salicylate complex on powered PUFS at pH about 8.0. Uranium could be achieved in 85 % from a 500 mL uranium solution (0.1 μgmL -1 ) which shows the suitability of salicylate foam for preconcentration analysis. (author)

An optical authentication system based on imaging of excitation-selected lanthanide luminescence.

Science.gov (United States)

Carro-Temboury, Miguel R; Arppe, Riikka; Vosch, Tom; Sørensen, Thomas Just

2018-01-01

Secure data encryption relies heavily on one-way functions, and copy protection relies on features that are difficult to reproduce. We present an optical authentication system based on lanthanide luminescence from physical one-way functions or physical unclonable functions (PUFs). They cannot be reproduced and thus enable unbreakable encryption. Further, PUFs will prevent counterfeiting if tags with unique PUFs are grafted onto products. We have developed an authentication system that comprises a hardware reader, image analysis, and authentication software and physical keys that we demonstrate as an anticounterfeiting system. The physical keys are PUFs made from random patterns of taggants in polymer films on glass that can be imaged following selected excitation of particular lanthanide(III) ions doped into the individual taggants. This form of excitation-selected imaging ensures that by using at least two lanthanide(III) ion dopants, the random patterns cannot be copied, because the excitation selection will fail when using any other emitter. With the developed reader and software, the random patterns are read and digitized, which allows a digital pattern to be stored. This digital pattern or digital key can be used to authenticate the physical key in anticounterfeiting or to encrypt any message. The PUF key was produced with a staggering nominal encoding capacity of 7 3600 . Although the encoding capacity of the realized authentication system reduces to 6 × 10 104 , it is more than sufficient to completely preclude counterfeiting of products.

Neutron spectra of /sup 239/Pu-Be neutron sources

Energy Technology Data Exchange (ETDEWEB)

Kumar, A; Nagarajan, P S [Bhabha Atomic Research Centre, Bombay (India). Div. of Radiation Protection

1977-01-01

Neutron spectra of /sup 239/Pu-Be(..cap alpha..,n) sources have been calculated by using the most recent data on the differential cross sections and angular distributions. The contribution from the multibody break-up reaction /sup 9/Be(..cap alpha..,..cap alpha..n)/sup 8/Be has also been incorporated. Modifications to the primary spectrum due to the secondary interactions in the source such as elastic scattering with beryllium, oxygen and plutonium and the /sup 9/Be(n,2n) and /sup 239/Pu(n,f) reaction have been calculated for different strengths and geometries. The present calculation has shown that the spectrum changes considerably because of these events within the source by way of smearing of peaks and filling up of valleys and raising the low energy part of the spectrum. Increase in H/D value leads to channeling of extra neutrons into the equatorial plane at the cost of the neutrons along the axial direction. The present calculations show that inclusion of secondary interactions to the extent considered in this work does not account completely for the increased intensity in the lower energy end of the measured spectrum.

PubMed search strings for the study of agricultural workers' diseases.

Science.gov (United States)

Mattioli, Stefano; Gori, Davide; Di Gregori, Valentina; Ricotta, Lara; Baldasseroni, Alberto; Farioli, Andrea; Zanardi, Francesca; Galletti, Stefania; Colosio, Claudio; Curti, Stefania; Violante, Francesco S

2013-12-01

Several optimized search strategies have been developed in Medicine, and more recently in Occupational Medicine. The aim of this study was to identify efficient PubMed search strategies to retrieve articles regarding putative occupational determinants of agricultural workers' diseases. We selected the Medical Subjects Heading (MeSH) term agricultural workers' diseases and six MeSH terms describing farm work (agriculture, agrochemicals NOT pesticides, animal husbandry, pesticides, rural health, rural population) alongside 61 other promising terms. We estimated proportions of articles containing potentially pertinent information regarding occupational etiology to formulate two search strategies (one "more specific," one "more sensitive"). We applied these strategies to retrieve information on the possible occupational etiology among agricultural workers of kidney cancer, knee osteoarthritis, and multiple sclerosis. We evaluated the number of needed to read (NNR) abstracts to identify one potentially pertinent article in the context of these pathologies. The "more specific" search string was based on the combination of terms that yielded the highest proportion (40%) of potentially pertinent abstracts. The "more sensitive" string was based on use of broader search fields and additional coverage provided by other search terms under study. Using the "more specific" string, the NNR to find one potentially pertinent article were: 1.1 for kidney cancer; 1.4 for knee osteoarthritis; 1.2 for multiple sclerosis. Using the sensitive strategy, the NNR were 1.4, 3.6, and 6.3, respectively. The proposed strings could help health care professionals explore putative occupational etiology for agricultural workers' diseases (even if not generally thought to be work related). © 2013 Wiley Periodicals, Inc.

Genetic manipulation of longevity-related genes as a tool to regulate yeast life span and metabolite production during winemaking.

Science.gov (United States)

Orozco, Helena; Matallana, Emilia; Aranda, Agustín

2013-01-02

Yeast viability and vitality are essential for different industrial processes where the yeast Saccharomyces cerevisiae is used as a biotechnological tool. Therefore, the decline of yeast biological functions during aging may compromise their successful biotechnological use. Life span is controlled by a variety of molecular mechanisms, many of which are connected to stress tolerance and genomic stability, although the metabolic status of a cell has proven a main factor affecting its longevity. Acetic acid and ethanol accumulation shorten chronological life span (CLS), while glycerol extends it. Different age-related gene classes have been modified by deletion or overexpression to test their role in longevity and metabolism. Overexpression of histone deacetylase SIR2 extends CLS and reduces acetate production, while overexpression of SIR2 homolog HST3 shortens CLS, increases the ethanol level, and reduces acetic acid production. HST3 overexpression also enhances ethanol tolerance. Increasing tolerance to oxidative stress by superoxide dismutase SOD2 overexpression has only a moderate positive effect on CLS. CLS during grape juice fermentation has also been studied for mutants on several mRNA binding proteins that are regulators of gene expression at the posttranscriptional level; we found that NGR1 and UTH4 deletions decrease CLS, while PUF3 and PUB1 deletions increase it. Besides, the pub1Δ mutation increases glycerol production and blocks stress granule formation during grape juice fermentation. Surprisingly, factors relating to apoptosis, such as caspase Yca1 or apoptosis-inducing factor Aif1, play a positive role in yeast longevity during winemaking as their deletions shorten CLS. Manipulation of regulators of gene expression at both transcriptional (i.e., sirtuins) and posttranscriptional (i.e., mRNA binding protein Pub1) levels allows to modulate yeast life span during its biotechnological use. Due to links between aging and metabolism, it also influences the

Biodegradation of cypermethrin by immobilized cells of Micrococcus sp. strain CPN 1.

Science.gov (United States)

Tallur, Preeti N; Mulla, Sikandar I; Megadi, Veena B; Talwar, Manjunatha P; Ninnekar, Harichandra Z

2015-01-01

Pyrethroid pesticide cypermethrin is a environmental pollutant because of its widespread use, toxicity and persistence. Biodegradation of such chemicals by microorganisms may provide an cost-effective method for their detoxification. We have investigated the degradation of cypermethrin by immobilized cells of Micrococcus sp. strain CPN 1 in various matrices such as, polyurethane foam (PUF), polyacrylamide, sodium alginate and agar. The optimum temperature and pH for the degradation of cypermethrin by immobilized cells of Micrococcus sp. were found to be 30 °C and 7.0, respectively. The rate of degradation of 10 and 20 mM of cypermethrin by freely suspended cells were compared with that of immobilized cells in batches and semi-continuous with shaken cultures. PUF-immobilized cells showed higher degradation of cypermethrin (10 mM and 20 mM) than freely suspended cells and cells immobilized in other matrices. The PUF-immobilized cells of Micrococcus sp. strain CPN 1 were retain their degradation capacity. Thus, they can be reused for more than 32 cycles, without losing their degradation capacity. Hence, the PUF-immobilized cells of Micrococcus sp. could potentially be used in the bioremediation of cypermethrin contaminated water.

Enhanced degradation of 2-nitrotoluene by immobilized cells of Micrococcus sp. strain SMN-1.

Science.gov (United States)

Mulla, Sikandar I; Talwar, Manjunatha P; Bagewadi, Zabin K; Hoskeri, Robertcyril S; Ninnekar, Harichandra Z

2013-02-01

Nitrotoluenes are the toxic pollutants of the environment because of their large scale use in the production of explosives. Biodegradation of such chemicals by microorganisms may provide an effective method for their detoxification. We have studied the degradation of 2-nitrotoluene by cells of Micrococcus sp. strain SMN-1 immobilized in various matrices such as polyurethane foam (PUF), sodium alginate (SA), sodium alginate-polyvinyl alcohol (SA-PVA), agar and polyacrylamide. The rate of degradation of 15 and 30 mM 2-nitrotoluene by freely suspended cells and immobilized cells in batches and fed-batch with shaken cultures were compared. The PUF-immobilized cells achieved higher degradation of 15 and 30 mM 2-nitrotoluene than freely suspended cells and the cells immobilized in SA-PVA, polyacrylamide, SA and agar. The PUF-immobilized cells could be reused more than 24 cycles without loosing their degradation capacity and showed more tolerance to pH and temperature changes than freely suspended cells. These results revealed the enhanced rate of degradation of 2-nitrotoluene by PUF-immobilized cells of Micrococcus sp. strain SMN-1. Copyright © 2012 Elsevier Ltd. All rights reserved.

Experimental investigation of density behaviors in front of the lower hybrid launcher in experimental advanced superconducting tokamak

International Nuclear Information System (INIS)

Zhang, L.; Ding, B. J.; Li, M. H.; Kong, E. H.; Wei, W.; Liu, F. K.; Shan, J. F.; Wu, Z. G.; Zhu, L.; Ma, W. D.; Tong, Y. Y.; Li, Y. C.; Wang, M.; Zhao, L. M.; Hu, H. C.; Liu, L.

2013-01-01

A triple Langmuir probe is mounted on the top of the Lower Hybrid (LH) antenna to measure the electron density near the LH grills in Experimental Advanced Superconducting Tokamak. In this work, the LH power density ranges from 2.3 MWm −2 to 10.3 MWm −2 and the rate of puffing gas varies from 1.7 × 10 20 el/s to 14 × 10 20 el/s. The relation between the edge density (from 0.3 × n e-cutoff to 20 × n e-cutoff , where n e-cutoff is the cutoff density, n e-cutoff = 0.74 × 10 17 m −3 for 2.45 GHz lower hybrid current drive) near the LH grill and the LH power reflection coefficients is investigated. The factors, including the gap between the LH grills and the last closed magnetic flux surface, line-averaged density, LH power, edge safety factor, and gas puffing, are analyzed. The experiments show that injection of LH power is beneficial for increasing edge density. Gas puffing is beneficial for increasing grill density but excess gas puffing is unfavorable for coupling and current drive

Pitfall of the Strongest Cells in Static Random Access Memory Physical Unclonable Functions

Directory of Open Access Journals (Sweden)

Mingyang Gong

2018-06-01

Full Text Available Static Random Access Memory (SRAM Physical Unclonable Functions (PUFs are some of the most popular PUFs that provide a highly-secured solution for secret key storage. Given that PUF responses are noisy, the key reconstruction must use error correcting code (ECC to reduce the noise. Repetition code is widely used in resource constrained systems as it is concise and lightweight, however, research has shown that repetition codes can lead to information leakage. In this paper we found that the strongest cell distribution in a SRAM array may leak information of the responses of SRAM PUF when the repetition code is directly applied. Experimentally, on an ASIC platform with the HHGRACE 0.13 μm process, we recovered 8.3% of the measured response using the strongest cells revealed by the helper data, and we finally obtained a clone response 79% similar to weak response using the public helper data. We therefore propose Error Resistant Fuzzy Extractor (ERFE, a 4-bit error tolerant fuzzy extractor, that extracts the value of the sum of the responses as a unique key and reduces the failure rate to 1.8 × 10−8 with 256 bit entropy.

Transition of Plasmodium sporozoites into liver stage-like forms is regulated by the RNA binding protein Pumilio

KAUST Repository

Gomes-Santos, Carina S. S.

2011-05-19

Many eukaryotic developmental and cell fate decisions that are effected post-transcriptionally involve RNA binding proteins as regulators of translation of key mRNAs. In malaria parasites (Plasmodium spp.), the development of round, non-motile and replicating exo-erythrocytic liver stage forms from slender, motile and cell-cycle arrested sporozoites is believed to depend on environmental changes experienced during the transmission of the parasite from the mosquito vector to the vertebrate host. Here we identify a Plasmodium member of the RNA binding protein family PUF as a key regulator of this transformation. In the absence of Pumilio-2 (Puf2) sporozoites initiate EEF development inside mosquito salivary glands independently of the normal transmission-associated environmental cues. Puf2- sporozoites exhibit genome-wide transcriptional changes that result in loss of gliding motility, cell traversal ability and reduction in infectivity, and, moreover, trigger metamorphosis typical of early Plasmodium intra-hepatic development. These data demonstrate that Puf2 is a key player in regulating sporozoite developmental control, and imply that transformation of salivary gland-resident sporozoites into liver stage-like parasites is regulated by a post-transcriptional mechanism. 2011 Gomes-Santos et al.

Biodegradation of cypermethrin by immobilized cells of Micrococcus sp. strain CPN 1

Directory of Open Access Journals (Sweden)

Preeti N. Tallur

2015-09-01

Full Text Available Pyrethroid pesticide cypermethrin is a environmental pollutant because of its widespread use, toxicity and persistence. Biodegradation of such chemicals by microorganisms may provide an cost-effective method for their detoxification. We have investigated the degradation of cypermethrin by immobilized cells of Micrococcus sp. strain CPN 1 in various matrices such as, polyurethane foam (PUF, polyacrylamide, sodium alginate and agar. The optimum temperature and pH for the degradation of cypermethrin by immobilized cells of Micrococcus sp. were found to be 30 °C and 7.0, respectively. The rate of degradation of 10 and 20 mM of cypermethrin by freely suspended cells were compared with that of immobilized cells in batches and semi-continuous with shaken cultures. PUF-immobilized cells showed higher degradation of cypermethrin (10 mM and 20 mM than freely suspended cells and cells immobilized in other matrices. The PUF-immobilized cells of Micrococcus sp. strain CPN 1 were retain their degradation capacity. Thus, they can be reused for more than 32 cycles, without losing their degradation capacity. Hence, the PUF-immobilized cells of Micrococcus sp. could potentially be used in the bioremediation of cypermethrin contaminated water.

Bibliometric Analysis of Traditional Chinese Medicine Scientific Production between 1982 and 2016 Indexed in PubMed.

Science.gov (United States)

Consentino, Ricardo; Santos, Maria João; Matos, Luís Carlos; Machado, Jorge Pereira

2018-05-03

Background: Traditional Chinese medicine (TCM) may be understood as a system of sensations and findings designed to establish the functional vegetative state of the body. This state may be treated by several therapeutic methods such as acupuncture, Chinese pharmacotherapy, dietetics, Tuina , and Qigong . Nowadays, as a result of several evidence-based reported beneficial effects over specific pathological conditions, there is an increasing tendency to integrate some of these practices in Western medicine. The main goal of this study was to perform a bibliometric analysis of TCM scientific production between 1982 and 2016 indexed in PubMed, by analyzing several parameters including time and location distribution, publication quality, experimental design, and treatment methods. Methods: The methodology was based on the quantitative inventory of published scientific research indexed in PubMed medical subject headings (MeSH), sorted within the broad term “Traditional Chinese Medicine” and integrating the following criteria as limit filters: “Species: Humans”, “Article Type: Clinical Trial”. In addition, the articles’ triage was ruled by temporal limitations set between 1945 and 2016. Results: The overall analysis of data allowed observation of an average annual growth of approximately 33%, with a productive peak of 122 articles in 2007. The scientific production was distributed in 27 countries, led by China (76.1%), followed by the United States of America (3.0%) and South Korea (2.1%). A significant amount of references were published in Chinese journals: more than 50%; however, these journals had a low impact factor. The most cited treatments in the keywords section of the articles were phytotherapy (55%) and acupuncture (40%). Conclusion: The increasing demand for TCM seems to be due to factors such as lower side effects and greater efficacy in some patients not responding well to conventional therapy. As a result, a considerable amount of TCM science

Pramana – Journal of Physics | Indian Academy of Sciences

Indian Academy of Sciences (India)

A high resistance, meandering type horizontal strip connects the anodes at one end and aids in position sensing by charge division method. The detector is tested with gas mixtures 3He+Kr (1 : 2) and 3He+CF4 (2 : 1) at pressure of 3 atmospheres and using a Pu-Be neutron source. The pulse height spectrum shows energy ...

Utilization of colemanite as a radiation protection material

International Nuclear Information System (INIS)

Bayulken, Ahmet; Aksut, Cem

1986-01-01

In experiments utilizing neutrons, a good shielding is very important. For developing countries, economics of the protection system is also a very important factor. In this work, a new material for protection blocks is investigated. These blocks are fabricated with colemanite powder in a paraffin wax matrix, and their behaviour as a neutron shield are investigated with a Pu-Be neutron source. (author)

Wishing away Plagiarism in Scientific Publications! Will it work? A situational analysis of Plagiarism policy of journals in PubMed.

Science.gov (United States)

Debnath, Jyotindu; Cariappa, M P

2018-04-01

Plagiarism remains a scourge for the modern academia. There are inconsistencies in the plagiarism policy scientific journals. The aims of this study was to analyze types of published articles on 'Plagiarism' available on PubMed over last two decades against a backdrop of the plagiarism policy of the journals publishing such articles. A literature search on PubMed (https://www.ncbi.nlm.nih.gov/pubmed) was made using the search term "plagiarism" from 01 January 1997 till 29 March 17. All publications having 'plagiarism' in the title formed the study group. The following were noted: types of articles published, ethical and plagiarism policy of the journal as available in the Instructions to authors and or in the journal home page. A total of 582 publications from 320 journals were studied. Editorials (165, 28.3%) and Letters to the Editor (159, 27.3%) formed the bulk. Research articles (56, 9.6%), Review articles (51, 8.7%) and Commentaries (47, 8%) formed the remainder. Detailed ethical guidelines were present in 221 (69%). Outline ethical guidelines only were present in 15 (4.7%) journals. 49 (15.3%) journals did not have any ethical guidelines. Detailed description of the policy on plagiarism was found in 80 (25%) journals. Only an outline description was found in 29 (9%) journals while a plagiarism policy/statement was totally absent in 176 (55%) journals. There is a need to have a well defined plagiarism policy/statement for all scholarly journals easily visible on their home pages on the internet and also in their Instructions to Authors.

Microtask crowdsourcing for disease mention annotation in PubMed abstracts.

Science.gov (United States)

Good, Benjamin M; Nanis, Max; Wu, Chunlei; Su, Andrew I

2015-01-01

Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon's Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the 'training set' of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http://figshare.com/articles/Disease_Mention_Annotation_with_Mechanical_Turk/1126402.

pubmed.mineR: an R package with text-mining algorithms to analyse PubMed abstracts.

Science.gov (United States)

Rani, Jyoti; Shah, A B Rauf; Ramachandran, Srinivasan

2015-10-01

The PubMed literature database is a valuable source of information for scientific research. It is rich in biomedical literature with more than 24 million citations. Data-mining of voluminous literature is a challenging task. Although several text-mining algorithms have been developed in recent years with focus on data visualization, they have limitations such as speed, are rigid and are not available in the open source. We have developed an R package, pubmed.mineR, wherein we have combined the advantages of existing algorithms, overcome their limitations, and offer user flexibility and link with other packages in Bioconductor and the Comprehensive R Network (CRAN) in order to expand the user capabilities for executing multifaceted approaches. Three case studies are presented, namely, 'Evolving role of diabetes educators', 'Cancer risk assessment' and 'Dynamic concepts on disease and comorbidity' to illustrate the use of pubmed.mineR. The package generally runs fast with small elapsed times in regular workstations even on large corpus sizes and with compute intensive functions. The pubmed.mineR is available at http://cran.rproject. org/web/packages/pubmed.mineR.

NEMO: Extraction and normalization of organization names from PubMed affiliations.

Science.gov (United States)

Jonnalagadda, Siddhartha Reddy; Topham, Philip

2010-10-04

Today, there are more than 18 million articles related to biomedical research indexed in MEDLINE, and information derived from them could be used effectively to save the great amount of time and resources spent by government agencies in understanding the scientific landscape, including key opinion leaders and centers of excellence. Associating biomedical articles with organization names could significantly benefit the pharmaceutical marketing industry, health care funding agencies and public health officials and be useful for other scientists in normalizing author names, automatically creating citations, indexing articles and identifying potential resources or collaborators. Large amount of extracted information helps in disambiguating organization names using machine-learning algorithms. We propose NEMO, a system for extracting organization names in the affiliation and normalizing them to a canonical organization name. Our parsing process involves multi-layered rule matching with multiple dictionaries. The system achieves more than 98% f-score in extracting organization names. Our process of normalization that involves clustering based on local sequence alignment metrics and local learning based on finding connected components. A high precision was also observed in normalization. NEMO is the missing link in associating each biomedical paper and its authors to an organization name in its canonical form and the Geopolitical location of the organization. This research could potentially help in analyzing large social networks of organizations for landscaping a particular topic, improving performance of author disambiguation, adding weak links in the co-author network of authors, augmenting NLM's MARS system for correcting errors in OCR output of affiliation field, and automatically indexing the PubMed citations with the normalized organization name and country. Our system is available as a graphical user interface available for download along with this paper.

Countries’ Biomedical Publications and Attraction Scores. A PubMed-based assessment

Science.gov (United States)

Xu, Qinyi; Boggio, Andrea; Ballabeni, Andrea

2015-01-01

Studying publication volumes at the country level is key to understanding and improving a country’s research system. PubMed is a public search engine of publications in all life sciences areas. Here, we show how this search engine can be used to assess the outputs of life science-related research by country. We have measured the numbers of publications during different time periods based on the country of affiliation of the first authors. Moreover, we have designed scores, which we have named Attraction Scores, to appraise the relative focus either toward particular types of studies, such as clinical trials or reviews, or toward specific research areas, such as public health and pharmacogenomics, or toward specific topics, for instance embryonic stem cells; we have also investigated a possible use of these Attraction Scores in connection with regulatory policies. We have weighed the statistics against general indicators such as country populations and gross domestic products (GDP). During the 5-year period 2008-2012, the United States was the country with the highest number of publications and Denmark the one with the highest number of publications per capita. Among the 40 countries with the highest GDPs, Israel had the highest publications-to-GDP ratio. Among the 20 countries with the most publications, Japan had the highest Attraction Score for induced pluripotent stem (iPS) cells and Italy the highest proportion of review publications. More than 50% of publications in English were from countries in which English is not the primary language. We show an assorted and extensive collection of rankings and charts that will inform scholars and policymakers in studying and improving the research systems both at the national and international level. PMID:26401263

Drosophila Pumilio protein contains multiple autonomous repression domains that regulate mRNAs independently of Nanos and brain tumor.

Science.gov (United States)

Weidmann, Chase A; Goldstrohm, Aaron C

2012-01-01

Drosophila melanogaster Pumilio is an RNA-binding protein that potently represses specific mRNAs. In developing embryos, Pumilio regulates a key morphogen, Hunchback, in collaboration with the cofactor Nanos. To investigate repression by Pumilio and Nanos, we created cell-based assays and found that Pumilio inhibits translation and enhances mRNA decay independent of Nanos. Nanos robustly stimulates repression through interactions with the Pumilio RNA-binding domain. We programmed Pumilio to recognize a new binding site, which garners repression of new target mRNAs. We show that cofactors Brain Tumor and eIF4E Homologous Protein are not obligatory for Pumilio and Nanos activity. The conserved RNA-binding domain of Pumilio was thought to be sufficient for its function. Instead, we demonstrate that three unique domains in the N terminus of Pumilio possess the major repressive activity and can function autonomously. The N termini of insect and vertebrate Pumilio and Fem-3 binding factors (PUFs) are related, and we show that corresponding regions of human PUM1 and PUM2 have repressive activity. Other PUF proteins lack these repression domains. Our findings suggest that PUF proteins have evolved new regulatory functions through protein sequences appended to their conserved PUF repeat RNA-binding domains.

Semi-insulating GaAs detectors of fast neutrons

International Nuclear Information System (INIS)

Sagatova, A.; Sedlackova, K.; Necas, V.; Zatko, B.; Dubecky, F.; Bohacek, P.

2012-01-01

The present work deals with the technology of HDPE neutron conversion layer application on the surface of semi-insulating (SI) GaAs detectors via developed polypropylene (PP) based glue. The influence of glue deposition on the electric properties of the detectors was studied as well as the ability of the detectors to register the fast neutrons from "2"3"9Pu-Be neutron source. (authors)

Detection and identification of explosives and illicit drugs using neutron based techniques

International Nuclear Information System (INIS)

Papp, A.; Csikai, J.; Debrecen University,

2011-01-01

Some methods developed in collaboration between the ATOMKI and IEP for bulk hydrogen analysis and for the detection and identification of illicit drugs are presented. Advantages and limitations of neutron techniques (reflection, transmission, elastic and inelastic scatterings, leakage spectra and angular yields of Be(d,n), Pu-Be, D-D, D-T and 252 Cf neutrons transmitted from thick samples, effects of hidden materials) are discussed. (author)

Preliminary comparison of the Essie and PubMed search engines for answering clinical questions using MD on Tap, a PDA-based program for accessing biomedical literature.

Science.gov (United States)

Sutton, Victoria R; Hauser, Susan E

2005-01-01

MD on Tap, a PDA application that searches and retrieves biomedical literature, is specifically designed for use by mobile healthcare professionals. With the goal of improving the usability of the application, a preliminary comparison was made of two search engines (PubMed and Essie) to determine which provided most efficient path to the desired clinically-relevant information.

Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.

Science.gov (United States)

Karthikeyan, M; Krishnan, S; Pandey, Anil Kumar; Bender, Andreas; Tropsha, Alexander

2008-04-01

We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.ncl.res.in/chemstar/.

PageRank without hyperlinks: Reranking with PubMed related article networks for biomedical text retrieval

Directory of Open Access Journals (Sweden)

Lin Jimmy

2008-06-01

Full Text Available Abstract Background Graph analysis algorithms such as PageRank and HITS have been successful in Web environments because they are able to extract important inter-document relationships from manually-created hyperlinks. We consider the application of these techniques to biomedical text retrieval. In the current PubMed® search interface, a MEDLINE® citation is connected to a number of related citations, which are in turn connected to other citations. Thus, a MEDLINE record represents a node in a vast content-similarity network. This article explores the hypothesis that these networks can be exploited for text retrieval, in the same manner as hyperlink graphs on the Web. Results We conducted a number of reranking experiments using the TREC 2005 genomics track test collection in which scores extracted from PageRank and HITS analysis were combined with scores returned by an off-the-shelf retrieval engine. Experiments demonstrate that incorporating PageRank scores yields significant improvements in terms of standard ranked-retrieval metrics. Conclusion The link structure of content-similarity networks can be exploited to improve the effectiveness of information retrieval systems. These results generalize the applicability of graph analysis algorithms to text retrieval in the biomedical domain.

PageRank without hyperlinks: reranking with PubMed related article networks for biomedical text retrieval.

Science.gov (United States)

Lin, Jimmy

2008-06-06

Graph analysis algorithms such as PageRank and HITS have been successful in Web environments because they are able to extract important inter-document relationships from manually-created hyperlinks. We consider the application of these techniques to biomedical text retrieval. In the current PubMed(R) search interface, a MEDLINE(R) citation is connected to a number of related citations, which are in turn connected to other citations. Thus, a MEDLINE record represents a node in a vast content-similarity network. This article explores the hypothesis that these networks can be exploited for text retrieval, in the same manner as hyperlink graphs on the Web. We conducted a number of reranking experiments using the TREC 2005 genomics track test collection in which scores extracted from PageRank and HITS analysis were combined with scores returned by an off-the-shelf retrieval engine. Experiments demonstrate that incorporating PageRank scores yields significant improvements in terms of standard ranked-retrieval metrics. The link structure of content-similarity networks can be exploited to improve the effectiveness of information retrieval systems. These results generalize the applicability of graph analysis algorithms to text retrieval in the biomedical domain.

The effects of smoking status and ventilation on environmental tobacco smoke concentrations in public areas of UK pubs and bars

Science.gov (United States)

Carrington, Joanna; Watson, Adrian F. R.; Gee, Ivan L.

UK public houses generally allow smoking to occur and consequently customer ETS exposure can take place. To address this, in 1999 the UK Government and the hospitality industry initiated the Public Places Charter (PPC) to increase non-smoking facilities and provide better ventilation in public houses. A study involving 60 UK pubs, located in Greater Manchester, was conducted to investigate the effects of smoking area status and ventilation on ETS concentrations. ETS markers RSP, UVPM, FPM, SolPM and nicotine were sampled and analysed using established methodologies. ETS marker concentrations were significantly higher ( P mobile in these environments and tends to remain in the smoking areas. This result, together with the much higher reductions in nicotine concentrations between smoking and non-smoking areas compared to other markers, suggests that nicotine is not the most suitable marker to use in these environments as an indicator of the effectiveness of tobacco control policies. The use of ventilation systems (sophisticated HVAC systems and extractor fans in either the on or off mode) did not have a significant effect ( P > 0.05) on ETS marker concentrations in either the smoking or non-smoking areas. The PPC aims to reduce non-smoking customers' exposure through segregation and ventilation and provide customer choice though appropriate signs. This study indicates that although ETS levels are lower in non-smoking sections and signs will assist customers in reducing their exposure, some exposure will still occur because ETS was detected in non-smoking areas. Existing ventilation provision was not effective in reducing exposure and signs advertising ventilated premises may be misleading to customers. Improvements in the design and management of ventilation systems in pubs and bars are required to reduce customer exposure to ETS, if the aims of the PPC are to be met.

Using Clinical Data, Hypothesis Generation Tools and PubMed Trends to Discover the Association between Diabetic Retinopathy and Antihypertensive Drugs

Energy Technology Data Exchange (ETDEWEB)

Senter, Katherine G [ORNL; Sukumar, Sreenivas R [ORNL; Patton, Robert M [ORNL; Chaum, Ed [University of Tennessee, Knoxville (UTK)

2015-01-01

Diabetic retinopathy (DR) is a leading cause of blindness and common complication of diabetes. Many diabetic patients take antihypertensive drugs to prevent cardiovascular problems, but these drugs may have unintended consequences on eyesight. Six common classes of antihypertensive drug are angiotensin converting enzyme (ACE) inhibitors, alpha blockers, angiotensin receptor blockers (ARBs), -blockers, calcium channel blockers, and diuretics. Analysis of medical history data might indicate which of these drugs provide safe blood pressure control, and a literature review is often used to guide such analyses. Beyond manual reading of relevant publications, we sought to identify quantitative trends in literature from the biomedical database PubMed to compare with quantitative trends in the clinical data. By recording and analyzing PubMed search results, we found wide variation in the prevalence of each antihypertensive drug in DR literature. Drug classes developed more recently such as ACE inhibitors and ARBs were most prevalent. We also identified instances of change-over-time in publication patterns. We then compared these literature trends to a dataset of 500 diabetic patients from the UT Hamilton Eye Institute. Data for each patient included class of antihypertensive drug, presence and severity of DR. Graphical comparison revealed that older drug classes such as diuretics, calcium channel blockers, and -blockers were much more prevalent in the clinical data than in the DR and antihypertensive literature. Finally, quantitative analysis of the dataset revealed that patients taking -blockers were statistically more likely to have DR than patients taking other medications, controlling for presence of hypertension and year of diabetes onset. This finding was concerning given the prevalence of -blockers in the clinical data. We determined that clinical use of -blockers should be minimized in diabetic patients to prevent retinal damage.

Cassava and turmeric flour blends as new raw materials to extruded snacks

Directory of Open Access Journals (Sweden)

Alessandra Mussato Spinello

2014-02-01

Full Text Available Short cooking time and ability to blend varieties of food ingredients have made extrusion cooking a medium for low-cost and nutritionally improved food products. The effect of moisture, extrusion temperature and amount of turmeric flour mixed with cassava flour on physical characteristic of puffed snacks was evaluated in this work. Extrusion process was carried out using a single-screw extruder in a factorial central composite design with four factors. Results showed effect of extrusion parameters on dependents variables. High expansion, low browning, low water solubility index, intermediate water absorption index and high crispness desirable characteristics to puffed snacks are obtained in conditions of 12% moisture, 5% turmeric flour, 105º C of temperature and 250 rpm of screw speed. These paper point to the potential still unexplored of the use of flours of cassava and turmeric as raw materials in the development of extruded puffed snacks.

Estimation of peak heat flux onto the targets for CFETR with extended divertor leg

International Nuclear Information System (INIS)

Zhang, Chuanjia; Chen, Bin; Xing, Zhe; Wu, Haosheng; Mao, Shifeng; Luo, Zhengping; Peng, Xuebing; Ye, Minyou

2016-01-01

Highlights: • A hypothetical geometry is assumed to extend the outer divertor leg in CFETR. • Density scan SOLPS simulation is done to study the peak heat flux onto target. • Attached–detached regime transition in out divertor occurs at lower puffing rate. • Unexpected delay of attached–detached regime transition occurs in inner divertor. - Abstract: China Fusion Engineering Test Reactor (CFETR) is now in conceptual design phase. CFETR is proposed as a good complement to ITER for demonstrating of fusion energy. Divertor is a crucial component which faces the plasmas and handles huge heat power for CFETR and future fusion reactor. To explore an effective way for heat exhaust, various methods to reduce the heat flux to divertor target should be considered for CFETR. In this work, the effect of extended out divertor leg on the peak heat flux is studied. The magnetic configuration of the long leg divertor is obtained by EFIT and Tokamak Simulation Code (TSC), while a hypothetical geometry is assumed to extend the out divertor leg as long as possible inside vacuum vessel. A SOLPS simulation is performed to study peak heat flux of the long leg divertor for CFETR. D 2 gas puffing is used and increasing of the puffing rate means increase of plasma density. Both peak heat flux onto inner and outer targets are below 10 MW/m 2 is achieved. A comparison between the peak heat flux between long leg and conventional divertor shows that an attached–detached regime transition of out divertor occurs at lower gas puffing gas puffing rate for long leg divertor. While for the inner divertor, even the configuration is almost the same, the situation is opposite.

Estimation of peak heat flux onto the targets for CFETR with extended divertor leg

Energy Technology Data Exchange (ETDEWEB)

Zhang, Chuanjia; Chen, Bin [School of Nuclear Science and Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026 (China); Xing, Zhe [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); Wu, Haosheng [School of Nuclear Science and Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026 (China); Mao, Shifeng, E-mail: sfmao@ustc.edu.cn [School of Nuclear Science and Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026 (China); Luo, Zhengping; Peng, Xuebing [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); Ye, Minyou [School of Nuclear Science and Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026 (China); Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China)

2016-11-01

Highlights: • A hypothetical geometry is assumed to extend the outer divertor leg in CFETR. • Density scan SOLPS simulation is done to study the peak heat flux onto target. • Attached–detached regime transition in out divertor occurs at lower puffing rate. • Unexpected delay of attached–detached regime transition occurs in inner divertor. - Abstract: China Fusion Engineering Test Reactor (CFETR) is now in conceptual design phase. CFETR is proposed as a good complement to ITER for demonstrating of fusion energy. Divertor is a crucial component which faces the plasmas and handles huge heat power for CFETR and future fusion reactor. To explore an effective way for heat exhaust, various methods to reduce the heat flux to divertor target should be considered for CFETR. In this work, the effect of extended out divertor leg on the peak heat flux is studied. The magnetic configuration of the long leg divertor is obtained by EFIT and Tokamak Simulation Code (TSC), while a hypothetical geometry is assumed to extend the out divertor leg as long as possible inside vacuum vessel. A SOLPS simulation is performed to study peak heat flux of the long leg divertor for CFETR. D{sub 2} gas puffing is used and increasing of the puffing rate means increase of plasma density. Both peak heat flux onto inner and outer targets are below 10 MW/m{sup 2} is achieved. A comparison between the peak heat flux between long leg and conventional divertor shows that an attached–detached regime transition of out divertor occurs at lower gas puffing gas puffing rate for long leg divertor. While for the inner divertor, even the configuration is almost the same, the situation is opposite.

Reproducibility in Natural Language Processing: A Case Study of Two R Libraries for Mining PubMed/MEDLINE

Science.gov (United States)

Cohen, K. Bretonnel; Xia, Jingbo; Roeder, Christophe; Hunter, Lawrence E.

2018-01-01

There is currently a crisis in science related to highly publicized failures to reproduce large numbers of published studies. The current work proposes, by way of case studies, a methodology for moving the study of reproducibility in computational work to a full stage beyond that of earlier work. Specifically, it presents a case study in attempting to reproduce the reports of two R libraries for doing text mining of the PubMed/MEDLINE repository of scientific publications. The main findings are that a rational paradigm for reproduction of natural language processing papers can be established; the advertised functionality was difficult, but not impossible, to reproduce; and reproducibility studies can produce additional insights into the functioning of the published system. Additionally, the work on reproducibility lead to the production of novel user-centered documentation that has been accessed 260 times since its publication—an average of once a day per library. PMID:29568821

Secure key storage with PUFs

NARCIS (Netherlands)

Tuyls, P.T.; Schrijen, G.J.; Willems, F.M.J.; Ignatenko, T.; Skoric, B.; Tuyls, P.T.; Skoric, B.; Kevenaar, T.A.M.

2007-01-01

Nowadays, people carry around devices (cell phones, PDAs, bank passes, etc.) that have a high value. That value is often contained in the data stored in it or lies in the services the device can grant access to (by using secret identification information stored in it). These devices often operate in

Medicare Referring Provider DMEPOS PUF

Data.gov (United States)

U.S. Department of Health & Human Services — This dataset, which is part of CMSs Medicare Provider Utilization and Payment Data, details information on Durable Medical Equipment, Prosthetics, Orthotics and...

Secure Key Storage with PUFs

Science.gov (United States)

Skoric, Boris; Schrijen, Geert-Jan; Tuyls, Pim; Ignatenko, Tanya; Willems, Frans

Nowadays, people carry around devices (cell phones, PDAs, bank passes, etc.) that have a high value. That value is often contained in the data stored in it or lies in the services the device can grant access to (by using secret identification information stored in it). These devices often operate in hostile environments and their protection level is not adequate to deal with that situation. Bank passes and credit cards contain a magnetic stripe where identification information is stored. In the case of bank passes, a PIN is additionally required to withdraw money from an ATM (Automated Teller Machine). At various occasions, it has been shown that by placing a small coil in the reader, the magnetic information stored in the stripe can easily be copied and used to produce a cloned card. Together with eavesdropping the PIN (by listening to the keypad or recording it with a camera), an attacker can easily impersonate the legitimate owner of the bank pass by using the cloned card in combination with the eavesdropped PIN.

Role of recycling flux in gas fuelling in the Large Helical Device

International Nuclear Information System (INIS)

Miyazawa, J.; Masuzaki, S.; Yamada, H.

2004-01-01

The 'effective' fuelling efficiency of hydrogen gas puffing ranges from 10% to 50% in the Large Helical Device. A local increase in neutral particle pressure at the gas puff port was measured in the experiment. The pressure increase rate corresponds to ∼ 10% of the gas puff flux. The other 90% of the gas puff flux increases the density and/or the plasma outflow. A particle balance model reveals that the recycling flux estimated from the particle flux on the divertor plates increases during the gas puffing. It is shown that the high effective fuelling efficiency is possibly due to the large recycling flux. At the limit of small recycling flux, the effective fuelling efficiency decreases to ∼10%. In the helium gas puff discharge, the effective fuelling efficiency is larger than the hydrogen gas puffing and approaches 100%. This can be related to the large recycling coefficient of more than 0.95. (author)

Development of a radiative divertor for DIII-D

International Nuclear Information System (INIS)

Allen, S.L.; Brooks, N.H.; Campbell, R.B.; Fenstermacher, M.E.; Hill, D.N.; Hyatt, A.W.; Knoll, D.; Lasnier, C.J.; Lazarus, E.A.; Leonard, A.W.; Lippmann, S.I.; Mahdavi, M.A.; Maingi, R.; Meyer, W.; Moyer, R.A.; Petrie, T.W.; Porter, G.D.; Rensink, M.E.; Rognlien, T.D.; Schaffer, M.J.; Smith, J.P.; Staebler, G.M.; Stambaugh, R.D.; West, W.P.; Wood, R.D.

1995-01-01

We have used experiments and modeling to develop a new radiative divertor configuration for DIII-D. Gas puffing experiments with the existing open divertor have shown the creation of a localized ( similar 10 cm diameter) radiation zone which results in substantial reduction (3-10) in the divertor heat flux while τ E remains similar 2 times ITER-89P scaling. However, n e increases with D 2 puffing, and Z eff increases with neon puffing. Divertor structures are required to minimize the effects on the core plasma. The UEDGE fluid code, benchmarked with DIII-D data, and the DEGAS neutrals transport code are used to estimate the effectiveness of divertor configurations; slots reduce the core ionization more than baffles. The overall divertor shape is set by confinement studies which indicate that high triangularity (δ∼0.8) is important for high τ E VH-modes. Results from engineering feasibility studies, including diagnostic access, will be presented. ((orig.))

Estudo da sorção do corante catiônico violeta cristal por espuma de poliuretano em meio aquoso contendo dodecilsulfato de sódio Sorption of crystal violet by polyurethane foam from aqueous medium containing sodium dodecylsulfate

Directory of Open Access Journals (Sweden)

Mariana Mori

2009-01-01

Full Text Available This work presents a detailed study about the sorption of crystal violet (CV cationic dye onto polyether type polyurethane foam (PUF. The sorption process was based on the formation of an ionic-pair between cationic dye and dodecylsulfate anion (SDS, which presented high affinity by PUF. Set-up employed in the study was built up by adjusting a 200 mg cylinder of PUF to the arm of an overhead stirrer. The system was characterized in relation to equilibrium and kinetic aspects and it was modeled by employing Langmuir and Freundlich isotherms. Obtained results showed that the ratio between SDS and MB concentrations played an important role on the sorption process. According to results found it was possible to retain up to 3.4 mg of dye from 200 mL of a 5.0 x 10-5 mol L-1 CV solution containing 1.25 x 10-4 mol L-1 SDS, which represented a removal efficiency of around 92%.

Development of a radiative divertor for DIII-D

Energy Technology Data Exchange (ETDEWEB)

Allen, S.L. [Lawrence Livermore National Lab., CA (United States); Brooks, N.H. [General Atomics, San Diego, CA (United States); Campbell, R.B. [Sandia National Labs., Albuquerque, NM (United States); Fenstermacher, M.E. [Lawrence Livermore National Lab., CA (United States); Hill, D.N. [Lawrence Livermore National Lab., CA (United States); Hyatt, A.W. [General Atomics, San Diego, CA (United States); Knoll, D.; Lasnier, C.J. [Lawrence Livermore National Lab., CA (United States); Lazarus, E.A. [Oak Ridge National Lab., TN (United States); Leonard, A.W. [General Atomics, San Diego, CA (United States); Lippmann, S.I. [General Atomics, San Diego, CA (United States); Mahdavi, M.A. [General Atomics, San Diego, CA (United States); Maingi, R. [Oak Ridge National Lab., TN (United States); Meyer, W. [Lawrence Livermore National Lab., CA (United States); Moyer, R.A. [California Univ., Los Angeles, CA (United States); Petrie, T.W. [General Atomics, San Diego, CA (United States); Porter, G.D. [Lawrence Livermore National Lab., CA (United States); Rensink, M.E. [Lawrence Livermore National Lab., CA (United States); Rognlien, T.D. [Lawrence Livermore National Lab., CA (United States); Schaffer, M.J. [General Atomics, San Diego, CA (United States); Smith, J.P. [General Atomics, San Diego, CA (United States); Staebler, G.M. [General Atomics, San Diego, CA (United States); Stambaugh, R.D. [General Atomics, San Diego, CA (United States); West, W.P. [General Atomics, San Diego, CA (United States); Wood, R.D. [Lawrence Livermore National Lab., CA (United States)

1995-04-01

We have used experiments and modeling to develop a new radiative divertor configuration for DIII-D. Gas puffing experiments with the existing open divertor have shown the creation of a localized ( similar 10 cm diameter) radiation zone which results in substantial reduction (3-10) in the divertor heat flux while {tau}{sub E} remains similar 2 times ITER-89P scaling. However, n{sub e} increases with D{sub 2} puffing, and Z{sub eff} increases with neon puffing. Divertor structures are required to minimize the effects on the core plasma. The UEDGE fluid code, benchmarked with DIII-D data, and the DEGAS neutrals transport code are used to estimate the effectiveness of divertor configurations; slots reduce the core ionization more than baffles. The overall divertor shape is set by confinement studies which indicate that high triangularity ({delta}{approx}0.8) is important for high {tau}{sub E} VH-modes. Results from engineering feasibility studies, including diagnostic access, will be presented. ((orig.)).

Langmuir probe measurements of the scrape-off plasma in ISX-A

International Nuclear Information System (INIS)

Namkung, W.; England, A.C.; Eldridge, O.C.

1978-11-01

A fixed double Langmuir probe was used to investigate the temporal behavior of the scrape-off plasma in the ISX-A tokamak. During gas puffing, the ion saturation current dropped rapidly to a very low level while the line average density showed a steady increase. This sudden transition was due mainly to a density change of more than a factor of five while the electron temperature remained relatively constant at approximately 10 eV. This behavior was easily observed at points away from the limiter with mild and moderate gas puffing rates, and near the inner edge of the limiter with strong gas puffing. In order to explain the phenomenon, it is suggested that there may be two distinct layers in the scrape-off plasma and that the boundary between the layers moves inward toward the limiter. The existence of the boundary has been confirmed indirectly by sudden shifts of the plasma during feedback control experiments

Passive non destructive assay of hull waste by gross neutron counting method

International Nuclear Information System (INIS)

Andola, Sanjay; Sur, Amit; Rawool, A.M.; Sharma, B.; Kaushik, T.C.; Gupta, S.C.; Basu, Sekhar; Raman Kumar; Agarwal, K.

2014-01-01

The special nuclear material accounting (SNMA) is an important and necessary issue now in nuclear waste management. The hull waste generated from dissolution of spent fuel contains small amounts of Uranium and Plutonium and other actinides due to undissolved trapped material inside zircoalloy tubes. We report here on the development of a Passive Hull monitoring system using gross neutron counting technique and its implementation with semiautomatic instrumentation. The overall sensitivity of the 3 He detector banks placed at 75 cm from the centre of loaded hull cask comes out to 5.2 x 10 -3 counts per neutron (c/n) while with standard Pu-Be source placed in same position it comes out to be 3.1 x 10 3 c/n. The difference in the efficiency is mainly because of the differences in the geometry and size of hull cask as well as difference in the energy spectrum of hull waste and Pu-Be source. This is accounted through Monte Carlo computations. The Pu mass in solid waste comes out as expected and varies with the surface dose rate of drum in almost a proportional manner. Being simple and less time consuming, this setup has been installed for routine assay of solid Hull waste at NRB, Tarapur

Virtuous suffering and the predicament of being handicapped. Towards a theology of the ‘disabled God puffing in a wheelchair’

Directory of Open Access Journals (Sweden)

Daniel J. Louw

2014-04-01

Full Text Available The reality of disablement, being handicapped and physical disfigurement, opens up anew the theological debate regarding God-images in human suffering. It is argued that the Hellenistic understanding of the power of God, God as a pantokrator [Almighty], presupposes the immutability of an apathetic God. In terms of the logic of a cause-effect paradigm, God becomes the deterministic principle behind human suffering. With reference to a theologia crucis [theology of the Cross], the paradigm of theopaschitic theology proposes a pathetic understanding of God. Weakness and vulnerability (astheneia describes an authentic identification of God with human suffering. Forsakenness (derelictio reframes power as compassionate weakness or vulnerability and divine disability. The disabled God is, in terms of the New Testament a connection between divine compassion and human predicament (ta splanchna, the passionate God. Bowel categories make it possible to speak of the ‘puffing God in the wheelchair’. A theology of the cross should be supplemented by a theology of ability (theologia resurrectionis. The resurrection introduces the spiritual ability parrhesia − the transformation of the weakness of suffering into the fortigenitics of hope. Lyding tussen lot en deug binne die dilemma van gestremdheid. Die onwikkeling van ’n teologie van die ‘gestremde God, hygend in ’n rolstoel’. Die gegewendheid en realiteit van verskillende vorme van gestremdheid onderstreep menslike weerloosheid en magteloosheid. Vir gelowiges wat worstel met die vraag na sin in lyding, roep dit onder andere die vraag op na die verband tussen lyding en die almag en krag van God. Die basiese argument is dat die Hellenistiese konsep en paradigma van die mag van God, God as pantokrator, die starre onbeweeglikheid van ’n apatiese God voorveronderstel. Met behulp van die oorsaak-gevolg skema van denke, word God, in terme van die menslike logika, ’n deterministiese

Adei .pub

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Adei .pub

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of the challenges that affect the Poultry indus- try reflected in .... government's 2010 budget and financial state- ment restored duties ... jects were examined and the relationships be- tween them ..... paves the way for customers who buy within.

Yebaoh .pub

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Keywords: teenage pregnancy, social support, pre-natal clinic visits, pregnancy outcomes. INTRODUCTION .... In this sense, social support has meliorating influence on the ..... graphic Change, Mexico, 25-28 October,. 1994. Oppong, C.

Development of plasma fueling on EAST

International Nuclear Information System (INIS)

Yao, X.J.; Zheng, X.W.; Li, C.Z.; Chen, Y.

2015-01-01

To achieve better plasma density control, experimental advanced superconducting tokamak (EAST) has already equipped with gas puffing (GP), supersonic molecular beam injection (SMBI) and pellet injection (PI). During the past few years, lots of experiments and ameliorations have been done. The performance of the SMBI and gas puffing (GP) feedback systems were used and compared. And the preliminary result of pellet injection was also presented here. The results shows the PI and SMBI were more compatible to the long pulse high density discharge on EAST. (author)

Physically unclonable functions constructions, properties and applications

CERN Document Server

Maes, Roel

2013-01-01

Physically unclonable functions (PUFs) are innovative physical security primitives that produce unclonable and inherent instance-specific measurements of physical objects; in many ways they are the inanimate equivalent of biometrics for human beings. Since they are able to securely generate and store secrets, they allow us to bootstrap the physical implementation of an information security system. In this book the author discusses PUFs in all their facets: the multitude of their physical constructions, the algorithmic and physical properties which describe them, and the techniques required to

LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC.

Science.gov (United States)

Allot, Alexis; Peng, Yifan; Wei, Chih-Hsuan; Lee, Kyubum; Phan, Lon; Lu, Zhiyong

2018-05-14

The identification and interpretation of genomic variants play a key role in the diagnosis of genetic diseases and related research. These tasks increasingly rely on accessing relevant manually curated information from domain databases (e.g. SwissProt or ClinVar). However, due to the sheer volume of medical literature and high cost of expert curation, curated variant information in existing databases are often incomplete and out-of-date. In addition, the same genetic variant can be mentioned in publications with various names (e.g. 'A146T' versus 'c.436G>A' versus 'rs121913527'). A search in PubMed using only one name usually cannot retrieve all relevant articles for the variant of interest. Hence, to help scientists, healthcare professionals, and database curators find the most up-to-date published variant research, we have developed LitVar for the search and retrieval of standardized variant information. In addition, LitVar uses advanced text mining techniques to compute and extract relationships between variants and other associated entities such as diseases and chemicals/drugs. LitVar is publicly available at https://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/LitVar.

Sports medicine clinical trial research publications in academic medical journals between 1996 and 2005: an audit of the PubMed MEDLINE database.

Science.gov (United States)

Nichols, A W

2008-11-01

To identify sports medicine-related clinical trial research articles in the PubMed MEDLINE database published between 1996 and 2005 and conduct a review and analysis of topics of research, experimental designs, journals of publication and the internationality of authorships. Sports medicine research is international in scope with improving study methodology and an evolution of topics. Structured review of articles identified in a search of a large electronic medical database. PubMed MEDLINE database. Sports medicine-related clinical research trials published between 1996 and 2005. Review and analysis of articles that meet inclusion criteria. Articles were examined for study topics, research methods, experimental subject characteristics, journal of publication, lead authors and journal countries of origin and language of publication. The search retrieved 414 articles, of which 379 (345 English language and 34 non-English language) met the inclusion criteria. The number of publications increased steadily during the study period. Randomised clinical trials were the most common study type and the "diagnosis, management and treatment of sports-related injuries and conditions" was the most popular study topic. The knee, ankle/foot and shoulder were the most frequent anatomical sites of study. Soccer players and runners were the favourite study subjects. The American Journal of Sports Medicine had the highest number of publications and shared the greatest international diversity of authorships with the British Journal of Sports Medicine. The USA, Australia, Germany and the UK produced a good number of the lead authorships. In all, 91% of articles and 88% of journals were published in English. Sports medicine-related research is internationally diverse, clinical trial publications are increasing and the sophistication of research design may be improving.

Modernization of the irradiation apparatus for nuclear instrument calibration laboratory of the Paks Nuclear Power Plant, Hungary

International Nuclear Information System (INIS)

Orban, M.; Csete, I.; Lenart, A.

1993-01-01

The National Office of Measures, OMH of Hungary, has made several proposals for improving technical and personal conditions of metrological inspection of calibration apparatuses at PNPP, Hungary. Some recent improvement of irradiation facilities are described, including the collimator system of the large gamma irradiation facility, the small gamma irradiation gun, and the Pu-Be neutron gun. The upgrading operations and results of these equipment are presented. (N.T.) 4 figs.; 1 tab

[An analysis of Chilean biomedical publications in PubMed in the years 2008-2009].

Science.gov (United States)

Valdés S, Gloria; Pérez G, Fernanda; Reyes B, Humberto

2015-08-01

During the years 2008 and 2009, 1,191 biomedical articles authored by Chilean investigators working in Chile were indexed in PubMed. To evaluate the potential visibility of those articles, according to scientometric indexes of the journals where they were published. Those journals where the articles had been published were identified and each journal’s Impact Factor (JIF), 5-year JIF, SCImago Journal Rank (SJR), SCImago Quartiles (Q) for 2010 and the Source Normalized Impact per Paper (SNIP) for 2008-2009 were identified. Three hundred and twelve articles (26,2%) were dedicated to experimental studies in animals, tissues or cells and they were classified as “Biomedicine”, while 879 (73,8%) were classified as “Clinical Medicine”; in both areas the main type of articles were original reports (90% and 73.6%, respectively). Revista Médica de Chile and Revista Chilena de Infectología concentrated the greater number of publications. Articles classified in Biomedicine were published more frequently in English and in journals with higher scientometric indexes than those classified in Clinical Medicine. Biomedical articles dealing with clinical topics, particularly case reports, were published mostly in national journals or in foreign journals with low scientometric indexes. It can be partly attributable to the authors’ interest in reaching local readers. The evaluation of research productivity should combine several scientometric indexes, selected according to the field of research, the institution's and investigators’ interests, with a qualitative and multifactorial assessment.

Baltimore PM2.5 Supersite: highly time-resolved organic compounds--sampling duration and phase distribution--implications for health effects studies.

Science.gov (United States)

Rogge, Wolfgang F; Ondov, John M; Bernardo-Bricker, Anna; Sevimoglu, Orhan

2011-12-01

As part of the Baltimore PM2.5 Supersite study, intensive three-hourly continuous PM2.5 sampling was conducted for nearly 4 weeks in summer of 2002 and as well in winter of 2002/2003. Close to 120 individual organic compounds have been quantified separately in filter and polyurethane foam (PUF) plug pairs for 17 days for each sampling period. Here, the focus is on (1) describing briefly the new sampling system, (2) discussing filter/PUF plugs breakthrough experiments for semi-volatile compounds, (3) providing insight into phase distribution of semi-volatile organic species, and (4) discussing the impact of air pollution sampling time on human exposure with information on maximum 3- and 24-h averaged ambient concentrations of potentially adverse health effects causing organic pollutants. The newly developed sampling system consisted of five electronically controlled parallel sampling channels that are operated in a sequential mode. Semi-volatile breakthrough experiments were conducted in three separate experiments over 3, 4, and 5 h each using one filter and three PUF plugs. Valuable insight was obtained about the transfer of semi-volatile organic compounds through the sequence of PUF plugs and a cut-off could be defined for complete sampling of semi-volatile compounds on only one filter/PUF plug pair, i.e., the setup finally used during the seasonal PM2.5 sampling campaign. Accordingly, n-nonadecane (C19) with a vapor pressure (vp) of 3.25 × 10(-4) Torr is collected with > 95% on the filter/PUF pair. Applied to phenanthrene, the most abundant the PAH sampled, phenanthrene (vp, 6.2 × 10(-5) Torr) was collected completely in wintertime and correlates very well with three-hourly PM2.5 ambient concentrations. Valuable data on the fractional partitioning for semi-volatile organics as a function of season is provided here and can be used to differentiate the human uptake of an organic pollutant of interest via gas- and particle-phase exposure. Health effects studies

Genetic manipulation of longevity-related genes as a tool to regulate yeast life span and metabolite production during winemaking

Directory of Open Access Journals (Sweden)

Orozco Helena

2013-01-01

Full Text Available Abstract Background Yeast viability and vitality are essential for different industrial processes where the yeast Saccharomyces cerevisiae is used as a biotechnological tool. Therefore, the decline of yeast biological functions during aging may compromise their successful biotechnological use. Life span is controlled by a variety of molecular mechanisms, many of which are connected to stress tolerance and genomic stability, although the metabolic status of a cell has proven a main factor affecting its longevity. Acetic acid and ethanol accumulation shorten chronological life span (CLS, while glycerol extends it. Results Different age-related gene classes have been modified by deletion or overexpression to test their role in longevity and metabolism. Overexpression of histone deacetylase SIR2 extends CLS and reduces acetate production, while overexpression of SIR2 homolog HST3 shortens CLS, increases the ethanol level, and reduces acetic acid production. HST3 overexpression also enhances ethanol tolerance. Increasing tolerance to oxidative stress by superoxide dismutase SOD2 overexpression has only a moderate positive effect on CLS. CLS during grape juice fermentation has also been studied for mutants on several mRNA binding proteins that are regulators of gene expression at the posttranscriptional level; we found that NGR1 and UTH4 deletions decrease CLS, while PUF3 and PUB1 deletions increase it. Besides, the pub1Δ mutation increases glycerol production and blocks stress granule formation during grape juice fermentation. Surprisingly, factors relating to apoptosis, such as caspase Yca1 or apoptosis-inducing factor Aif1, play a positive role in yeast longevity during winemaking as their deletions shorten CLS. Conclusions Manipulation of regulators of gene expression at both transcriptional (i.e., sirtuins and posttranscriptional (i.e., mRNA binding protein Pub1 levels allows to modulate yeast life span during its biotechnological use. Due to

Puffers and Chuggers: Statistical Curiosities in Volcano World

Science.gov (United States)

Lees, J. M.

2002-12-01

Several on-going, low level volcanic explosions exhibit background phenomena commonly known as puffing, or in some cases chugging. Recently these events have been scrutinized because of the initiation of infrasonic monitoring, whereas earlier the events may have gone undetected. The activity associated with a puffer at a volcanic vent is generally small in magnitude and is often not observed audibly. The low frequency signals are readily observed on sensitive acoustic instrumentation and they provide a new dimension for our understanding of volcanic processes at volcanoes like Stromboli and Etna that have constant puffing signals. At other volcanoes, like Karymsky volcano in Kamchatka and Sangay Volcano in Ecuador, chugging signals associated with Strombolian style eruptions also provides new insights into the physics of the conduit systems. Here we present a statistical method of event detection, and event cluster association. When multiple vents work in unison it may be difficult to separate out chugging and puffing signals between spatially separated vents. The cluster analysis automatically differentiates between the vents based on waveform characteristics in the acoustic and seismic wavefields. Data examples from May, 2001, at Stromboli and Etna, show extensive periods of puffing (1-5 second frequency) superimposed on a background of vigorous, small-scale explosive activity. At Karymsky and Sangay non-linear, dynamic models explain the fluid flow through vents which gives rise to chugging. Furthermore, the frequency of chugging events appears to be associated with the intensity of lava flows and eruption rate.

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.

Science.gov (United States)

Kafkas, Şenay; Kim, Jee-Hyub; Pi, Xingjun; McEntyre, Johanna R

2015-01-01

In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe PubMed Central. Our aim is to investigate whether supplementary data files should be considered as a source of information for integrating the literature with biomolecular databases. Using text-mining methods to identify and extract a variety of core biological database accession numbers, we found that the supplemental data files contain many more database citations than the body of the article, and that those citations often take the form of a relatively small number of articles citing large collections of accession numbers in text-based files. Moreover, citation of value-added databases derived from submission databases (such as Pfam, UniProt or Ensembl) is common, demonstrating the reuse of these resources as datasets in themselves. All the database accession numbers extracted from the supplementary data are publicly accessible from http://dx.doi.org/10.5281/zenodo.11771. Our study suggests that supplementary data should be considered when linking articles with data, in curation pipelines, and in information retrieval tasks in order to make full use of the entire research article. These observations highlight the need to improve the management of supplemental data in general, in order to make this information more discoverable and useful.

A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records

DEFF Research Database (Denmark)

Jiang, Li; Edwards, Stefan M.; Thomsen, Bo

2014-01-01

from PubMed abstracts, OMIM, and GeneRIF records. We also investigated the validity of several vocabulary filters and different likelihood thresholds for predicted protein-protein interactions in terms of their effect on the network-based gene-prioritization approach, which relies on text-mining......Background: Prioritizing genetic variants is a challenge because disease susceptibility loci are often located in genes of unknown function or the relationship with the corresponding phenotype is unclear. A global data-mining exercise on the biomedical literature can establish the phenotypic...

Designing a mini subcritical nuclear reactor

International Nuclear Information System (INIS)

Escobedo G, C. R.; Vega C, H. R.; Davila H, V. M.

2015-10-01

In this work the design of a mini subcritical nuclear reactor formed by means of light water moderator, uranium as fuel, and isotopic neutron source of 239 PuBe was carried out. The design was done by Monte Carlo methods with the code MCNP5 in which uranium was modeled in an array of concentric holes cylinders of 8.5, 14.5, 20.5, 26.5, 32.5 cm of internal radius and 3 cm of thickness, 36 cm of height. Different models were made from a single fuel cylinder (natural uranium) to five. The neutron source of 239 PuBe was situated in the center of the mini reactor; in each arrangement was used water as moderator. Cross sections libraries Endf/Vi were used and the number of stories was large enough to ensure less uncertainty than 3%. For each case the effective multiplication factor k e -f f , the amplification factor and the power was calculated. Outside the mini reactor the ambient dose equivalent H (10) was calculated for different cases. The value of k eff , the amplification factor and power are directly related to the number of cylinders of uranium as fuel. Although the average energy of the neutrons 239 PuBe is between 4.5 and 5 MeV in the case of the mini reactor for a cylinder, in the neutron spectrum the presence of thermal neutrons does not exist, so that produced fissions are generated with fast neutrons, and in designs of two and three rings the neutron spectra shows the presence of thermal neutrons, however the fissions are being generated with fast neutrons. Finally in the four and five cases the amount of moderator is enough to thermalized the neutrons and thereby produce the fission. The maximum value for k eff was 0.82; this value is very close to the assembly of Universidad Autonoma de Zacatecas generating a k eff of 0.86. According to the safety and radiation protection standards for the design of mini reactor of one, two and three cylinders they comply with the established safety, while designs of four and five cylinders not met. (Author)

Designing a mini subcritical nuclear reactor; Diseno de un mini reactor nuclear subcritico

Energy Technology Data Exchange (ETDEWEB)

Escobedo G, C. R.; Vega C, H. R.; Davila H, V. M., E-mail: rafelaescobedo@hotmail.com [Universidad Autonoma de Zacatecas, Unidad Academica de Estudios Nucleares, Jardin Juarez 147, Col. Centro, 98000 Zacatecas, Zac. (Mexico)

2015-10-15

In this work the design of a mini subcritical nuclear reactor formed by means of light water moderator, uranium as fuel, and isotopic neutron source of {sup 239}PuBe was carried out. The design was done by Monte Carlo methods with the code MCNP5 in which uranium was modeled in an array of concentric holes cylinders of 8.5, 14.5, 20.5, 26.5, 32.5 cm of internal radius and 3 cm of thickness, 36 cm of height. Different models were made from a single fuel cylinder (natural uranium) to five. The neutron source of {sup 239}PuBe was situated in the center of the mini reactor; in each arrangement was used water as moderator. Cross sections libraries Endf/Vi were used and the number of stories was large enough to ensure less uncertainty than 3%. For each case the effective multiplication factor k{sub e}-f{sub f}, the amplification factor and the power was calculated. Outside the mini reactor the ambient dose equivalent H (10) was calculated for different cases. The value of k{sub eff}, the amplification factor and power are directly related to the number of cylinders of uranium as fuel. Although the average energy of the neutrons {sup 239}PuBe is between 4.5 and 5 MeV in the case of the mini reactor for a cylinder, in the neutron spectrum the presence of thermal neutrons does not exist, so that produced fissions are generated with fast neutrons, and in designs of two and three rings the neutron spectra shows the presence of thermal neutrons, however the fissions are being generated with fast neutrons. Finally in the four and five cases the amount of moderator is enough to thermalized the neutrons and thereby produce the fission. The maximum value for k{sub eff} was 0.82; this value is very close to the assembly of Universidad Autonoma de Zacatecas generating a k{sub eff} of 0.86. According to the safety and radiation protection standards for the design of mini reactor of one, two and three cylinders they comply with the established safety, while designs of four and five

Neutron-based techniques for detection of explosives and drugs

Energy Technology Data Exchange (ETDEWEB)

Kiraly, B.; Olah, L.; Csikai, J. E-mail: csikai@falcon.phys.klte.hu

2001-06-01

Systematic measurements were carried out on the possible use of elastically backscattered Pu-Be neutrons combined with the thermal neutron reflection method for the identification of land mines and illicit drugs via he detection of H, C, N, and O elements as their major constituents. While ur present results show that these methods are capable of indicating the anomalies in bulky materials and observation of the major elements, e termination of the exact atom fractions needs further investigation.

Neutron-based techniques for detection of explosives and drugs

CERN Document Server

Kiraly, B; Csikai, J

2001-01-01

Systematic measurements were carried out on the possible use of elastically backscattered Pu-Be neutrons combined with the thermal neutron reflection method for the identification of land mines and illicit drugs via he detection of H, C, N, and O elements as their major constituents. While ur present results show that these methods are capable of indicating the anomalies in bulky materials and observation of the major elements, e termination of the exact atom fractions needs further investigation.

Co-culturing of Lactobacillus paracasei subsp. paracasei with a Lactobacillus delbrueckii subsp. delbrueckii mutant to make high cell density for increased lactate productivity from cassava bagasse hydrolysate.

Science.gov (United States)

John, Rojan Pappy; Nampoothiri, K Madhavan

2011-03-01

To increase the productivity of lactic acid, a co-culture of lactobacilli was made by mixing 1:1 ratio of Lactobacillus paracasei subsp. paracasei and a fast growing L. delbrueckii subsp. delbrueckii mutant. The culture was embedded on to polyurethane foam (PUF) cubes as a biofilm and used for fermentation. In order to prevent the cell leakage, the PUF cubes were further entrapped in calcium cross-linked alginate. The maximum lactic acid production using a high cell density free culture was >38 g l(-1) from ~40 g l(-1) of reducing sugar within 12 h of fermentation. Using PUF biofilms, the same yield of lactic acid attained after 24 h. When the cubes were further coated with alginate it took 36 h for the maximum yield. Even though, the productivity is slightly lesser with the alginate coating, cell leakage was decreased and cubes were reused without much decrease in production in repeated batches. Using a conventional control inoculum (3%, w/v), it took 120 h to yield same amount of lactic acid.

A role of neutral hydrogen in CHS plasmas with reheat and collapse and comparison with JIPP T-IIU tokamak plasmas

International Nuclear Information System (INIS)

Morita, S.; Yamada, H.; Iguchi, H.

1992-09-01

Results are described on NBI plasmas of the Compact Helical System (CHS). An increase in the stored energy, which is called plasma 'reheat', is observed with density peaking when gas puffing is turned off in the high density region. A plasma collapse with large increase in radiation loss occurs even in discharges whose Z eff values (typically, less than 2-3) do not show any increase when the gas puffing is continued. Both phenomena are basically explained by the edge electron temperature due to the difference in the amount of edge hydrogen neutrals. After turning off the gas puffing, the central electron density n e0 shows an increase of 80% and the density peaking factor (n e0 /n-bar e ) changes from 1.0 to 2.0, in typical cases, and a high inward velocity of the impurities appears (v = 20 m/s). The accumulation is studied in relation to the poloidal rotation and the edge temperature. These results are compared with results from plasmas with IOC- and H-modes in the JIPPT-IIU tokamak. (author)

A bestiary of ordinary vent activities at Stromboli (and what it tells us about vent conditions)

Science.gov (United States)

Gaudin, Damien; Taddeucci, Jacopo; Scarlato, Piergiorgio

2015-04-01

Normal active degassing at Stromboli (Aeolian Islands, Italy) is traditionally divided in two classes. Puffing correspond to the frequent (~1 Hz) release of small gas pockets (0.5 - 1 m of diameter) at low exit velocities (5 - 15 m/s). Whereas, Strombolian explosions occur at a frequency of 1 - 10 per hour, and are characterized the ejection of bombs and/or ash at high velocities (50 - 400 m/s). In order to get a broader overview of two types of degassing, we used a thermal high speed FLIR SC655 camera to monitor the temperature anomalies generated by the expelled gas, ash, and/or bombs. The enhanced time and spatial resolutions of the camera (200 frames per second, 15 cm wide pixels) enables to use numerical algorithms to distinguish and characterize individual ejection events. In particular, for each explosion and puff, we compute the temperature, the volume, the exit point and the rise velocities of the expelled material. These values, as well as the frequency of the release events, are used to portray a total of 12 vent activities, observed during three field campaigns in 2012, 2013 and 2014. Sustained puffing was visible on 7 cases, with an intensity ranging on at least two orders of magnitude. Although the released gas volume is sometimes highly variable, on some cases, constant sized puffs allows to define a typical discharge frequency ranging between 0.4 and 1.5 Hz. Regular Strombolian explosions, with various duration, intensity and ash contents, are reported in 6 cases, 2 of them simultaneously presenting a puffing activity. In some cases, we noticed modifications of the vent activity just before the explosions. These precursors, usually lasting about 1 second but occasionally reaching 10 seconds, can be sorted into 1) increase of the puffing activity ; 2) emission of gas plumes ; 3) inflation of the visible vent surface. Finally, one vent activity was hybrid between puffing and Strombolian explosions, with frequent explosions (1 Hz) ejecting numerous

Robust Secure Authentication and Data Storage with Perfect Secrecy

Directory of Open Access Journals (Sweden)

Sebastian Baur

2018-04-01

Full Text Available We consider an authentication process that makes use of biometric data or the output of a physical unclonable function (PUF, respectively, from an information theoretical point of view. We analyse different definitions of achievability for the authentication model. For the secrecy of the key generated for authentication, these definitions differ in their requirements. In the first work on PUF based authentication, weak secrecy has been used and the corresponding capacity regions have been characterized. The disadvantages of weak secrecy are well known. The ultimate performance criteria for the key are perfect secrecy together with uniform distribution of the key. We derive the corresponding capacity region. We show that, for perfect secrecy and uniform distribution of the key, we can achieve the same rates as for weak secrecy together with a weaker requirement on the distribution of the key. In the classical works on PUF based authentication, it is assumed that the source statistics are known perfectly. This requirement is rarely met in applications. That is why the model is generalized to a compound model, taking into account source uncertainty. We also derive the capacity region for the compound model requiring perfect secrecy. Additionally, we consider results for secure storage using a biometric or PUF source that follow directly from the results for authentication. We also generalize known results for this problem by weakening the assumption concerning the distribution of the data that shall be stored. This allows us to combine source compression and secure storage.

On eco-efficient technologies to minimize industrial water consumption

Science.gov (United States)

Amiri, Mohammad C.; Mohammadifard, Hossein; Ghaffari, Ghasem

2016-07-01

Purpose - Water scarcity will further stress on available water systems and decrease the security of water in many areas. Therefore, innovative methods to minimize industrial water usage and waste production are of paramount importance in the process of extending fresh water resources and happen to be the main life support systems in many arid regions of the world. This paper demonstrates that there are good opportunities for many industries to save water and decrease waste water in softening process by substituting traditional with echo-friendly methods. The patented puffing method is an eco-efficient and viable technology for water saving and waste reduction in lime softening process. Design/methodology/approach - Lime softening process (LSP) is a very sensitive process to chemical reactions. In addition, optimal monitoring not only results in minimizing sludge that must be disposed of but also it reduces the operating costs of water conditioning. Weakness of the current (regular) control of LSP based on chemical analysis has been demonstrated experimentally and compared with the eco-efficient puffing method. Findings - This paper demonstrates that there is a good opportunity for many industries to save water and decrease waste water in softening process by substituting traditional method with puffing method, a patented eco-efficient technology. Originality/value - Details of the required innovative works to minimize industrial water usage and waste production are outlined in this paper. Employing the novel puffing method for monitoring of lime softening process results in saving a considerable amount of water while reducing chemical sludge.

Experimental study of heat and mass transfer in a buoyant countercurrent exchange flow

Science.gov (United States)

Conover, Timothy Allan

Buoyant Countercurrent Exchange Flow occurs in a vertical vent through which two miscible fluids communicate, the higher-density fluid, residing above the lower-density fluid, separated by the vented partition. The buoyancy- driven zero net volumetric flow through the vent transports any passive scalars, such as heat and toxic fumes, between the two compartments as the fluids seek thermodynamic and gravitational equilibrium. The plume rising from the vent into the top compartment resembles a pool fire plume. In some circumstances both countercurrent flows and pool fires can ``puff'' periodically, with distinct frequencies. One experimental test section containing fresh water in the top compartment and brine (NaCl solution) in the bottom compartment provided a convenient, idealized flow for study. This brine flow decayed in time as the concentrations approached equilibrium. A second test section contained fresh water that was cooled by heat exchangers above and heated by electrical elements below and operated steadily, allowing more time for data acquisition. Brine transport was reduced to a buoyancy- scaled flow coefficient, Q*, and heat transfer was reduced to an analogous coefficient, H*. Results for vent diameter D = 5.08 cm were consistent between test sections and with the literature. Some results for D = 2.54 cm were inconsistent, suggesting viscosity and/or molecular diffusion of heat become important at smaller scales. Laser Doppler Velocimetry was used to measure velocity fields in both test sections, and in thermal flow a small thermocouple measured temperature simultaneously with velocity. Measurement fields were restricted to the plume base region, above the vent proper. In baseline periodic flow, instantaneous velocity and temperature were ensemble averaged, producing a movie of the average variation of each measure during a puffing flow cycle. The temperature movie revealed the previously unknown cold core of the puff during its early development. The

ZK DrugResist 2.0: A TextMiner to extract semantic relations of drug resistance from PubMed.

Science.gov (United States)

Khalid, Zoya; Sezerman, Osman Ugur

2017-05-01

Extracting useful knowledge from an unstructured textual data is a challenging task for biologists, since biomedical literature is growing exponentially on a daily basis. Building an automated method for such tasks is gaining much attention of researchers. ZK DrugResist is an online tool that automatically extracts mutations and expression changes associated with drug resistance from PubMed. In this study we have extended our tool to include semantic relations extracted from biomedical text covering drug resistance and established a server including both of these features. Our system was tested for three relations, Resistance (R), Intermediate (I) and Susceptible (S) by applying hybrid feature set. From the last few decades the focus has changed to hybrid approaches as it provides better results. In our case this approach combines rule-based methods with machine learning techniques. The results showed 97.67% accuracy with 96% precision, recall and F-measure. The results have outperformed the previously existing relation extraction systems thus can facilitate computational analysis of drug resistance against complex diseases and further can be implemented on other areas of biomedicine. Copyright © 2017 Elsevier Inc. All rights reserved.

Self-titration by experienced e-cigarette users: blood nicotine delivery and subjective effects.

Science.gov (United States)

Dawkins, Lynne E; Kimber, Catherine F; Doig, Mira; Feyerabend, Colin; Corcoran, Olivia

2016-08-01

Self-titration is well documented in the tobacco literature. The extent to which e-cigarette users (vapers) self-titrate is unknown. This study explored the effects of high and low nicotine strength liquid on puffing topography, nicotine delivery and subjective effects in experienced vapers. Eleven experienced male vapers completed 60 min of ad libitum vaping under low (6 mg/mL) and high (24 mg/mL) nicotine liquid conditions in two separate sessions. Measurements included puffing topography (puff number, puff duration, volume of liquid consumed) and changes in plasma nicotine levels, craving, withdrawal symptoms, self-reported hit, satisfaction and adverse effects. Liquid consumption and puff number were higher and puff duration longer, in the low nicotine strength condition (all ps < 0.01). The mean difference in nicotine boost from baseline in the low condition was 8.59 (7.52) ng/mL, 16.99 (11.72) ng/mL and 22.03 (16.19) ng/mL at 10, 30 and 60 min, respectively. Corresponding values for the high condition were 33.77 (34.88) ng/mL, 35.48 (28.31) ng/mL and 43.57 (34.78) ng/mL (ps < 0.05). There were no statistically significant differences between conditions in self-reported craving, withdrawal symptoms, satisfaction, hit or adverse effects. Vapers engaged in compensatory puffing with lower nicotine strength liquid, doubling their consumption. Whilst compensatory puffing was sufficient to reduce craving and withdrawal discomfort, self-titration was incomplete with significantly higher plasma nicotine levels in the high condition.

Trends and topics in eye disease research in PubMed from 2010 to 2014.

Science.gov (United States)

Boudry, Christophe; Denion, Eric; Mortemousque, Bruno; Mouriaux, Fréderic

2016-01-01

The purpose of this study is to provide a report on scientific production during the period 2010-2014 in order to identify the major topics as well as the predominant actors (journals, countries, continents) involved in the field of eye disease. A PubMed search was carried out to extract articles related to eye diseases during the period 2010-2014. Data were downloaded and processed through developed PHP scripts for further analysis. A total of 62,123 articles were retrieved. A total of 3,368 different journals were found, and 19 journals were identified as "core journals" according to Braford's law. English was by far the predominant language. A total of 853,182 MeSH terms were found, representing an average of 13.73 (SD = 4.98) MeSH terms per article. Among these 853,182 MeSH terms, 14,689 different MeSH terms were identified. Vision Disorders, Glaucoma, Diabetic Retinopathy, Macular Degeneration, and Cataract were the most frequent five MeSH terms related to eye diseases. The analysis of the total number of publications showed that Europe and Asia were the most productive continents, and the USA and China the most productive countries. Interestingly, using the mean Five-Year Impact Factor, the two most productive continents were North America and Oceania. After adjustment for population, the overall ranking positions changed in favor of smaller countries (i.e. Iceland, Switzerland, Denmark, and New Zealand), while after adjustment for Gross Domestic Product (GDP), the overall ranking positions changed in favor of some developing countries (Malawi, Guatemala, Singapore). Due to the large number of articles included and the numerous parameters analyzed, this study provides a wide view of scientific productivity related to eye diseases during the period 2010-2014 and allows us to better understand this field.

International Clean Energy System Using Hydrogen Conversion (WE-NET). subtask 5. Development of hydrogen transport/storage technology (development of tanker for liquid hydrogen); Suiso riyo kokusai clean energy system gijutsu (WE-NET). subtask 5. Suiso yuso chozo gijutsu no kaihatsu (ekitai suiso yuso tanker no kaihatsu)

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-03-01

As a part of the WE-NET project, the tanker for liquid hydrogen transport was studied. In fiscal 1996, some experiments and numerical analyses were proposed which are necessary to solve technological issues extracted in fiscal 1995 for heat insulation structure. The issue was roughly classified into vacuum and non-vacuum insulation, and their basic functions and required performance were arranged. Boil-off rate of 0.2-0.4%/d was targeted. The insulation system which applies polyurethane form (PUF) to tank surfaces and injects atmospheric N2 gas into the surrounding hold space, could achieve the targeted insulation performance by PUF of 1m in thickness. The system of vacuum panel insulation and atmospheric N2 gas injection into a hold space required the panel of 500mm in thickness because of the large effect of metallic outer panel material. The system of vacuum hold and PUF panels was faced with the essential issue for realizing and maintaining vacuum hold. The super insulation system featured by layered insulation materials and vacuum layer spaces was also strongly affected by degree of vacuum. 23 figs., 8 tabs.

Setup and Calibration of SLAC's Peripheral Monitoring Stations

Energy Technology Data Exchange (ETDEWEB)

Cooper, C.

2004-09-03

or measured). Detector response for both detectors is dependent upon the energy of the incident radiation; this trend had to be accounted for in the calibration of the BF{sub 3} detector. Energy dependence did not have to be taken into consideration when calibrating the GM detectors since GM detector response is only dependent on radiation energy below 100 keV; SLAC only produces a spectrum of gamma radiation above 100 keV. For the GM detector, calibration consisted of bringing a {sup 137}Cs source and a NIST-calibrated RADCAL Radiation Monitor Controller (model 9010) out to the field; the absolute dose rate was determined by the RADCAL device while simultaneously irradiating the GM detector to obtain a scaler reading corresponding to counts per minute. Detector response was then calculated. Calibration of the BF{sub 3} detector was done using NIST certified neutron sources of known emission rates and energies. Five neutron sources ({sup 238}PuBe, {sup 238}PuB, {sup 238}PuF4, {sup 238}PuLi and {sup 252}Cf) with different energies were used to account for the energy dependence of the response. The actual neutron dose rate was calculated by date-correcting NIST source data and considering the direct dose rate and scattered dose rate. Once the total dose rate (sum of the direct and scattered dose rates) was known, the response vs. energy curve was plotted. The first station calibrated (PMS6) was calibrated with these five neutron sources; all subsequent stations were calibrated with one neutron source and the energy dependence was assumed to be the same.

Spectrochemical determination of tantalum in plutonium metal using direct current plasma emission spectrometry

International Nuclear Information System (INIS)

Fadeff, S.K.; Morris, W.F.

1983-01-01

Tantalum is determined by direct current plasma spectrometry after separation of plutonium from solution as PuF 3 . After centrifugation of the PuF 3 precipitate, a low level of plutonium remains in solution in sufficient quantity to cause spectral interferences. It is necessary to determine the plutonium by dc plasma spectrometry and apply a correction to determine low tantalum concentrations with good accuracy and precision. Tantalum can be determined down to 0.4 ppM in solution with a relative standard deviation of 10 percent. Better precision can be achieved at higher concentrations. The procedure is simple and convenient for glovebox work. 5 references, 1 figure, 1 table

A transportable system for the determination of phosphorus in sheep bone by in vivo neutron activation analysis

International Nuclear Information System (INIS)

Whineray, S.; Thomas, B.J.; Ternouth, J.H.; Davies, H.M.S.

1980-01-01

An apparatus was constructed which measures the phosphorus in sheep leg bone, non-invasively, by neutron activation analysis. The results obtained show that with two 10 Ci isotopic neutron sources ( 241 Am/Be or 238 Pu/Be) and a single 7.5 x 7.5 cm NaI(Tl) detector, serial changes in leg bone phosphorus may be determined with a precision of 13% in 15 min of experimental time. This precision could be reduced to 5% by incorporating two large detectors into the system. (author)

Thermal neutron absorption cross section of small samples

International Nuclear Information System (INIS)

Nghiep, T.D.; Vinh, T.T.; Son, N.N.; Vuong, T.V.; Hung, N.T.

1989-01-01

A modified steady method for determining the macroscopic thermal neutron absorption cross section of small samples 500 cm 3 in volume is described. The method uses a moderating block of paraffin, Pu-Be neutron source emitting 1.1x10 6 n.s. -1 , SNM-14 counter and ordinary counting equipment. The interval of cross section from 2.6 to 1.3x10 4 (10 -3 cm 2 g -1 ) was measured. The experimental data are described by calculation formulae. 7 refs.; 4 figs

Kwarteng Frimpong.pub

African Journals Online (AJOL)

User

The staff audit showed that the district assem- bly was understaffed as key positions such as. Deputy District Coordination Director (DCD),. Assistant Planning .... determine the fiscal performance of the assem- bly during the period under consideration. Like many other DAs in the country, Internally Gen- erated Revenue ...

Gendered discourses of youth sexualities--an exploration of PubMed articles on prevention of sexually transmissible infections.

Science.gov (United States)

Johansson, Eva E; Alex, Lena; Christianson, Monica

2014-10-01

To explore how gender is addressed in medical articles on the prevention of sexually transmissible infections (STI) among adolescents. Sixtyone articles were retrieved from a PubMed search and scrutinized by qualitative content analysis. Most articles were affiliated with North American research institutions, but there were also reports from Europe, Africa, South America, and Asia. Gender turned up in the following four recurrent discourses: Gendered Receptiveness for Information, Stereotyped Heterosexual Expectations, Power Imbalance in Sexual Relations, and Gendered Prevention Approaches. Young women were described as knowledgeable, communicative, and responsible, but at risk because of feminine ideals and a lack of negotiating power. Men were described as less informed, more reluctant to discuss, and more risk taking due to masculine ideals and power dominance. Prevention approaches concerned how to postpone sex and/or tailor gender-sensitive programs for specific groups of young women and men. Researchers' own gender expectations might have a substantial impact on how sex and sexual health is considered in prevention research. To avoid reconstruction of current inequalities and stereotypes regarding sexual practices of young women and men, the impact of gender, the power structures in intimate relations, and the cultural context should be considered. Medical research on STI prevention could benefit from including a wider array of gender perspectives. Copyright © 2014 Elsevier B.V. All rights reserved.

A study of the influence of task familiarity on user behaviors and performance with a MeSH term suggestion interface for PubMed bibliographic search.

Science.gov (United States)

Tang, Muh-Chyun; Liu, Ying-Hsang; Wu, Wan-Ching

2013-09-01

Previous research has shown that information seekers in biomedical domain need more support in formulating their queries. A user study was conducted to evaluate the effectiveness of a metadata based query suggestion interface for PubMed bibliographic search. The study also investigated the impact of search task familiarity on search behaviors and the effectiveness of the interface. A real user, user search request and real system approach was used for the study. Unlike tradition IR evaluation, where assigned tasks were used, the participants were asked to search requests of their own. Forty-four researchers in Health Sciences participated in the evaluation - each conducted two research requests of their own, alternately with the proposed interface and the PubMed baseline. Several performance criteria were measured to assess the potential benefits of the experimental interface, including users' assessment of their original and eventual queries, the perceived usefulness of the interfaces, satisfaction with the search results, and the average relevance score of the saved records. The results show that, when searching for an unfamiliar topic, users were more likely to change their queries, indicating the effect of familiarity on search behaviors. The results also show that the interface scored higher on several of the performance criteria, such as the "goodness" of the queries, perceived usefulness, and user satisfaction. Furthermore, in line with our hypothesis, the proposed interface was relatively more effective when less familiar search requests were attempted. Results indicate that there is a selective compatibility between search familiarity and search interface. One implication of the research for system evaluation is the importance of taking into consideration task familiarity when assessing the effectiveness of interactive IR systems. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A critical assessment of passive air samplers for per- and polyfluoroalkyl substances

Science.gov (United States)

Karásková, Pavlína; Codling, Garry; Melymuk, Lisa; Klánová, Jana

2018-07-01

Since their inclusion in the Stockholm Convention, there has been a need for global monitoring of perfluorooctane sulfonate (PFOS), its salts and perfluorooctanesulfonyl fluoride (PFOSF), along with other non-listed highly fluorinated compounds. Passive air samplers (PAS) are ideal for geographic coverage of atmospheric monitoring. The most common type of PAS, using polyurethane foam (PUF) as a sorbent, was primarily developed for non-polar semivolatile organic compounds (SVOCs) and are not well-validated for polar substances such as the per- and polyfluoroalkyl substances (PFASs), however, they have been used for some PFASs, particularly PFOS. To evaluate their applicability, PAS were deployed for measurement of PFASs in outdoor and indoor air. Outdoors, two types of PAS, one consisting of PUF and one of XAD-2 resin, were deployed in an 18-week calibration study in parallel with a low-volume active air sampler (LV-AAS) in a suburban area. Indoors, PUF-PAS were similarly deployed over 12 weeks to evaluate their applicability for indoor monitoring. Samples were analysed for perfluoroalkyl carboxylic acids (PFCAs), perfluoroalkyl sulfonates (PFSAs), perfluorooctane sulfonamides (FOSAs), and perfluorooctane sulfonamidoethanols (FOSEs). In outdoor air, 17 out of the 21 PFAS were detected in more than 50% of samples, with a median ∑17PFASs of 18.0 pg m-3 while 20 compounds were detected in indoor air with a median concentration ∑20PFASs of 76.6 pg m-3 using AAS samplers. PFOS was the most common PFAS in the outdoor air while PFBA was most common indoors. Variability between PAS and AAS was observed and comparing gas phase and particle phase separately or in combination did not account for the variation observed. PUF-PAS may still have a valuable use in PFAS monitoring but more work is needed to identify the applicability of passive samplers for ionic PFAS.

An integrable low-cost hardware random number generator

Science.gov (United States)

Ranasinghe, Damith C.; Lim, Daihyun; Devadas, Srinivas; Jamali, Behnam; Zhu, Zheng; Cole, Peter H.

2005-02-01

A hardware random number generator is different from a pseudo-random number generator; a pseudo-random number generator approximates the assumed behavior of a real hardware random number generator. Simple pseudo random number generators suffices for most applications, however for demanding situations such as the generation of cryptographic keys, requires an efficient and a cost effective source of random numbers. Arbiter-based Physical Unclonable Functions (PUFs) proposed for physical authentication of ICs exploits statistical delay variation of wires and transistors across integrated circuits, as a result of process variations, to build a secret key unique to each IC. Experimental results and theoretical studies show that a sufficient amount of variation exits across IC"s. This variation enables each IC to be identified securely. It is possible to exploit the unreliability of these PUF responses to build a physical random number generator. There exists measurement noise, which comes from the instability of an arbiter when it is in a racing condition. There exist challenges whose responses are unpredictable. Without environmental variations, the responses of these challenges are random in repeated measurements. Compared to other physical random number generators, the PUF-based random number generators can be a compact and a low-power solution since the generator need only be turned on when required. A 64-stage PUF circuit costs less than 1000 gates and the circuit can be implemented using a standard IC manufacturing processes. In this paper we have presented a fast and an efficient random number generator, and analysed the quality of random numbers produced using an array of tests used by the National Institute of Standards and Technology to evaluate the randomness of random number generators designed for cryptographic applications.

Calibration and intercomparison of neutron moderation spectrometers

International Nuclear Information System (INIS)

Rimpler, A.; Hermanska, J.; Prouza, Z.

1989-01-01

Results have been reported of comparative measurements of neutron fields from bare PuBe and Cf sources using multisphere (Bonner) spectrometers. The experiments were carried out by the Institute of Biophysics and Nuclear Medicine at Charles University in Prague and the National Board for Atomic Safety and Radiation Protection in Berlin. Both sides agreed upon uniform measuring conditions and calibration factors thus rendering possible the comparability of the dosimetric parameters which have been determined and verified, respectively, to an accuracy of ± 10%. 20 refs., 10 tabs., 2 figs. (author)

Implementing the ban on smoking in Israeli pubs: measuring airborne nicotine and enforcement by local authorities.

Science.gov (United States)

Satran, Carmit; Drach-Zahavy, Anat; Hammond, S Katharine; Baron-Epel, Orna

2014-06-01

In 2007 an amendment to the law restricting smoking in pubs and bars (P&Bs) was enacted in Israel. However, a year after the ban only slight decreases in airborne smoke in P&Bs in one city have been reported. We aimed to assess levels of airborne nicotine in Israeli P&Bs and to measure ifself-reported enforcement of the law by local officials was associated with levels of airborne nicotine in P&Bs. Airborne nicotine levels were measured in 72 P&Bs in 29 towns in Israel; this consisted of 90% of eligible towns. In addition, 73 local authority officials were interviewed in 25 of these towns. The officials were asked to assess the local authority's level of enforcement of the law banning smoking in P&Bs. The association of levels of airborne nicotine with the levels of enforcement of the law was calculated. Data were collected during 2009-2010 and analyzed in 2010-2011. Levels of airborne nicotine were comparatively high in P&Bs. No association was detected between levels of nicotine and the P&Bs' characteristics. In the larger towns, levels of airborne nicotine were higher. In 16% of towns the local authority officials reported high levels of law enforcement. Generally, levels of reported enforcement by local authorities were low and did not predict levels of airborne nicotine in the P&Bs. Self-reported local authorities' law enforcement was not associated with levels of airborne nicotine in P&Bs in these towns. There is a need to develop ways to increase law enforcement by the local authorities or other agencies.

Size selective isocyanate aerosols personal air sampling using porous plastic foams

International Nuclear Information System (INIS)

Cong Khanh Huynh; Trinh Vu Duc

2009-01-01

As part of a European project (SMT4-CT96-2137), various European institutions specialized in occupational hygiene (BGIA, HSL, IOM, INRS, IST, Ambiente e Lavoro) have established a program of scientific collaboration to develop one or more prototypes of European personal samplers for the collection of simultaneous three dust fractions: inhalable, thoracic and respirable. These samplers based on existing sampling heads (IOM, GSP and cassettes) use Polyurethane Plastic Foam (PUF) according to their porosity to support sampling and separator size of the particles. In this study, the authors present an original application of size selective personal air sampling using chemical impregnated PUF to perform isocyanate aerosols capturing and derivatizing in industrial spray-painting shops.

Area-efficient physically unclonable function circuit architecture

Science.gov (United States)

Gurrieri, Thomas; Hamlet, Jason; Bauer, Todd; Helinski, Ryan; Pierson, Lyndon G

2015-04-28

Generating a physically a physically unclonable function ("PUF") circuit value includes comparing each of first identification components in a first bank to each of second identification components in a second bank. A given first identification component in the first bank is not compared to another first identification component in the first bank and a given second identification component in the second bank is not compared to another second identification component in the second bank. A digital bit value is generated for each comparison made while comparing each of the first identification components to each of the second identification components. A PUF circuit value is generated from the digital bit values from each comparison made.

MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank.

Science.gov (United States)

Mao, Yuqing; Lu, Zhiyong

2017-04-17

MeSH indexing is the task of assigning relevant MeSH terms based on a manual reading of scholarly publications by human indexers. The task is highly important for improving literature retrieval and many other scientific investigations in biomedical research. Unfortunately, given its manual nature, the process of MeSH indexing is both time-consuming (new articles are not immediately indexed until 2 or 3 months later) and costly (approximately ten dollars per article). In response, automatic indexing by computers has been previously proposed and attempted but remains challenging. In order to advance the state of the art in automatic MeSH indexing, a community-wide shared task called BioASQ was recently organized. We propose MeSH Now, an integrated approach that first uses multiple strategies to generate a combined list of candidate MeSH terms for a target article. Through a novel learning-to-rank framework, MeSH Now then ranks the list of candidate terms based on their relevance to the target article. Finally, MeSH Now selects the highest-ranked MeSH terms via a post-processing module. We assessed MeSH Now on two separate benchmarking datasets using traditional precision, recall and F 1 -score metrics. In both evaluations, MeSH Now consistently achieved over 0.60 in F-score, ranging from 0.610 to 0.612. Furthermore, additional experiments show that MeSH Now can be optimized by parallel computing in order to process MEDLINE documents on a large scale. We conclude that MeSH Now is a robust approach with state-of-the-art performance for automatic MeSH indexing and that MeSH Now is capable of processing PubMed scale documents within a reasonable time frame. http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/MeSHNow/ .

Polyurethane foam loaded with sodium dodecylsulfate for the extraction of 'quat' pesticides from aqueous medium: Optimization of loading conditions.

Science.gov (United States)

Vinhal, Jonas O; Lima, Claudio F; Cassella, Ricardo J

2016-09-01

The cationic herbicides paraquat, diquat and difenzoquat are largely used in different cultures worldwide. With this, there is an intrinsic risk of environmental contamination when these herbicides achieve natural waters. The goal of this work was to propose a novel and low-cost sorbent for the removal of the cited herbicides from aqueous medium. The proposed sorbent was prepared by loading polyurethane foam with sodium dodecylsulfate. The influence of several parameters (SDS concentration, HCl concentration and shaking time) on the loading process was investigated. The results obtained in this work demonstrated that all studied variables influenced the loading process, having significant effect on the extraction efficiency of the resulted PUF-SDS. At optimized conditions, the PUF was loaded by shaking 200mg of crushed foam with 200mL of a solution containing 5.0×10(-3)molL(-1) SDS and 0.25molL(-1) HCl, for 30min. The obtained PUF-SDS was efficient for removing the three herbicides from aqueous medium, achieving extraction percentages higher than 90%. The sorption process followed a pseudo second-order kinetics, which presented excellent predictive capacity of the amount of herbicide retained with time. Copyright © 2016 Elsevier Inc. All rights reserved.

Aerobic Anoxygenic Photosynthesis Is Commonly Present within the Genus Limnohabitans.

Science.gov (United States)

Kasalický, Vojtěch; Zeng, Yonghui; Piwosz, Kasia; Šimek, Karel; Kratochvilová, Hana; Koblížek, Michal

2018-01-01

The genus Limnohabitans ( Comamonadaceae , Betaproteobacteria ) is a common and a highly active component of freshwater bacterioplanktonic communities. To date, the genus has been considered to contain only heterotrophic species. In this study, we detected the photosynthesis genes pufLM and bchY in 28 of 46 strains from three Limnohabitans lineages. The pufM sequences obtained are very closely related to environmental pufM sequences detected in various freshwater habitats, indicating the ubiquity and potential importance of photoheterotrophic Limnohabitans in nature. Additionally, we sequenced and analyzed the genomes of 5 potentially photoheterotrophic Limnohabitans strains, to gain further insights into their phototrophic capacity. The structure of the photosynthesis gene cluster turned out to be highly conserved within the genus Limnohabitans and also among all potentially photosynthetic Betaproteobacteria strains. The expression of photosynthetic complexes was detected in a culture of Limnohabitans planktonicus II-D5 T using spectroscopic and pigment analyses. This was further verified by a novel combination of infrared microscopy and fluorescent in situ hybridization. IMPORTANCE The data presented document that the capacity to perform anoxygenic photosynthesis is common among the members of the genus Limnohabitans , indicating that they may have a novel role in freshwater habitats. Copyright © 2017 American Society for Microbiology.

Experimental investigation of molecular beam injection in HL-1 tokamak

International Nuclear Information System (INIS)

Yao Lianghua; Diao Guangyao; Wang Zhanhe; Deng Huichen; Luo Junlin; Duan Xuru; Cui Zhengying

1993-07-01

A new method of gas puffing is presented. The molecular beam, formed by high pressure deuterium gas through Larval nozzle and skimmer slit, is injected into the HL-1 vacuum vessel. The deuterium molecular current from the nozzle passing through the skimmer is about 3 x 10 20 /s. At the line average electron density of 5.2 x 10 19 m -3 , the beam velocity is about 100 m/s. As the plasma density and temperature increasing, the influxes of deuterium particles attenuate quickly. When the molecular beam injection (MBI) just returned to normal gas puffing, the D α emission rapidly decreases, meanwhile, the particles move toward plasma center, the electron density is continuously peaking. The line average electron density rising lasts 45 ms. The thermal energy of plasma and confinement time for particles and energy are also increasing. the MBI is a direct and efficient gas fuelling mode, and the injected particles can reach to inside about 8 cm of plasma and q ≅ 2 confinement region. Its efficiency of injection is about 50%. After the MBI, the particle recycling coefficient R on the wall is 0.6 which is 10% lower than that of normal gas puffing

In the pursuit of a semantic similarity metric based on UMLS annotations for articles in PubMed Central Open Access.

Science.gov (United States)

Garcia Castro, Leyla Jael; Berlanga, Rafael; Garcia, Alexander

2015-10-01

Although full-text articles are provided by the publishers in electronic formats, it remains a challenge to find related work beyond the title and abstract context. Identifying related articles based on their abstract is indeed a good starting point; this process is straightforward and does not consume as many resources as full-text based similarity would require. However, further analyses may require in-depth understanding of the full content. Two articles with highly related abstracts can be substantially different regarding the full content. How similarity differs when considering title-and-abstract versus full-text and which semantic similarity metric provides better results when dealing with full-text articles are the main issues addressed in this manuscript. We have benchmarked three similarity metrics - BM25, PMRA, and Cosine, in order to determine which one performs best when using concept-based annotations on full-text documents. We also evaluated variations in similarity values based on title-and-abstract against those relying on full-text. Our test dataset comprises the Genomics track article collection from the 2005 Text Retrieval Conference. Initially, we used an entity recognition software to semantically annotate titles and abstracts as well as full-text with concepts defined in the Unified Medical Language System (UMLS®). For each article, we created a document profile, i.e., a set of identified concepts, term frequency, and inverse document frequency; we then applied various similarity metrics to those document profiles. We considered correlation, precision, recall, and F1 in order to determine which similarity metric performs best with concept-based annotations. For those full-text articles available in PubMed Central Open Access (PMC-OA), we also performed dispersion analyses in order to understand how similarity varies when considering full-text articles. We have found that the PubMed Related Articles similarity metric is the most suitable for

MMLEADS Public Use File

Data.gov (United States)

U.S. Department of Health & Human Services — The Medicare-Medicaid Linked Enrollee Analytic Data Source (MMLEADS) Public Use File (PUF) contains demographic, enrollment, condition prevalence, utilization, and...

Report: EPA Office of Inspector General’s Report on Reducing Fraud, Waste, and Abuse in the Small Business Innovative Research Program, as Required by the National Defense Authorization Act for Fiscal Year 2012, Pub. L. 112-81 (2012)

Science.gov (United States)

September 28, 2012. The EPA OIG is required by Section 5143 of the NDA Act for Fiscal Year 201 2, Pub. L. No. 112-81 (2012), to report on reducing vulnerability to fraud, waste and abuse in the Small Business Innovative Research (SBIR) program.

Medicare Provider Payment Data - Skilled Nursing Facilities

Data.gov (United States)

U.S. Department of Health & Human Services — The Skilled Nursing Facility Utilization and Payment Public Use File (Skilled Nursing Facility PUF) provides information on services provided to Medicare...

Medicare Provider Payment Data - Home Health Agencies

Data.gov (United States)

U.S. Department of Health & Human Services — The Home Health Agency PUF contains information on utilization, payment (Medicare payment and standard payment), and submitted charges organized by CMS Certification...

Medicare Provider Utilization and Payment Data - Outpatient

Data.gov (United States)

U.S. Department of Health & Human Services — The Outpatient Utilization and Payment Public Use File (Outpatient PUF) presents information on common outpatient services provided to Medicare fee-for-service...