Characterization of Malaysian Trichoderma isolates using random amplified microsatellites (RAMS).

Science.gov (United States)

Siddiquee, Shafiquzzaman; Tan, Soon Guan; Yusuf, Umi Kalsom; Fatihah, Nur Hasan Nudin; Hasan, Md Mainul

2012-01-01

Trichoderma species are commercially applied as biocontrol agents against numerous plant pathogenic fungi due to their production of antifungal metabolites, competition for nutrients and space, and mycoparasitism. However, currently the identification of Trichoderma species from throughout the world based on micro-morphological descriptions is tedious and prone to error. The correct identification of Trichoderma species is important as several traits are species-specific. The Random Amplified Microsatellites (RAMS) analysis done using five primers in this study showed different degrees of the genetic similarity among 42 isolates of this genus. The genetic similarity values were found to be in the range of 12.50-85.11% based on a total of 76 bands scored in the Trichoderma isolates. Of these 76 bands, 96.05% were polymorphic, 3.95% were monomorphic and 16% were exclusive bands. Two bands (250 bp and 200 bp) produced by primer LR-5 and one band (250 bp) by primer P1A were present in all the Trichoderma isolates collected from healthy and infected oil palm plantation soils. Cluster analysis based on UPGMA of the RAMS marker data showed that T. harzianum, T. virens and T. longibrachiatum isolates were grouped into different clades and lineages. In this study we found that although T. aureoviride isolates were morphologically different when compared to T. harzianum isolates, the UPGMA cluster analysis showed that the majority isolates of T. aureoviride (seven from nine) were closely related to the isolates of T. harzianum.

Isolation and characterization of Acinetobacter baumannii recovered from Campylobacter selective medium.

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Dinesh M Fernando

2016-11-01

Full Text Available Acinetobacter baumannii, a Gram-negative opportunistic pathogen, is known to cause multidrug resistant infections. This organism has primarily been isolated from clinical environments and its environmental reservoirs remain largely unknown. In the present study, we recovered seven isolates of A. baumannii growing under conditions selective for Campylobacter spp. (microaerophilic at 42 oC and in the presence of antibiotics from dairy cattle manure storage tank or surface water impacted by livestock effluents. Antibiotic susceptibility tests revealed that all of these isolates were less susceptible to at least two different clinically relevant antibiotics, compared to the type strain A. baumannii ATCC17978. Expression of resistance-nodulation-division efflux pumps, an important mechanism of intrinsic resistance in these organisms, was analyzed and adeB was found to be overexpressed in one and adeJ was overexpressed in three isolates. Comparison of these isolates using genomic DNA Macro-Restriction Fragment Pattern Analysis (MRFPA revealed relatively low relatedness among themselves or with some of the clinical isolates from previous studies. This study suggests that A. baumannii isolates are capable of growing under selective conditions for Campylobacter spp. and that this organism can be present in manure and water.

A radiation-hardened 1K-bit dielectrically isolated random access memory

International Nuclear Information System (INIS)

Sandors, T.J.; Boarman, J.W.; Kasten, A.J.; Wood, G.M.

1982-01-01

Dielectric Isolation has been used for many years as the bipolar technology for latch-up free, radiation hardened integrated circuits in strategic systems. The state-of-the-art up to this point has been the manufacture of MSI functions containing a maximum of several hundred isolated components. This paper discusses a 1024 Bit Random Access Memory chip containing over 4000 dielectrically isolated components which has been designed for strategic radiation environments. The process utilized and the circuit design of the 1024 Bit RAM have been previously discussed. The techniques used are similar to those employed for the MX digital integrated circuits except for specific items required to make this a true LSI technology. These techniques, along with electrical and radiation data for the RAM, are presented

Selective medium for the isolation of Bacteroides gingivalis.

OpenAIRE

Hunt, D E; Jones, J V; Dowell, V R

1986-01-01

Bacteroides gingivalis has been implicated in various forms of periodontal disease and may be responsible for other diseases in humans. The role of B. gingivalis in disease has been difficult to assess, because it is inhibited by most selective media commonly used by clinical laboratories to aid in isolating gram-negative, nonsporeforming anaerobes. We have developed a new medium, Bacteroides gingivalis agar, which contains bacitracin, colistin, and nalidixic acid as selective agents. This me...

Genomic signatures of geographic isolation and natural selection in coral reef fishes.

Science.gov (United States)

Gaither, Michelle R; Bernal, Moisés A; Coleman, Richard R; Bowen, Brian W; Jones, Shelley A; Simison, W Brian; Rocha, Luiz A

2015-04-01

The drivers of speciation remain among the most controversial topics in evolutionary biology. Initially, Darwin emphasized natural selection as a primary mechanism of speciation, but the architects of the modern synthesis largely abandoned that view in favour of divergence by geographic isolation. The balance between selection and isolation is still at the forefront of the evolutionary debate, especially for the world's tropical oceans where biodiversity is high, but isolating barriers are few. Here, we identify the drivers of speciation in Pacific reef fishes of the genus Acanthurus by comparative genome scans of two peripheral populations that split from a large Central-West Pacific lineage at roughly the same time. Mitochondrial sequences indicate that populations in the Hawaiian Archipelago and the Marquesas Islands became isolated approximately 0.5 Ma. The Hawaiian lineage is morphologically indistinguishable from the widespread Pacific form, but the Marquesan form is recognized as a distinct species that occupies an unusual tropical ecosystem characterized by upwelling, turbidity, temperature fluctuations, algal blooms and little coral cover. An analysis of 3737 SNPs reveals a strong signal of selection at the Marquesas, with 59 loci under disruptive selection including an opsin Rh2 locus. While both the Hawaiian and Marquesan populations indicate signals of drift, the former shows a weak signal of selection that is comparable with populations in the Central-West Pacific. This contrast between closely related lineages reveals one population diverging due primarily to geographic isolation and genetic drift, and the other achieving taxonomic species status under the influence of selection. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Design and Analysis of Shock and Random Vibration Isolation of Operating Hard Disk Drive in Harsh Environment

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Hendri Harmoko

2009-01-01

Full Text Available An effective vibration isolation system is important for hard disk drives (HDD used in a harsh mechanical environment. This paper describes how to design, simulate, test and evaluate vibration isolation systems for operating HDD subjected to severe shock and random vibrations based on military specifications MIL-STD-810E. The well-defined evaluation criteria proposed in this paper can be used to effectively assess the performance of HDD vibration isolation system. Design concepts on how to achieve satisfactory shock and vibration isolation for HDD are described. The concepts are tested and further enhanced by the two design case studies presented here. It is shown that an effective vibration isolation system, that will allow a HDD to operate well when subjected to severe shock and random vibration, is feasible.

Selective isolation and characterization of agriculturally beneficial endopytic bacteria from wild hemp using canola

International Nuclear Information System (INIS)

Afzal, I.; Iqrar, I.

2015-01-01

Endophytic bacteria can provide a useful alternative to synthetic fertilizers to improve plant growth. Wild plants are little investigated as a source of growth promoting endophytic bacteria for commercial application to crops. In present study, endophytic bacteria were isolated from Cannabis sativa L. (hemp) using two different methods to examine their ability to promote canola growth. Besides direct isolation from the roots, endophytic bacteria were also selectively isolated from the rhizosphere of C. sativa using canola. Under gnotobiotic conditions, six bacteria from the selective isolation significantly improved canola root growth, as compared to the two bacteria isolated from direct method. Overall, three isolates performed distinctly well, namely, Pantoea vagans MOSEL-t13, Pseudomonas geniculata MOSEL-tnc1, and Serratia marcescens MOSEL-w2. These bacteria tolerated high salt concentrations and promoted canola growth under salt stress. Further, the isolated bacteria possessed plant growth promoting traits like IAA production, phosphate solubilization, and siderophore production. Most isolates produced plant cell-wall degrading enzymes, cellulase and pectinase. Some isolates were also effective in hindering the growth of two phytopathogenic fungi in dual culture assay, and displayed chitinase and protease activity. Paenibacillus sp. MOSEL-w13 displayed the greatest antifungal activity among all the isolates. Present findings conclude that wild plants can be a good source for isolating beneficial microbes, and validates the employed selective isolation for improved isolation of plant-beneficial endophytic bacteria. (author)

Isolated galaxies

International Nuclear Information System (INIS)

Einasto, Maret

1990-01-01

To test for the possible presence of really isolated galaxies, which form a randomly distributed population in voids, we compare the distribution of most isolated galaxies in an observed sample with distributions of the same number of random points using the nearest neighbour test. The results show that the random population of really isolated galaxies does not exist - even the most isolated galaxies are connected with systems of galaxies, forming their outlying parts. (author)

Glycine-containing selective medium for isolation of Legionellaceae from environmental specimens.

Science.gov (United States)

Wadowsky, R M; Yee, R B

1981-11-01

Glycine, at a final concentration of 0.3%, has been shown to be an excellent selective agent for the isolation of Legionellaceae. Stock cultures of Legionella pneumophila were not inhibited on buffered charcoal-yeast extract agar containing the amino acid. Among the other Legionellaceae tested, only one of two strains of L. dumoffii and two of six strains of L. micdadei were appreciably inhibited. This medium permitted the isolation of L. pneumophila from environmental specimens with marked inhibition of many non-Legionellaceae bacteria. The selectivity of the medium was subsequently improved by the incorporation of vancomycin (5 microgram/ml) and polymyxin B (100 U/ml). This selective medium, glycine-vancomycin-polymyxin B agar, should facilitate the recovery of Legionellaceae from environmental sources.

[Isolation of Actinomycetales from the soil of Kazakhstan on selective media with antibiotics].

Science.gov (United States)

Vetlugina, L A; Adiiatova, Zh F; Khozhamuratova, S Sh; Rymzhanova, Z A; Trenozhnikova, L P; Kopytina, M N

1990-02-01

About 3000 actinomycetes were isolated from various soil samples collected in 11 regions of Kazakhstan. 62.7 per cent of them proved to be antagonists. For isolation of the strains, selective media supplemented with antibiotics were used. Kanamycin promoted growth of Actinomadura and Nocardia. Rubomycin promoted growth of Actinomadura. Tavromycetin and roseofungin were used as selective agents for the first time. Tavromycetin favoured isolation of Actinomadura and Nocardia. Roseofungin favoured isolation of Actinomadura. Light chestnut and serozemic soils were the most rich in antagonists (67.1 and 61.3 per cent, respectively) while saline and chestnut soils were the poorest in antagonists (32.2 and 30.6 per cent, respectively). Actinomadura were more frequent in light-chestnut light-loamy and serozemic soils. Half of the antibiotics isolated in the form of concentrates were identified with the known antibiotics or classified as belonging to various groups. A culture producing a novel antibiotic was isolated.

Evidence for estrogen receptor beta-selective activity of Vitex agnus-castus and isolated flavones.

Science.gov (United States)

Jarry, Hubertus; Spengler, Barbara; Porzel, Andrea; Schmidt, Juergen; Wuttke, Wolfgang; Christoffel, Volker

2003-10-01

Recent cell culture experiments indicated that extracts of Vitex agnus-castus (VAC) may contain yet unidentified phytoestrogens. Estrogenic actions are mediated via estrogen receptors (ER). To investigate whether VAC compounds bind to the currently known isoforms ERalpha or ERss, ligand binding assays (LBA) were performed. Subtype specific ER-LBA revealed a binding of VAC to ERss only. To isolate the ERss-selective compounds, the extract was fractionated by bio-guidance. The flavonoid apigenin was isolated and identified as the most active ERss-selective phytoestrogen in VAC. Other isolated compounds were vitexin and penduletin. These data demonstrate that the phytoestrogens in VAC are ERss-selective.

Selection, isolation, and identification of fungi for bioherbicide production

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Angélica Rossana Castro de Souza

Full Text Available Abstract Production of a bioherbicide for biological control of weeds requires a series of steps, from selection of a suitable microbial strain to final formulation. Thus, this study aimed to select fungi for production of secondary metabolites with herbicidal activity using biological resources of the Brazilian Pampa biome. Phytopathogenic fungi were isolated from infected tissues of weeds in the Pampa biome. A liquid synthetic culture medium was used for production of metabolites. The phytotoxicity of fungal metabolites was assessed via biological tests using the plant Cucumis sativus L., and the most promising strain was identified by molecular analysis. Thirty-nine fungi were isolated, and 28 presented some phytotoxic symptoms against the target plant. Fungus VP51 belonging to the genus Diaporthe showed the most pronounced herbicidal activity. The Brazilian Pampa biome is a potential resource for the development of new and sustainable chemical compounds for modern agriculture.

Selective Osmotic Shock (SOS)-Based Islet Isolation for Microencapsulation.

Science.gov (United States)

Enck, Kevin; McQuilling, John Patrick; Orlando, Giuseppe; Tamburrini, Riccardo; Sivanandane, Sittadjody; Opara, Emmanuel C

2017-01-01

Islet transplantation (IT) has recently been shown to be a promising alternative to pancreas transplantation for reversing diabetes. IT requires the isolation of the islets from the pancreas, and these islets can be used to fabricate a bio-artificial pancreas. Enzymatic digestion is the current gold standard procedure for islet isolation but has lingering concerns. One such concern is that it has been shown to damage the islets due to nonselective tissue digestion. This chapter provides a detailed description of a nonenzymatic method that we are exploring in our lab as an alternative to current enzymatic digestion procedures for islet isolation from human and nonhuman pancreatic tissues. This method is based on selective destruction and protection of specific cell types and has been shown to leave the extracellular matrix (ECM) of islets intact, which may thus enhance islet viability and functionality. We also show that these SOS-isolated islets can be microencapsulated for transplantation.

Selection of Infective Arbuscular Mycorrhizal Fungal Isolates for Field Inoculation

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Elisa Pellegrino

2010-09-01

Full Text Available Arbuscular mycorrhizal (AM fungi play a key role in host plant growth and health, nutrient and water uptake, plant community diversity and dynamics. AM fungi differ in their symbiotic performance, which is the result of the interaction of two fungal characters, infectivity and efficiency. Infectivity is the ability of a fungal isolate to establish rapidly an extensive mycorrhizal symbiosis and is correlated with pre-symbiotic steps of fungal life cycle, such as spore germination and hyphal growth. Here, different AM fungal isolates were tested, with the aim of selecting infective endophytes for field inoculation. Greenhouse and microcosm experiments were performed in order to assess the ability of 12 AM fungal isolates to produce spores, colonize host roots and to perform initial steps of symbiosis establishment, such as spore germination and hyphal growth. AM fungal spore production and root colonization were significantly different among AM fungal isolates. Spore and sporocarp densities ranged from 0.8 to 7.4 and from 0.6 to 2.0 per gram of soil, respectively, whereas root colonization ranged from 2.9 to 72.2%. Percentage of spore or sporocarp germination ranged from 5.8 to 53.3% and hyphal length from 4.7 to 79.8 mm. The ordination analysis (Redundancy Analysis, RDA showed that environmental factors explained about 60% of the whole variance and their effect on fungal infectivity variables was significant (P = 0.002. The biplot clearly showed that variables which might be used to detect infective AM fungal isolates were hyphal length and root colonization. Such analysis may allow the detection of the best parameters to select efficient AM fungal isolates to be used in agriculture.

Analysis of isolates within species of anuran trypanosomes using random amplified polymorphic DNA.

Science.gov (United States)

Lun, Z R; Desser, S S

1996-01-01

A total of 20 decamer primers were used to generate random applied polymorphic DNA (RAPD) markers from 5 isolates of Trypanosoma fallisi, 3 isolates of T. ranarum, 2 isolates of T. rotatorium, and 2 isolates of T. rotatorium-like trypanosomes in addition to 2 species from the American Type Culture Collection, T. chattoni (ATCC 50294) and Trypanosoma sp. (ATCC 50295). A slight polymorphism was observed among the four isolates of T. fallisi obtained form American toads, Bufo americanus, collected in Algonquin Park, Ontario, Canada, and an isolate obtained from the same species of host collected in Marquette, Michigan, United States, and produced similarity coefficients ranging from 80.7% to 96.9%. Pronounced polymorphism was recorded among the three isolates of T. ranarum from bullfrogs, Rana catesbeiana, collected in Ontario, Canada, and in Maryland, United States, and from a Northern leopard frog, R. pipiens, collected in Minnesota (USA). The similarity coefficients ranged from 54.7% to 59.5%, suggesting that alleles of these isolates were conserved over a wide geographic range. The high degree of polymorphism observed in two isolates of T. rotatorium from a bullfrog collected in Ontario and two isolates of a T. rotatorium-like parasite from the green frog R. clamitans, collected in Louisiana (USA) suggests that they are different species. These results reflect the high similarity among isolates from the same geographic location and the pronounced polymorphism apparent among isolates from distant geographic locations.

Selection of cellulolytic fungi isolated from diverse substrates

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Mônica Caramez Triches Damaso

2012-08-01

Full Text Available The aim of the present work was to select filamentous fungi isolated from diverse substrates to obtain the strains with potential to produce the hydrolytic enzymes. From a total of 215 strains, seven strains from the soils, six from the plants and one from sugarcane bagasse were selected and identified as belonging to the Trichoderma, Penicillium and Aspergillus genera. The best hydrolytic activities obtained by semi-solid fermentation using these strains were approximately: 35; 1; 160; 170 and 120 U/gdm (CMCase, FPase, β-glucosidase, xylanase and polygalacturonase, respectively, demonstrating their potential to synthesize the enzymes compared with the results reported in the literature.

Star formation rates in isolated galaxies selected from the Two-Micron All-Sky Survey

Science.gov (United States)

Melnyk, O.; Karachentseva, V.; Karachentsev, I.

2015-08-01

We have considered the star formation properties of 1616 isolated galaxies from the 2MASS XSC (Extended Source Catalog) selected sample (2MIG) with the far-ultraviolet GALEX magnitudes. This sample was then compared with corresponding properties of isolated galaxies from the Local Orphan Galaxies (LOG) catalogue and paired galaxies. We found that different selection algorithms define different populations of isolated galaxies. The population of the LOG catalogue, selected from non-clustered galaxies in the Local Supercluster volume, mostly consists of low-mass spiral and late-type galaxies. The specific star formation rate (SSFR) upper limit in isolated and paired galaxies does not exceed the value of ˜dex(-9.4). This is probably common for galaxies of differing activity and environment (at least at z processes is the galaxy mass. However, the environmental influence is notable: paired massive galaxies with logM* > 11.5 have higher (S)SFR than isolated galaxies. Our results suggest that the environment helps to trigger the star formation in the highest mass galaxies. We found that the fraction of AGN in the paired sample is only a little higher than in our isolated galaxy sample. We assume that AGN phenomenon is probably defined by secular galaxy evolution.

Technique for selection of transient radiation-hard junction-isolated integrated circuits

International Nuclear Information System (INIS)

Crowley, J.L.; Junga, F.A.; Stultz, T.J.

1976-01-01

A technique is presented which demonstrates the feasibility of selecting junction-isolated integrated circuits (JI/ICS) for use in transient radiation environments. The procedure guarantees that all PNPN paths within the integrated circuit are identified and describes the methods used to determine whether the paths represent latchup susceptible structures. Two examples of the latchup analysis are given involving an SSI and an LSI bipolar junction-isolated integrated circuit

Patagonian red wines: selection of Lactobacillus plantarum isolates as potential starter cultures for malolactic fermentation.

Science.gov (United States)

Bravo-Ferrada, Bárbara Mercedes; Hollmann, Axel; Delfederico, Lucrecia; Valdés La Hens, Danay; Caballero, Adriana; Semorile, Liliana

2013-09-01

The aim of this study was to evaluate fifty-three Lactobacillus plantarum isolates obtained from a Patagonian red wine, molecularly identified and typified using RAPD analysis, in order to select starter cultures for malolactic fermentation (MLF). The results obtained suggest a considerable genetic diversity, taking into account that all L. plantarum isolates were obtained from one cellar and one vintage. Based on the capacity to tolerate a concentration of 14 % ethanol in MRS broth for 2 days, eight isolates were selected for the subsequent analysis. The incidence of various wine stress factors (ethanol, acid pH, lysozyme and sulfur dioxide) on isolates growth was studied. Besides, glucosidase and tannase activities were evaluated, and the presence of genes involved in the synthesis of biogenic amines was examined by PCR. A previously characterized indigenous Oenococcus oeni strain was included with comparative purposes. Differences in technologically relevant characteristics were observed among the eight L. plantarum selected isolates, revealing an isolate-dependent behavior. Detectable glucosidase and tannase activities were found in all isolates. The presence of genes encoding histidine and tyrosine descarboxylases and putrescine carbamoyltransferase was not detected. The ability of L. plantarum isolates to grow and consume L-malic acid in simulated laboratory-scale vinifications revealed that two of them could be considered as possible MLF starter cultures for Patagonian red wines. These isolates will be subjected to further analysis, for a final winery technological characterization.

DEVELOPMENT AND EVALUATION OF A SELECTIVE AND INDICATIVE MEDIUM FOR ISOLATION OF ACTINOBACILLUS-PLEUROPNEUMONIAE FROM TONSILS

DEFF Research Database (Denmark)

Jakobsen, Marianne; Nielsen, Jens

1995-01-01

In order to isolate ActinobacillIus pleuropneumoniae from mixed bacterial flora a selective and indicative medium was developed. The optimal concentrations of antibiotics were determined for selective chocolate agar (S-TSA) and selective blood agar (S-MBA) using a set of 25 strains of A. pleuropn......In order to isolate ActinobacillIus pleuropneumoniae from mixed bacterial flora a selective and indicative medium was developed. The optimal concentrations of antibiotics were determined for selective chocolate agar (S-TSA) and selective blood agar (S-MBA) using a set of 25 strains of A...

Molecular profiles of Venezuelan isolates of Trypanosoma sp. by random amplified polymorphic DNA method.

Science.gov (United States)

Perrone, T M; Gonzatti, M I; Villamizar, G; Escalante, A; Aso, P M

2009-05-12

Nine Trypanosoma sp. Venezuelan isolates, initially presumed to be T. evansi, were collected from three different hosts, capybara (Apure state), horse (Apure state) and donkey (Guarico state) and compared by the random amplification polymorphic DNA technique (RAPD). Thirty-one to 46 reproducible fragments were obtained with 12 of the 40 primers that were used. Most of the primers detected molecular profiles with few polymorphisms between the seven horse, capybara and donkey isolates. Quantitative analyses of the RAPD profiles of these isolates revealed a high degree of genetic conservation with similarity coefficients between 85.7% and 98.5%. Ten of the primers generated polymorphic RAPD profiles with two of the three Trypanosoma sp. horse isolates, namely TeAp-N/D1 and TeGu-N/D1. The similarity coefficient between these two isolates and the rest, ranged from 57.9% to 68.4% and the corresponding dendrogram clustered TeAp-N/D1 and Te Gu-N/D1 in a genetically distinct group.

40 CFR 761.308 - Sample selection by random number generation on any two-dimensional square grid.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Sample selection by random number... § 761.79(b)(3) § 761.308 Sample selection by random number generation on any two-dimensional square... area created in accordance with paragraph (a) of this section, select two random numbers: one each for...

Applications of random forest feature selection for fine-scale genetic population assignment.

Science.gov (United States)

Sylvester, Emma V A; Bentzen, Paul; Bradbury, Ian R; Clément, Marie; Pearce, Jon; Horne, John; Beiko, Robert G

2018-02-01

Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine-learning algorithms (random forest, regularized random forest and guided regularized random forest) compared with F ST ranking for selection of single nucleotide polymorphisms (SNP) for fine-scale population assignment. We applied these methods to an unpublished SNP data set for Atlantic salmon ( Salmo salar ) and a published SNP data set for Alaskan Chinook salmon ( Oncorhynchus tshawytscha ). In each species, we identified the minimum panel size required to obtain a self-assignment accuracy of at least 90% using each method to create panels of 50-700 markers Panels of SNPs identified using random forest-based methods performed up to 7.8 and 11.2 percentage points better than F ST -selected panels of similar size for the Atlantic salmon and Chinook salmon data, respectively. Self-assignment accuracy ≥90% was obtained with panels of 670 and 384 SNPs for each data set, respectively, a level of accuracy never reached for these species using F ST -selected panels. Our results demonstrate a role for machine-learning approaches in marker selection across large genomic data sets to improve assignment for management and conservation of exploited populations.

Genetic polymorphism and natural selection of Duffy binding protein of Plasmodium vivax Myanmar isolates

Science.gov (United States)

2012-01-01

Background Plasmodium vivax Duffy binding protein (PvDBP) plays an essential role in erythrocyte invasion and a potential asexual blood stage vaccine candidate antigen against P. vivax. The polymorphic nature of PvDBP, particularly amino terminal cysteine-rich region (PvDBPII), represents a major impediment to the successful design of a protective vaccine against vivax malaria. In this study, the genetic polymorphism and natural selection at PvDBPII among Myanmar P. vivax isolates were analysed. Methods Fifty-four P. vivax infected blood samples collected from patients in Myanmar were used. The region flanking PvDBPII was amplified by PCR, cloned into Escherichia coli, and sequenced. The polymorphic characters and natural selection of the region were analysed using the DnaSP and MEGA4 programs. Results Thirty-two point mutations (28 non-synonymous and four synonymous mutations) were identified in PvDBPII among the Myanmar P. vivax isolates. Sequence analyses revealed that 12 different PvDBPII haplotypes were identified in Myanmar P. vivax isolates and that the region has evolved under positive natural selection. High selective pressure preferentially acted on regions identified as B- and T-cell epitopes of PvDBPII. Recombination may also be played a role in the resulting genetic diversity of PvDBPII. Conclusions PvDBPII of Myanmar P. vivax isolates displays a high level of genetic polymorphism and is under selective pressure. Myanmar P. vivax isolates share distinct types of PvDBPII alleles that are different from those of other geographical areas. These results will be useful for understanding the nature of the P. vivax population in Myanmar and for development of PvDBPII-based vaccine. PMID:22380592

Isolation of cells for selective treatment and analysis using a magnetic microfluidic chip

KAUST Repository

Yassine, Omar

2014-05-01

This study describes the development and testing of a magnetic microfluidic chip (MMC) for trapping and isolating cells tagged with superparamagnetic beads (SPBs) in a microfluidic environment for selective treatment and analysis. The trapping and isolation are done in two separate steps; first, the trapping of the tagged cells in a main channel is achieved by soft ferromagnetic disks and second, the transportation of the cells into side chambers for isolation is executed by tapered conductive paths made of Gold (Au). Numerical simulations were performed to analyze the magnetic flux and force distributions of the disks and conducting paths, for trapping and transporting SPBs. The MMC was fabricated using standard microfabrication processes. Experiments were performed with E. coli (K12 strand) tagged with 2.8 μm SPBs. The results showed that E. coli can be separated from a sample solution by trapping them at the disk sites, and then isolated into chambers by transporting them along the tapered conducting paths. Once the E. coli was trapped inside the side chambers, two selective treatments were performed. In one chamber, a solution with minimal nutrition content was added and, in another chamber, a solution with essential nutrition was added. The results showed that the growth of bacteria cultured in the second chamber containing nutrient was significantly higher, demonstrating that the E. coli was not affected by the magnetically driven transportation and the feasibility of performing different treatments on selectively isolated cells on a single microfluidic platform.

Interference-aware random beam selection for spectrum sharing systems

KAUST Repository

Abdallah, Mohamed M.

2012-09-01

Spectrum sharing systems have been introduced to alleviate the problem of spectrum scarcity by allowing secondary unlicensed networks to share the spectrum with primary licensed networks under acceptable interference levels to the primary users. In this paper, we develop interference-aware random beam selection schemes that provide enhanced throughput for the secondary link under the condition that the interference observed at the primary link is within a predetermined acceptable value. For a secondary transmitter equipped with multiple antennas, our schemes select a random beam, among a set of power- optimized orthogonal random beams, that maximizes the capacity of the secondary link while satisfying the interference constraint at the primary receiver for different levels of feedback information describing the interference level at the primary receiver. For the proposed schemes, we develop a statistical analysis for the signal-to-noise and interference ratio (SINR) statistics as well as the capacity of the secondary link. Finally, we present numerical results that study the effect of system parameters including number of beams and the maximum transmission power on the capacity of the secondary link attained using the proposed schemes. © 2012 IEEE.

Glycine-containing selective medium for isolation of Legionellaceae from environmental specimens.

OpenAIRE

Wadowsky, R M; Yee, R B

1981-01-01

Glycine, at a final concentration of 0.3%, has been shown to be an excellent selective agent for the isolation of Legionellaceae. Stock cultures of Legionella pneumophila were not inhibited on buffered charcoal-yeast extract agar containing the amino acid. Among the other Legionellaceae tested, only one of two strains of L. dumoffii and two of six strains of L. micdadei were appreciably inhibited. This medium permitted the isolation of L. pneumophila from environmental specimens with marked i...

Interference-aware random beam selection for spectrum sharing systems

KAUST Repository

Abdallah, Mohamed M.; Sayed, Mostafa M.; Alouini, Mohamed-Slim; Qaraqe, Khalid A.

2012-01-01

. In this paper, we develop interference-aware random beam selection schemes that provide enhanced throughput for the secondary link under the condition that the interference observed at the primary link is within a predetermined acceptable value. For a secondary

Susceptibility of Mycosphaerella fijiensis isolates to the Higromicine B and Carbendazim selection agents

Directory of Open Access Journals (Sweden)

Mileidy Cruz-Martín

2006-10-01

Full Text Available The  study  of  Musa  -  Mycosphaerella  fijiensis  interactions  supported  by  molecular  tools  such  as  the  genetic transformation could contribute to elucidate new mechanisms related with the pathogenesis and through it to allow  the  development  of  new  selective  fungicides  as  well  as  the  elaboration  of  more  durable  resistance strategies.  This  work  had  as  objective,  to  determine  the  Minimum  Inhibitory  Concentration  (MIC  of  different antimicrobial substances commonly used as selection agents in the genetic transformation study of different species of Mycosphaerella (Hygromycin B and carbendazim. The agar dilution method was used and mycelial suspensions of nine of M. fijiensis isolated by several regions of Villa Clara and Ciego de Ávila was used as inoculums. Concentrations of these substances from 32.0 to 0.015 mg.l l -1  were rehearsed. It was possible to determine  the  MIC  of  both  antimicrobials  substances  against  the  M.fijiensis  isolated  using  this  method.  The MCI of the Hygromycin B for 100% of the isolated was less to 8 μg.ml l -1 and the rehearsed 90% of the isolated ones showed, for the carbendazim, MIC less or similar to 0.125 μg.ml l -1 . CCIBP-Pf-57 isolated did not achieve to be inhibited to the rehearsed concentrations of the Carbendazim. The results obtained in this work evidence the importance of knowing the MIC of the selective agents that are used in the transformation avoiding escapes in the selection. Key words: antimicrobial substance, genetic transformation, Minimal inhibitory concentration, mycelia suspension, Pseudosercospora  fijiensis

The signature of positive selection at randomly chosen loci.

OpenAIRE

Przeworski, Molly

2002-01-01

In Drosophila and humans, there are accumulating examples of loci with a significant excess of high-frequency-derived alleles or high levels of linkage disequilibrium, relative to a neutral model of a random-mating population of constant size. These are features expected after a recent selective sweep. Their prevalence suggests that positive directional selection may be widespread in both species. However, as I show here, these features do not persist long after the sweep ends: The high-frequ...

Simulated Performance Evaluation of a Selective Tracker Through Random Scenario Generation

DEFF Research Database (Denmark)

Hussain, Dil Muhammad Akbar

2006-01-01

performance assessment. Therefore, a random target motion scenario is adopted. Its implementation in particular for testing the proposed selective track splitting algorithm using Kalman filters is investigated through a number of performance parameters which gives the activity profile of the tracking scenario......  The paper presents a simulation study on the performance of a target tracker using selective track splitting filter algorithm through a random scenario implemented on a digital signal processor.  In a typical track splitting filter all the observation which fall inside a likelihood ellipse...... are used for update, however, in our proposed selective track splitting filter less number of observations are used for track update.  Much of the previous performance work [1] has been done on specific (deterministic) scenarios. One of the reasons for considering the specific scenarios, which were...

Minimization over randomly selected lines

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Ismet Sahin

2013-07-01

Full Text Available This paper presents a population-based evolutionary optimization method for minimizing a given cost function. The mutation operator of this method selects randomly oriented lines in the cost function domain, constructs quadratic functions interpolating the cost function at three different points over each line, and uses extrema of the quadratics as mutated points. The crossover operator modifies each mutated point based on components of two points in population, instead of one point as is usually performed in other evolutionary algorithms. The stopping criterion of this method depends on the number of almost degenerate quadratics. We demonstrate that the proposed method with these mutation and crossover operations achieves faster and more robust convergence than the well-known Differential Evolution and Particle Swarm algorithms.

Selection for altruism through random drift in variable size populations

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Houchmandzadeh Bahram

2012-05-01

Full Text Available Abstract Background Altruistic behavior is defined as helping others at a cost to oneself and a lowered fitness. The lower fitness implies that altruists should be selected against, which is in contradiction with their widespread presence is nature. Present models of selection for altruism (kin or multilevel show that altruistic behaviors can have ‘hidden’ advantages if the ‘common good’ produced by altruists is restricted to some related or unrelated groups. These models are mostly deterministic, or assume a frequency dependent fitness. Results Evolutionary dynamics is a competition between deterministic selection pressure and stochastic events due to random sampling from one generation to the next. We show here that an altruistic allele extending the carrying capacity of the habitat can win by increasing the random drift of “selfish” alleles. In other terms, the fixation probability of altruistic genes can be higher than those of a selfish ones, even though altruists have a smaller fitness. Moreover when populations are geographically structured, the altruists advantage can be highly amplified and the fixation probability of selfish genes can tend toward zero. The above results are obtained both by numerical and analytical calculations. Analytical results are obtained in the limit of large populations. Conclusions The theory we present does not involve kin or multilevel selection, but is based on the existence of random drift in variable size populations. The model is a generalization of the original Fisher-Wright and Moran models where the carrying capacity depends on the number of altruists.

Selection bias and subject refusal in a cluster-randomized controlled trial

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Rochelle Yang

2017-07-01

Full Text Available Abstract Background Selection bias and non-participation bias are major methodological concerns which impact external validity. Cluster-randomized controlled trials are especially prone to selection bias as it is impractical to blind clusters to their allocation into intervention or control. This study assessed the impact of selection bias in a large cluster-randomized controlled trial. Methods The Improved Cardiovascular Risk Reduction to Enhance Rural Primary Care (ICARE study examined the impact of a remote pharmacist-led intervention in twelve medical offices. To assess eligibility, a standardized form containing patient demographics and medical information was completed for each screened patient. Eligible patients were approached by the study coordinator for recruitment. Both the study coordinator and the patient were aware of the site’s allocation prior to consent. Patients who consented or declined to participate were compared across control and intervention arms for differing characteristics. Statistical significance was determined using a two-tailed, equal variance t-test and a chi-square test with adjusted Bonferroni p-values. Results were adjusted for random cluster variation. Results There were 2749 completed screening forms returned to research staff with 461 subjects who had either consented or declined participation. Patients with poorly controlled diabetes were found to be significantly more likely to decline participation in intervention sites compared to those in control sites. A higher mean diastolic blood pressure was seen in patients with uncontrolled hypertension who declined in the control sites compared to those who declined in the intervention sites. However, these findings were no longer significant after adjustment for random variation among the sites. After this adjustment, females were now found to be significantly more likely to consent than males (odds ratio = 1.41; 95% confidence interval = 1.03, 1

Selection of Beauveria bassiana and Metarhizium anisopliae Isolates to Control Triatoma infestans

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Luz Christian

1998-01-01

Full Text Available Twenty three isolates of Beauveria bassiana and 13 isolates of Metarhizium anisopliae were tested on third instar nymphs of Triatoma infestans, a serious vector of Chagas disease. Pathogenicity tests at saturated humidity showed that this insect is very susceptible to fungal infection. At lower relative humidity (50%, conditions expected in the vector microhabitat, virulence was significantly different among isolates. Cumulative mortality 15 days after treatment varied from 17.5 to 97.5%, and estimates of 50% survival time varied from 6 to 11 days. Maintaining lower relative humidity, four B. bassiana and two M. anisopliae isolates were selected for analysis of virulence at different conidial concentrations and temperatures. Lethal concentrations sufficient to kill 50% of insects (LC50 varied from 7.1x105 to 4.3x106 conidia/ml, for a B. bassiana isolate (CG 14 and a M. anisopliae isolate (CG 491 respectively. Most isolates, particularly B. bassiana isolates CG 24 and CG 306, proved to be more virulent at 25 and 30°C, compared to 15 and 20°C. The differential virulence at 50% humidity observed among some B. bassiana isolates was not correlated to phenetic groups in cluster analysis of RAPD markers. In fact, the B. bassiana isolates analyzed presented a high homogeneity (> 73% similarity.

An Improved Test Selection Optimization Model Based on Fault Ambiguity Group Isolation and Chaotic Discrete PSO

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Xiaofeng Lv

2018-01-01

Full Text Available Sensor data-based test selection optimization is the basis for designing a test work, which ensures that the system is tested under the constraint of the conventional indexes such as fault detection rate (FDR and fault isolation rate (FIR. From the perspective of equipment maintenance support, the ambiguity isolation has a significant effect on the result of test selection. In this paper, an improved test selection optimization model is proposed by considering the ambiguity degree of fault isolation. In the new model, the fault test dependency matrix is adopted to model the correlation between the system fault and the test group. The objective function of the proposed model is minimizing the test cost with the constraint of FDR and FIR. The improved chaotic discrete particle swarm optimization (PSO algorithm is adopted to solve the improved test selection optimization model. The new test selection optimization model is more consistent with real complicated engineering systems. The experimental result verifies the effectiveness of the proposed method.

Chemical rationale for selection of isolates for genome sequencing

DEFF Research Database (Denmark)

Rank, Christian; Larsen, Thomas Ostenfeld; Frisvad, Jens Christian

The advances in gene sequencing will in the near future enable researchers to affordably acquire the full genomes of handpicked isolates. We here present a method to evaluate the chemical potential of an entire species and select representatives for genome sequencing. The selection criteria for new...... strains to be sequenced can be manifold, but for studying the functional phenotype, using a metabolome based approach offers a cheap and rapid assessment of critical strains to cover the chemical diversity. We have applied this methodology on the complex A. flavus/A. oryzae group. Though these two species...... are in principal identical, they represent two different phenotypes. This is clearly presented through a correspondence analysis of selected extrolites, in which the subtle chemical differences are visually dispersed. The results points to a handful of strains, which, if sequenced, will likely enhance our...

Interference-aware random beam selection schemes for spectrum sharing systems

KAUST Repository

Abdallah, Mohamed; Qaraqe, Khalid; Alouini, Mohamed-Slim

2012-01-01

users. In this work, we develop interference-aware random beam selection schemes that provide enhanced performance for the secondary network under the condition that the interference observed by the receivers of the primary network is below a

Selection on plant male function genes identifies candidates for reproductive isolation of yellow monkeyflowers.

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Jan E Aagaard

Full Text Available Understanding the genetic basis of reproductive isolation promises insight into speciation and the origins of biological diversity. While progress has been made in identifying genes underlying barriers to reproduction that function after fertilization (post-zygotic isolation, we know much less about earlier acting pre-zygotic barriers. Of particular interest are barriers involved in mating and fertilization that can evolve extremely rapidly under sexual selection, suggesting they may play a prominent role in the initial stages of reproductive isolation. A significant challenge to the field of speciation genetics is developing new approaches for identification of candidate genes underlying these barriers, particularly among non-traditional model systems. We employ powerful proteomic and genomic strategies to study the genetic basis of conspecific pollen precedence, an important component of pre-zygotic reproductive isolation among yellow monkeyflowers (Mimulus spp. resulting from male pollen competition. We use isotopic labeling in combination with shotgun proteomics to identify more than 2,000 male function (pollen tube proteins within maternal reproductive structures (styles of M. guttatus flowers where pollen competition occurs. We then sequence array-captured pollen tube exomes from a large outcrossing population of M. guttatus, and identify those genes with evidence of selective sweeps or balancing selection consistent with their role in pollen competition. We also test for evidence of positive selection on these genes more broadly across yellow monkeyflowers, because a signal of adaptive divergence is a common feature of genes causing reproductive isolation. Together the molecular evolution studies identify 159 pollen tube proteins that are candidate genes for conspecific pollen precedence. Our work demonstrates how powerful proteomic and genomic tools can be readily adapted to non-traditional model systems, allowing for genome-wide screens

Continuous-Time Mean-Variance Portfolio Selection with Random Horizon

International Nuclear Information System (INIS)

Yu, Zhiyong

2013-01-01

This paper examines the continuous-time mean-variance optimal portfolio selection problem with random market parameters and random time horizon. Treating this problem as a linearly constrained stochastic linear-quadratic optimal control problem, I explicitly derive the efficient portfolios and efficient frontier in closed forms based on the solutions of two backward stochastic differential equations. Some related issues such as a minimum variance portfolio and a mutual fund theorem are also addressed. All the results are markedly different from those in the problem with deterministic exit time. A key part of my analysis involves proving the global solvability of a stochastic Riccati equation, which is interesting in its own right

Continuous-Time Mean-Variance Portfolio Selection with Random Horizon

Energy Technology Data Exchange (ETDEWEB)

Yu, Zhiyong, E-mail: yuzhiyong@sdu.edu.cn [Shandong University, School of Mathematics (China)

2013-12-15

This paper examines the continuous-time mean-variance optimal portfolio selection problem with random market parameters and random time horizon. Treating this problem as a linearly constrained stochastic linear-quadratic optimal control problem, I explicitly derive the efficient portfolios and efficient frontier in closed forms based on the solutions of two backward stochastic differential equations. Some related issues such as a minimum variance portfolio and a mutual fund theorem are also addressed. All the results are markedly different from those in the problem with deterministic exit time. A key part of my analysis involves proving the global solvability of a stochastic Riccati equation, which is interesting in its own right.

TEHRAN AIR POLLUTANTS PREDICTION BASED ON RANDOM FOREST FEATURE SELECTION METHOD

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A. Shamsoddini

2017-09-01

Full Text Available Air pollution as one of the most serious forms of environmental pollutions poses huge threat to human life. Air pollution leads to environmental instability, and has harmful and undesirable effects on the environment. Modern prediction methods of the pollutant concentration are able to improve decision making and provide appropriate solutions. This study examines the performance of the Random Forest feature selection in combination with multiple-linear regression and Multilayer Perceptron Artificial Neural Networks methods, in order to achieve an efficient model to estimate carbon monoxide and nitrogen dioxide, sulfur dioxide and PM2.5 contents in the air. The results indicated that Artificial Neural Networks fed by the attributes selected by Random Forest feature selection method performed more accurate than other models for the modeling of all pollutants. The estimation accuracy of sulfur dioxide emissions was lower than the other air contaminants whereas the nitrogen dioxide was predicted more accurate than the other pollutants.

Tehran Air Pollutants Prediction Based on Random Forest Feature Selection Method

Science.gov (United States)

Shamsoddini, A.; Aboodi, M. R.; Karami, J.

2017-09-01

Air pollution as one of the most serious forms of environmental pollutions poses huge threat to human life. Air pollution leads to environmental instability, and has harmful and undesirable effects on the environment. Modern prediction methods of the pollutant concentration are able to improve decision making and provide appropriate solutions. This study examines the performance of the Random Forest feature selection in combination with multiple-linear regression and Multilayer Perceptron Artificial Neural Networks methods, in order to achieve an efficient model to estimate carbon monoxide and nitrogen dioxide, sulfur dioxide and PM2.5 contents in the air. The results indicated that Artificial Neural Networks fed by the attributes selected by Random Forest feature selection method performed more accurate than other models for the modeling of all pollutants. The estimation accuracy of sulfur dioxide emissions was lower than the other air contaminants whereas the nitrogen dioxide was predicted more accurate than the other pollutants.

Hebbian Learning in a Random Network Captures Selectivity Properties of the Prefrontal Cortex

Science.gov (United States)

Lindsay, Grace W.

2017-01-01

Complex cognitive behaviors, such as context-switching and rule-following, are thought to be supported by the prefrontal cortex (PFC). Neural activity in the PFC must thus be specialized to specific tasks while retaining flexibility. Nonlinear “mixed” selectivity is an important neurophysiological trait for enabling complex and context-dependent behaviors. Here we investigate (1) the extent to which the PFC exhibits computationally relevant properties, such as mixed selectivity, and (2) how such properties could arise via circuit mechanisms. We show that PFC cells recorded from male and female rhesus macaques during a complex task show a moderate level of specialization and structure that is not replicated by a model wherein cells receive random feedforward inputs. While random connectivity can be effective at generating mixed selectivity, the data show significantly more mixed selectivity than predicted by a model with otherwise matched parameters. A simple Hebbian learning rule applied to the random connectivity, however, increases mixed selectivity and enables the model to match the data more accurately. To explain how learning achieves this, we provide analysis along with a clear geometric interpretation of the impact of learning on selectivity. After learning, the model also matches the data on measures of noise, response density, clustering, and the distribution of selectivities. Of two styles of Hebbian learning tested, the simpler and more biologically plausible option better matches the data. These modeling results provide clues about how neural properties important for cognition can arise in a circuit and make clear experimental predictions regarding how various measures of selectivity would evolve during animal training. SIGNIFICANCE STATEMENT The prefrontal cortex is a brain region believed to support the ability of animals to engage in complex behavior. How neurons in this area respond to stimuli—and in particular, to combinations of stimuli (�

Performance Evaluation of User Selection Protocols in Random Networks with Energy Harvesting and Hardware Impairments

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Tan Nhat Nguyen

2016-01-01

Full Text Available In this paper, we evaluate performances of various user selection protocols under impact of hardware impairments. In the considered protocols, a Base Station (BS selects one of available Users (US to serve, while the remaining USs harvest the energy from the Radio Frequency (RF transmitted by the BS. We assume that all of the US randomly appear around the BS. In the Random Selection Protocol (RAN, the BS randomly selects a US to transmit the data. In the second proposed protocol, named Minimum Distance Protocol (MIND, the US that is nearest to the BS will be chosen. In the Optimal Selection Protocol (OPT, the US providing the highest channel gain between itself and the BS will be served. For performance evaluation, we derive exact and asymptotic closed-form expressions of average Outage Probability (OP over Rayleigh fading channels. We also consider average harvested energy per a US. Finally, Monte-Carlo simulations are then performed to verify the theoretical results.

Multivariate fault isolation of batch processes via variable selection in partial least squares discriminant analysis.

Science.gov (United States)

Yan, Zhengbing; Kuang, Te-Hui; Yao, Yuan

2017-09-01

In recent years, multivariate statistical monitoring of batch processes has become a popular research topic, wherein multivariate fault isolation is an important step aiming at the identification of the faulty variables contributing most to the detected process abnormality. Although contribution plots have been commonly used in statistical fault isolation, such methods suffer from the smearing effect between correlated variables. In particular, in batch process monitoring, the high autocorrelations and cross-correlations that exist in variable trajectories make the smearing effect unavoidable. To address such a problem, a variable selection-based fault isolation method is proposed in this research, which transforms the fault isolation problem into a variable selection problem in partial least squares discriminant analysis and solves it by calculating a sparse partial least squares model. As different from the traditional methods, the proposed method emphasizes the relative importance of each process variable. Such information may help process engineers in conducting root-cause diagnosis. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

The reliability of randomly selected final year pharmacy students in ...

African Journals Online (AJOL)

Employing ANOVA, factorial experimental analysis, and the theory of error, reliability studies were conducted on the assessment of the drug product chloroquine phosphate tablets. The G–Study employed equal numbers of the factors for uniform control, and involved three analysts (randomly selected final year Pharmacy ...

Random selection of items. Selection of n1 samples among N items composing a stratum

International Nuclear Information System (INIS)

Jaech, J.L.; Lemaire, R.J.

1987-02-01

STR-224 provides generalized procedures to determine required sample sizes, for instance in the course of a Physical Inventory Verification at Bulk Handling Facilities. The present report describes procedures to generate random numbers and select groups of items to be verified in a given stratum through each of the measurement methods involved in the verification. (author). 3 refs

PREDOMOS study, impact of a social intervention program for socially isolated elderly cancer patients: study protocol for a randomized controlled trial.

Science.gov (United States)

Crétel-Durand, Elodie; Nouguerède, Emilie; Le Caer, Hervé; Rousseau, Frédérique; Retornaz, Frédérique; Guillem, Olivier; Couderc, Anne-Laure; Greillier, Laurent; Norguet, Emmanuelle; Cécile, Maud; Boulahssass, Rabia; Le Caer, Francoise; Tournier, Sandrine; Butaud, Chantal; Guillet, Pierre; Nahon, Sophie; Poudens, Laure; Kirscher, Sylvie; Loubière, Sandrine; Diaz, Nadine; Dhorne, Jean; Auquier, Pascal; Baumstarck, Karine

2017-04-12

Cancer incidence and social isolation increase along with advanced age, and social isolation potentiates the relative risk of death by cancer. Once spotted, social isolation can be averted with the intervention of a multidisciplinary team. Techniques of automation and remote assistance have already demonstrated their positive impact on falls prevention and quality of life (QoL), though little is known about their impact on socially isolated elderly patients supported for cancer. The primary objective of the PREDOMOS study is to evaluate the impact of establishing a Program of Social intervention associated with techniques of Domotic and Remote assistance (PS-DR) on the improvement of QoL of elderly isolated patients, treated for locally advanced or metastatic cancer. The secondary objectives include treatment failure, tolerance, survival, and autonomy. This trial is a multicenter, prospective, randomized, placebo-controlled, open-label, two-parallel group study. The setting is 10 French oncogeriatric centers. Inclusion criteria are patients aged at least 70 years with a social isolation risk and a histological diagnosis of cancer, locally advanced or metastatic disease. The groups are (1) the control group, receiving usual care; (2) the experimental group, receiving usual care associating with monthly social assistance, domotic, and remote assistance. Participants are randomized in a 1:1 allocation ratio. Evaluation times involve inclusion (randomization) and follow-up (12 months). The primary endpoint is QoL at 3 months (via European Organization for Research and Treatment of Cancer (EORTC) QLQ C30); secondary endpoints are social isolation, time to treatment failure, toxicity, dose response-intensity, survival, autonomy, and QoL at 6 months. For the sample size, 320 individuals are required to obtain 90% power to detect a 10-point difference (standard deviation 25) in QoL score between the two groups (20% loss to follow-up patients expected). The randomized

The mathematics of random mutation and natural selection for multiple simultaneous selection pressures and the evolution of antimicrobial drug resistance.

Science.gov (United States)

Kleinman, Alan

2016-12-20

The random mutation and natural selection phenomenon act in a mathematically predictable behavior, which when understood leads to approaches to reduce and prevent the failure of the use of these selection pressures when treating infections and cancers. The underlying principle to impair the random mutation and natural selection phenomenon is to use combination therapy, which forces the population to evolve to multiple selection pressures simultaneously that invoke the multiplication rule of probabilities simultaneously as well. Recently, it has been seen that combination therapy for the treatment of malaria has failed to prevent the emergence of drug-resistant variants. Using this empirical example and the principles of probability theory, the derivation of the equations describing this treatment failure is carried out. These equations give guidance as to how to use combination therapy for the treatment of cancers and infectious diseases and prevent the emergence of drug resistance. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Selection of oleuropein-degrading lactic acid bacteria strains isolated from fermenting Moroccan green olives

Energy Technology Data Exchange (ETDEWEB)

Ghabbour, N.; Lamzira, Z.; Thonart, P.; Cidalia, P.; Markaouid, M.; Asehraoua, A.

2011-07-01

A total of 177 strains of lactic acid bacteria (LAB) were isolated from early-stage Moroccan Picholine green olive fermentation, including Lactobacillus plantarum (44.63%), Lactobacillus pentosus (25.99%), Lactobacillus brevis (9.61%) and Pediococcus pentosaceus (19.77%). All the isolates were screened for their tolerance to olive leaf extract and oleuropein. Most of the isolates (85.3%) were found able to degrade oleuropein, when evaluated by either oleuropein or 5-Bromo-4-chloro-3-indolyl {beta}-D-glucuronide (X-Gluc) as substrates. The biodegradation capacity of the selected strains of each species was confirmed by HPLC analysis. (Author).

A Bayesian random effects discrete-choice model for resource selection: Population-level selection inference

Science.gov (United States)

Thomas, D.L.; Johnson, D.; Griffith, B.

2006-01-01

Modeling the probability of use of land units characterized by discrete and continuous measures, we present a Bayesian random-effects model to assess resource selection. This model provides simultaneous estimation of both individual- and population-level selection. Deviance information criterion (DIC), a Bayesian alternative to AIC that is sample-size specific, is used for model selection. Aerial radiolocation data from 76 adult female caribou (Rangifer tarandus) and calf pairs during 1 year on an Arctic coastal plain calving ground were used to illustrate models and assess population-level selection of landscape attributes, as well as individual heterogeneity of selection. Landscape attributes included elevation, NDVI (a measure of forage greenness), and land cover-type classification. Results from the first of a 2-stage model-selection procedure indicated that there is substantial heterogeneity among cow-calf pairs with respect to selection of the landscape attributes. In the second stage, selection of models with heterogeneity included indicated that at the population-level, NDVI and land cover class were significant attributes for selection of different landscapes by pairs on the calving ground. Population-level selection coefficients indicate that the pairs generally select landscapes with higher levels of NDVI, but the relationship is quadratic. The highest rate of selection occurs at values of NDVI less than the maximum observed. Results for land cover-class selections coefficients indicate that wet sedge, moist sedge, herbaceous tussock tundra, and shrub tussock tundra are selected at approximately the same rate, while alpine and sparsely vegetated landscapes are selected at a lower rate. Furthermore, the variability in selection by individual caribou for moist sedge and sparsely vegetated landscapes is large relative to the variability in selection of other land cover types. The example analysis illustrates that, while sometimes computationally intense, a

Population genetic structure and natural selection of apical membrane antigen-1 in Plasmodium vivax Korean isolates.

Science.gov (United States)

Kang, Jung-Mi; Lee, Jinyoung; Cho, Pyo-Yun; Moon, Sung-Ung; Ju, Hye-Lim; Ahn, Seong Kyu; Sohn, Woon-Mok; Lee, Hyeong-Woo; Kim, Tong-Soo; Na, Byoung-Kuk

2015-11-16

Plasmodium vivax apical membrane antigen-1 (PvAMA-1) is a leading candidate antigen for blood stage malaria vaccine. However, antigenic variation is a major obstacle in the development of an effective vaccine based on this antigen. In this study, the genetic structure and the effect of natural selection of PvAMA-1 among Korean P. vivax isolates were analysed. Blood samples were collected from 66 Korean patients with vivax malaria. The entire PvAMA-1 gene was amplified by polymerase chain reaction and cloned into a TA cloning vector. The PvAMA-1 sequence of each isolate was sequenced and the polymorphic characteristics and effect of natural selection were analysed using the DNASTAR, MEGA4, and DnaSP programs. Thirty haplotypes of PvAMA-1, which were further classified into seven different clusters, were identified in the 66 Korean P. vivax isolates. Domain II was highly conserved among the sequences, but substantial nucleotide diversity was observed in domains I and III. The difference between the rates of non-synonymous and synonymous mutations suggested that the gene has evolved under natural selection. No strong evidence indicating balancing or positive selection on PvAMA-1 was identified. Recombination may also play a role in the resulting genetic diversity of PvAMA-1. This study is the first comprehensive analysis of nucleotide diversity across the entire PvAMA-1 gene using a single population sample from Korea. Korean PvAMA-1 had limited genetic diversity compared to PvAMA-1 in global isolates. The overall pattern of genetic polymorphism of Korean PvAMA-1 differed from other global isolates and novel amino acid changes were also identified in Korean PvAMA-1. Evidences for natural selection and recombination event were observed, which is likely to play an important role in generating genetic diversity across the PvAMA-1. These results provide useful information for the understanding the population structure of P. vivax circulating in Korea and have important

The signature of positive selection at randomly chosen loci.

Science.gov (United States)

Przeworski, Molly

2002-03-01

In Drosophila and humans, there are accumulating examples of loci with a significant excess of high-frequency-derived alleles or high levels of linkage disequilibrium, relative to a neutral model of a random-mating population of constant size. These are features expected after a recent selective sweep. Their prevalence suggests that positive directional selection may be widespread in both species. However, as I show here, these features do not persist long after the sweep ends: The high-frequency alleles drift to fixation and no longer contribute to polymorphism, while linkage disequilibrium is broken down by recombination. As a result, loci chosen without independent evidence of recent selection are not expected to exhibit either of these features, even if they have been affected by numerous sweeps in their genealogical history. How then can we explain the patterns in the data? One possibility is population structure, with unequal sampling from different subpopulations. Alternatively, positive selection may not operate as is commonly modeled. In particular, the rate of fixation of advantageous mutations may have increased in the recent past.

Design and methods of a social network isolation study for reducing respiratory infection transmission: The eX-FLU cluster randomized trial.

Science.gov (United States)

Aiello, Allison E; Simanek, Amanda M; Eisenberg, Marisa C; Walsh, Alison R; Davis, Brian; Volz, Erik; Cheng, Caroline; Rainey, Jeanette J; Uzicanin, Amra; Gao, Hongjiang; Osgood, Nathaniel; Knowles, Dylan; Stanley, Kevin; Tarter, Kara; Monto, Arnold S

2016-06-01

Social networks are increasingly recognized as important points of intervention, yet relatively few intervention studies of respiratory infection transmission have utilized a network design. Here we describe the design, methods, and social network structure of a randomized intervention for isolating respiratory infection cases in a university setting over a 10-week period. 590 students in six residence halls enrolled in the eX-FLU study during a chain-referral recruitment process from September 2012-January 2013. Of these, 262 joined as "seed" participants, who nominated their social contacts to join the study, of which 328 "nominees" enrolled. Participants were cluster-randomized by 117 residence halls. Participants were asked to respond to weekly surveys on health behaviors, social interactions, and influenza-like illness (ILI) symptoms. Participants were randomized to either a 3-Day dorm room isolation intervention or a control group (no isolation) upon illness onset. ILI cases reported on their isolation behavior during illness and provided throat and nasal swab specimens at onset, day-three, and day-six of illness. A subsample of individuals (N=103) participated in a sub-study using a novel smartphone application, iEpi, which collected sensor and contextually-dependent survey data on social interactions. Within the social network, participants were significantly positively assortative by intervention group, enrollment type, residence hall, iEpi participation, age, gender, race, and alcohol use (all Pisolation from social networks in a university setting. These data provide an unparalleled opportunity to address questions about isolation and infection transmission, as well as insights into social networks and behaviors among college-aged students. Several important lessons were learned over the course of this project, including feasible isolation durations, the need for extensive organizational efforts, as well as the need for specialized programmers and server

Environmental considerations in the selection of isolation gowns: A life cycle assessment of reusable and disposable alternatives.

Science.gov (United States)

Vozzola, Eric; Overcash, Michael; Griffing, Evan

2018-04-11

Isolation gowns serve a critical role in infection control by protecting healthcare workers, visitors, and patients from the transfer of microorganisms and body fluids. The decision of whether to use a reusable or disposable garment system is a selection process based on factors including sustainability, barrier effectiveness, cost, and comfort. Environmental sustainability is increasingly being used in the decision-making process. Life cycle assessment is the most comprehensive and widely used tool used to evaluate environmental performance. The environmental impacts of market-representative reusable and disposable isolation gown systems were compared using standard life cycle assessment procedures. The basis of comparison was 1,000 isolation gown uses in a healthcare setting. The scope included the manufacture, use, and end-of-life stages of the gown systems. At the healthcare facility, compared to the disposable gown system, the reusable gown system showed a 28% reduction in energy consumption, a 30% reduction in greenhouse gas emissions, a 41% reduction in blue water consumption, and a 93% reduction in solid waste generation. Selecting reusable garment systems may result in significant environmental benefits compared to selecting disposable garment systems. By selecting reusable isolation gowns, healthcare facilities can add these quantitative benefits directly to their sustainability scorecards. Copyright © 2018 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Differential privacy-based evaporative cooling feature selection and classification with relief-F and random forests.

Science.gov (United States)

Le, Trang T; Simmons, W Kyle; Misaki, Masaya; Bodurka, Jerzy; White, Bill C; Savitz, Jonathan; McKinney, Brett A

2017-09-15

Classification of individuals into disease or clinical categories from high-dimensional biological data with low prediction error is an important challenge of statistical learning in bioinformatics. Feature selection can improve classification accuracy but must be incorporated carefully into cross-validation to avoid overfitting. Recently, feature selection methods based on differential privacy, such as differentially private random forests and reusable holdout sets, have been proposed. However, for domains such as bioinformatics, where the number of features is much larger than the number of observations p≫n , these differential privacy methods are susceptible to overfitting. We introduce private Evaporative Cooling, a stochastic privacy-preserving machine learning algorithm that uses Relief-F for feature selection and random forest for privacy preserving classification that also prevents overfitting. We relate the privacy-preserving threshold mechanism to a thermodynamic Maxwell-Boltzmann distribution, where the temperature represents the privacy threshold. We use the thermal statistical physics concept of Evaporative Cooling of atomic gases to perform backward stepwise privacy-preserving feature selection. On simulated data with main effects and statistical interactions, we compare accuracies on holdout and validation sets for three privacy-preserving methods: the reusable holdout, reusable holdout with random forest, and private Evaporative Cooling, which uses Relief-F feature selection and random forest classification. In simulations where interactions exist between attributes, private Evaporative Cooling provides higher classification accuracy without overfitting based on an independent validation set. In simulations without interactions, thresholdout with random forest and private Evaporative Cooling give comparable accuracies. We also apply these privacy methods to human brain resting-state fMRI data from a study of major depressive disorder. Code

In vitro selection and characterization of putative probiotics isolated from the gut of Acipenser baerii (Brandt, 1869)

NARCIS (Netherlands)

Geraylou, Z.; Vanhove, M.P.M.; Souffreau, C.; Rurangwa, E.; Buyse, J.; Ollevier, F.

2014-01-01

To select and characterize potential probiotic bacteria from the gut microbiota of Siberian sturgeon (Acipenser baerii), 129 strains isolated from the hindgut were screened for antagonistic activity against five fish pathogens. Ten isolates showed antagonism towards three or more pathogens. Nine of

Impact of social isolation on behavioral health in elderly: Systematic review.

Science.gov (United States)

Choi, Hanbyul; Irwin, Michael R; Cho, Hyong Jin

2015-12-22

To examine and compare the effects of subjective and objective social isolation on behavioral health in elderly adults. A systematic search of PubMed was performed for original research articles from peer-reviewed journals examining one of the following topics: "Social isolation and sleep disturbance", "social isolation and depression", or "social isolation and fatigue in older adults". Studies were selected following the criteria established based on the aim of this review. Data were extracted from the articles by two independent reviewers. Due to the heterogeneity in study designs and outcome measures of the included studies, qualitative and narrative analyses were conducted. The set criteria were used to select a total of 16 studies for the review. Of the 16, 13 were cross-sectional studies. The characteristics of study populations were identified as follows. A total of 12 studies randomly selected subjects irrespective of pre-existing health conditions. Consequently, an unspecified number of the study subjects had chronic diseases in the studies compared. In addition, cultural and ethnic backgrounds of studies in this review were diverse, and included subjects living in North America, South America, Asia, Europe, and Oceania. Both subjective and objective types of social isolation increased behavioral symptoms, such as sleep disturbance, depressive symptoms, and fatigue in older adults. Furthermore, a few recent studies reported stronger effects of subjective social isolation than objective social isolation on sleep disturbance and depressive symptoms. Social isolation affects behavioral health in older adults. Compared to the objective social isolation, subjective social isolation contributes more significantly to sleep disturbance and depression.

Resistance of Bacteria Isolated from Otamiri River to Heavy Metals and Some Selected Antibiotics

OpenAIRE

I.C. Mgbemena; J.C. Nnokwe; L.A. Adjeroh; N.N. Onyemekara

2012-01-01

This study is aimed at determining the resistance of bacteria to heavy metals and some antibiotics. The ability of aquatic bacteria isolates from Otamiri River at Ihiagwa in Owerri North, Imo State to tolerate or resist the presence of certain selected heavy metals: Pb+, Zn2+ and Fe2+ and some antibiotics was investigated. Identification tests for the bacteria isolates from Otamiri River revealed them to belong to the genera Pseudomonas, Aeromonas, Bacillus, Escherichia, Micrococcus and Prote...

Selection and characterization of Argentine isolates of Trichoderma harzianum for effective biocontrol of Septoria leaf blotch of wheat.

Science.gov (United States)

Stocco, Marina C; Mónaco, Cecilia I; Abramoff, Cecilia; Lampugnani, Gladys; Salerno, Graciela; Kripelz, Natalia; Cordo, Cristina A; Consolo, Verónica F

2016-03-01

Species of the genus Trichoderma are economically important as biocontrol agents, serving as a potential alternative to chemical control. The applicability of Trichoderma isolates to different ecozones will depend on the behavior of the strains selected from each zone. The present study was undertaken to isolate biocontrol populations of Trichoderma spp. from the Argentine wheat regions and to select and characterize the best strains of Trichoderma harzianum by means of molecular techniques. A total of 84 out of the 240 strains of Trichoderma were able to reduce the disease severity of the leaf blotch of wheat. Thirty-seven strains were selected for the reduction equal to or greater than 50% of the severity, compared with the control. The percentage values of reduction of the pycnidial coverage ranged between 45 and 80%. The same last strains were confirmed as T. harzianum by polymerase chain reaction amplification of internal transcribed spacers, followed by sequencing. Inter-simple sequence repeat was used to examine the genetic variability among isolates. This resulted in a total of 132 bands. Further numerical analysis revealed 19 haplotypes, grouped in three clusters (I, II, III). Shared strains, with different geographical origins and isolated in different years, were observed within each cluster. The origin of the isolates and the genetic group were partially related. All isolates from Paraná were in cluster I, all isolates from Lobería were in cluster II, and all isolates from Pergamino and Santa Fe were in cluster III. Our results suggest that the 37 native strains of T. harzianum are important in biocontrol programs and could be advantageous for the preparation of biopesticides adapted to the agroecological conditions of wheat culture.

Pulmonary vein isolation using a second-generation cryoballoon catheter: a randomized comparison of ablation duration and method of deflation.

Science.gov (United States)

Andrade, Jason G; Dubuc, Marc; Guerra, Peter G; Landry, Evelyn; Coulombe, Nicolas; Leduc, Hugues; Rivard, Léna; Macle, Laurent; Thibault, Bernard; Talajic, Mario; Roy, Denis; Khairy, Paul

2013-06-01

Optimal cryoballoon ablation parameters for pulmonary vein (PV) isolation remain to be defined. We conducted a randomized preclinical trial to compare 2- versus 4-minute ablation lesions and assess the safety of active (forced) cryoballoon deflation. Thirty-two dogs underwent PV isolation with a second-generation 23 mm cryoballoon catheter. The left superior (LSPV) and inferior (LIPV) PVs were randomized in a factorial design to (1) a single 2- versus 4-minute cryoapplication, and (2) passive versus active cryoballoon deflation. Animals were survived for 30 days, after which histopathologic analysis was performed. Acute PV isolation was attained in 89.8% of PVs after a single application (93.8% LSPV, 85.2% LIPV; P = 0.2823). Mean time to PV isolation was 29.5 ± 18.5 seconds. Although 4-minute lesions were associated with a thicker neointima than 2-minute lesions (223.8 μm versus 135.6 μm; P = 0.007), no differences were observed in procedural characteristics (freezing temperature, rewarming time), rates of acute PV isolation, or the achievement of complete circumferentially transmural lesions at 30 days (78.7% overall; 86.2% for 2 minutes vs 70.0% for 4 minutes; P = 0.285). Active deflation was associated with faster balloon rewarming but not with significant differences in mean or maximum neointimal thickness. A single application with the second-generation cryoballoon catheter results in a high rate of PV isolation. The degree of vascular injury was not increased by active balloon deflation and no differences in acute efficacy or mature transmural circumferential lesions were observed with 2- versus 4-minute applications. © 2013 Wiley Periodicals, Inc.

Interference-aware random beam selection schemes for spectrum sharing systems

KAUST Repository

Abdallah, Mohamed

2012-10-19

Spectrum sharing systems have been recently introduced to alleviate the problem of spectrum scarcity by allowing secondary unlicensed networks to share the spectrum with primary licensed networks under acceptable interference levels to the primary users. In this work, we develop interference-aware random beam selection schemes that provide enhanced performance for the secondary network under the condition that the interference observed by the receivers of the primary network is below a predetermined/acceptable value. We consider a secondary link composed of a transmitter equipped with multiple antennas and a single-antenna receiver sharing the same spectrum with a primary link composed of a single-antenna transmitter and a single-antenna receiver. The proposed schemes select a beam, among a set of power-optimized random beams, that maximizes the signal-to-interference-plus-noise ratio (SINR) of the secondary link while satisfying the primary interference constraint for different levels of feedback information describing the interference level at the primary receiver. For the proposed schemes, we develop a statistical analysis for the SINR statistics as well as the capacity and bit error rate (BER) of the secondary link.

Partial Sequencing of 16S rRNA Gene of Selected Staphylococcus aureus Isolates and its Antibiotic Resistance

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Harsi Dewantari Kusumaningrum

2016-08-01

Full Text Available The choice of primer used in 16S rRNA sequencing for identification of Staphylococcus species found in food is important. This study aimed to characterize Staphylococcus aureus isolates by partial sequencing based on 16S rRNA gene employing primers 16sF, 63F or 1387R. The isolates were isolated from milk, egg dishes and chicken dishes and selected based on the presence of sea gene that responsible for formation of enterotoxin-A. Antibiotic susceptibility of the isolates towards six antibiotics was also tested. The use of 16sF resulted generally in higher identity percentage and query coverage compared to the sequencing by 63F or 1387R. BLAST results of all isolates, sequenced by 16sF, showed 99% homology to complete genome of four S. aureus strains, with different characteristics on enterotoxin production and antibiotic resistance. Considering that all isolates were carrying sea gene, indicated by the occurence of 120 bp amplicon after PCR amplification using primer SEA1/SEA2,  the isolates were most in agreeing to S. aureus subsp. aureus ST288. This study indicated that 4 out of 8 selected isolates were resistant towards streptomycin. The 16S rRNA gene sequencing using 16sF is useful for identification of S. aureus. However, additional analysis such as PCR employing specific gene target, should give a valuable supplementary information, when specific characteristic is expected.

Topology-selective jamming of fully-connected, code-division random-access networks

Science.gov (United States)

Polydoros, Andreas; Cheng, Unjeng

1990-01-01

The purpose is to introduce certain models of topology selective stochastic jamming and examine its impact on a class of fully-connected, spread-spectrum, slotted ALOHA-type random access networks. The theory covers dedicated as well as half-duplex units. The dominant role of the spatial duty factor is established, and connections with the dual concept of time selective jamming are discussed. The optimal choices of coding rate and link access parameters (from the users' side) and the jamming spatial fraction are numerically established for DS and FH spreading.

Sexual selection, sexual isolation and pheromones in Drosophila melanogaster strains after long-term maintaining on different diets.

Science.gov (United States)

Trajković, Jelena; Miličić, Dragana; Savić, Tatjana; Pavković-Lučić, Sofija

2017-07-01

Evolution of reproductive isolation may be a consequence of a variety of signals used in courtship and mate preferences. Pheromones play an important role in both sexual selection and sexual isolation. The abundance of pheromones in Drosophila melanogaster may depend on different environmental factors, including diet. The aim of this study was to ascertain to which degree principal pheromones affect sexual selection in D. melanogaster. We used D. melanogaster strains reared for 14 years on four substrates: standard cornmeal substrate and those containing tomato, banana and carrot. We have previously determined that long-term maintaining of these dietary strains resulted in differences in their cuticular hydrocarbons profile (CHs). In this work, we have tested the level of sexual selection and sexual isolation between aforementioned strains. We found that the high levels of cis-vaccenyl acetate, 7-pentacosene and 7,11-nonacosadiene in the strain reared on a substrate containing carrot affected the individual attractiveness and influenced sexual isolation between flies of this strain and flies reared on a substrate containing banana. Based on these results, long-term different diets, may contribute, to sexual behaviour of D. melanogaster via the effects of principal pheromones. Copyright © 2017 Elsevier B.V. All rights reserved.

Peculiarities of the statistics of spectrally selected fluorescence radiation in laser-pumped dye-doped random media

Science.gov (United States)

Yuvchenko, S. A.; Ushakova, E. V.; Pavlova, M. V.; Alonova, M. V.; Zimnyakov, D. A.

2018-04-01

We consider the practical realization of a new optical probe method of the random media which is defined as the reference-free path length interferometry with the intensity moments analysis. A peculiarity in the statistics of the spectrally selected fluorescence radiation in laser-pumped dye-doped random medium is discussed. Previously established correlations between the second- and the third-order moments of the intensity fluctuations in the random interference patterns, the coherence function of the probe radiation, and the path difference probability density for the interfering partial waves in the medium are confirmed. The correlations were verified using the statistical analysis of the spectrally selected fluorescence radiation emitted by a laser-pumped dye-doped random medium. Water solution of Rhodamine 6G was applied as the doping fluorescent agent for the ensembles of the densely packed silica grains, which were pumped by the 532 nm radiation of a solid state laser. The spectrum of the mean path length for a random medium was reconstructed.

Selective cultures for the isolation of biosurfactant producing bacteria: comparison of different combinations of environmental inocula and hydrophobic carbon sources.

Science.gov (United States)

Domingues, Patrícia M; Louvado, António; Oliveira, Vanessa; Coelho, Francisco J C R; Almeida, Adelaide; Gomes, Newton C M; Cunha, Angela

2013-01-01

The potential of estuarine microniches as reservoirs of biosurfactant-producing bacteria was evaluated by testing different combinations of inocula and hydrophobic carbon sources. Selective cultures using diesel, petroleum, or paraffin as hydrophobic carbon sources were prepared and inoculated with water from the surface microlayer, bulk sediments, and sediment of the rhizosphere of Halimione portulacoides. These inocula were compared regarding the frequency of biosurfactant-producing strains among selected isolates. The community structure of the selective cultures was profiled using denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene fragments at the end of the incubation. The DGGE profiles corresponding to the communities established in selective cultures at the end of the incubation revealed that communities were different in terms of structural diversity. The highest diversity was observed in the selective cultures containing paraffin (H (') = 2.5). Isolates were obtained from the selective cultures (66) and tested for biosurfactant production by the atomized oil assay. Biosurfactant production was detected in 17 isolates identified as Microbacterium, Pseudomonas, Rhodococcus, and Serratia. The combination of estuarine surface microlayer (SML) water as inoculum and diesel as carbon source seems promising for the isolation of surfactant-producing bacteria. Supplemental materials are available for this article. Go to the publisher's online edition of Preparative Biochemistry and Biotechnology to view the supplemental file.

The use of naturally occurring selectively isolated bacteria for inhibiting paraffin deposition

International Nuclear Information System (INIS)

Lazar, I.; Voicu, A.; Dobrota, S.; Petrisor, I.G.; Stefanescu, M.; Sandulescu, L.; Nicolescu, C.; Mucenica, D.

1999-01-01

One of the most severe problems at any oil fields producing paraffinic oils is that of paraffin depositions. Romania which has a long experience in oil production is also faced with this problem in many oil fields. The microbial treatment, based on the activity of naturally occurring, selectively isolated bacteria, is already proved as an effective alternative to conventional methods to prevent and remove paraffin damage. Using such kind of bacterial products, exciting results for inhibiting paraffin depositions have been obtained. In this paper results concerning the naturally occurring bacteria selectively isolated from hydrocarbon polluted sites as well as from paraffinic oils, semi-solid and solid paraffin depositions are presented. After a laboratory screening, 15 bacterial strains (BS 1-15), three bacterial consortia (BC 1-3) and a Special Bacterial Consortium (SBC1) were selected. For the selection of bacterial consortia, the classical enrichment culture method has been used. The Special Bacterial Consortium resulted from a mixture of BS 1-15 and BC 1-3 following the steps of the classical enrichment culture method. The BS 1-15, BC 1-3 and SBC1 have been tested for their performances in producing biosurfactants and biosolvents as well as for hydrocarbon utilisation. The SBC1 has been tested for its ability in degradation of hydrocarbons contained in several types of paraffinic or non-paraffinic oils, and then for inhibiting paraffin deposition on a 'flow equipment' using two types of paraffinic oils. The SBC1 has been also tested for degradation of hydrocarbons contained in semi-solid and solid paraffin depositions. The results obtained could support further applications to prevent and control paraffin depositions

The use of naturally occurring selectively isolated bacteria for inhibiting paraffin deposition

Energy Technology Data Exchange (ETDEWEB)

Lazar, I.; Voicu, A.; Dobrota, S.; Petrisor, I.G.; Stefanescu, M.; Sandulescu, L. [Institute of Biology of the Romanian Academy, Spl. Independentei 296, Bucharest (Romania); Nicolescu, C.; Mucenica, D. [PETROSTAR Ploiesti, Bdul Bucuresti 35, Ploiesti (Romania)

1999-01-01

One of the most severe problems at any oil fields producing paraffinic oils is that of paraffin depositions. Romania which has a long experience in oil production is also faced with this problem in many oil fields. The microbial treatment, based on the activity of naturally occurring, selectively isolated bacteria, is already proved as an effective alternative to conventional methods to prevent and remove paraffin damage. Using such kind of bacterial products, exciting results for inhibiting paraffin depositions have been obtained. In this paper results concerning the naturally occurring bacteria selectively isolated from hydrocarbon polluted sites as well as from paraffinic oils, semi-solid and solid paraffin depositions are presented. After a laboratory screening, 15 bacterial strains (BS 1-15), three bacterial consortia (BC 1-3) and a Special Bacterial Consortium (SBC1) were selected. For the selection of bacterial consortia, the classical enrichment culture method has been used. The Special Bacterial Consortium resulted from a mixture of BS 1-15 and BC 1-3 following the steps of the classical enrichment culture method. The BS 1-15, BC 1-3 and SBC1 have been tested for their performances in producing biosurfactants and biosolvents as well as for hydrocarbon utilisation. The SBC1 has been tested for its ability in degradation of hydrocarbons contained in several types of paraffinic or non-paraffinic oils, and then for inhibiting paraffin deposition on a `flow equipment` using two types of paraffinic oils. The SBC1 has been also tested for degradation of hydrocarbons contained in semi-solid and solid paraffin depositions. The results obtained could support further applications to prevent and control paraffin depositions

Isolating E.Coli Bacteriophage from Raw Sewage and Determining its Selectivity to the Host Cell

Directory of Open Access Journals (Sweden)

SM Imeni

2016-05-01

Full Text Available Introduction: Bacteriophages are viruses that infect and destroy prokaryote cells, specifically the bacteria. They act too selective, so as each bacteriophage affects only on specific type of bacteria. Due to their specific features, bacteriophages can be used as an appropriate substitute for antibiotics in infectious diseases treatment. Therefore, this study aimed to isolate E. coli-specific bacteriophage from raw sewage. Methods: Eight samples of raw sewage, each containing approximately 50 ml of raw sewage with 10 minute gap, were prepared from Zargandeh wastewater treatment plant, Tehran, Iran. The sewages were mixed with Brain-heart infusion medium (BHI as a liquid culture medium in order to let the microorganisms grow. Incubation, purification and determination of bacteria were followed repeatedly to isolate the bacteriophage. Then it was tested on E.coli (ATCC 25922, Enterococcus faecalis (ATCC 19433, Staphylococcus aureus (ATCC 2392, and Yersinia enterocolitica (ATCC 9610 in order to determine the bacteriophage selectivity. Results: The E.coli bacteriophages were successfully isolated from all the eight samples, that were completely able to lyse and destroy E.coli bacterial cells, though no effect was observed on other types of bacteria. Conclusion: The study findings revealed that bacteriophages act selectively. Considering the raise of antibiotic resistance in the world, bacteriophages can serve as a good substitute for antibiotics in treating infectious diseases.

High-Tg Polynorbornene-Based Block and Random Copolymers for Butanol Pervaporation Membranes

Science.gov (United States)

Register, Richard A.; Kim, Dong-Gyun; Takigawa, Tamami; Kashino, Tomomasa; Burtovyy, Oleksandr; Bell, Andrew

Vinyl addition polymers of substituted norbornene (NB) monomers possess desirably high glass transition temperatures (Tg); however, until very recently, the lack of an applicable living polymerization chemistry has precluded the synthesis of such polymers with controlled architecture, or copolymers with controlled sequence distribution. We have recently synthesized block and random copolymers of NB monomers bearing hydroxyhexafluoroisopropyl and n-butyl substituents (HFANB and BuNB) via living vinyl addition polymerization with Pd-based catalysts. Both series of polymers were cast into the selective skin layers of thin film composite (TFC) membranes, and these organophilic membranes investigated for the isolation of n-butanol from dilute aqueous solution (model fermentation broth) via pervaporation. The block copolymers show well-defined microphase-separated morphologies, both in bulk and as the selective skin layers on TFC membranes, while the random copolymers are homogeneous. Both block and random vinyl addition copolymers are effective as n-butanol pervaporation membranes, with the block copolymers showing a better flux-selectivity balance. While polyHFANB has much higher permeability and n-butanol selectivity than polyBuNB, incorporating BuNB units into the polymer (in either a block or random sequence) limits the swelling of the polyHFANB and thereby improves the n-butanol pervaporation selectivity.

Isolation, selection and characterization of root-associated growth promoting bacteria in Brazil Pine (Araucaria angustifolia).

Science.gov (United States)

Ribeiro, Carlos Marcelo; Cardoso, Elke Jurandy Bran Nogueira

2012-01-20

Araucaria angustifolia, a unique species of this genus that occurs naturally in Brazil, has a high socio-economic and environmental value and is critically endangered of extinction, since it has been submitted to intense predatory exploitation during the last century. Root-associated bacteria from A. angustifolia were isolated, selected and characterized for their biotechnological potential of growth promotion and biocontrol of plant pathogenic fungi. Ninety-seven strains were isolated and subjected to chemical tests. All isolates presented at least one positive feature, characterizing them as potential PGPR. Eighteen isolates produced indole-3-acetic acid (IAA), 27 were able to solubilize inorganic phosphate, 21 isolates were presumable diazotrophs, with pellicle formation in nitrogen-free culture medium, 83 were phosphatases producers, 37 were positive for siderophores and 45 endospore-forming isolates were antagonistic to Fusarium oxysporum, a pathogen of conifers. We also observed the presence of bacterial strains with multiple beneficial mechanisms of action. Analyzing the fatty acid methyl ester (FAME) and partial sequencing of the 16S rRNA gene of these isolates, it was possible to characterize the most effective isolates as belonging to Bacillaceae (9 isolates), Enterobacteriaceae (11) and Pseudomonadaceae (1). As far as we know, this is the first study to include the species Ewingella americana as a PGPR. Copyright © 2011 Elsevier GmbH. All rights reserved.

Selection of Leuconostoc strains isolated from artisanal Serrano Catarinense cheese for use as adjuncts in cheese manufacture.

Science.gov (United States)

Seixas, Felipe Nael; Rios, Edson Antônio; Martinez de Oliveira, André Luiz; Beloti, Vanerli; Poveda, Justa Maria

2018-08-01

Serrano Catarinense cheese is a raw bovine milk cheese produced in the region of Santa Catarina, Brazil. Twelve representative strains of Leuconostoc isolated from 20 samples of this artisanal cheese were selected and submitted for evaluation of the acidifying, proteolytic, autolytic, aminopeptidase and lipolytic activities, NaCl and acid resistance, production of dextran and biogenic amines and antimicrobial activity. The aim was to genetically and technologically characterize the Leuconostoc strains in order to use them in mixed starter cultures for cheese manufacture. Leuconostoc mesenteroides subsp. mesenteroides was the species that accounted for the largest proportion of isolates of Leuconostoc genus. Two leuconostoc isolates stood out in the acidifying activity, with reduction in pH of 1.12 and 1.04 units. The isolates showed low proteolytic and autolytic activity. Most of the isolates were dextran producers, presented good resistance to the salt and pH conditions of the cheese and showed antimicrobial activity against cheese pathogen bacteria, and none of them produced biogenic amines. These results allowed the selection of five strains (UEL 04, UEL 12, UEL 18, UEL 21 and UEL 28) as good candidates for use as adjunct cultures for cheese manufacture. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

Blind Measurement Selection: A Random Matrix Theory Approach

KAUST Repository

Elkhalil, Khalil

2016-12-14

This paper considers the problem of selecting a set of $k$ measurements from $n$ available sensor observations. The selected measurements should minimize a certain error function assessing the error in estimating a certain $m$ dimensional parameter vector. The exhaustive search inspecting each of the $n\\\\choose k$ possible choices would require a very high computational complexity and as such is not practical for large $n$ and $k$. Alternative methods with low complexity have recently been investigated but their main drawbacks are that 1) they require perfect knowledge of the measurement matrix and 2) they need to be applied at the pace of change of the measurement matrix. To overcome these issues, we consider the asymptotic regime in which $k$, $n$ and $m$ grow large at the same pace. Tools from random matrix theory are then used to approximate in closed-form the most important error measures that are commonly used. The asymptotic approximations are then leveraged to select properly $k$ measurements exhibiting low values for the asymptotic error measures. Two heuristic algorithms are proposed: the first one merely consists in applying the convex optimization artifice to the asymptotic error measure. The second algorithm is a low-complexity greedy algorithm that attempts to look for a sufficiently good solution for the original minimization problem. The greedy algorithm can be applied to both the exact and the asymptotic error measures and can be thus implemented in blind and channel-aware fashions. We present two potential applications where the proposed algorithms can be used, namely antenna selection for uplink transmissions in large scale multi-user systems and sensor selection for wireless sensor networks. Numerical results are also presented and sustain the efficiency of the proposed blind methods in reaching the performances of channel-aware algorithms.

Isolation, Characterization, and Selection of Molds Associated to Fermented Black Table Olives

Directory of Open Access Journals (Sweden)

Simona L. Bavaro

2017-07-01

Full Text Available Table olives are one of the most important fermented food in the Mediterranean countries. Apart from lactic acid bacteria and yeasts that mainly conduct the olive fermentation, molds can develop on the brine surface, and can have either deleterious or useful effects on this process. From the food safety point of view, occurring molds could also produce mycotoxins, so, it is important to monitor and control them. In this respect, identification of molds associated to two Italian and two Greek fermented black table olives cultivars, was carried out. Sixty strains were isolated and molecularly identified as Penicillium crustosum (21, P. roqueforti (29, P. paneum (1, P. expansum (6, P. polonicum (2, P. commune (1. A group of 20 selected isolates was subjected to technological (beta-glucosidase, cellulolytic, ligninolytic, pectolytic, and xylanolytic activities; proteolytic enzymes and safety (biogenic amines and secondary metabolites, including mycotoxins characterization. Combining both technological (presence of desired and absence of undesired enzymatic activities and safety aspects (no or low production of biogenic amines and regulated mycotoxins, it was possible to select six strains with biotechnological interest. These are putative candidates for future studies as autochthonous co-starters with yeasts and lactic acid bacteria for black table olive production.

Contributions of natural and sexual selection to the evolution of premating reproductive isolation: a research agenda.

Science.gov (United States)

Safran, Rebecca J; Scordato, Elizabeth S C; Symes, Laurel B; Rodríguez, Rafael L; Mendelson, Tamra C

2013-11-01

Speciation by divergent natural selection is well supported. However, the role of sexual selection in speciation is less well understood due to disagreement about whether sexual selection is a mechanism of evolution separate from natural selection, as well as confusion about various models and tests of sexual selection. Here, we outline how sexual selection and natural selection are different mechanisms of evolutionary change, and suggest that this distinction is critical when analyzing the role of sexual selection in speciation. Furthermore, we clarify models of sexual selection with respect to their interaction with ecology and natural selection. In doing so, we outline a research agenda for testing hypotheses about the relative significance of divergent sexual and natural selection in the evolution of reproductive isolation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Evaluation of a commercial microarray as a confirmation test for the presence of extended-spectrum beta-lactamases in isolates from the routine clinical setting.

NARCIS (Netherlands)

Platteel, T.N.; Stuart, J.W.; Voets, G.M.; Scharringa, J.; Sande, N. van de; Fluit, A.C.; Leverstein-van Hall, M.A.; Sturm, P.D.J.; et al.,

2011-01-01

Since the diagnostic characteristics of the Check-KPC ESBL microarray as a confirmation test on isolates obtained in a routine clinical setting have not been determined, we evaluated the microarray in a random selection of 346 clinical isolates with a positive ESBL screen test (MIC >1 mg/L for

Isolation of two independent allyl alcohol resistant Adh-1 null mutants following selection of pollen and seeds.

NARCIS (Netherlands)

Wisman, E.; Ramanna, M.S.; Zabel, P.

1993-01-01

The Adh-1 null mutant (B15-1-8) isolated previously was used to establish conditions that allow the selection of ADH-deficient pollen grains and seeds of tomato. New Adh-1 null mutants were then selected among the progenies derived from crosses between the genetically unstable tomato lines Yvms,

Using ArcMap, Google Earth, and Global Positioning Systems to select and locate random households in rural Haiti.

Science.gov (United States)

Wampler, Peter J; Rediske, Richard R; Molla, Azizur R

2013-01-18

A remote sensing technique was developed which combines a Geographic Information System (GIS); Google Earth, and Microsoft Excel to identify home locations for a random sample of households in rural Haiti. The method was used to select homes for ethnographic and water quality research in a region of rural Haiti located within 9 km of a local hospital and source of health education in Deschapelles, Haiti. The technique does not require access to governmental records or ground based surveys to collect household location data and can be performed in a rapid, cost-effective manner. The random selection of households and the location of these households during field surveys were accomplished using GIS, Google Earth, Microsoft Excel, and handheld Garmin GPSmap 76CSx GPS units. Homes were identified and mapped in Google Earth, exported to ArcMap 10.0, and a random list of homes was generated using Microsoft Excel which was then loaded onto handheld GPS units for field location. The development and use of a remote sensing method was essential to the selection and location of random households. A total of 537 homes initially were mapped and a randomized subset of 96 was identified as potential survey locations. Over 96% of the homes mapped using Google Earth imagery were correctly identified as occupied dwellings. Only 3.6% of the occupants of mapped homes visited declined to be interviewed. 16.4% of the homes visited were not occupied at the time of the visit due to work away from the home or market days. A total of 55 households were located using this method during the 10 days of fieldwork in May and June of 2012. The method used to generate and field locate random homes for surveys and water sampling was an effective means of selecting random households in a rural environment lacking geolocation infrastructure. The success rate for locating households using a handheld GPS was excellent and only rarely was local knowledge required to identify and locate households. This

Using ArcMap, Google Earth, and Global Positioning Systems to select and locate random households in rural Haiti

Directory of Open Access Journals (Sweden)

Wampler Peter J

2013-01-01

Full Text Available Abstract Background A remote sensing technique was developed which combines a Geographic Information System (GIS; Google Earth, and Microsoft Excel to identify home locations for a random sample of households in rural Haiti. The method was used to select homes for ethnographic and water quality research in a region of rural Haiti located within 9 km of a local hospital and source of health education in Deschapelles, Haiti. The technique does not require access to governmental records or ground based surveys to collect household location data and can be performed in a rapid, cost-effective manner. Methods The random selection of households and the location of these households during field surveys were accomplished using GIS, Google Earth, Microsoft Excel, and handheld Garmin GPSmap 76CSx GPS units. Homes were identified and mapped in Google Earth, exported to ArcMap 10.0, and a random list of homes was generated using Microsoft Excel which was then loaded onto handheld GPS units for field location. The development and use of a remote sensing method was essential to the selection and location of random households. Results A total of 537 homes initially were mapped and a randomized subset of 96 was identified as potential survey locations. Over 96% of the homes mapped using Google Earth imagery were correctly identified as occupied dwellings. Only 3.6% of the occupants of mapped homes visited declined to be interviewed. 16.4% of the homes visited were not occupied at the time of the visit due to work away from the home or market days. A total of 55 households were located using this method during the 10 days of fieldwork in May and June of 2012. Conclusions The method used to generate and field locate random homes for surveys and water sampling was an effective means of selecting random households in a rural environment lacking geolocation infrastructure. The success rate for locating households using a handheld GPS was excellent and only

Optimizing Event Selection with the Random Grid Search

Energy Technology Data Exchange (ETDEWEB)

Bhat, Pushpalatha C. [Fermilab; Prosper, Harrison B. [Florida State U.; Sekmen, Sezen [Kyungpook Natl. U.; Stewart, Chip [Broad Inst., Cambridge

2017-06-29

The random grid search (RGS) is a simple, but efficient, stochastic algorithm to find optimal cuts that was developed in the context of the search for the top quark at Fermilab in the mid-1990s. The algorithm, and associated code, have been enhanced recently with the introduction of two new cut types, one of which has been successfully used in searches for supersymmetry at the Large Hadron Collider. The RGS optimization algorithm is described along with the recent developments, which are illustrated with two examples from particle physics. One explores the optimization of the selection of vector boson fusion events in the four-lepton decay mode of the Higgs boson and the other optimizes SUSY searches using boosted objects and the razor variables.

Non-random mating for selection with restricted rates of inbreeding and overlapping generations

NARCIS (Netherlands)

Sonesson, A.K.; Meuwissen, T.H.E.

2002-01-01

Minimum coancestry mating with a maximum of one offspring per mating pair (MC1) is compared with random mating schemes for populations with overlapping generations. Optimum contribution selection is used, whereby $\\\\\\\\Delta F$ is restricted. For schemes with $\\\\\\\\Delta F$ restricted to 0.25% per

Selection of antagonistic bacteria isolated from the Physalis peruviana rhizosphere against Fusarium oxysporum.

Science.gov (United States)

Urrea, R; Cabezas, L; Sierra, R; Cárdenas, M; Restrepo, S; Jiménez, P

2011-09-01

Cape gooseberries (Physalis peruviana) have become increasingly important in Colombia for both domestic consumption and the international export market. Vascular wilting caused by Fusarium oxysporum is the most damaging disease to P. peruviana crops in Colombia. The control of this pathogen is mainly carried out by chemical and cultural practices, increasing production costs and generating resistance. Therefore, the objectives of this study were to test rhizobacteria isolates from P. peruviana rhizosphere against F. oxysporum under in vitro and in vivo conditions. Over 120 strains were isolated, and five were selected for their high inhibition of F. oxysporum growth and conidia production under in vitro conditions. These strains inhibited growth by 41-58% and reduced three- to fivefold conidia production. In the in vivo assays, all the tested isolates significantly reduced fungal pathogenicity in terms of virulence. Isolate B-3.4 was the most efficient in delaying the onset of the first symptoms. All isolates were identified as belonging to the genus Pseudomonas except for A-19 (Bacillus sp.). Our results confirmed that there are prospective rhizobacteria strains that can be used as biological control agents; some of them being able to inhibit in vitro F. oxysporum growth and sporulation. Incorporating these bacteria into biological control strategies for the disease that causes high economical losses in the second most exported fruit from Colombia would result in a reduced impact on environment and economy. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

Comparative Evaluations of Randomly Selected Four Point-of-Care Glucometer Devices in Addis Ababa, Ethiopia.

Science.gov (United States)

Wolde, Mistire; Tarekegn, Getahun; Kebede, Tedla

2018-05-01

Point-of-care glucometer (PoCG) devices play a significant role in self-monitoring of the blood sugar level, particularly in the follow-up of high blood sugar therapeutic response. The aim of this study was to evaluate blood glucose test results performed with four randomly selected glucometers on diabetes and control subjects versus standard wet chemistry (hexokinase) methods in Addis Ababa, Ethiopia. A prospective cross-sectional study was conducted on randomly selected 200 study participants (100 participants with diabetes and 100 healthy controls). Four randomly selected PoCG devices (CareSens N, DIAVUE Prudential, On Call Extra, i-QARE DS-W) were evaluated against hexokinase method and ISO 15197:2003 and ISO 15197:2013 standards. The minimum and maximum blood sugar values were recorded by CareSens N (21 mg/dl) and hexokinase method (498.8 mg/dl), respectively. The mean sugar values of all PoCG devices except On Call Extra showed significant differences compared with the reference hexokinase method. Meanwhile, all four PoCG devices had strong positive relationship (>80%) with the reference method (hexokinase). On the other hand, none of the four PoCG devices fulfilled the minimum accuracy measurement set by ISO 15197:2003 and ISO 15197:2013 standards. In addition, the linear regression analysis revealed that all four selected PoCG overestimated the glucose concentrations. The overall evaluation of the selected four PoCG measurements were poorly correlated with standard reference method. Therefore, before introducing PoCG devices to the market, there should be a standardized evaluation platform for validation. Further similar large-scale studies on other PoCG devices also need to be undertaken.

Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms

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Ramoni Marco F

2007-03-01

Full Text Available Abstract Background Recent studies have shown that when individuals are grouped on the basis of genetic similarity, group membership corresponds closely to continental origin. There has been considerable debate about the implications of these findings in the context of larger debates about race and the extent of genetic variation between groups. Some have argued that clustering according to continental origin demonstrates the existence of significant genetic differences between groups and that these differences may have important implications for differences in health and disease. Others argue that clustering according to continental origin requires the use of large amounts of genetic data or specifically chosen markers and is indicative only of very subtle genetic differences that are unlikely to have biomedical significance. Results We used small numbers of randomly selected single nucleotide polymorphisms (SNPs from the International HapMap Project to train naïve Bayes classifiers for prediction of ancestral continent of origin. Predictive accuracy was tested on two independent data sets. Genetically similar groups should be difficult to distinguish, especially if only a small number of genetic markers are used. The genetic differences between continentally defined groups are sufficiently large that one can accurately predict ancestral continent of origin using only a minute, randomly selected fraction of the genetic variation present in the human genome. Genotype data from only 50 random SNPs was sufficient to predict ancestral continent of origin in our primary test data set with an average accuracy of 95%. Genetic variations informative about ancestry were common and widely distributed throughout the genome. Conclusion Accurate characterization of ancestry is possible using small numbers of randomly selected SNPs. The results presented here show how investigators conducting genetic association studies can use small numbers of arbitrarily

Phylodynamic analysis of clinical and environmental Vibrio cholerae isolates from Haiti reveals diversification driven by positive selection.

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Azarian, Taj; Ali, Afsar; Johnson, Judith A; Mohr, David; Prosperi, Mattia; Veras, Nazle M; Jubair, Mohammed; Strickland, Samantha L; Rashid, Mohammad H; Alam, Meer T; Weppelmann, Thomas A; Katz, Lee S; Tarr, Cheryl L; Colwell, Rita R; Morris, J Glenn; Salemi, Marco

2014-12-23

Phylodynamic analysis of genome-wide single-nucleotide polymorphism (SNP) data is a powerful tool to investigate underlying evolutionary processes of bacterial epidemics. The method was applied to investigate a collection of 65 clinical and environmental isolates of Vibrio cholerae from Haiti collected between 2010 and 2012. Characterization of isolates recovered from environmental samples identified a total of four toxigenic V. cholerae O1 isolates, four non-O1/O139 isolates, and a novel nontoxigenic V. cholerae O1 isolate with the classical tcpA gene. Phylogenies of strains were inferred from genome-wide SNPs using coalescent-based demographic models within a Bayesian framework. A close phylogenetic relationship between clinical and environmental toxigenic V. cholerae O1 strains was observed. As cholera spread throughout Haiti between October 2010 and August 2012, the population size initially increased and then fluctuated over time. Selection analysis along internal branches of the phylogeny showed a steady accumulation of synonymous substitutions and a progressive increase of nonsynonymous substitutions over time, suggesting diversification likely was driven by positive selection. Short-term accumulation of nonsynonymous substitutions driven by selection may have significant implications for virulence, transmission dynamics, and even vaccine efficacy. Cholera, a dehydrating diarrheal disease caused by toxigenic strains of the bacterium Vibrio cholerae, emerged in 2010 in Haiti, a country where there were no available records on cholera over the past 100 years. While devastating in terms of morbidity and mortality, the outbreak provided a unique opportunity to study the evolutionary dynamics of V. cholerae and its environmental presence. The present study expands on previous work and provides an in-depth phylodynamic analysis inferred from genome-wide single nucleotide polymorphisms of clinical and environmental strains from dispersed geographic settings in

Fuzzy Random λ-Mean SAD Portfolio Selection Problem: An Ant Colony Optimization Approach

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Thakur, Gour Sundar Mitra; Bhattacharyya, Rupak; Mitra, Swapan Kumar

2010-10-01

To reach the investment goal, one has to select a combination of securities among different portfolios containing large number of securities. Only the past records of each security do not guarantee the future return. As there are many uncertain factors which directly or indirectly influence the stock market and there are also some newer stock markets which do not have enough historical data, experts' expectation and experience must be combined with the past records to generate an effective portfolio selection model. In this paper the return of security is assumed to be Fuzzy Random Variable Set (FRVS), where returns are set of random numbers which are in turn fuzzy numbers. A new λ-Mean Semi Absolute Deviation (λ-MSAD) portfolio selection model is developed. The subjective opinions of the investors to the rate of returns of each security are taken into consideration by introducing a pessimistic-optimistic parameter vector λ. λ-Mean Semi Absolute Deviation (λ-MSAD) model is preferred as it follows absolute deviation of the rate of returns of a portfolio instead of the variance as the measure of the risk. As this model can be reduced to Linear Programming Problem (LPP) it can be solved much faster than quadratic programming problems. Ant Colony Optimization (ACO) is used for solving the portfolio selection problem. ACO is a paradigm for designing meta-heuristic algorithms for combinatorial optimization problem. Data from BSE is used for illustration.

Pediatric selective mutism therapy: a randomized controlled trial.

Science.gov (United States)

Esposito, Maria; Gimigliano, Francesca; Barillari, Maria R; Precenzano, Francesco; Ruberto, Maria; Sepe, Joseph; Barillari, Umberto; Gimigliano, Raffaele; Militerni, Roberto; Messina, Giovanni; Carotenuto, Marco

2017-10-01

Selective mutism (SM) is a rare disease in children coded by DSM-5 as an anxiety disorder. Despite the disabling nature of the disease, there is still no specific treatment. The aims of this study were to verify the efficacy of six-month standard psychomotor treatment and the positive changes in lifestyle, in a population of children affected by SM. Randomized controlled trial registered in the European Clinical Trials Registry (EuDract 2015-001161-36). University third level Centre (Child and Adolescent Neuropsychiatry Clinic). Study population was composed by 67 children in group A (psychomotricity treatment) (35 M, mean age 7.84±1.15) and 71 children in group B (behavioral and educational counseling) (37 M, mean age 7.75±1.36). Psychomotor treatment was administered by trained child therapists in residential settings three times per week. Each child was treated for the whole period by the same therapist and all the therapists shared the same protocol. The standard psychomotor session length is of 45 minutes. At T0 and after 6 months (T1) of treatments, patients underwent a behavioral and SM severity assessment. To verify the effects of the psychomotor management, the Child Behavior Checklist questionnaire (CBCL) and Selective Mutism Questionnaire (SMQ) were administered to the parents. After 6 months of psychomotor treatment SM children showed a significant reduction among CBCL scores such as in social relations, anxious/depressed, social problems and total problems (Pselective mutism, even if further studies are needed. The present study identifies in psychomotricity a safe and efficacy therapy for pediatric selective mutism.

Primitive polynomials selection method for pseudo-random number generator

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Anikin, I. V.; Alnajjar, Kh

2018-01-01

In this paper we suggested the method for primitive polynomials selection of special type. This kind of polynomials can be efficiently used as a characteristic polynomials for linear feedback shift registers in pseudo-random number generators. The proposed method consists of two basic steps: finding minimum-cost irreducible polynomials of the desired degree and applying primitivity tests to get the primitive ones. Finally two primitive polynomials, which was found by the proposed method, used in pseudorandom number generator based on fuzzy logic (FRNG) which had been suggested before by the authors. The sequences generated by new version of FRNG have low correlation magnitude, high linear complexity, less power consumption, is more balanced and have better statistical properties.

Cholecalciferol treatment to reduce blood pressure in older patients with isolated systolic hypertension: the VitDISH randomized controlled trial.

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Witham, Miles D; Price, Rosemary J G; Struthers, Allan D; Donnan, Peter T; Messow, Claudia-Martina; Ford, Ian; McMurdo, Marion E T

2013-10-14

Observational data link low 25-hydroxyvitamin D levels to both prevalent blood pressure and incident hypertension. No clinical trial has yet examined the effect of vitamin D supplementation in isolated systolic hypertension, the most common pattern of hypertension in older people. To test whether high-dose, intermittent cholecalciferol supplementation lowers blood pressure in older patients with isolated systolic hypertension. Parallel group, double-blind, placebo-controlled randomized trial. Primary care clinics and hospital clinics. Patients 70 years and older with isolated systolic hypertension (supine systolic blood pressure >140 mm Hg and supine diastolic blood pressure blood pressure, 24-hour blood pressure, arterial stiffness, endothelial function, cholesterol level, insulin resistance, and b-type natriuretic peptide level during 12 months. A total of 159 participants were randomized (mean age, 77 years). Mean baseline office systolic blood pressure was 163/78 mm Hg. Mean baseline 25-hydroxyvitamin D level was 18 ng/mL. 25-Hydroxyvitamin D levels increased in the treatment group compared with the placebo group (+8 ng/mL at 1 year, P blood pressure (−1 [−6 to 4]/−2 [−4 to 1] mm Hg at 3 months and 1 [−2 to 4]/0 [−2 to 2] mm Hg overall treatment effect). No significant treatment effect was evident for any of the secondary outcomes (24-hour blood pressure, arterial stiffness, endothelial function, cholesterol level, glucose level, and walking distance). There was no excess of adverse events in the treatment group, and the total number of falls was nonsignificantly lower in the group receiving vitamin D (36 vs 46, P = .24). Vitamin D supplementation did not improve blood pressure or markers of vascular health in older patients with isolated systolic hypertension. isrctn.org Identifier: ISRCTN92186858.

Functional investigation of β-adrenoceptors in human isolated detrusor focusing on the novel selective β3-adrenoceptor agonist KUC-7322

NARCIS (Netherlands)

Igawa, Yasuhiko; Schneider, Tim; Yamazaki, Yoshinobu; Tatemichi, Satoshi; Homma, Yukio; Nishizawa, Osamu; Michel, Martin C.

2012-01-01

This study aimed to characterize the β-adrenoceptor (β-AR) subtype mediating relaxation of isolated human bladder strips and to explore relaxation by the novel β3-AR-selective agonist KUC-7322 for its relaxant effect on the human isolated detrusor and for its effect on the carbachol (CCh)-induced

Population genetic structure and natural selection of Plasmodium falciparum apical membrane antigen-1 in Myanmar isolates.

Science.gov (United States)

Kang, Jung-Mi; Lee, Jinyoung; Moe, Mya; Jun, Hojong; Lê, Hương Giang; Kim, Tae Im; Thái, Thị Lam; Sohn, Woon-Mok; Myint, Moe Kyaw; Lin, Khin; Shin, Ho-Joon; Kim, Tong-Soo; Na, Byoung-Kuk

2018-02-07

Plasmodium falciparum apical membrane antigen-1 (PfAMA-1) is one of leading blood stage malaria vaccine candidates. However, genetic variation and antigenic diversity identified in global PfAMA-1 are major hurdles in the development of an effective vaccine based on this antigen. In this study, genetic structure and the effect of natural selection of PfAMA-1 among Myanmar P. falciparum isolates were analysed. Blood samples were collected from 58 Myanmar patients with falciparum malaria. Full-length PfAMA-1 gene was amplified by polymerase chain reaction and cloned into a TA cloning vector. PfAMA-1 sequence of each isolate was sequenced. Polymorphic characteristics and effect of natural selection were analysed with using DNASTAR, MEGA4, and DnaSP programs. Polymorphic nature and natural selection in 459 global PfAMA-1 were also analysed. Thirty-seven different haplotypes of PfAMA-1 were identified in 58 Myanmar P. falciparum isolates. Most amino acid changes identified in Myanmar PfAMA-1 were found in domains I and III. Overall patterns of amino acid changes in Myanmar PfAMA-1 were similar to those in global PfAMA-1. However, frequencies of amino acid changes differed by country. Novel amino acid changes in Myanmar PfAMA-1 were also identified. Evidences for natural selection and recombination event were observed in global PfAMA-1. Among 51 commonly identified amino acid changes in global PfAMA-1 sequences, 43 were found in predicted RBC-binding sites, B-cell epitopes, or IUR regions. Myanmar PfAMA-1 showed similar patterns of nucleotide diversity and amino acid polymorphisms compared to those of global PfAMA-1. Balancing natural selection and intragenic recombination across PfAMA-1 are likely to play major roles in generating genetic diversity in global PfAMA-1. Most common amino acid changes in global PfAMA-1 were located in predicted B-cell epitopes where high levels of nucleotide diversity and balancing natural selection were found. These results highlight the

Randomizing Roaches: Exploring the "Bugs" of Randomization in Experimental Design

Science.gov (United States)

Wagler, Amy; Wagler, Ron

2014-01-01

Understanding the roles of random selection and random assignment in experimental design is a central learning objective in most introductory statistics courses. This article describes an activity, appropriate for a high school or introductory statistics course, designed to teach the concepts, values and pitfalls of random selection and assignment…

Social isolation and risk for malnutrition among older people.

Science.gov (United States)

Boulos, Christa; Salameh, Pascale; Barberger-Gateau, Pascale

2017-02-01

Social isolation and loneliness are emerging issues among the geriatric population. The relationships between both, and their impact on health and nutritional status in older people are complex. The purpose of the present study was to evaluate the association between three components of social isolation: social network, feeling of loneliness, commensality and nutritional status. A total of 1200 randomly selected elderly individuals aged ≥65 years and living in rural areas of Lebanon participated in the present study. Data were collected during a face-to-face interview including nutritional status (Mini-Nutritional Assessment), measures of social isolation (Lubben Social Network Scale), subjective loneliness (Jong-Gierveld Loneliness Scale), sociodemographic conditions, and health and functional status. Both social isolation and loneliness were independently associated with a higher risk of malnutrition (OR 1.58, P = 0.011; OR 1.15, P = 0.020, respectively). However no association was found between the frequency of sharing meals and the risk of malnutrition. The present study showed that social isolation and subjective loneliness are two independent risk factors for malnutrition among older people. Geriatr Gerontol Int 2017; 17: 286-294. © 2016 Japan Geriatrics Society.

Materials selection for oxide-based resistive random access memories

International Nuclear Information System (INIS)

Guo, Yuzheng; Robertson, John

2014-01-01

The energies of atomic processes in resistive random access memories (RRAMs) are calculated for four typical oxides, HfO 2 , TiO 2 , Ta 2 O 5 , and Al 2 O 3 , to define a materials selection process. O vacancies have the lowest defect formation energy in the O-poor limit and dominate the processes. A band diagram defines the operating Fermi energy and O chemical potential range. It is shown how the scavenger metal can be used to vary the O vacancy formation energy, via controlling the O chemical potential, and the mean Fermi energy. The high endurance of Ta 2 O 5 RRAM is related to its more stable amorphous phase and the adaptive lattice rearrangements of its O vacancy

Genetic relatedness of Trichoderma isolates antagonistic against Fusarium oxysporum f.sp. dianthi inflicting carnation wilt.

Science.gov (United States)

Shanmugam, V; Sharma, Vivek; Ananthapadmanaban

2008-01-01

Twenty-eight isolates of Trichoderma belonging to four different species were screened in vitro for their antagonistic ability against Fusarium oxysporum f.sp. dianthi causing carnation wilt. Three different levels of antagonism observed in dual plate assay were further confirmed by cell-free culture filtrate experiments. Isolates showing class I level of antagonism produced maximum lytic enzymes, chitinases and beta-1,3-glucanases. Genetic variability of 25 selected isolates was assessed by random amplified polymorphic DNA technique and the amplified products were correlated for their level of antagonism. Unweighed pair-group method with arithmetical averages cluster analysis revealed prominent inter-and intraspecific genetic variation among the isolates. Based on their genetic relationship, the isolates were mainly distributed into 3 major groups representing T. atroviride, T. pseudokoningii and T. harzianum, with 20-35% interspecific dissimilarity. However, the polymorphism shown by the isolates did not correlate to their level of antagonism.

Antimicrobial susceptibilities and random amplified polymorphic DNA-PCR fingerprint characterization of Lactococcus lactis ssp. lactis and Lactococcus garvieae isolated from bovine intramammary infections.

Science.gov (United States)

Plumed-Ferrer, C; Barberio, A; Franklin-Guild, R; Werner, B; McDonough, P; Bennett, J; Gioia, G; Rota, N; Welcome, F; Nydam, D V; Moroni, P

2015-09-01

In total, 181 streptococci-like bacteria isolated from intramammary infections (IMI) were submitted by a veterinary clinic to Quality Milk Production Services (QMPS, Cornell University, Ithaca, NY). The isolates were characterized by sequence analysis, and 46 Lactococcus lactis ssp. lactis and 47 Lactococcus garvieae were tested for susceptibility to 17 antibiotics. No resistant strains were found for β-lactam antibiotics widely used in clinical practice (penicillin, ampicillin, and amoxicillin), and all minimum inhibitory concentrations (MIC) were far from the resistance breakpoints. Eight strains had MIC intermediate to cefazolin. The random amplification of polymorphic DNA (RAPD)-PCR fingerprint patterns showed a slightly higher heterogeneity for Lc. lactis ssp. lactis isolates than for Lc. garvieae isolates. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Emergence of multilevel selection in the prisoner's dilemma game on coevolving random networks

International Nuclear Information System (INIS)

Szolnoki, Attila; Perc, Matjaz

2009-01-01

We study the evolution of cooperation in the prisoner's dilemma game, whereby a coevolutionary rule is introduced that molds the random topology of the interaction network in two ways. First, existing links are deleted whenever a player adopts a new strategy or its degree exceeds a threshold value; second, new links are added randomly after a given number of game iterations. These coevolutionary processes correspond to the generic formation of new links and deletion of existing links that, especially in human societies, appear frequently as a consequence of ongoing socialization, change of lifestyle or death. Due to the counteraction of deletions and additions of links the initial heterogeneity of the interaction network is qualitatively preserved, and thus cannot be held responsible for the observed promotion of cooperation. Indeed, the coevolutionary rule evokes the spontaneous emergence of a powerful multilevel selection mechanism, which despite the sustained random topology of the evolving network, maintains cooperation across the whole span of defection temptation values.

Assessing the accuracy and stability of variable selection methods for random forest modeling in ecology

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Random forest (RF) modeling has emerged as an important statistical learning method in ecology due to its exceptional predictive performance. However, for large and complex ecological datasets there is limited guidance on variable selection methods for RF modeling. Typically, e...

Optimization of the Dutch Matrix Test by Random Selection of Sentences From a Preselected Subset

Directory of Open Access Journals (Sweden)

Rolph Houben

2015-04-01

Full Text Available Matrix tests are available for speech recognition testing in many languages. For an accurate measurement, a steep psychometric function of the speech materials is required. For existing tests, it would be beneficial if it were possible to further optimize the available materials by increasing the function’s steepness. The objective is to show if the steepness of the psychometric function of an existing matrix test can be increased by selecting a homogeneous subset of recordings with the steepest sentence-based psychometric functions. We took data from a previous multicenter evaluation of the Dutch matrix test (45 normal-hearing listeners. Based on half of the data set, first the sentences (140 out of 311 with a similar speech reception threshold and with the steepest psychometric function (≥9.7%/dB were selected. Subsequently, the steepness of the psychometric function for this selection was calculated from the remaining (unused second half of the data set. The calculation showed that the slope increased from 10.2%/dB to 13.7%/dB. The resulting subset did not allow the construction of enough balanced test lists. Therefore, the measurement procedure was changed to randomly select the sentences during testing. Random selection may interfere with a representative occurrence of phonemes. However, in our material, the median phonemic occurrence remained close to that of the original test. This finding indicates that phonemic occurrence is not a critical factor. The work highlights the possibility that existing speech tests might be improved by selecting sentences with a steep psychometric function.

Isolation and characterization of putative endophytic bacteria antagonistic to Phoma tracheiphila and Verticillium albo-atrum.

Science.gov (United States)

Kalai-Grami, Leila; Saidi, Sabrine; Bachkouel, Sarra; Ben Slimene, Imen; Mnari-Hattab, Monia; Hajlaoui, Mohamed Rebah; Limam, Ferid

2014-09-01

A collection of 200 bacterial isolates recovered from citrus plants (Citrus limon, Citrus sinensis, and Citrus reticulata), Medicago truncatula and Laurus nobilis, was established. In vitro screening indicated that 28 isolates exhibited an inhibitory activity against the vascular pathogens Phoma tracheiphila and Verticillium albo-atrum. Isolates were screened according to their hydrolytic activities, plant growth-promoting bacteria (PGPB) abilities, as well as for the presence of nonribosomal peptide synthetase (NRPS) genes responsible of the lipopeptide biosynthesis. The results were positive for 16 isolates which exhibited at least two PGPB activities and a single NRPS gene. Genetic diversity of the selected isolates was studied using random amplified polymorphic DNA (RAPD) and repetitive element PCR (REP) tools that showed clustering of strains into three major groups (I, II, and III) (i, ii, and iii), respectively. Clustering was further confirmed by the 16S rDNA sequencing that assigned nine isolates to Bacillus velezensis, four isolates to Bacillus methyltrophicus, one isolate to Bacillus amyloliquefaciens, and two isolates to Bacillus mojavensis. Organ-bacterial genotype interaction as well as positive correlation with NRPS genes are discussed.

Random drift versus selection in academic vocabulary: an evolutionary analysis of published keywords.

Science.gov (United States)

Bentley, R Alexander

2008-08-27

The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example.

Antibiotic susceptibility of Brachyspira hyodysenteriae isolates from Czech swine farms: a 10-year follow-up study

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Josef Prášek

2014-01-01

Full Text Available Brachyspira hyodysenteriae is the causative agent of swine dysentery. Loss of clinical efficacy of some antimicrobial agents authorized for treating swine dysentery was observed on certain Czech pig farms. The aim of the present study was to evaluate the antimicrobial sensitivity of six antibiotics using a set of 202 randomly selected B. hyodysenteriae isolates obtained from farms in the Czech Republic between years 1997 and 2006. Minimum inhibitory concentration of antibiotics tylosin, lincomycin, tylvalosin, chlortetracyclin, tiamulin and valnemulin were tested, using an agar dilution method. All antibiotics tested showed an increase in minimal inhibitory concentrations. Continual decrease in susceptibility of B. hyodysenteriae isolates to tiamulin and valnemulin was observed. Multiresistant B. hyodysenteriae were isolated more frequently in the past years. Only a careful use of antibiotics can ensure their efficacy, especially in case of pleuromutilins, in the strategic therapy of swine dysentery. This rare study demonstrates the minimal inhibitory concentration changes of selected antidysenterics among Czech isolates of Brachyspira hyodysenteriae during a ten-year period.

Fourier transform IR studies on the interaction of selected chemicals with isolated cuticles

International Nuclear Information System (INIS)

Luque, P.; Ramirez, F.J.; Heredia, A.; Bukovac, M.J.

1994-01-01

It is known that the plant cuticle represents the first barrier that must be overcome by any chemical reaching the plant surface from the atmosphere before entering the plant. Because of the importance of the cuticle as a barrier to penetration of a wide variety of compounds, its morphology, chemistry, and permeability have been extensively studied. However, only limited information is available on the nature of functional chemical groups present and their interaction and role during the penetration process. The usefulness of in situ Fourier transform infrared spectroscopy studies in identifying functional groups present in isolated cuticles is described and their relationships to the structure of the cuticular membrane are discussed. Applications of infrared spectroscopy on the presence and role of phenolics in the cuticle structure and during the cuticle development, nitrogen oxide binding to isolated cuticles, and the interactions between selected chemical probes during sorption by the cuticle are also described. (orig.)

Materials selection for oxide-based resistive random access memories

Energy Technology Data Exchange (ETDEWEB)

Guo, Yuzheng; Robertson, John [Engineering Department, Cambridge University, Cambridge CB2 1PZ (United Kingdom)

2014-12-01

The energies of atomic processes in resistive random access memories (RRAMs) are calculated for four typical oxides, HfO{sub 2}, TiO{sub 2}, Ta{sub 2}O{sub 5}, and Al{sub 2}O{sub 3}, to define a materials selection process. O vacancies have the lowest defect formation energy in the O-poor limit and dominate the processes. A band diagram defines the operating Fermi energy and O chemical potential range. It is shown how the scavenger metal can be used to vary the O vacancy formation energy, via controlling the O chemical potential, and the mean Fermi energy. The high endurance of Ta{sub 2}O{sub 5} RRAM is related to its more stable amorphous phase and the adaptive lattice rearrangements of its O vacancy.

Site selection and evaluation studies of the Waste Isolation Pilot Plant (WIPP), Los Medanos, Eddy County, NM

International Nuclear Information System (INIS)

Griswold, G.B.

1977-12-01

Bedded-salt deposits of the Salado Formation have been selected for evaluation for a proposed Waste Isolation Pilot Plant (WIPP) to be located in Eddy County, NM, approximately 26 mi east of Carlsbad. Site selection and evaluation studies that included geologic mapping, geophysical surveys, drilling, and resource appraisal were conducted over and under the prospective location. The lower portion of the Salado meets essential criteria for waste isolation. Beds chosen for waste storage lie 2074 to 2730 ft below the surface. High-purity salt exists at these depths, and the geologic structure revealed by geophysical surveys indicates that these beds are essentially flat. Additional geophysical surveys are now under way. The initial interpretation of the new data indicates that more structure may exist in the salt beds in the northern portion of the site area. Full evaluation of potentially commercial deposits of potash and natural gas within the WIPP site will be reported by separate studies, as will be the hydrologic details of the region

40 CFR 761.306 - Sampling 1 meter square surfaces by random selection of halves.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Sampling 1 meter square surfaces by...(b)(3) § 761.306 Sampling 1 meter square surfaces by random selection of halves. (a) Divide each 1 meter square portion where it is necessary to collect a surface wipe test sample into two equal (or as...

From Protocols to Publications: A Study in Selective Reporting of Outcomes in Randomized Trials in Oncology

Science.gov (United States)

Raghav, Kanwal Pratap Singh; Mahajan, Sminil; Yao, James C.; Hobbs, Brian P.; Berry, Donald A.; Pentz, Rebecca D.; Tam, Alda; Hong, Waun K.; Ellis, Lee M.; Abbruzzese, James; Overman, Michael J.

2015-01-01

Purpose The decision by journals to append protocols to published reports of randomized trials was a landmark event in clinical trial reporting. However, limited information is available on how this initiative effected transparency and selective reporting of clinical trial data. Methods We analyzed 74 oncology-based randomized trials published in Journal of Clinical Oncology, the New England Journal of Medicine, and The Lancet in 2012. To ascertain integrity of reporting, we compared published reports with their respective appended protocols with regard to primary end points, nonprimary end points, unplanned end points, and unplanned analyses. Results A total of 86 primary end points were reported in 74 randomized trials; nine trials had greater than one primary end point. Nine trials (12.2%) had some discrepancy between their planned and published primary end points. A total of 579 nonprimary end points (median, seven per trial) were planned, of which 373 (64.4%; median, five per trial) were reported. A significant positive correlation was found between the number of planned and nonreported nonprimary end points (Spearman r = 0.66; P < .001). Twenty-eight studies (37.8%) reported a total of 65 unplanned end points; 52 (80.0%) of which were not identified as unplanned. Thirty-one (41.9%) and 19 (25.7%) of 74 trials reported a total of 52 unplanned analyses involving primary end points and 33 unplanned analyses involving nonprimary end points, respectively. Studies reported positive unplanned end points and unplanned analyses more frequently than negative outcomes in abstracts (unplanned end points odds ratio, 6.8; P = .002; unplanned analyses odd ratio, 8.4; P = .007). Conclusion Despite public and reviewer access to protocols, selective outcome reporting persists and is a major concern in the reporting of randomized clinical trials. To foster credible evidence-based medicine, additional initiatives are needed to minimize selective reporting. PMID:26304898

Joint random beam and spectrum selection for spectrum sharing systems with partial channel state information

KAUST Repository

Abdallah, Mohamed M.

2013-11-01

In this work, we develop joint interference-aware random beam and spectrum selection scheme that provide enhanced performance for the secondary network under the condition that the interference observed at the primary receiver is below a predetermined acceptable value. We consider a secondary link composed of a transmitter equipped with multiple antennas and a single-antenna receiver sharing the same spectrum with a set of primary links composed of a single-antenna transmitter and a single-antenna receiver. The proposed schemes jointly select a beam, among a set of power-optimized random beams, as well as the primary spectrum that maximizes the signal-to-interference-plus-noise ratio (SINR) of the secondary link while satisfying the primary interference constraint. In particular, we consider the case where the interference level is described by a q-bit description of its magnitude, whereby we propose a technique to find the optimal quantizer thresholds in a mean square error (MSE) sense. © 2013 IEEE.

Joint random beam and spectrum selection for spectrum sharing systems with partial channel state information

KAUST Repository

Abdallah, Mohamed M.; Sayed, Mostafa M.; Alouini, Mohamed-Slim; Qaraqe, Khalid A.

2013-01-01

In this work, we develop joint interference-aware random beam and spectrum selection scheme that provide enhanced performance for the secondary network under the condition that the interference observed at the primary receiver is below a predetermined acceptable value. We consider a secondary link composed of a transmitter equipped with multiple antennas and a single-antenna receiver sharing the same spectrum with a set of primary links composed of a single-antenna transmitter and a single-antenna receiver. The proposed schemes jointly select a beam, among a set of power-optimized random beams, as well as the primary spectrum that maximizes the signal-to-interference-plus-noise ratio (SINR) of the secondary link while satisfying the primary interference constraint. In particular, we consider the case where the interference level is described by a q-bit description of its magnitude, whereby we propose a technique to find the optimal quantizer thresholds in a mean square error (MSE) sense. © 2013 IEEE.

The RANDOM computer program: A linear congruential random number generator

Science.gov (United States)

Miles, R. F., Jr.

1986-01-01

The RANDOM Computer Program is a FORTRAN program for generating random number sequences and testing linear congruential random number generators (LCGs). The linear congruential form of random number generator is discussed, and the selection of parameters of an LCG for a microcomputer described. This document describes the following: (1) The RANDOM Computer Program; (2) RANDOM.MOD, the computer code needed to implement an LCG in a FORTRAN program; and (3) The RANCYCLE and the ARITH Computer Programs that provide computational assistance in the selection of parameters for an LCG. The RANDOM, RANCYCLE, and ARITH Computer Programs are written in Microsoft FORTRAN for the IBM PC microcomputer and its compatibles. With only minor modifications, the RANDOM Computer Program and its LCG can be run on most micromputers or mainframe computers.

Analysis and applications of a frequency selective surface via a random distribution method

International Nuclear Information System (INIS)

Xie Shao-Yi; Huang Jing-Jian; Yuan Nai-Chang; Liu Li-Guo

2014-01-01

A novel frequency selective surface (FSS) for reducing radar cross section (RCS) is proposed in this paper. This FSS is based on the random distribution method, so it can be called random surface. In this paper, the stacked patches serving as periodic elements are employed for RCS reduction. Previous work has demonstrated the efficiency by utilizing the microstrip patches, especially for the reflectarray. First, the relevant theory of the method is described. Then a sample of a three-layer variable-sized stacked patch random surface with a dimension of 260 mm×260 mm is simulated, fabricated, and measured in order to demonstrate the validity of the proposed design. For the normal incidence, the 8-dB RCS reduction can be achieved both by the simulation and the measurement in 8 GHz–13 GHz. The oblique incidence of 30° is also investigated, in which the 7-dB RCS reduction can be obtained in a frequency range of 8 GHz–14 GHz. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

The Effectiveness of Seismic Isolation System for Nuclear Equipment

International Nuclear Information System (INIS)

Kim, Min-Kyu; Choun, Young-Sun; Seo, Jeong-Moon

2005-04-01

In this study, the Emergency Diesel Generator and Off-site Transformer were selected for isolation. For the selection of the most suitable base isolation system, the literature review and the numerical analysis were performed. For the decision of the parameter of isolation system, the sensitivity analysis was performed. Finally the conceptual design of each equipment was performed. In case of EDG, the Coil Spring and Viscous Damper system was selected for isolation system and 45% isolation effect was determined. For the OST, the FPS was selected and 69% isolation effect was determined

The Effectiveness of Seismic Isolation System for Nuclear Equipment

Energy Technology Data Exchange (ETDEWEB)

Kim, Min-Kyu; Choun, Young-Sun; Seo, Jeong-Moon

2005-04-15

In this study, the Emergency Diesel Generator and Off-site Transformer were selected for isolation. For the selection of the most suitable base isolation system, the literature review and the numerical analysis were performed. For the decision of the parameter of isolation system, the sensitivity analysis was performed. Finally the conceptual design of each equipment was performed. In case of EDG, the Coil Spring and Viscous Damper system was selected for isolation system and 45% isolation effect was determined. For the OST, the FPS was selected and 69% isolation effect was determined.

Random drift versus selection in academic vocabulary: an evolutionary analysis of published keywords.

Directory of Open Access Journals (Sweden)

R Alexander Bentley

Full Text Available The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example.

On theoretical models of gene expression evolution with random genetic drift and natural selection.

Directory of Open Access Journals (Sweden)

Osamu Ogasawara

2009-11-01

Full Text Available The relative contributions of natural selection and random genetic drift are a major source of debate in the study of gene expression evolution, which is hypothesized to serve as a bridge from molecular to phenotypic evolution. It has been suggested that the conflict between views is caused by the lack of a definite model of the neutral hypothesis, which can describe the long-run behavior of evolutionary change in mRNA abundance. Therefore previous studies have used inadequate analogies with the neutral prediction of other phenomena, such as amino acid or nucleotide sequence evolution, as the null hypothesis of their statistical inference.In this study, we introduced two novel theoretical models, one based on neutral drift and the other assuming natural selection, by focusing on a common property of the distribution of mRNA abundance among a variety of eukaryotic cells, which reflects the result of long-term evolution. Our results demonstrated that (1 our models can reproduce two independently found phenomena simultaneously: the time development of gene expression divergence and Zipf's law of the transcriptome; (2 cytological constraints can be explicitly formulated to describe long-term evolution; (3 the model assuming that natural selection optimized relative mRNA abundance was more consistent with previously published observations than the model of optimized absolute mRNA abundances.The models introduced in this study give a formulation of evolutionary change in the mRNA abundance of each gene as a stochastic process, on the basis of previously published observations. This model provides a foundation for interpreting observed data in studies of gene expression evolution, including identifying an adequate time scale for discriminating the effect of natural selection from that of random genetic drift of selectively neutral variations.

From Protocols to Publications: A Study in Selective Reporting of Outcomes in Randomized Trials in Oncology.

Science.gov (United States)

Raghav, Kanwal Pratap Singh; Mahajan, Sminil; Yao, James C; Hobbs, Brian P; Berry, Donald A; Pentz, Rebecca D; Tam, Alda; Hong, Waun K; Ellis, Lee M; Abbruzzese, James; Overman, Michael J

2015-11-01

The decision by journals to append protocols to published reports of randomized trials was a landmark event in clinical trial reporting. However, limited information is available on how this initiative effected transparency and selective reporting of clinical trial data. We analyzed 74 oncology-based randomized trials published in Journal of Clinical Oncology, the New England Journal of Medicine, and The Lancet in 2012. To ascertain integrity of reporting, we compared published reports with their respective appended protocols with regard to primary end points, nonprimary end points, unplanned end points, and unplanned analyses. A total of 86 primary end points were reported in 74 randomized trials; nine trials had greater than one primary end point. Nine trials (12.2%) had some discrepancy between their planned and published primary end points. A total of 579 nonprimary end points (median, seven per trial) were planned, of which 373 (64.4%; median, five per trial) were reported. A significant positive correlation was found between the number of planned and nonreported nonprimary end points (Spearman r = 0.66; P medicine, additional initiatives are needed to minimize selective reporting. © 2015 by American Society of Clinical Oncology.

Isolation and Fatty Acid Profile of Selected Microalgae Strains from the Red Sea for Biofuel Production

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Khalid M. Abu-Salah

2013-05-01

Full Text Available The isolation of lipid-rich autochthonous strains of microalgae is a crucial stage for the development of a microalgae-based biofuel production plant, as these microalgae already have the necessary adaptations to withstand competition, predation and the temperatures observed at each production site. This is particularly important in extreme climates such as in Saudi Arabia. Resorting to fluorescence activated cell sorting (FACS we screened for and isolated several microalgal strains from samples collected from the Red Sea. Relying on the fluorescence of BODIPY 505/515 (4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diazasindacene and growth performance, four promising candidates were identified and the total lipid content and fatty acid profile was assessed for biofuels production. Selected isolates were classified as chlorophytes, belonging to three different genera: Picochlorum, Nannochloris and Desmochloris. The lipid contents were assessed microscopically by means of BODIPY 505/515-associated fluorescence to detect intracellular lipid bodies, which revealed several lipid drops in all selected strains. This result was confirmed by lipid gravimetric determination, which demonstrated that all strains under study presented inner cell lipid contents ranging from 20% to 25% of the biomass dry weight. Furthermore, the fatty acid methyl esters profile of all strains seems ideal for biodiesel production due to a low degree of polyunsaturated fatty acid methyl esters and high amount of palmitic and oleic acids.

Visual search in scenes involves selective and non-selective pathways

Science.gov (United States)

Wolfe, Jeremy M; Vo, Melissa L-H; Evans, Karla K; Greene, Michelle R

2010-01-01

How do we find objects in scenes? For decades, visual search models have been built on experiments in which observers search for targets, presented among distractor items, isolated and randomly arranged on blank backgrounds. Are these models relevant to search in continuous scenes? This paper argues that the mechanisms that govern artificial, laboratory search tasks do play a role in visual search in scenes. However, scene-based information is used to guide search in ways that had no place in earlier models. Search in scenes may be best explained by a dual-path model: A “selective” path in which candidate objects must be individually selected for recognition and a “non-selective” path in which information can be extracted from global / statistical information. PMID:21227734

Isolation, characterization, and evaluation of wild isolates of Lactobacillus reuteri from pig feces.

Science.gov (United States)

Lee, Deog Yong; Seo, Yeon-Soo; Rayamajhi, Nabin; Kang, Mi Lan; Lee, Su In; Yoo, Han Sang

2009-12-01

Lactic acid bacteria (LAB) are a well-used probiotics for health improvements in both humans and animals. Despite of several benefits, non-host-specific LAB showed poor probiotics effects due to difficulty in colonization and competition with normal flora. Therefore, the feasibility of porcine LAB isolates was evaluated as a probiotics. Ten of 49 Lactobacillus spp. isolates harbored 2 approximately 10 kb plasmid DNA. Seven strains were selected based on the safety test, such as hemolytic activity, ammonia, indole, and phenylalanine production. After safety test, five strains were selected again by several tests, such as epithelial adherence, antimicrobial activity, tolerance against acid, bile, heat, and cold-drying, and production of acid and hydrogen peroxide. Then, enzyme profiles (ZYM test) and antibiotics resistance were analyzed for further characterization. Five Lactobacillus reuteri isolates from pig feces were selected by safety and functional tests. The plasmid DNA which was able to develop vector system was detected in the isolates. Together with these approaches, pig-specific Lactobacillus spp. originated from pigs were selected. These strains may be useful tools to develop oral delivery system.

Sensitivity Analysis on Elbow Piping Components in Seismically Isolated NPP under Seismic Loading

Energy Technology Data Exchange (ETDEWEB)

Ju, Hee Kun; Hahm, Dae Gi; Kim, Min Kyu [KAERI, Daejeon (Korea, Republic of); Jeon, Bub Gyu; Kim, Nam Sik [Pusan National University, Busan (Korea, Republic of)

2016-05-15

In this study, the FE model is verified using specimen test results and simulation with parameter variations are conducted. Effective parameters will randomly sampled and used as input values for simulations to be applied to the fragility analysis. pipelines are representative of them because they could undergo larger displacements when they are supported on both isolated and non-isolated structures simultaneously. Especially elbows are critical components of pipes under severed loading conditions such as earthquake action because strain is accumulated on them during the repeated bending of the pipe. Therefore, seismic performance of pipe elbow components should be examined thoroughly based on the fragility analysis. Fragility assessment of interface pipe should take different sources of uncertainty into account. However, selection of important sources and repeated tests with many random input values are very time consuming and expensive, so numerical analysis is commonly used. In the present study, finite element (FE) model of elbow component will be validated using the dynamic test results of elbow components. Using the verified model, sensitivity analysis will be implemented as a preliminary process of seismic fragility of piping system. Several important input parameters are selected and how the uncertainty of them are apportioned to the uncertainty of the elbow response is to be studied. Piping elbows are critical components under cyclic loading conditions as they are subjected large displacement. In a seismically isolated NPP, seismic capacity of piping system should be evaluated with caution. Seismic fragility assessment preliminarily needs parameter sensitivity analysis about the output of interest with different input parameter values.

Antimicrobial and antibiofilm effects of selected food preservatives against Salmonella spp. isolated from chicken samples.

Science.gov (United States)

Er, Buket; Demirhan, Burak; Onurdag, Fatma Kaynak; Ozgacar, Selda Özgen; Oktem, Aysel Bayhan

2014-03-01

Salmonella spp. are widespread foodborne pathogens that contaminate egg and poultry meats. Attachment, colonization, as well as biofilm formation capacity of Salmonella spp. on food and contact surfaces of food may cause continuous contamination. Biofilm may play a crucial role in the survival of salmonellae under unfavorable environmental conditions, such as in animal slaughterhouses and processing plants. This could serve as a reservoir compromising food safety and human health. Addition of antimicrobial preservatives extends shelf lives of food products, but even when products are supplemented with adequate amounts of preservatives, it is not always possible to inhibit the microorganisms in a biofilm community. In this study, our aims were i) to determine the minimum inhibitory concentrations (MIC) and minimum biofilm inhibitory concentrations (MBIC) of selected preservatives against planktonic and biofilm forms of Salmonella spp. isolated from chicken samples and Salmonella Typhimurium SL1344 standard strain, ii) to show the differences in the susceptibility patterns of same strains versus the planktonic and biofilm forms to the same preservative agent, and iii) to determine and compare antimicrobial and antibiofilm effects of selected food preservatives against Salmonella spp. For this purpose, Salmonella Typhimurium SL1344 standard strain and 4 Salmonella spp. strains isolated from chicken samples were used. Investigation of antimicrobial and antibiofilm effects of selected food preservatives against Salmonella spp. was done according to Clinical and Laboratory Standards Institute M100-S18 guidelines and BioTimer assay, respectively. As preservative agents, pure ciprofloxacin, sodium nitrite, potassium sorbate, sodium benzoate, methyl paraben, and propyl paraben were selected. As a result, it was determined that MBIC values are greater than the MIC values of the preservatives. This result verified the resistance seen in a biofilm community to food

Pace-capture-guided ablation after contact-force-guided pulmonary vein isolation: results of the randomized controlled DRAGON trial.

Science.gov (United States)

Masuda, Masaharu; Fujita, Masashi; Iida, Osamu; Okamoto, Shin; Ishihara, Takayuki; Nanto, Kiyonori; Kanda, Takashi; Sunaga, Akihiro; Tsujimura, Takuya; Matsuda, Yasuhiro; Ohashi, Takuya; Uematsu, Masaaki

2017-11-17

Before the discovery of contact-force guidance, eliminating pacing capture along the pulmonary vein (PV) isolation line had been reported to improve PV isolation durability and rhythm outcomes. DRAGON (UMIN-CTR, UMIN000015332) aimed to elucidate the efficacy of pace-capture-guided ablation following contact-force-guided PV isolation ablation in paroxysmal atrial fibrillation (AF) patients. A total of 156 paroxysmal AF patients with AF-trigger ectopies from any of the four PVs induced by isoproterenol were randomly assigned to undergo pace-capture-guided ablation along a contact-force-guided isolation line around AF-trigger PVs (PC group, n = 76) or contact-force-guided PV isolation ablation alone (control group, n = 80). Follow-up of at least 1 year commenced with serial 24 h Holter and symptom-triggered ambulatory monitoring. There was no significant difference in acute PV reconnection rates during a 20 min waiting period after the last ablation or adenosine infusion testing between the PC and the control groups (per patient, 21% vs. 27%, P = 0.27; per AF-trigger PV, 5.9% vs. 7.3%, P = 0.70; and per non-AF-trigger PV, 7.1% vs. 7.4%, P = 0.92). Atrial tachyarrhythmia-free survival rates off antiarrhythmic drugs after the initial session were comparable at 19.3 ± 6.2 months between the two groups (82% vs. 80%, P = 0.80). Among 22 patients who required a second ablation procedure, there was no difference between the PC and the control groups in the PV reconnection rates at both previously AF-trigger (29% vs. 43%, P = 0.70) and non-AF-trigger PVs (18% vs. 19%, P = 0.88). Pace-capture-guided ablation performed after contact-force-guided PV isolation demonstrated no improvement in PV isolation durability or rhythm outcome. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2017. For permissions, please email: journals.permissions@oup.com.

High Entropy Random Selection Protocols

NARCIS (Netherlands)

H. Buhrman (Harry); M. Christandl (Matthias); M. Koucky (Michal); Z. Lotker (Zvi); B. Patt-Shamir; M. Charikar; K. Jansen; O. Reingold; J. Rolim

2007-01-01

textabstractIn this paper, we construct protocols for two parties that do not trust each other, to generate random variables with high Shannon entropy. We improve known bounds for the trade off between the number of rounds, length of communication and the entropy of the outcome.

Selection of hyperproduction of AmpC and SME-1 in a carbapenem-resistant Serratia marcescens isolate during antibiotic therapy.

Science.gov (United States)

Hemarajata, Peera; Amick, Thomas; Yang, Shangxin; Gregson, Aric; Holzmeyer, Cameron; Bush, Karen; Humphries, Romney M

2018-02-19

Antibiotic selective pressure may result in changes to antimicrobial susceptibility throughout the course of infection, especially for organisms that harbour chromosomally encoded AmpC β-lactamases, notably Enterobacter spp., in which hyperexpression of ampC may be induced following treatment with cephalosporins. In this study, we document a case of bacteraemia caused by a blaSME-1-harbouring Serratia marcescens that subsequently developed resistance to expanded-spectrum cephalosporins, piperacillin/tazobactam and fluoroquinolones, over the course of several months of treatment with piperacillin/tazobactam and ciprofloxacin. Susceptibility testing and WGS were performed on three S. marcescens isolates from the patient. β-Lactamase activity in the presence or absence of induction by imipenem was measured by nitrocefin hydrolysis assays. Expression of ampC and blaSME-1 under the same conditions was determined by real-time PCR. WGS demonstrated accumulation of missense and nonsense mutations in ampD associated with stable derepression of AmpC. Gene expression and β-lactamase activity of both AmpC and SME-1 were inducible in the initial susceptible isolate, but were constitutively high in the resistant isolate, in which total β-lactamase activity was increased by 128-fold. Although development of such in vitro resistance due to selective pressure imposed by antibiotics is reportedly low in S. marcescens, our findings highlight the need to evaluate isolates on a regular basis during long-term antibiotic therapy.

Selection, assessment of virulence to Alphitobius diaperinus, and Pr1 enzyme production of Beauveria bassiana (Bals. Vuill. isolates cultured at stress temperatures

Directory of Open Access Journals (Sweden)

Kelly Christiane Constanski

2015-12-01

Full Text Available The entomopathogenic fungus Beauveria bassiana is a promising agent for use in insect control. Its pathogenic activity, as well as other factors such as temperature that can interfere with its development, should be assessed, thus, establishing the foundations for B. bassiana use in biological control programs. The objective of this study was to select and induce tolerance of B. bassiana isolates to high and low temperatures and to assess their virulence before and after exposure to those temperatures. A pre-selection test was performed, in which the tolerance of isolates to stress temperatures was tested and compared to the ideal growth temperature of 25 °C for this organism. For the isolates/temperature combinations resulting in growth, conidia germination and colony-forming units (CFUs were assessed. The isolates Unioeste 4 and Unioeste 40 exhibited >95% germinated conidia at 16 and 31 °C. Thereafter, they underwent four consecutive passages at maximum and minimum tolerated temperatures (10 and 37 °C. A significant difference in germination was observed between the two isolates at all temperatures tested. More CFUs were observed for Unioeste 4 compared to Unioeste 40 at all temperatures, and in the case of the latter, there was no difference in CFU formation at 10 and 25 °C. For both isolates, decreased vegetative growth was observed at 37 °C. Recovery of virulence was observed in both isolates, as determined by insect mortality. No relationship was observed between production of the enzyme Pr1 and the virulence of the isolates.

Compost as a source of microbial isolates for the bioremediation of heavy metals: In vitro selection

International Nuclear Information System (INIS)

Vargas-García, María del Carmen; López, María José; Suárez-Estrella, Francisca; Moreno, Joaquín

2012-01-01

Heavy metal pollution has become a major environmental concern nowadays and the bioremediation of polluted habitats is an increasingly popular strategy due to both its efficiency and safety. A screening and selection protocol based on different composting processes was designed in order to isolate heavy metal-resistant microorganisms. A collection of 51 microorganisms was obtained and most of them showed the capability to tolerate heavy metals in multi-polluted aqueous systems (Cd(II), Cr(VI), Ni, Pb, Zn(II)), as well as to remove them. The highest detoxification ratios were observed for Pb. Some of the isolates detoxifying more than a 90% of this metal, while the other metals were removed in a range between 20% and 60%. The best isolates (Graphium putredinis, Fusarium solani, Fusarium sp. and Penicillium chrysogenum) were further assayed in order to determine the predominant removal mechanism and the potential use of their dead biomass as a biosorbent. Intracellular accumulation was the prevalent mechanism for most isolates and metals, with the exception of Ni. In this case, the proportion removed by extracellular adsorption was similar or even higher than that removed by intracellular accumulation. Thus, the efficiency of living cells was higher than that of dead biomass except in the case of Ni. - Highlights: ► Composting is a good reservoir for the isolation of HM-resistant microorganisms. ► Pb was the most removed heavy metal in multi-polluted aqueous systems. ► Intracellular accumulation was the predominant mechanism for heavy metal removal. ► Graphium putredinis, which detoxifies organic pollutants, was the most efficient isolate.

Optimization of Culture Parameters for Maximum Polyhydroxybutyrate Production by Selected Bacterial Strains Isolated from Rhizospheric Soils.

Science.gov (United States)

Lathwal, Priyanka; Nehra, Kiran; Singh, Manpreet; Jamdagni, Pragati; Rana, Jogender S

2015-01-01

The enormous applications of conventional non-biodegradable plastics have led towards their increased usage and accumulation in the environment. This has become one of the major causes of global environmental concern in the present century. Polyhydroxybutyrate (PHB), a biodegradable plastic is known to have properties similar to conventional plastics, thus exhibiting a potential for replacing conventional non-degradable plastics. In the present study, a total of 303 different bacterial isolates were obtained from soil samples collected from the rhizospheric area of three crops, viz., wheat, mustard and sugarcane. All the isolates were screened for PHB (Poly-3-hydroxy butyric acid) production using Sudan Black staining method, and 194 isolates were found to be PHB positive. Based upon the amount of PHB produced, the isolates were divided into three categories: high, medium and low producers. Representative isolates from each category were selected for biochemical characterization; and for optimization of various culture parameters (carbon source, nitrogen source, C/N ratio, different pH, temperature and incubation time periods) for maximizing PHB accumulation. The highest PHB yield was obtained when the culture medium was supplemented with glucose as the carbon source, ammonium sulphate at a concentration of 1.0 g/l as the nitrogen source, and by maintaining the C/N ratio of the medium as 20:1. The physical growth parameters which supported maximum PHB accumulation included a pH of 7.0, and an incubation temperature of 30 degrees C for a period of 48 h. A few isolates exhibited high PHB accumulation under optimized conditions, thus showing a potential for their industrial exploitation.

The angiotensin II receptor antagonist telmisartan reduces urinary albumin excretion in patients with isolated systolic hypertension: results of a randomized, double-blind, placebo-controlled trial

NARCIS (Netherlands)

Vogt, Liffert; Navis, Gerjan; Koester, Juergen; Manolis, Athanasios J.; Reid, John L.; de Zeeuw, Dick

2005-01-01

Objective To examine the effect of telmisartan or hydrochlorothiazide on the control of urinary albumin excretion (UAE) in patients with isolated systolic hypertension (ISH) unselected for albuminuria in a pre-planned substudy of a large, multicentre, double-blind, placebo-controlled, randomized

Selection and identification of oleaginous yeast isolated from soil, animal feed and ruminal fluid for use as feed supplement in dairy cattle.

Science.gov (United States)

Paserakung, A; Pattarajinda, V; Vichitphan, K; Froetschel, M A

2015-10-01

The purpose of this study was to select oleaginous yeast for microbial lipid production. Sixty-four yeast isolates were obtained from soil (GSY1-12), animal feeds (FDY1-21), and ruminal fluid (RMY1-31) using yeast extract peptone dextrose (YPD) agar. The cultivation of these isolates on nitrogen limited-medium revealed that GSY2 to GSY6, GSY10, FDY2, FDY12 and FDY14 accumulated lipid over 20% of dry biomass. Therefore, they were preliminarily classified as oleaginous yeast. In subsequent experiment, an 8 × 3 factorial in completely randomized design was conducted to examine the effect of eight oleaginous yeast strains and three nitrogen sources (peptone, (NH4 )2 SO4 , urea) on lipid accumulation when using molasses as substrate. The result illustrated that only GSY3 and GSY10 accumulated lipid over 20% of biomass when using peptone or (NH4 )2 SO4 but urea did not. However, GSY10 gave higher biomass and lipid yield than GSY3 (P yeast for microbial lipid production from molasses. This study illustrated the ability of T. asahii GSY10 to utilize molasses and (NH4 )2 SO4 for synthesizing and accumulating cellular lipid of which oleic acid (C18:1 ) was predominant. This yeast would be used for microbial lipid production used as feed supplement in dairy cattle. © 2015 The Society for Applied Microbiology.

Sympathicotomy for isolated facial blushing

DEFF Research Database (Denmark)

Licht, Peter Bjørn; Pilegaard, Hans K; Ladegaard, Lars

2012-01-01

Background. Facial blushing is one of the most peculiar of human expressions. The pathophysiology is unclear, and the prevalence is unknown. Thoracoscopic sympathectomy may cure the symptom and is increasingly used in patients with isolated facial blushing. The evidence base for the optimal level...... of targeting the sympathetic chain is limited to retrospective case studies. We present a randomized clinical trial. Methods. 100 patients were randomized (web-based, single-blinded) to rib-oriented (R2 or R2-R3) sympathicotomy for isolated facial blushing at two university hospitals during a 6-year period...... between R2 and R2-R3 sympathicotomy for isolated facial blushing. Both were effective, and QOL increased significantly. Despite very frequent side effects, the vast majority of patients were satisfied. Surprisingly, many patients experienced mild recurrent symptoms within the first year; this should...

Integrated Behavior Therapy for Selective Mutism: a randomized controlled pilot study.

Science.gov (United States)

Bergman, R Lindsey; Gonzalez, Araceli; Piacentini, John; Keller, Melody L

2013-10-01

To evaluate the feasibility, acceptability, and preliminary efficacy of a novel behavioral intervention for reducing symptoms of selective mutism and increasing functional speech. A total of 21 children ages 4 to 8 with primary selective mutism were randomized to 24 weeks of Integrated Behavior Therapy for Selective Mutism (IBTSM) or a 12-week Waitlist control. Clinical outcomes were assessed using blind independent evaluators, parent-, and teacher-report, and an objective behavioral measure. Treatment recipients completed a three-month follow-up to assess durability of treatment gains. Data indicated increased functional speaking behavior post-treatment as rated by parents and teachers, with a high rate of treatment responders as rated by blind independent evaluators (75%). Conversely, children in the Waitlist comparison group did not experience significant improvements in speaking behaviors. Children who received IBTSM also demonstrated significant improvements in number of words spoken at school compared to baseline, however, significant group differences did not emerge. Treatment recipients also experienced significant reductions in social anxiety per parent, but not teacher, report. Clinical gains were maintained over 3 month follow-up. IBTSM appears to be a promising new intervention that is efficacious in increasing functional speaking behaviors, feasible, and acceptable to parents and teachers. Copyright © 2013 Elsevier Ltd. All rights reserved.

Field-based random sampling without a sampling frame: control selection for a case-control study in rural Africa.

Science.gov (United States)

Crampin, A C; Mwinuka, V; Malema, S S; Glynn, J R; Fine, P E

2001-01-01

Selection bias, particularly of controls, is common in case-control studies and may materially affect the results. Methods of control selection should be tailored both for the risk factors and disease under investigation and for the population being studied. We present here a control selection method devised for a case-control study of tuberculosis in rural Africa (Karonga, northern Malawi) that selects an age/sex frequency-matched random sample of the population, with a geographical distribution in proportion to the population density. We also present an audit of the selection process, and discuss the potential of this method in other settings.

Treatment selection in a randomized clinical trial via covariate-specific treatment effect curves.

Science.gov (United States)

Ma, Yunbei; Zhou, Xiao-Hua

2017-02-01

For time-to-event data in a randomized clinical trial, we proposed two new methods for selecting an optimal treatment for a patient based on the covariate-specific treatment effect curve, which is used to represent the clinical utility of a predictive biomarker. To select an optimal treatment for a patient with a specific biomarker value, we proposed pointwise confidence intervals for each covariate-specific treatment effect curve and the difference between covariate-specific treatment effect curves of two treatments. Furthermore, to select an optimal treatment for a future biomarker-defined subpopulation of patients, we proposed confidence bands for each covariate-specific treatment effect curve and the difference between each pair of covariate-specific treatment effect curve over a fixed interval of biomarker values. We constructed the confidence bands based on a resampling technique. We also conducted simulation studies to evaluate finite-sample properties of the proposed estimation methods. Finally, we illustrated the application of the proposed method in a real-world data set.

Cluster Head Selection in a Homogeneous Wireless Sensor Network Ensuring Full Connectivity with Minimum Isolated Nodes

Directory of Open Access Journals (Sweden)

Tapan Kumar Jain

2014-01-01

Full Text Available The research work proposes a cluster head selection algorithm for a wireless sensor network. A node can be a cluster head if it is connected to at least one unique neighbor node where the unique neighbor is the one that is not connected to any other node. If there is no connected unique node then the CH is selected on the basis of residual energy and the number of neighbor nodes. With the increase in number of clusters, the processing energy of the network increases; hence, this algorithm proposes minimum number of clusters which further leads to increased network lifetime. The major novel contribution of the proposed work is an algorithm that ensures a completely connected network with minimum number of isolated nodes. An isolated node will remain only if it is not within the transmission range of any other node. With the maximum connectivity, the coverage of the network is automatically maximized. The superiority of the proposed design is verified by simulation results done in MATLAB, where it clearly depicts that the total numbers of rounds before the network dies out are maximum compared to other existing protocols.

Isolation and selection of new biosurfactant producing bacteria from degraded palm kernel cake under liquid state fermentation.

Science.gov (United States)

Jamal, Parveen; Mir, Shajrat; Alam, Md Zahangir; Wan Nawawi, Wan M Fazli

2014-01-01

Biosurfactants are surface-active compounds produced by different microorganisms. The aim of this study was to introduce palm kernel cake (PKC) as a novel substrate for biosurfactant production using a potent bacterial strain under liquid state fermentation. This study was primarily based on the isolation and identification of biosurfactant-producing bacteria that could utilize palm kernel cake as a new major substrate. Potential bacterial strains were isolated from degraded PKC and screened for biosurfactant production with the help of the drop collapse assay and by analyzing the surface tension activity. From the screened isolates, a new strain, SM03, showed the best and most consistent results, and was therefore selected as the most potent biosurfactant-producing bacterial strain. The new strain was identified as Providencia alcalifaciens SM03 using the Gen III MicroPlate Biolog Microbial Identification System. The yield of the produced biosurfactant was 8.3 g/L.

Isolation of human simple repeat loci by hybridization selection.

Science.gov (United States)

Armour, J A; Neumann, R; Gobert, S; Jeffreys, A J

1994-04-01

We have isolated short tandem repeat arrays from the human genome, using a rapid method involving filter hybridization to enrich for tri- or tetranucleotide tandem repeats. About 30% of clones from the enriched library cross-hybridize with probes containing trimeric or tetrameric tandem arrays, facilitating the rapid isolation of large numbers of clones. In an initial analysis of 54 clones, 46 different tandem arrays were identified. Analysis of these tandem repeat loci by PCR showed that 24 were polymorphic in length; substantially higher levels of polymorphism were displayed by the tetrameric repeat loci isolated than by the trimeric repeats. Primary mapping of these loci by linkage analysis showed that they derive from 17 chromosomes, including the X chromosome. We anticipate the use of this strategy for the efficient isolation of tandem repeats from other sources of genomic DNA, including DNA from flow-sorted chromosomes, and from other species.

Genetic Variability of Macrophomina phaseolina Isolates from Dry Beans in Turkey

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Serkan Yeşil

2016-04-01

Full Text Available Charcoal rot is a soil and seed borne, economically important fungal disease on dry bean in Turkey. Twenty bean isolates of M. phaseolina collected from different locations in Turkey during 2008 and 2012 years were studied for genetic variability using random amplified polymorphic DNA (RAPD assay, chlorate sensitivity on medium supplemented with 120mM of potassium, phenotype of colony, and pathogenicity. Isolates were identified as M. phaseolina based on morhological features and PCR assays using species-specific primers (MPKF1and MPKR1. Isolates of M. phaseolina were analysed for their aggressiveness on the susceptible bean cv. Akman 98, by soil inoculation method. Isolates exhibiting a dense chlorate phenotype were chlorate-resistant, while those possessing feathery and restricted chlorate phenotypes were chlorate-sensitive. More than half of the isolates (55% were resistant to chlorate and produced dense phenotype, while 35% isolates showed feathery and two isolates (10% showed restricted growth. DNA from 20 isolates was subjected to genetic diversity analysis by the RAPD method using 14 randomly chosen 10-base random primers, and low genetic diversity (33.3% was observed among the tested isolates.

The angiotensin II receptor antagonist telmisartan reduces urinary albumin excretion in patients with isolated systolic hypertension: results of a randomized, double-blind, placebo-controlled trial

NARCIS (Netherlands)

Vogt, Liffert; Navis, Gerjan; Köster, Jürgen; Manolis, Athanasios J.; Reid, John L.; de Zeeuw, Dick

2005-01-01

To examine the effect of telmisartan or hydrochlorothiazide on the control of urinary albumin excretion (UAE) in patients with isolated systolic hypertension (ISH) unselected for albuminuria in a pre-planned substudy of a large, multicentre, double-blind, placebo-controlled, randomized study. The

Isolating GaSb Membranes Grown Metamorphically on GaAs Substrates Using Highly Selective Substrate Removal Etch Processes

Science.gov (United States)

Renteria, E. J.; Muniz, A. J.; Addamane, S. J.; Shima, D. M.; Hains, C. P.; Balakrishnan, G.

2015-05-01

The etch rates of NH4OH:H2O2 and C6H8O7:H2O2 for GaAs and GaSb have been investigated to develop a selective etch for GaAs substrates and to isolate GaSb epilayers grown on GaAs. The NH4OH:H2O2 solution has a greater etch rate differential for the GaSb/GaAs material system than C6H8O7:H2O2 solution. The selectivity of NH4OH:H2O2 for GaAs/GaSb under optimized etch conditions has been observed to be as high as 11,000 ± 2000, whereas that of C6H8O7:H2O2 has been measured up to 143 ± 2. The etch contrast has been verified by isolating 2- μm-thick GaSb epilayers that were grown on GaAs substrates. GaSb membranes were tested and characterized with high- resolution x-ray diffraction and atomic force microscopy.

Selective isolation of gonyautoxins 1,4 from the dinoflagellate Alexandrium minutum based on molecularly imprinted solid-phase extraction.

Science.gov (United States)

Lian, Ziru; Wang, Jiangtao

2017-09-15

Gonyautoxins 1,4 (GTX1,4) from Alexandrium minutum samples were isolated selectively and recognized specifically by an innovative and effective extraction procedure based on molecular imprinting technology. Novel molecularly imprinted polymer microspheres (MIPMs) were prepared by double-templated imprinting strategy using caffeine and pentoxifylline as dummy templates. The synthesized polymers displayed good affinity to GTX1,4 and were applied as sorbents. Further, an off-line molecularly imprinted solid-phase extraction (MISPE) protocol was optimized and an effective approach based on the MISPE coupled with HPLC-FLD was developed for selective isolation of GTX1,4 from the cultured A. minutum samples. The separation method showed good extraction efficiency (73.2-81.5%) for GTX1,4 and efficient removal of interferences matrices was also achieved after the MISPE process for the microalgal samples. The outcome demonstrated the superiority and great potential of the MISPE procedure for direct separation of GTX1,4 from marine microalgal extracts. Copyright © 2017. Published by Elsevier Ltd.

Isolation of a random cosmid clone, cX5, which defines a new polymorphic locus DXS148 near the locus for Duchenne muscular dystrophy

NARCIS (Netherlands)

Hofker, M. H.; Bergen, A. A.; Skraastad, M. I.; Bakker, E.; Francke, U.; Wieringa, B.; Bartley, J.; van Ommen, G. J.; Pearson, P. L.

1986-01-01

We have isolated a random cosmid cX5 (DXS148), which maps into a small Xp21 deletion associated with Duchenne muscular dystrophy (DMD), chronic granulomatous disease (CGD), retinitis pigmentosa (RP) and McLeod syndrome, cX5 maps proximally outside several other deletions associated with DMD,

Isolated Calyx Mistaken for a Cyst: Inappropriately Performed Catheter-Directed Sclerotherapy and Safe Removal of the Catheter After Selective Embolization

Energy Technology Data Exchange (ETDEWEB)

Gwak, Jng Won, E-mail: jjungwonie@hanmail.net; Lee, Seung Hwa, E-mail: gareureung@daum.net; Chung, Hwan Hoon, E-mail: chungmic@korea.ac.kr; Je, Bo Kyung, E-mail: purity21@hanmail.net; Yeom, Suk kyu, E-mail: pagoda20@hanmail.net [Korea University College of Medicine, Department of Radiology, Ansan Hospital (Korea, Republic of); Sung, Deuk Jae, E-mail: urora@korea.ac.kr [Korea University College of Medicine, Department of Radiology, Anam Hospital (Korea, Republic of)

2015-02-15

We present a case of isolated calyx that was mistaken for a large cyst. A 47-year-old woman was referred for sclerotherapy of a large cystic lesion on her left kidney. Computed tomography (CT) and ultrasound showed that the cystic lesion was a large cyst. We noticed that the cystic lesion was not a typical simple cyst, even after two sessions of catheter-mediated sclerotherapy. Isolated calyx was presumed by medical history review and was confirmed by aspirated fluid analysis and far delayed-phase CT after intravenous contrast injection. We performed meticulous selective arterial embolization for an isolated calyx and inserted a catheter that could be removed without complication.

Nickel nanoparticle decorated graphene for highly selective isolation of polyhistidine-tagged proteins

Science.gov (United States)

Liu, Jia-Wei; Yang, Ting; Ma, Lin-Yu; Chen, Xu-Wei; Wang, Jian-Hua

2013-12-01

Nickel nanoparticle decorated graphene (GP-Ni) is prepared by one-pot hydrothermal reduction of graphene oxide and nickel cations by hydrazine hydrate in the presence of poly(sodium-p-styrenesulfonate) (PSS). The GP-Ni hybrid is characterized by XRD, TEM, SEM, XPS, Raman and FT-IR spectra, demonstrating the formation of poly-dispersed nickel nanoparticles with an average size of 83 nm attached on the surface of graphene sheets. The GP-Ni hybrid exhibits ferromagnetic behavior with a magnetization saturation of 31.1 emu g-1 at 10 000 Oersted (Oe). The GP-Ni also possesses favorable stability in aqueous medium and rapid magnetic response to an external magnetic field. These make it a novel magnetic adsorbent for the separation/isolation of His6-tagged recombinant proteins from a complex sample matrix (cell lysate). The targeted protein species is captured onto the surface of the GP-Ni hybrid via specific metal affinity force between polyhistidine groups and nickel nanoparticles. The SDS-PAGE assay indicates highly selective separation of His6-tagged Smt A from cell lysate. The GP-Ni hybrid displays favorable performance on the separation/isolation of His6-tagged recombinant proteins with respect to the commercial NTA-Ni2+ column.

Environmental carbonate chemistry selects for phenotype of recently isolated strains of Emiliania huxleyi

Science.gov (United States)

Rickaby, Rosalind E. M.; Hermoso, Michaël; Lee, Renee B. Y.; Rae, Benjamin D.; Heureux, Ana M. C.; Balestreri, Cecilia; Chakravarti, Leela; Schroeder, Declan C.; Brownlee, Colin

2016-05-01

Coccolithophorid algae, particularly Emiliania huxleyi, are prolific biomineralisers that, under many conditions, dominate communities of marine eukaryotic plankton. Their ability to photosynthesise and form calcified scales (coccoliths) has placed them in a unique position in the global carbon cycle. Contrasting reports have been made with regards to the response of E. huxleyi to ocean acidification. Therefore, there is a pressing need to further determine the fate of this key organism in a rising CO2 world. In this paper, we investigate the phenotype of newly isolated, genetically diverse, strains of E. huxleyi from UK Ocean Acidification Research Programme (UKOA) cruises around the British Isles, the Arctic, and the Southern Ocean. We find a continuum of diversity amongst the physiological and photosynthetic parameters of different strains of E. huxleyi morphotype A under uniform, ambient conditions imposed in the laboratory. This physiology is best explained by adaptation to carbonate chemistry in the former habitat rather than being prescribed by genetic fingerprints such as the coccolithophore morphology motif (CMM). To a first order, the photosynthetic capacity of each strain is a function of both aqueous CO2 availability, and calcification rate, suggestive of a link between carbon concentrating ability and calcification. The calcification rate of each strain is related linearly to the natural environmental [CO32-] at the site of isolation, but a few exceptional strains display low calcification rates at the highest [CO32-] when calcification is limited by low CO2 availability and/or a lack of a carbon concentrating mechanism. We present O2-electrode measurements alongside coccolith oxygen isotopic composition and the uronic acid content (UAC) of the coccolith associated polysaccharide (CAP), that act as indirect tools to show the differing carbon concentrating ability of the strains. The environmental selection revealed amongst our recently isolated strain

Selective isolation and screening of fungi with herbicidal potential ...

African Journals Online (AJOL)

The respective fungal isolates were cultivated in modified Fries media under standard condition. The mycelia and the filtrate were extracted with ethyl acetate and the concentrated extract was evaluated for the herbicidal activity adopting leaf necrosis assay. Among the different isolates, extract prepared from A. alternata and ...

Selective decontamination in pediatric liver transplants. A randomized prospective study.

Science.gov (United States)

Smith, S D; Jackson, R J; Hannakan, C J; Wadowsky, R M; Tzakis, A G; Rowe, M I

1993-06-01

Although it has been suggested that selective decontamination of the digestive tract (SDD) decreases postoperative aerobic Gram-negative and fungal infections in orthotopic liver transplantation (OLT), no controlled trials exist in pediatric patients. This prospective, randomized controlled study of 36 pediatric OLT patients examines the effect of short-term SDD on postoperative infection and digestive tract flora. Patients were randomized into two groups. The control group received perioperative parenteral antibiotics only. The SDD group received in addition polymyxin E, tobramycin, and amphotericin B enterally and by oropharyngeal swab postoperatively until oral intake was tolerated (6 +/- 4 days). Indications for operation, preoperative status, age, and intensive care unit and hospital length of stay were no different in SDD (n = 18) and control (n = 18) groups. A total of 14 Gram-negative infections (intraabdominal abscess 7, septicemia 5, pneumonia 1, urinary tract 1) developed in the 36 patients studied. Mortality was not significantly different in the two groups. However, there were significantly fewer patients with Gram-negative infections in the SDD group: 3/18 patients (11%) vs. 11/18 patients (50%) in the control group, P < 0.001. There was also significant reduction in aerobic Gram-negative flora in the stool and pharynx in patients receiving SDD. Gram-positive and anaerobic organisms were unaffected. We conclude that short-term postoperative SDD significantly reduces Gram-negative infections in pediatric OLT patients.

Compost as a source of microbial isolates for the bioremediation of heavy metals: In vitro selection

Energy Technology Data Exchange (ETDEWEB)

Vargas-Garcia, Maria del Carmen, E-mail: mcvargas@ual.es; Lopez, Maria Jose, E-mail: mllopez@ual.es; Suarez-Estrella, Francisca, E-mail: fsuarez@ual.es; Moreno, Joaquin, E-mail: jcasco@ual.es

2012-08-01

Heavy metal pollution has become a major environmental concern nowadays and the bioremediation of polluted habitats is an increasingly popular strategy due to both its efficiency and safety. A screening and selection protocol based on different composting processes was designed in order to isolate heavy metal-resistant microorganisms. A collection of 51 microorganisms was obtained and most of them showed the capability to tolerate heavy metals in multi-polluted aqueous systems (Cd(II), Cr(VI), Ni, Pb, Zn(II)), as well as to remove them. The highest detoxification ratios were observed for Pb. Some of the isolates detoxifying more than a 90% of this metal, while the other metals were removed in a range between 20% and 60%. The best isolates (Graphium putredinis, Fusarium solani, Fusarium sp. and Penicillium chrysogenum) were further assayed in order to determine the predominant removal mechanism and the potential use of their dead biomass as a biosorbent. Intracellular accumulation was the prevalent mechanism for most isolates and metals, with the exception of Ni. In this case, the proportion removed by extracellular adsorption was similar or even higher than that removed by intracellular accumulation. Thus, the efficiency of living cells was higher than that of dead biomass except in the case of Ni. - Highlights: Black-Right-Pointing-Pointer Composting is a good reservoir for the isolation of HM-resistant microorganisms. Black-Right-Pointing-Pointer Pb was the most removed heavy metal in multi-polluted aqueous systems. Black-Right-Pointing-Pointer Intracellular accumulation was the predominant mechanism for heavy metal removal. Black-Right-Pointing-Pointer Graphium putredinis, which detoxifies organic pollutants, was the most efficient isolate.

Day-ahead load forecast using random forest and expert input selection

International Nuclear Information System (INIS)

Lahouar, A.; Ben Hadj Slama, J.

2015-01-01

Highlights: • A model based on random forests for short term load forecast is proposed. • An expert feature selection is added to refine inputs. • Special attention is paid to customers behavior, load profile and special holidays. • The model is flexible and able to handle complex load signal. • A technical comparison is performed to assess the forecast accuracy. - Abstract: The electrical load forecast is getting more and more important in recent years due to the electricity market deregulation and integration of renewable resources. To overcome the incoming challenges and ensure accurate power prediction for different time horizons, sophisticated intelligent methods are elaborated. Utilization of intelligent forecast algorithms is among main characteristics of smart grids, and is an efficient tool to face uncertainty. Several crucial tasks of power operators such as load dispatch rely on the short term forecast, thus it should be as accurate as possible. To this end, this paper proposes a short term load predictor, able to forecast the next 24 h of load. Using random forest, characterized by immunity to parameter variations and internal cross validation, the model is constructed following an online learning process. The inputs are refined by expert feature selection using a set of if–then rules, in order to include the own user specifications about the country weather or market, and to generalize the forecast ability. The proposed approach is tested through a real historical set from the Tunisian Power Company, and the simulation shows accurate and satisfactory results for one day in advance, with an average error exceeding rarely 2.3%. The model is validated for regular working days and weekends, and special attention is paid to moving holidays, following non Gregorian calendar

Isolation and characterization of bioactive fungi from shark Carcharodon carcharias' gill with biopharmaceutical prospects

Science.gov (United States)

Zhang, Yi; Han, Jinyuan; Feng, Yan; Mu, Jun; Bao, Haiyan; Kulik, Andreas; Grond, Stephanie

2016-01-01

Until recently, little was known about the fungi found in shark gills and their biomedicinal potential. In this article, we described the isolation, bioactivity, diversity, and secondary metabolites of bioactive fungi from the gill of a shark ( Carcharodon carcharias). A total of 115 isolates were obtained and grown in 12 culture media. Fifty-eight of these isolates demonstrated significant activity in four antimicrobial, pesticidal, and cytotoxic bioassay models. Four randomly selected bioactive isolates inhibited human cancer cell proliferation during re-screening. These active isolates were segregated into 6 genera using the internal transcribed spacer-large subunit (ITS-LSU) rDNA-sequence BLAST comparison. Four genera, Penicillium, Aspergillus, Mucor, and Chaetomium were the dominant taxa. A phylogenic tree illustrated their intergenera and intragenera genetic diversity. HPLC-DAD-HRMS analysis and subsequent database searching revealed that nine representative strains produced diverse bioactive compound profiles. These results detail the broad range of bioactive fungi found in a shark's gills, revealing their biopharmaceutical potential. To the best of our knowledge, this is the first study characterizing shark gill fungi and their bioactivity.

Detection of Extended Spectrum Beta-Lactamases Resistance Genes among Bacteria Isolated from Selected Drinking Water Distribution Channels in Southwestern Nigeria.

Science.gov (United States)

Adesoji, Ayodele T; Ogunjobi, Adeniyi A

2016-01-01

Extended Spectrum Beta-Lactamases (ESBL) provide high level resistance to beta-lactam antibiotics among bacteria. In this study, previously described multidrug resistant bacteria from raw, treated, and municipal taps of DWDS from selected dams in southwestern Nigeria were assessed for the presence of ESBL resistance genes which include bla TEM, bla SHV, and bla CTX by PCR amplification. A total of 164 bacteria spread across treated (33), raw (66), and municipal taps (68), belonging to α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Flavobacteriia, Bacilli, and Actinobacteria group, were selected for this study. Among these bacteria, the most commonly observed resistance was for ampicillin and amoxicillin/clavulanic acid (61 isolates). Sixty-one isolates carried at least one of the targeted ESBL genes with bla TEM being the most abundant (50/61) and bla CTX being detected least (3/61). Klebsiella was the most frequently identified genus (18.03%) to harbour ESBL gene followed by Proteus (14.75%). Moreover, combinations of two ESBL genes, bla SHV + bla TEM or bla CTX + bla TEM, were observed in 11 and 1 isolate, respectively. In conclusion, classic bla TEM ESBL gene was present in multiple bacterial strains that were isolated from DWDS sources in Nigeria. These environments may serve as foci exchange of genetic traits in a diversity of Gram-negative bacteria.

Selected Lactobacillus strains isolated from sugary and milk kefir reduce Salmonella infection of epithelial cells in vitro.

Science.gov (United States)

Zavala, L; Golowczyc, M A; van Hoorde, K; Medrano, M; Huys, G; Vandamme, P; Abraham, A G

2016-09-01

The isolation of potentially probiotic strains and the subsequent study of their properties are very important steps to gain insight in the health benefits ascribed to sugary and milk kefir. The aim of the present study was to characterise fifteen Lactobacillus strains isolated from these beverages by determining some surface properties and their ability to antagonise enterocyte cell damage after Salmonella infection in vitro. Lactobacillus surface properties were determined by hydrophobicity, autoaggregation, and coaggregation assays with Salmonella. In addition, lactobacilli adhesion to Caco-2/TC-7 cells and the effect on Salmonella invasion were evaluated. Finally, the disassembly of F-actin cytoskeleton on intestinal epithelial cells was assayed in vitro when Salmonella infection was performed in the presence of selected Lactobacillus strains. Ten out of the 15 strains showed a high adhesion capacity to Caco-2/TC-7 cells. Most of the strains were hydrophilic and non-autoaggregating. Strains isolated from sugary kefir were non-coaggregating with Salmonella, while strains Lactobacillus paracasei CIDCA 83120, 83121, 83123, 83124, 8339, 83102 isolated from milk kefir were able to coaggregate after 1 h. L. paracasei CIDCA 8339 and Lactobacillus kefiri CIDCA 83102 were able to diminish Salmonella invasion to the enterocytes. An antagonistic effect on cytoskeleton disruption elicited by the pathogen was also demonstrated. Our results suggest that both strains isolated from milk kefir could be considered as appropriate probiotic candidates.

Comparative analysis of the genomes of two field isolates of the rice blast fungus Magnaporthe oryzae.

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Minfeng Xue

Full Text Available Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice worldwide. The fungal pathogen is notorious for its ability to overcome host resistance. To better understand its genetic variation in nature, we sequenced the genomes of two field isolates, Y34 and P131. In comparison with the previously sequenced laboratory strain 70-15, both field isolates had a similar genome size but slightly more genes. Sequences from the field isolates were used to improve genome assembly and gene prediction of 70-15. Although the overall genome structure is similar, a number of gene families that are likely involved in plant-fungal interactions are expanded in the field isolates. Genome-wide analysis on asynonymous to synonymous nucleotide substitution rates revealed that many infection-related genes underwent diversifying selection. The field isolates also have hundreds of isolate-specific genes and a number of isolate-specific gene duplication events. Functional characterization of randomly selected isolate-specific genes revealed that they play diverse roles, some of which affect virulence. Furthermore, each genome contains thousands of loci of transposon-like elements, but less than 30% of them are conserved among different isolates, suggesting active transposition events in M. oryzae. A total of approximately 200 genes were disrupted in these three strains by transposable elements. Interestingly, transposon-like elements tend to be associated with isolate-specific or duplicated sequences. Overall, our results indicate that gain or loss of unique genes, DNA duplication, gene family expansion, and frequent translocation of transposon-like elements are important factors in genome variation of the rice blast fungus.

CHROMagar COL-APSE: a selective bacterial culture medium for the isolation and differentiation of colistin-resistant Gram-negative pathogens

DEFF Research Database (Denmark)

Abdul Momin, Muhd Haziq F; Bean, David C; Hendriksen, Rene S.

2017-01-01

Purpose. A selective chromogenic culture medium for the laboratory isolation and differentiation of colistin resistant Acinetobacter, Pseudomonas, Stenotrophomonas and Enterobacteriaceae spp. (CHROMagar COL-APSE) was developed, evaluated and compared to an existing selective bacterial culture......-resistant non-fermentative bacteria (Acinetobacter, Pseudomonas and Stenotrophomonas). CHROMagar COL-APSE was also more sensitive in supporting the growth of Enterobacteriaceae with COL resistance associated with the carriage of mcr-1. Conclusion. CHROMagar COL-APSE is a sensitive and specific medium...

Distribution of orientation selectivity in recurrent networks of spiking neurons with different random topologies.

Science.gov (United States)

Sadeh, Sadra; Rotter, Stefan

2014-01-01

Neurons in the primary visual cortex are more or less selective for the orientation of a light bar used for stimulation. A broad distribution of individual grades of orientation selectivity has in fact been reported in all species. A possible reason for emergence of broad distributions is the recurrent network within which the stimulus is being processed. Here we compute the distribution of orientation selectivity in randomly connected model networks that are equipped with different spatial patterns of connectivity. We show that, for a wide variety of connectivity patterns, a linear theory based on firing rates accurately approximates the outcome of direct numerical simulations of networks of spiking neurons. Distance dependent connectivity in networks with a more biologically realistic structure does not compromise our linear analysis, as long as the linearized dynamics, and hence the uniform asynchronous irregular activity state, remain stable. We conclude that linear mechanisms of stimulus processing are indeed responsible for the emergence of orientation selectivity and its distribution in recurrent networks with functionally heterogeneous synaptic connectivity.

Influence of selected Rhizoctonia solani isolates on sugar beet seedlings

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Skonieczek Paweł

2016-04-01

Full Text Available From 2008 to 2010 the levels of sugar beet seedlings infection caused by Rhizoctonia solani were compared in laboratory tests. Seven sugar beet lines were tested: H56, H66, S2, S3, S4, S5 and S6 as well as three control cultivars: Carlos, Esperanza and Janosik. Sugar beet lines with tolerance to rhizoctoniosis and cultivars without tolerance were infected artificially by R. solani isolates: R1, R28a and R28b. These isolates belong to the second anastomosis group (AG, which is usually highly pathogenic to beet roots. The aim of the experiment was to test whether the tolerance of sugar beet genotypes to R. solani AG 2 prevents both root rot, and damping-off of seedlings, induced by the pathogen. Sugar beet lines tolerant to brown root rot in laboratory tests were significantly less sensitive to infection of the seedlings by R. solani AG 2 isolates in comparison to control cultivars. Rhizoctonia solani AG 2 isolates demonstrated considerable differences in pathogenicity against seedlings of sugar beet lines and cultivars. The strongest infection of sugar beet seedlings occurred with the isolate R28b. The greatest tolerance to infection by AG 2 isolates was found for the S5 and S3 breeding lines.

Typing of Candida isolates from patients with invasive infection and concomitant colonization

DEFF Research Database (Denmark)

Brillowska-Dabrowska, A.; Bergmann, O.; Jensen, Irene Møller

2010-01-01

We investigated the relationship between colonizing and invasive isolates from patients with candidaemia. Molecular typing was performed using random amplification of polymorphic DNA (RAPD) and multilocus sequence typing (MLST). We found MLST to be sufficient for typing Candida isolates, and that......We investigated the relationship between colonizing and invasive isolates from patients with candidaemia. Molecular typing was performed using random amplification of polymorphic DNA (RAPD) and multilocus sequence typing (MLST). We found MLST to be sufficient for typing Candida isolates...

Summary of computational support and general documentation for computer code (GENTREE) used in Office of Nuclear Waste Isolation Pilot Salt Site Selection Project

International Nuclear Information System (INIS)

Beatty, J.A.; Younker, J.L.; Rousseau, W.F.; Elayat, H.A.

1983-01-01

A Decision Tree Computer Model was adapted for the purposes of a Pilot Salt Site Selection Project conducted by the Office of Nuclear Waste Isolation (ONWI). A deterministic computer model was developed to structure the site selection problem with submodels reflecting the five major outcome categories (Cost, Safety, Delay, Environment, Community Impact) to be evaluated in the decision process. Time-saving modifications were made in the tree code as part of the effort. In addition, format changes allowed retention of information items which are valuable in directing future research and in isolation of key variabilities in the Site Selection Decision Model. The deterministic code was linked to the modified tree code and the entire program was transferred to the ONWI-VAX computer for future use by the ONWI project

Selection of bacteria with hydrocarbon degrading capacity isolated from Colombian Caribbean sediments

International Nuclear Information System (INIS)

Narvaez Florez, Silvia; Gomez, Martha L; Martinez Maria M

2008-01-01

Thirty one bacterial isolations in minimal salts supplemented medium with hydrocarbons (ACPM or crude oil) as sole carbon source were isolated from sediment samples from the Colombian Caribbean. Bacterial strains underwent selection tests in different concentrations of hydrocarbons; 11 tolerant crude oil and ACPM strains in a range of 1-8%v/v were chosen. A mixed bacterial culture was created and assessed its ability to degrade hydrocarbons in a laboratory-scale test, with a concentration of 2% v/v of ACPM over a period of 21 days. Measurements of biomass in Colony Forming Units (CFU)/mL were used to develop the growth curve of the mixed culture. Hydrocarbons remotion was measured by mass chromatography. The mixed culture was able to degrade the 68.6% of aliphatic hydrocarbons in preference of long chain n- alkenes (C12- C31), reaching a maximum growth of 3.13 x 10 9 UFC / mL. Degradation of aromatic hydrocarbons was not evidenced under the observation time. Nine of the eleven strains were identified using the biochemical systems BBL and API 50 CHB/E; they belonged to the genus Klebsiella, Chromobacterium, Flavimonas, Enterobacter,Pseudomonas, and Bacillus. The evaluated strains have enzymatic potential to degrade hydrocarbons and it is necessary to characterize them at molecular level in order to develop and effective consortium for field application

Selection and geographic isolation influence hummingbird speciation: genetic, acoustic and morphological divergence in the wedge-tailed sabrewing (Campylopterus curvipennis

Directory of Open Access Journals (Sweden)

Ornelas Juan

2011-02-01

Full Text Available Abstract Background Mesoamerica is one of the most threatened biodiversity hotspots in the world, yet we are far from understanding the geologic history and the processes driving population divergence and speciation for most endemic taxa. In species with highly differentiated populations selective and/or neutral factors can induce rapid changes to traits involved in mate choice, promoting reproductive isolation between allopatric populations that can eventually lead to speciation. We present the results of genetic differentiation, and explore drift and selection effects in promoting acoustic and morphological divergence among populations of Campylopterus curvipennis, a lekking hummingbird with an extraordinary vocal variability across Mesoamerica. Results Analyses of two mitochondrial genes and ten microsatellite loci genotyped for 160 individuals revealed the presence of three lineages with no contemporary gene flow: C. c. curvipennis, C. c. excellens, and C. c. pampa disjunctly distributed in the Sierra Madre Oriental, the Tuxtlas region and the Yucatan Peninsula, respectively. Sequence mtDNA and microsatellite data were congruent with two diversification events: an old vicariance event at the Isthmus of Tehuantepec (c. 1.4 Ma, and a more recent Pleistocene split, isolating populations in the Tuxtlas region. Hummingbirds of the excellens group were larger, and those of the pampa group had shorter bills, and lineages that have been isolated the longest shared fewer syllables and differed in spectral and temporal traits of a shared syllable. Coalescent simulations showed that fixation of song types has occurred faster than expected under neutrality but the null hypothesis that morphological divergence resulted from drift was not rejected. Conclusions Our phylogeographic analyses uncovered the presence of three Mesoamerican wedge-tailed sabrewing lineages, which diverged at different time scales. These results highlight the importance of the

Genotypic characterization of Azotobacteria isolated from Argentinean soils and plant-growth-promoting traits of selected strains with prospects for biofertilizer production.

Science.gov (United States)

Rubio, Esteban Julián; Montecchia, Marcela Susana; Tosi, Micaela; Cassán, Fabricio Darío; Perticari, Alejandro; Correa, Olga Susana

2013-01-01

The genetic diversity among 31 putative Azotobacter isolates obtained from agricultural and non-agricultural soils was assessed using rep-PCR genomic fingerprinting and identified to species level by ARDRA and partial 16S rRNA gene sequence analysis. High diversity was found among the isolates, identified as A. chroococcum, A. salinestris, and A. armeniacus. Selected isolates were characterized on the basis of phytohormone biosynthesis, nitrogenase activity, siderophore production, and phosphate solubilization. Indole-3 acetic-acid (IAA), gibberellin (GA3) and zeatin (Z) biosynthesis, nitrogenase activity, and siderophore production were found in all evaluated strains, with variation among them, but no phosphate solubilization was detected. Phytohormones excreted to the culture medium ranged in the following concentrations: 2.2-18.2 μ g IAA mL(-1), 0.3-0.7 μ g GA3 mL(-1), and 0.5-1.2 μ g Z mL(-1). Seed inoculations with further selected Azotobacter strains and treatments with their cell-free cultures increased the number of seminal roots and root hairs in wheat seedlings. This latter effect was mimicked by treatments with IAA-pure solutions, but it was not related to bacterial root colonization. Our survey constitutes a first approach to the knowledge of Azotobacter species inhabiting Argentinean soils in three contrasting geographical regions. Moreover, this phenotypic characterization constitutes an important contribution to the selection of Azotobacter strains for biofertilizer formulations.

Mechanisms responsible for imipenem resistance among Pseudomonas aeruginosa clinical isolates exposed to imipenem concentrations within the mutant selection window.

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Vassilara, Foula; Galani, Irene; Souli, Maria; Papanikolaou, Konstantinos; Giamarellou, Helen; Papadopoulos, Antonios

2017-07-01

The aim of this study was to determine the propensities of imipenem to select for resistant Pseudomonas aeruginosa mutants by determining the mutant prevention concentrations (MPCs) for 9 unrelated clinical isolates and the accession of any relationship with mechanisms of resistance development. The MPC/MIC ratios ranged from 4 to 16. Detection of resistance mechanisms in the mutant derivatives of the nine isolates mainly revealed inactivating mutations in the gene coding for outer membrane protein OprD. Point mutations leading to premature stop codons or amino acid substitution S278P, ≥1bp deletion leading to frameshift mutations and interruption of the oprD by an insertion sequence, were observed. MPC and mutant selection window (MSW) are unique parameters that may guide the implementation of antimicrobial treatment, providing useful information about the necessary imipenem concentration needed in the infection area, in order to avoid the emergence of resistance, especially in clinical situations with high bacterial load. Copyright © 2017 Elsevier Inc. All rights reserved.

Ureaplasma parvum undergoes selection in utero resulting in genetically diverse isolates colonizing the chorioamnion of fetal sheep.

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Dando, Samantha J; Nitsos, Ilias; Polglase, Graeme R; Newnham, John P; Jobe, Alan H; Knox, Christine L

2014-02-01

Ureaplasmas are the microorganisms most frequently isolated from the amniotic fluid of pregnant women and can cause chronic intrauterine infections. These tiny bacteria are thought to undergo rapid evolution and exhibit a hypermutatable phenotype; however, little is known about how ureaplasmas respond to selective pressures in utero. Using an ovine model of chronic intraamniotic infection, we investigated if exposure of ureaplasmas to subinhibitory concentrations of erythromycin could induce phenotypic or genetic indicators of macrolide resistance. At 55 days gestation, 12 pregnant ewes received an intraamniotic injection of a nonclonal, clinical Ureaplasma parvum strain followed by (i) erythromycin treatment (intramuscularly, 30 mg/kg/day, n = 6) or (ii) saline (intramuscularly, n = 6) at 100 days gestation. Fetuses were then delivered surgically at 125 days gestation. Despite injecting the same inoculum into all the ewes, significant differences between amniotic fluid and chorioamnion ureaplasmas were detected following chronic intraamniotic infection. Numerous polymorphisms were observed in domain V of the 23S rRNA gene of ureaplasmas isolated from the chorioamnion (but not the amniotic fluid), resulting in a mosaiclike sequence. Chorioamnion isolates also harbored the macrolide resistance genes erm(B) and msr(D) and were associated with variable roxithromycin minimum inhibitory concentrations. Remarkably, this variability occurred independently of exposure of ureaplasmas to erythromycin, suggesting that low-level erythromycin exposure does not induce ureaplasmal macrolide resistance in utero. Rather, the significant differences observed between amniotic fluid and chorioamnion ureaplasmas suggest that different anatomical sites may select for ureaplasma subtypes within nonclonal, clinical strains. This may have implications for the treatment of intrauterine ureaplasma infections.

Antibiotic susceptibility of Brachyspira hyodysenteriae isolates from Czech swine farms: a 10-year follow-up study

OpenAIRE

Josef Prášek; Daniel Šperling; Dana Lobová; Jiří Smola; Alois Čížek

2014-01-01

Brachyspira hyodysenteriae is the causative agent of swine dysentery. Loss of clinical efficacy of some antimicrobial agents authorized for treating swine dysentery was observed on certain Czech pig farms. The aim of the present study was to evaluate the antimicrobial sensitivity of six antibiotics using a set of 202 randomly selected B. hyodysenteriae isolates obtained from farms in the Czech Republic between years 1997 and 2006. Minimum inhibitory concentration of antibiotics tylosin, linco...

Selection for autochthonous bifidobacteial isolates adapted to simulated gastrointestinal fluid

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H Jamalifar

2010-03-01

Full Text Available "nBackground and the purpose of the study: Bifidobacterial strains are excessively sensitive to acidic conditions and this can affect their living ability in the stomach and fermented foods, and as a result, restrict their use as live probiotic cultures. The aim of the present study was to obtain bifidobacterial isolates with augmented tolerance to simulated gastrointestinal condition using cross-protection method. "nMethods: Individual bifidobacterial strains were treated in acidic environment and also in media containing bile salts and NaCl. Viability of the acid and acid-bile-NaCl tolerant isolates was further examined in simulated gastric and small intestine by subsequent incubation of the probiotic bacteria in the corresponding media for 120 min. Antipathogenic activities of the adapted isolates were compared with those of the original strains. "nResults and major conclusion: The acid and acid-bile-NaCl adapted isolates showed improved viabilities significantly (p<0.05 in simulated gastric fluid compared to their parent strains. The levels of reduction in bacterial count (Log cfu/ml of the acid and acid-bile-NaCl adapted isolates obtained in simulated gastric fluid ranged from 0.64-3.06 and 0.36-2.43 logarithmic units after 120 min of incubation. There was no significant difference between the viability of the acid-bile-NaCl-tolerant isolates and the original strains in simulated small intestinal condition except for Bifidobacterium adolescentis (p<0.05. The presence of 15 ml of supernatants of acid-bile-NaCl-adapted isolates and also those of the initial Bifidobacterium strains inhibited pathogenic bacterial growth for 24 hrs. Probiotic bacteria with improved ability to survive in harsh gastrointestinal environment could be obtained by subsequent treatment of the strains in acid, bile salts and NaCl environments.

SENSITIVITY OF MOLDS ISOLATED FROM WAREHOUSES OF FOOD PRODUCTION FACILITY ON SELECTED ESSENTIAL OILS

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Łukasz Kręcidło

2015-07-01

Full Text Available Storage of raw materials is one of steps in food production chain. The aim of this study was to estimate the influence of selected essential oils on the growth of four fungal strains: Trichoderma viride, Rhizomucor miehei, Penicillium chrysogenum, Penicillium janthinellum. Strains were isolated from warehouses of the food production facility. Selected essential oils: thyme oil, rosewood oil and rosemary oil were used to assess antifungal activity. Chemical composition of essential oils was determined by Gas Chromatography-Mass Spectroscopy (GC-MS. Antifungal activity of essential oils was estimated in relative to peracetic acid (PAA and sterile water with Tween 80 (0,5%. The influence of essential oils on fungal growth was carried by medium poisoning method. Increment of fungal mycelium was measured every day by 10 days. The thyme essential oils totally inhibited fungal growth in the lowest concentration of 1 mm3·cm-3. The most resistant strain was Penicillium janthinellum.

The Implementation of a Hospital-wide Practice for the Selective Use of Carbapenems Based on the Monitoring of Susceptibility of Pseudomonas aeruginosa Isolates.

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Ohshima, Toshio; Asai, Satomi; Miyazawa, Miki; Yamamoto, Yukari; Hisada, Akifumi; Kumazawa, Chie; Hashimoto, Masayoshi; Fukawa, Katsuji; Iwashita, Hideo; Umezawa, Kazuo; Yamada, Sanetoshi; Yamamoto, Yoshiro; Miyachi, Hayato

2017-12-20

To control carbapenem-resistant Pseudomonas aeruginosa, we implemented a hospital-wide policy concerning the selective use of carbapenems based on the monitoring of P. aeruginosa isolates for susceptibility to five carbapenems using a customized dry plate method. In this study, we retrospectively investigated the outcome of our measures to control carbapenem-resistant P. aeruginosa. To select effective carbapenems, 100 clinical isolates were collected, and the minimum inhibitory concentration (MIC) to 5 carbapenems (IPM/CS, MEPM, DRPM, BIPM and PAPM/BP) was monitored using a customized dry plate method from 2006 to 2013. Carbapenems, which were associated with a high rate of drug resistance in P. aeruginosa, were restricted from use during our intervention study. The antimicrobial use density per 100 bed-days (AUD 100 ) of carbapenems and the detection rates of carbapenem (IPM/CS and MEPM)-resistant P. aeruginosa were determined during the period of the intervention. The isolates consistently showed higher rates of drug-resistant P. aeruginosa in IPM/CS and PAPM/BP. Thus, DRPM, MEPM and BIPM were adopted for hospital-wide use. The detection rates of all IPM/Cs and MEPM-resistant P. aeruginosa significantly decreased. Meanwhile, the consumption of carbapenems showed an increasing trend. The outcome of the hospital-wide implementation of the selective use of carbapenems based on periodic monitoring of the susceptibility of P. aeruginosa isolates was retrospectively studied. Implementation of this measure might have contributed in part to the control of carbapenem-resistant P. aeruginosa in our hospital.

Serological comparison of selected isolates of Aeromonas salmonicida ssp. Salmonicida

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Hahnel, G.B.; Gould, R.W.; Boatman, E.S.

1983-01-01

Eight isolates of Acronionus salmonicida ssp. salmonicida were collected during furunculosis epizootics in North American Pacific coast states and provinces. Both virulent and avirulent forms of each isolate, confirmed by challenge and electron microscopy, were examined. Serological comparisons by cross-absorption agglutination tests revealed no serological differences between isolates. Using the double diffusion precipitin test, a single band was observed when antigen from a sonicated virulent strain was reacted with antiserum against a sonicated, virulent strain absorbed with homologous, avirulent strain. The presence of the single band was eliminated by excess sonication.

Genetic Diversity Among Colletotrichum falcatum Isolates Causing Red Rot of Sugarcane in Subtropical Region of India

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Ratinderbir KAUR

2014-09-01

Full Text Available Silver Genetic diversity of Colletotrichum falcatum causing red rot of sugarcane was assessed based on morphological, pathological and molecular characteristics especially from sub-tropical Indian conditions. Sixteen isolates of this pathogen were collected based on the extensive survey on prominent varieties grown in the region along with some elite selections. Morphological observations (colony colour, mycelium pattern and sporulation grouped the isolates into two distinct types (C1: light type and C2: dark type. However, quantitative data on colony diameter showed five clusters for these isolates. Pathogenic characterization of these isolates on fourteen standard differentials formed six groups, ingroup 1: (CF-Pb-1 isolates Cf-157, Cf-249 and Cf-248 were the most virulent while group 6 (CF-Pb-6 isolates Cf-60 and Cf-247 were the least one. The genetic relatedness among the isolates using Random Amplified Polymorphic DNA (RAPD analysis revealed sufficient molecular polymorphism, which in turn confirmed the variation in virulence of different isolates. The data categorized different isolates into two major clusters and five independent lineages. Polymorphic information content (PIC ranged from 0.701 to 0.929. Isolate Cf-223 was found to be genetically most diverse among all the isolates. Present study inferred that morphological grouping of most of the isolates showed positive correlation with the pathogenic variability while molecular diversity did not showed such associations.

Isolation and selection of plant growth-promoting bacteria associated with sugarcane

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Ariana Alves Rodrigues

2016-06-01

Full Text Available Microorganisms play a vital role in maintaining soil fertility and plant health. They can act as biofertilizers and increase the resistance to biotic and abiotic stress. This study aimed at isolating and characterizing plant growth-promoting bacteria associated with sugarcane, as well as assessing their ability to promote plant growth. Endophytic bacteria from leaf, stem, root and rhizosphere were isolated from the RB 867515 commercial sugarcane variety and screened for indole acetic acid (IAA production, ability to solubilize phosphate, fix nitrogen and produce hydrogen cyanide (HCN, ammonia and the enzymes pectinase, cellulase and chitinase. A total of 136 bacteria were isolated, with 83 of them presenting some plant growth mechanism: 47 % phosphate solubilizers, 26 % nitrogen fixers and 57 % producing IAA, 0.7 % HCN and chitinase, 45 % ammonia, 30 % cellulose and 8 % pectinase. The seven best isolates were tested for their ability to promote plant growth in maize. The isolates tested for plant growth promotion belong to the Enterobacteriaceae family and the Klebsiella, Enterobacter and Pantoea genera. Five isolates promoted plant growth in greenhouse experiments, showing potential as biofertilizers.

The impact of the increased use of piperacillin/tazobactam on the selection of antibiotic resistance among invasive Escherichia coli and Klebsiella pneumoniae isolates.

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Lee, Jina; Oh, Chi Eun; Choi, Eun Hwa; Lee, Hoan Jong

2013-08-01

Increasing antimicrobial resistance is related to the selective pressure exerted by antibiotic usage. This study evaluated the impact of the increased use of piperacillin/tazobactam (TZP) on the selection of antibiotic resistance. From 1999 to 2010, Escherichia coli and Klebsiella pneumoniae invasive isolates obtained from hospitalized Korean children were analyzed in antibiotic susceptibility tests and subjected to characterization of the β-lactamase types. Antibiotic consumption data were also analyzed. Between January 1999 and December 2010, 409 invasive isolates of E. coli (n=170) and K. pneumoniae (n=239) were obtained. A rebound of extended-spectrum β-lactamase (ESBL) prevalence with an increase in total antibiotics was noted. Non-susceptibility to TZP was determined in 7.6% of E. coli isolates and 20.9% of K. pneumoniae isolates. Despite the increase in TZP usage, the overall prevalence of TZP resistance did not significantly increase over time, especially in E. coli. The mechanisms for TZP resistance included the presence of AmpC producers, possible TEM-1 hyperproducers, and multiple β-lactamases in individual organisms of a given isolate. Replacement of only the antibiotic class appears to be insufficient to control antibiotic resistance, and continued efforts to decrease overall antibiotic pressure are needed, especially in highly endemic situations. Copyright © 2013 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Avian influenza virus and Newcastle disease virus (NDV) surveillance in commercial breeding farm in China and the characterization of Class I NDV isolates.

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Hu, Beixia; Huang, Yanyan; He, Yefeng; Xu, Chuantian; Lu, Xishan; Zhang, Wei; Meng, Bin; Yan, Shigan; Zhang, Xiumei

2010-07-29

In order to determine the actual prevalence of avian influenza virus (AIV) and Newcastle disease virus (NDV) in ducks in Shandong province of China, extensive surveillance studies were carried out in the breeding ducks of an intensive farm from July 2007 to September 2008. Each month cloacal and tracheal swabs were taken from 30 randomly selected birds that appeared healthy. All of the swabs were negative for influenza A virus recovery, whereas 87.5% of tracheal swabs and 100% cloacal swabs collected in September 2007, were positive for Newcastle disease virus isolation. Several NDV isolates were recovered from tracheal and cloacal swabs of apparently healthy ducks. All of the isolates were apathogenic as determined by the MDT and ICPI. The HN gene and the variable region of F gene (nt 47-420) of four isolates selected at random were sequenced. A 374 bp region of F gene and the full length of HN gene were used for phylogenetic analysis. Four isolates were identified as the same isolate based on nucleotide sequences identities of 99.2-100%, displaying a closer phylogenetic relationship to lentogenic Class I viruses. There were 1.9-9.9% nucleotide differences between the isolates and other Class I virus in the variable region of F gene (nt 47-420), whereas there were 38.5-41.2% nucleotide difference between the isolates and Class II viruses. The amino acid sequences of the F protein cleavage sites in these isolates were 112-ERQERL-117. The full length of HN gene of these isolates was 1851 bp, coding 585 amino acids. The homology analysis of the nucleotide sequence of HN gene indicated that there were 2.0-4.2% nucleotide differences between the isolates and other Class I viruses, whereas there were 29.5-40.9% differences between the isolates and Class II viruses. The results shows that these isolates are not phylogenetically related to the vaccine strain (LaSota). This study adds to the understanding of the ecology of influenza viruses and Newcastle disease viruses in

Genotypic Characterization of Azotobacteria Isolated from Argentinean Soils and Plant-Growth-Promoting Traits of Selected Strains with Prospects for Biofertilizer Production

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Esteban Julián Rubio

2013-01-01

Full Text Available The genetic diversity among 31 putative Azotobacter isolates obtained from agricultural and non-agricultural soils was assessed using rep-PCR genomic fingerprinting and identified to species level by ARDRA and partial 16S rRNA gene sequence analysis. High diversity was found among the isolates, identified as A. chroococcum, A. salinestris, and A. armeniacus. Selected isolates were characterized on the basis of phytohormone biosynthesis, nitrogenase activity, siderophore production, and phosphate solubilization. Indole-3 acetic-acid (IAA, gibberellin (GA3 and zeatin (Z biosynthesis, nitrogenase activity, and siderophore production were found in all evaluated strains, with variation among them, but no phosphate solubilization was detected. Phytohormones excreted to the culture medium ranged in the following concentrations: 2.2–18.2 μg IAA mL−1, 0.3–0.7 μg GA3 mL−1, and 0.5–1.2 μg Z mL−1. Seed inoculations with further selected Azotobacter strains and treatments with their cell-free cultures increased the number of seminal roots and root hairs in wheat seedlings. This latter effect was mimicked by treatments with IAA-pure solutions, but it was not related to bacterial root colonization. Our survey constitutes a first approach to the knowledge of Azotobacter species inhabiting Argentinean soils in three contrasting geographical regions. Moreover, this phenotypic characterization constitutes an important contribution to the selection of Azotobacter strains for biofertilizer formulations.

Using Random Forests to Select Optimal Input Variables for Short-Term Wind Speed Forecasting Models

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Hui Wang

2017-10-01

Full Text Available Achieving relatively high-accuracy short-term wind speed forecasting estimates is a precondition for the construction and grid-connected operation of wind power forecasting systems for wind farms. Currently, most research is focused on the structure of forecasting models and does not consider the selection of input variables, which can have significant impacts on forecasting performance. This paper presents an input variable selection method for wind speed forecasting models. The candidate input variables for various leading periods are selected and random forests (RF is employed to evaluate the importance of all variable as features. The feature subset with the best evaluation performance is selected as the optimal feature set. Then, kernel-based extreme learning machine is constructed to evaluate the performance of input variables selection based on RF. The results of the case study show that by removing the uncorrelated and redundant features, RF effectively extracts the most strongly correlated set of features from the candidate input variables. By finding the optimal feature combination to represent the original information, RF simplifies the structure of the wind speed forecasting model, shortens the training time required, and substantially improves the model’s accuracy and generalization ability, demonstrating that the input variables selected by RF are effective.

Determination of the minimum inhibitory concentration (MIC and mutant prevention concentration (MPC of selected antimicrobials in bovine and swine Pasteurella multocida, Escherichia coli, and Staphylococcus aureus isolates

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Kateřina Nedbalcová

2015-01-01

Full Text Available We compared the values of the minimum inhibitory concentration (MIC and mutant prevention concentration (MPC values ​​of three antimicrobial agents for 72 bovine isolates of Pasteurella multocida, 80 swine isolates of P. multocida, 80 bovine isolates of Escherichia coli, 80 swine isolates of E. coli, and 80 isolates of Staphylococcus aureus from bovine mastitis. The ratio of MIC90​​/MPC90 which limited mutant selection window (MSW was ≤ 0.12/4 mg/l for enrofloxacin, 0.5/≥ 64 mg/l for florfenicol and 4/≥ 128 mg/l for tulathromycin in bovine P. multocida isolates, ≤ 0.12/2 mg/l for enrofloxacin, 0.5/≥ 64 mg/l for florfenicol and 4/≥ 128 mg/l for tulathromycin in swine P. multocida isolates, 1/16 mg/l for enrofloxacin, 8/≥ 64 mg/l for florfenicol and 8/≥ 128 mg/l for tulathromycin in bovine E. coli isolates, 0.5/16 mg/l for enrofloxacin, ≥ 64/≥ 64 mg/l for florfenicol and 8/≥ 128 mg/l for tulathromycin in swine E. coli isolates, and 0.25/16 mg/l for enrofloxacin, 4/≥ 64 mg/l for florfenicol and 4/≥ 128 mg/l for tulathromycin in S. aureus isolates. These findings indicate that the dosage of antimicrobial agents to achieve serum concentration equal to or higher than MPC could reduce selection of resistant bacterial subpopulation.

In vitro screening of selected probiotic properties of Lactobacillus strains isolated from traditional fermented cabbage and cucumber.

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Zielińska, Dorota; Rzepkowska, Anna; Radawska, Anna; Zieliński, Konrad

2015-02-01

Most important during probiotic selection are gastric acid and bile tolerance, the adhesion to the luminal epithelium to colonize the lower gastrointestinal tract of a human and safety for human consumption. The aim of this study was to evaluate the selected probiotic in vitro properties of Lactobacillus spp. Strains isolated from traditional fermented food. A total 38 strains were isolated from the pickled samples and 14 were identified as Lactobacillus spp. The survival of almost all strains after incubation at pH 2.5 did not change markedly, and remained at above 90 % (10(9) CFU/mL). The strains also exhibited a high survival rate at pH 3.5 (>90 %), whereas pH 1.5 all were died. Just four strains could survive 90 min. at pH 1.5 (survival rates of 81-94 % after 24 h, whereas after incubation in 2 and 4 % bile salt solution it was 59-94 %. All tested strains showed very good and good resistance to 0.4 % phenol addition, however only Lb. johnsonii K4 was able to multiply. The hydrophobic nature of the cell surface of the tested strains was moderated recording hydrophobicity of Lb. johnsonii K4 and Lb. rhamnosus K3 above 60 %. Safety evaluation excluded four of tested strains as candidate probiotics, according to antibiotic resistance patterns and certain metabolic activities. On the basis on the results 10 of the selected Lactobacillus strains are safe and can survive under gastrointestinal conditions, which requires them to future in vitro and in vivo probiotic studies.

Fusarium proliferatum isolated from garlic in Spain: identification, toxigenic potential and pathogenicity on related Allium species

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Daniel PALMERO

2012-05-01

Full Text Available Fusarium proliferatum has been reported on garlic in the Northwest USA, Spain and Serbia, causing water-soaked tan-colored lesions on cloves. In this work, Fusarium proliferatum was isolated from 300 symptomatic garlic bulbs. Morphological identification of Fusarium was confirmed using species-specific PCR assays and EF-1α sequencing. Confirmation of pathogenicity was conducted with eighteen isolates. Six randomly selected F. proliferatum isolates from garlic were tested for specific pathogenicity and screened for fusaric acid production. Additionally, pathogenicity of each F. proliferatum isolate was tested on healthy seedlings of onion (Allium cepa, leek (A. porrum, scallions (A. fistulosum, chives (A. schoenoprasum and garlic (A. sativum. A disease severity index (DSI was calculated as the mean severity on three plants of each species with four test replicates. Symptoms on onion and garlic plants were observed three weeks after inoculation. All isolates tested produced symptoms on all varieties inoculated. Inoculation of F. proliferatum isolates from diseased garlic onto other Allium species provided new information on host range and pathogenicity. The results demonstrated differences in susceptibility with respect to host species and cultivar. The F. proliferatum isolates tested all produced fusaric acid (FA; correlations between FA production and isolate pathogenicity are discussed. Additionally, all isolates showed the presence of the FUM1 gene suggesting the ability of Spanish isolates to produce fumonisins.

Selection of diazotrophic bacteria isolated from wastewater treatment plant sludge at a poultry slaughterhouse for their effect on maize plants

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Jorge Avelino Rodriguez Lozada

Full Text Available ABSTRACT The economic and environmental costs of nitrogen fertilization have intensified the search for technologies that reduce mineral fertilization, for example atmospheric nitrogen-fixing (diazotrophic bacteria inoculation. In this context, the present study addressed the isolation and quantification of diazotrophic bacteria in the sludge from treated wastewater of a poultry slaughterhouse; a description of the bacteria, based on cell and colony morphology; and an assessment of growth and N content of maize plants in response to inoculation. Sixteen morphotypes of bacteria were isolated in six N-free culture media (JMV, JMVL, NFb, JNFb, LGI, and LGI-P. The bacteria stained gram-positive, with 10 rod- and six coccoid-shaped isolates. To evaluate the potential of bacteria to promote plant growth, maize seeds were inoculated. The experiment consisted of 17 treatments (control plus 16 bacterial isolates and was carried out in a completely randomized design with six replicates. The experimental units consisted of one pot containing two maize plants in a greenhouse. Forty-five days after planting, the variables plant height, leaf number, stem diameter, root and shoot fresh and dry weight, and N content were measured. The highest values were obtained with isolate UFV L-162, which produced 0.68 g total dry matter per plant and increased N content to 22.14 mg/plant, representing increments of 74 and 133%, respectively, compared with the control. Diazotrophs inhabit sludge from treated wastewater of poultry slaughterhouses and can potentially be used to stimulate plant development and enrich inoculants.

Different Patterns of pfcrt and pfmdr1 Polymorphisms in P. falciparum Isolates from Nigeria and Brazil: The Potential Role of Antimalarial Drug Selection Pressure

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Gbotosho, Grace O.; Folarin, Onikepe A.; Bustamante, Carolina; Pereira da Silva, Luis Hildebrando; Mesquita, Elieth; Sowunmi, Akintunde; Zalis, Mariano G.; Oduola, Ayoade M. J.; Happi, Christian T.

2012-01-01

The effect of antimalarial drug selection on pfcrt and pfmdr1 polymorphisms in Plasmodium falciparum isolates from two distinct geographical locations was determined in 70 and 18 P. falciparum isolates from Nigeria and Brazil, respectively, using nested polymerase chain reaction and direct DNA sequencing approaches. All isolates from Brazil and 72% from Nigeria harbored the mutant SVMNT and CVIET pfcrt haplotype, respectively. The pfcrt CVMNT haplotype was also observed in (7%) of the Nigerian samples. One hundred percent (100%) and 54% of the parasites from Brazil and Nigeria, respectively, harbored wild-type pfmdr1Asn86. We provide first evidence of emergence of the CVMNT haplotype in West Africa. The high prevalence of pfcrt CVIET and SVMNT haplotypes in Nigeria and Brazil, respectively, is indicative of different selective pressure by chloroquine and amodiaquine. Continuous monitoring of pfcrt SVMNT haplotype is required in endemic areas of Africa, where artesunate-amodiaquine combination is used for treatment of acute uncomplicated malaria. PMID:22302850

Molecular mechanisms of membrane impermeability in clinical isolates of Enterobacteriaceae exposed to imipenem selective pressure.

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Pavez, Monica; Vieira, Camila; de Araujo, Maria Rita; Cerda, Alvaro; de Almeida, Lara Mendes; Lincopan, Nilton; Mamizuka, Elsa Masae

2016-07-01

Intrinsic mechanisms leading to carbapenem-induced membrane impermeability and multidrug resistance are poorly understood in clinical isolates of Enterobacteriaceae. In this study, molecular behaviours during the establishment of membrane impermeability in members of the Enterobacteriaceae family under imipenem selective pressure were investigated. Clinical isolates (n = 22) exhibiting susceptibility to multiple antibiotics or characterised as extended-spectrum β-lactamase (ESBL)- or AmpC-producers were submitted to progressive passages on Mueller-Hinton agar plates containing subclinical concentrations of imipenem [0.5 × the minimum inhibitory concentration (MIC)]. Changes in outer membrane permeability were evaluated by determination of antimicrobial MICs, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), and gene expression analysis related to membrane permeability (i.e. omp35-like, omp36-like and acrA) and regulatory mechanisms (i.e. marA and ompR) by quantitative reverse transcription PCR. Following imipenem induction, 73% of isolates showed increased carbapenem MICs by ≥2 doubling dilutions. At an early stage of treatment, imipenem modulated the expression of porins and efflux pump genes, represented by a reduction of 78% in omp36-like and a two-fold increase in acrA expression. Transcriptional factors marA and ompR were also affected by imipenem induction, increasing mRNA expression by 14- and 4-fold, respectively. High marA expression levels were associated with higher values of acrA expression. These results suggest that imipenem is an important factor in the development of an adaptive response to carbapenems by regulating key genes involved in the control of efflux pumps and porins, which could lead to a multidrug-resistant profile in clinical isolates, contributing to possible treatment failure. Copyright © 2016 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

The study of salinity and drought tolerance of Sinorhizobium meliloti isolated from province of Kerman in vivo condition

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mahboobe abolhasani zeraatkar

2009-06-01

Full Text Available It is well known that the host plant inoculation by native strains with high efficiency has a positive effect on plant yield and biological nitrogen fixation process. The main aim of this investigation was to based on salinity and drought experiments, four isolates of Sinorhizobium meliloti (S27K and S36K tolerant isolates, S109K semi-sensitive isolate, S56K sensitive isolate were selected for plant inoculation which was under drought stress in greenhouse condition. This experiment was carried out by using a factorial model in completely randomized design. Results showed that inoculation of alfalfa plants with high salinity and drought tolerant of Sinorhizobium meliloti bacteria could increased biological nitrogen fixation process (symbiotic efficiency, percent crude protein and yield of alfalfa under salinity and drought conditions significantly. There were not any significant differences between S27K and S36K isolates and positive control (no nitrogen limitation. Symbiotic efficiency increased 3.4 times higher than alfalfa plants were inoculated by sensitive isolates S56K when alfalfa plants were inoculated by S27K and S36K isolates.

Selection and identification of fungi isolated from sugarcane bagasse and their application for phenanthrene removal from soil.

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Cortés-Espinosa, D V; Fernández-Perrino, F J; Arana-Cuenca, A; Esparza-García, F; Loera, O; Rodríguez-Vázquez, R

2006-01-01

This work investigated the identification and selection of fungi isolated from sugarcane bagasse and their application for phenanthrene (Phe) removal from soil. Fungi were identified by PCR amplification of ITS regions as Aspergillus terrus, Aspergillus fumigatus and Aspergillus niger, Penicillium glabrum and Cladosporium cladosporioides. A primary selection of fungi was accomplished in plate, considering Phe tolerance of every strain in two different media: potato dextrose agar (PDA) and mineral medium (MM). The radial extension rate (r(r)) in PDA exhibited significant differences (p<0.05) at 200 and 400 ppm of Phe. A secondary selection of A. niger, C. cladosporoides, and P. glabrum sp. was achieved based on their tolerance to 200, 400, 600 and 800 ppm of Phe, in solid culture at a sugarcane bagasse/contaminated soil ratio of 95:5, in Toyamas, Czapeck and Wunder media. Under these conditions, a maximum (70%) Phe removal by A. niger was obtained. In addition C. cladosporioides and A. niger were able to remove high (800 ppm) Phe concentrations.

Optimal selective renewal policy for systems subject to propagated failures with global effect and failure isolation phenomena

International Nuclear Information System (INIS)

Maaroufi, Ghofrane; Chelbi, Anis; Rezg, Nidhal

2013-01-01

This paper considers a selective maintenance policy for multi-component systems for which a minimum level of reliability is required for each mission. Such systems need to be maintained between consecutive missions. The proposed strategy aims at selecting the components to be maintained (renewed) after the completion of each mission such that a required reliability level is warranted up to the next stop with the minimum cost, taking into account the time period allotted for maintenance between missions and the possibility to extend it while paying a penalty cost. This strategy is applied to binary-state systems subject to propagated failures with global effect, and failure isolation phenomena. A set of rules to reduce the solutions space for such complex systems is developed. A numerical example is presented to illustrate the modeling approach and the use of the reduction rules. Finally, the Monte-Carlo simulation is used in combination with the selective maintenance optimization model to deal with a number of successive missions

Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

Energy Technology Data Exchange (ETDEWEB)

Chandonia, John-Marc; Brenner, Steven E.

2004-07-14

The structural genomics project is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy which is medically and biologically relevant, of good value, and tractable. As an option to consider, we present the Pfam5000 strategy, which involves selecting the 5000 most important families from the Pfam database as sources for targets. We compare the Pfam5000 strategy to several other proposed strategies that would require similar numbers of targets. These include including complete solution of several small to moderately sized bacterial proteomes, partial coverage of the human proteome, and random selection of approximately 5000 targets from sequenced genomes. We measure the impact that successful implementation of these strategies would have upon structural interpretation of the proteins in Swiss-Prot, TrEMBL, and 131 complete proteomes (including 10 of eukaryotes) from the Proteome Analysis database at EBI. Solving the structures of proteins from the 5000 largest Pfam families would allow accurate fold assignment for approximately 68 percent of all prokaryotic proteins (covering 59 percent of residues) and 61 percent of eukaryotic proteins (40 percent of residues). More fine-grained coverage which would allow accurate modeling of these proteins would require an order of magnitude more targets. The Pfam5000 strategy may be modified in several ways, for example to focus on larger families, bacterial sequences, or eukaryotic sequences; as long as secondary consideration is given to large families within Pfam, coverage results vary only slightly. In contrast, focusing structural genomics on a single tractable genome would have only a limited impact in structural knowledge of other proteomes: a significant fraction (about 30-40 percent of the proteins, and 40-60 percent of the residues) of each proteome is classified in small

Genome-wide association data classification and SNPs selection using two-stage quality-based Random Forests.

Science.gov (United States)

Nguyen, Thanh-Tung; Huang, Joshua; Wu, Qingyao; Nguyen, Thuy; Li, Mark

2015-01-01

Single-nucleotide polymorphisms (SNPs) selection and identification are the most important tasks in Genome-wide association data analysis. The problem is difficult because genome-wide association data is very high dimensional and a large portion of SNPs in the data is irrelevant to the disease. Advanced machine learning methods have been successfully used in Genome-wide association studies (GWAS) for identification of genetic variants that have relatively big effects in some common, complex diseases. Among them, the most successful one is Random Forests (RF). Despite of performing well in terms of prediction accuracy in some data sets with moderate size, RF still suffers from working in GWAS for selecting informative SNPs and building accurate prediction models. In this paper, we propose to use a new two-stage quality-based sampling method in random forests, named ts-RF, for SNP subspace selection for GWAS. The method first applies p-value assessment to find a cut-off point that separates informative and irrelevant SNPs in two groups. The informative SNPs group is further divided into two sub-groups: highly informative and weak informative SNPs. When sampling the SNP subspace for building trees for the forest, only those SNPs from the two sub-groups are taken into account. The feature subspaces always contain highly informative SNPs when used to split a node at a tree. This approach enables one to generate more accurate trees with a lower prediction error, meanwhile possibly avoiding overfitting. It allows one to detect interactions of multiple SNPs with the diseases, and to reduce the dimensionality and the amount of Genome-wide association data needed for learning the RF model. Extensive experiments on two genome-wide SNP data sets (Parkinson case-control data comprised of 408,803 SNPs and Alzheimer case-control data comprised of 380,157 SNPs) and 10 gene data sets have demonstrated that the proposed model significantly reduced prediction errors and outperformed

Genetic Diversity Among Colletotrichum falcatum Isolates Causing Red Rot of Sugarcane in Subtropical Region of India

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Ratinderbir KAUR

2014-09-01

Full Text Available Silver Genetic diversity of Colletotrichum falcatum causing red rot of sugarcane was assessed based on morphological, pathological and molecular characteristics especially from sub-tropical Indian conditions. Sixteen isolates of this pathogen were collected based on the extensive survey on prominent varieties grown in the region along with some elite selections. Morphological observations (colony colour, mycelium pattern and sporulation grouped the isolates into two distinct types (C1: light type and C2: dark type. However, quantitative data on colony diameter showed five clusters for these isolates. Pathogenic characterization of these isolates on fourteen standard differentials formed six groups, ingroup 1: (CF-Pb-1 isolates Cf-157, Cf-249 and Cf-248 were the most virulent while group 6 (CF-Pb-6 isolates Cf-60 and Cf-247 were the least one. The genetic relatedness among the isolates using Random Amplified Polymorphic DNA (RAPD analysis revealed sufficient molecular polymorphism, which in turn confirmed the variation in virulence of different isolates. The data categorized different isolates into two major clusters and five independent lineages. Polymorphic information content (PIC ranged from 0.701 to 0.929. Isolate Cf-223 was found to be genetically most diverse among all the isolates. Present study inferred that morphological grouping of most of the isolates showed positive correlation with the pathogenic variability while molecular diversity did not showed such associations.

An analysis of the binding characteristics of a panel of recently selected ICAM-1 binding Plasmodium falciparum patient isolates

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Madkhali, Aymen M; Alkurbi, Mohammed O; Szestak, Tadge

2014-01-01

patterns of lab-adapted patient isolates after selecting on ICAM-1. We investigated the binding phenotypes using variant ICAM-1 proteins including ICAM-1Ref, ICAM-1Kilifi, ICAM-1S22/A, ICAM-1L42/A and ICAM-1L44/A using static assays. The study also examined ICAM-1 blocking by four anti-ICAM-1 monoclonal...

Isolating GaSb membranes grown metamorphically on GaAs substrates using highly selective substrate removal etch processes

Energy Technology Data Exchange (ETDEWEB)

Lavrova, Olga [Univ. of New Mexico, Albuquerque, NM (United States). Dept. of Electrical and Computer Engineering. Center for High Technology Materials; Balakrishnan, Ganesh [Univ. of New Mexico, Albuquerque, NM (United States). Dept. of Electrical and Computer Engineering. Center for High Technology Materials

2017-02-24

The etch rates of NH₄OH:H₂O₂ and C₆H₈O₇:H₂O₂ for GaAs and GaSb have been investigated to develop a selective etch for GaAs substrates and to isolate GaSb epilayers grown on GaAs. The NH₄OH:H₂O₂ solution has a greater etch rate differential for the GaSb/GaAs material system than C₆H₈O₇:H₂O₂ solution. The selectivity of NH₄OH:H₂O₂ for GaAs/GaSb under optimized etch conditions has been observed to be as high as 11471 ± 1691 whereas that of C₆H₈O₇:H₂O₂ has been measured up to 143 ± 2. The etch contrast has been verified by isolating 2 μm thick GaSb epi-layers that were grown on GaAs substrates. GaSb membranes were tested and characterized with high-resolution X-Ray diffraction (HR-XRD) and atomic force microscopy (AFM).

Isolation Effect in Immediate and Delayed Recall

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Bellezza, Francis S.; Cheney, Terry L.

1973-01-01

If the hypothesis of selective rehearsal is used to account for the isolation effect, then the recall of isolated items will depend both on the serial position of the isolated item and on whether recall is immediate or delayed. (Author)

Participant-selected music and physical activity in older adults following cardiac rehabilitation: a randomized controlled trial.

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Clark, Imogen N; Baker, Felicity A; Peiris, Casey L; Shoebridge, Georgie; Taylor, Nicholas F

2017-03-01

To evaluate effects of participant-selected music on older adults' achievement of activity levels recommended in the physical activity guidelines following cardiac rehabilitation. A parallel group randomized controlled trial with measurements at Weeks 0, 6 and 26. A multisite outpatient rehabilitation programme of a publicly funded metropolitan health service. Adults aged 60 years and older who had completed a cardiac rehabilitation programme. Experimental participants selected music to support walking with guidance from a music therapist. Control participants received usual care only. The primary outcome was the proportion of participants achieving activity levels recommended in physical activity guidelines. Secondary outcomes compared amounts of physical activity, exercise capacity, cardiac risk factors, and exercise self-efficacy. A total of 56 participants, mean age 68.2 years (SD = 6.5), were randomized to the experimental ( n = 28) and control groups ( n = 28). There were no differences between groups in proportions of participants achieving activity recommended in physical activity guidelines at Week 6 or 26. Secondary outcomes demonstrated between-group differences in male waist circumference at both measurements (Week 6 difference -2.0 cm, 95% CI -4.0 to 0; Week 26 difference -2.8 cm, 95% CI -5.4 to -0.1), and observed effect sizes favoured the experimental group for amounts of physical activity (d = 0.30), exercise capacity (d = 0.48), and blood pressure (d = -0.32). Participant-selected music did not increase the proportion of participants achieving recommended amounts of physical activity, but may have contributed to exercise-related benefits.

A method for selecting cis-acting regulatory sequences that respond to small molecule effectors

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Allas Ülar

2010-08-01

Full Text Available Abstract Background Several cis-acting regulatory sequences functioning at the level of mRNA or nascent peptide and specifically influencing transcription or translation have been described. These regulatory elements often respond to specific chemicals. Results We have developed a method that allows us to select cis-acting regulatory sequences that respond to diverse chemicals. The method is based on the β-lactamase gene containing a random sequence inserted into the beginning of the ORF. Several rounds of selection are used to isolate sequences that suppress β-lactamase expression in response to the compound under study. We have isolated sequences that respond to erythromycin, troleandomycin, chloramphenicol, meta-toluate and homoserine lactone. By introducing synonymous and non-synonymous mutations we have shown that at least in the case of erythromycin the sequences act at the peptide level. We have also tested the cross-activities of the constructs and found that in most cases the sequences respond most strongly to the compound on which they were isolated. Conclusions Several selected peptides showed ligand-specific changes in amino acid frequencies, but no consensus motif could be identified. This is consistent with previous observations on natural cis-acting peptides, showing that it is often impossible to demonstrate a consensus. Applying the currently developed method on a larger scale, by selecting and comparing an extended set of sequences, might allow the sequence rules underlying the activity of cis-acting regulatory peptides to be identified.

Pooled-DNA sequencing identifies genomic regions of selection in Nigerian isolates of Plasmodium falciparum.

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Oyebola, Kolapo M; Idowu, Emmanuel T; Olukosi, Yetunde A; Awolola, Taiwo S; Amambua-Ngwa, Alfred

2017-06-29

The burden of falciparum malaria is especially high in sub-Saharan Africa. Differences in pressure from host immunity and antimalarial drugs lead to adaptive changes responsible for high level of genetic variations within and between the parasite populations. Population-specific genetic studies to survey for genes under positive or balancing selection resulting from drug pressure or host immunity will allow for refinement of interventions. We performed a pooled sequencing (pool-seq) of the genomes of 100 Plasmodium falciparum isolates from Nigeria. We explored allele-frequency based neutrality test (Tajima's D) and integrated haplotype score (iHS) to identify genes under selection. Fourteen shared iHS regions that had at least 2 SNPs with a score > 2.5 were identified. These regions code for genes that were likely to have been under strong directional selection. Two of these genes were the chloroquine resistance transporter (CRT) on chromosome 7 and the multidrug resistance 1 (MDR1) on chromosome 5. There was a weak signature of selection in the dihydrofolate reductase (DHFR) gene on chromosome 4 and MDR5 genes on chromosome 13, with only 2 and 3 SNPs respectively identified within the iHS window. We observed strong selection pressure attributable to continued chloroquine and sulfadoxine-pyrimethamine use despite their official proscription for the treatment of uncomplicated malaria. There was also a major selective sweep on chromosome 6 which had 32 SNPs within the shared iHS region. Tajima's D of circumsporozoite protein (CSP), erythrocyte-binding antigen (EBA-175), merozoite surface proteins - MSP3 and MSP7, merozoite surface protein duffy binding-like (MSPDBL2) and serine repeat antigen (SERA-5) were 1.38, 1.29, 0.73, 0.84 and 0.21, respectively. We have demonstrated the use of pool-seq to understand genomic patterns of selection and variability in P. falciparum from Nigeria, which bears the highest burden of infections. This investigation identified known

r2VIM: A new variable selection method for random forests in genome-wide association studies.

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Szymczak, Silke; Holzinger, Emily; Dasgupta, Abhijit; Malley, James D; Molloy, Anne M; Mills, James L; Brody, Lawrence C; Stambolian, Dwight; Bailey-Wilson, Joan E

2016-01-01

Machine learning methods and in particular random forests (RFs) are a promising alternative to standard single SNP analyses in genome-wide association studies (GWAS). RFs provide variable importance measures (VIMs) to rank SNPs according to their predictive power. However, in contrast to the established genome-wide significance threshold, no clear criteria exist to determine how many SNPs should be selected for downstream analyses. We propose a new variable selection approach, recurrent relative variable importance measure (r2VIM). Importance values are calculated relative to an observed minimal importance score for several runs of RF and only SNPs with large relative VIMs in all of the runs are selected as important. Evaluations on simulated GWAS data show that the new method controls the number of false-positives under the null hypothesis. Under a simple alternative hypothesis with several independent main effects it is only slightly less powerful than logistic regression. In an experimental GWAS data set, the same strong signal is identified while the approach selects none of the SNPs in an underpowered GWAS. The novel variable selection method r2VIM is a promising extension to standard RF for objectively selecting relevant SNPs in GWAS while controlling the number of false-positive results.

The human clone ST22 SCCmec IV methicillin-resistant Staphylococcus aureus isolated from swine herds and wild primates in Nepal: is man the common source?

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Roberts, Marilyn C; Joshi, Prabhu Raj; Greninger, Alexander L; Melendez, Daira; Paudel, Saroj; Acharya, Mahesh; Bimali, Nabin Kishor; Koju, Narayan P; No, David; Chalise, Mukesh; Kyes, Randall C

2018-05-01

Swine nasal samples [n = 282] were collected from 12 randomly selected farms around Kathmandu, Nepal, from healthy animals. In addition, wild monkey (Macaca mulatta) saliva samples [n = 59] were collected near temples areas in Kathmandu using a non-invasive sampling technique. All samples were processed for MRSA using standardized selective media and conventional biochemical tests. MRSA verification was done and isolates characterized by SCCmec, multilocus sequence typing, whole genome sequencing [WGS] and antibiotic susceptibilities. Six (2.1%) swine MRSA were isolated from five of the different swine herds tested, five were ST22 type IV and one ST88 type V. Four (6.8%) macaques MRSA were isolated, with three ST22 SCCmec type IV and one ST239 type III. WGS sequencing showed that the eight ciprofloxacin resistant ST22 isolates carried gyrA mutation [S84L]. Six isolates carried the erm(C) genes, five isolates carried aacC-aphD genes and four isolates carried blaZ genes. The swine linezolid resistant ST22 did not carry any known acquired linezolid resistance genes but had a mutation in ribosomal protein L22 [A29V] and an insertion in L4 [68KG69], both previously associated with linezolid resistance. Multiple virulence factors were also identified. This is the first time MRSA ST22 SCCmec IV has been isolated from livestock or primates.

Selection of Lactic Acid Bacteria with Probiotic Potential Isolated from the Fermentation Process of "Cupuaçu" (Theobroma grandiflorum).

Science.gov (United States)

Ornellas, Roberta Maria Santos; Santos, Tiza Teles; Arcucio, Leonardo Borges; Sandes, Sávio Henrique Cicco; Oliveira, Mayara Messias; Dias, Cristiano Villela; de Carvalho Silva, Samuel; Uetanabaro, Ana Paula Trovatti; Vinderola, Gabriel; Nicoli, Jacques Robert

2017-01-01

In the present study, nine lactic acid bacteria isolated from the fermentation process of "cupuaçu" (Theobroma grandiflorum) were selected for probiotic use. In vitro (resistance to gastrointestinal environment, in vitro antagonism and co-aggregation with pathogens) and in vivo (intestinal colonization and ex vivo antagonism in germ-free mice, cumulative mortality, translocation to liver and spleen, histopathological examination of liver and ileum and mRNA cytokine gene expression during an experimental infection with S. Typhimurium) assays were used. Among the nine Lactobacillus strains isolated from the "cupuaçu" fermentation, L. plantarum 81 and L. plantarum 90 were selected as potential probiotics based on better results obtained in in vitro evaluations (production of diffusible inhibitory compounds and co-aggregation) as well as in vivo experiments (resistance to gastrointestinal environment, ex vivo antagonism, higher survival after enteropathogen challenge, lower hepatic translocation of enteropathogen, lower histopathological lesions in ileum and liver and anti-inflammatory pattern of immunological response). Concluding, L. plantarum 81 and L. plantarum 90 showed in vitro and in vivo capacities for probiotic use through different mechanisms of protection and its origin would allow an easier adaptation in an alimentary matrix for its administration.

Screening and characterization of phosphate solubilizing bacteria from isolate of thermophilic bacteria

Science.gov (United States)

Yulianti, Evy; Rakhmawati, Anna

2017-08-01

The aims of this study were to select bacteria that has the ability to dissolve phosphate from thermophilic bacteria isolates after the Merapi eruption. Five isolates of selected bacteria was characterized and continued with identification. Selection was done by using a pikovskaya selective medium. Bacterial isolates were grown in selective medium and incubated for 48 hours at temperature of 55 ° C. Characterization was done by looking at the cell and colony morphology, physiological and biochemical properties. Identification was done with the Profile Matching method based on the reference genus Oscillospira traced through Bergey's Manual of Determinative Bacteriology. Dendogram was created based on similarity index SSM. The results showed there were 14 isolates of bacteria that were able to dissolve phosphate indicated by a clear zone surrounding the bacterial colony on selective media. Five isolates were selected with the largest clear zone. Isolates D79, D92, D110a, D135 and D75 have different characters. The result of phenotypic characters identification with Genus Oscillospira profile has a percentage of 100% similarity to isolate D92 and D110a; 92.31% for isolates D79, and 84.6% for isolates D75 and D135. Dendogram generated from average linkage algorithm / UPGMA using the Simple Matching Coefficient (SSM) algorithms showed, isolate thermophilic bacteria D75 and D135 are combined together to form cluster 1. D110a and D92 form a sub cluster A. Sub cluster A and D79 form cluster 2

Reaction of common bean lines and aggressiveness of Sclerotinia sclerotiorum isolates.

Science.gov (United States)

Silva, P H; Santos, J B; Lima, I A; Lara, L A C; Alves, F C

2014-11-07

The aims of this study were to evaluate the reaction of common bean lines to white mold, the aggressiveness of different Sclerotinia sclerotiorum isolates from various common bean production areas in Brazil, and comparison of the diallel and GGE (genotype main effect plus genotype-by-environment interaction) biplot analysis procedures via study of the line-by-isolate interaction. Eleven common bean (Phaseolus vulgaris) lines derived from 3 backcross populations were used. Field experiments were performed in the experimental area of the Departamento de Biologia of the Universidade Federal de Lavras, Lavras, MG, Brazil, in the 2011 and 2012 dry crop season and 2011 winter crop season through a randomized block design with 3 replications. This study was also set up in a greenhouse. Inoculations were performed 28 days after sowing by means of the straw test method. The reaction of the bean lines to white mold was assessed according to a diagrammatic scale from 1 (plant without symptoms) to 9 (dead plant). Estimations of general reaction capacity (lines) and general aggressiveness capacity (isolates) indicated different horizontal levels of resistance in the lines and levels of aggressiveness in the isolates. Therefore, it was possible to select more resistant lines and foresee those crosses that are the most promising for increasing the level of resistance. It was also possible to identify the most aggressive isolates that were more efficient in distinguishing the lines. Both diallel and GGE biplot analyses were useful in identifying the genotypic values of lines and isolates.

Aspergillus species isolated from mangrove forests in Borneo Island, Sarawak, Malaysia

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J.S.S. Seelan

2009-06-01

Full Text Available A study on the occurrence of Aspergillus spp. on selected mangrove forests in Sarawak was conducted to find out their diversity and distribution. Samples were obtained from mangrove soils and leaf litters at different locations, i.e. Sematan, Lundu, Kampung Bako, Bako in Sarawak. Soil and leaf litter samples were taken randomly at different locations with five replicates from each area. A total of 138 isolates of Aspergillus species were obtained from the soil and leaf litter samples by using direct plating and Warcup method. Based on both macroscopic and microscopic observations, using an identification key, individual isolates were classified within the genus Aspergillus, belonging to three subgenera, four sections and five species. The fungi isolates were identified as A. terreus, A. flavipes, A. carneus, A. fumigatus and A. clavatus. The most frequent isolated species was A. flavipes (63.04%, followed by A. fumigatus (16.7%, A. terreus (13.04%, A. carneus (5.8% and A. clavatus (1.44%. All of the isolated Aspergillus species grew well on MEA and CYA at 25°C. A. carneus produced reddish sclerotia on MEA after seven days and this could be used as an important characteristic in this species identification. A. clavatus from mangrove soil in Kampung Bako has shown long conidiophores (ranging from 3-5 cm with swollen hyphal structures, while A. clavatus from Sematan area has shorter conidiophores (ranging from 2.5-3.5 cm on MEA.

Selective isolation and noninvasive analysis of circulating cancer stem cells through Raman imaging.

Science.gov (United States)

Cho, Hyeon-Yeol; Hossain, Md Khaled; Lee, Jin-Ho; Han, Jiyou; Lee, Hun Joo; Kim, Kyeong-Jun; Kim, Jong-Hoon; Lee, Ki-Bum; Choi, Jeong-Woo

2018-04-15

Circulating cancer stem cells (CCSCs), a rare circulating tumor cell (CTC) type, recently arose as a useful resource for monitoring and characterizing both cancers and their metastatic derivatives. However, due to the scarcity of CCSCs among hematologic cells in the blood and the complexity of the phenotype confirmation process, CCSC research can be extremely challenging. Hence, we report a nanoparticle-mediated Raman imaging method for CCSC characterization which profiles CCSCs based on their surface marker expression phenotypes. We have developed an integrated combinatorial Raman-Active Nanoprobe (RAN) system combined with a microfluidic chip to successfully process complete blood samples. CCSCs and CTCs were detected (90% efficiency) and classified in accordance with their respective surface marker expression via completely distinct Raman signals of RANs. Selectively isolated CCSCs (93% accuracy) were employed for both in vitro and in vivo tumor phenotyping to identify the tumorigenicity of the CCSCs. We utilized our new method to predict metastasis by screening blood samples from xenograft models, showing that upon CCSC detection, all subjects exhibited liver metastasis. Having highly efficient detection and noninvasive isolation capabilities, we have demonstrated that our RAN-based Raman imaging method will be valuable for predicting cancer metastasis and relapse via CCSC detection. Moreover, the exclusion of peak overlapping in CCSC analysis with our Raman imaging method will allow to expand the RAN families for various cancer types, therefore, increasing therapeutic efficacy by providing detailed molecular features of tumor subtypes. Copyright © 2017 Elsevier B.V. All rights reserved.

Identification of a novel clone, ST736, among Enterococcus faecium clinical isolates and its association with daptomycin nonsusceptibility.

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Wang, Guiqing; Kamalakaran, Sitharthan; Dhand, Abhay; Huang, Weihua; Ojaimi, Caroline; Zhuge, Jian; Yee, Leslie Lee; Mayigowda, Pramod; Surendraiah, Pavan Kumar Makam; Dimitrova, Nevenka; Fallon, John T

2014-08-01

Resistance to daptomycin in enterococcal clinical isolates remains rare but is being increasingly reported in the United States and worldwide. There are limited data on the genetic relatedness and microbiological and clinical characteristics of daptomycin-nonsusceptible enterococcal clinical isolates. In this study, we assessed the population genetics of daptomycin-nonsusceptible Enterococcus faecium (DNSE) clinical isolates by multilocus sequence typing (MLST) and whole-genome sequencing analysis. Forty-two nonduplicate DNSE isolates and 43 randomly selected daptomycin-susceptible E. faecium isolates were included in the analysis. All E. faecium isolates were recovered from patients at a tertiary care medical center in suburban New York City from May 2009 through December 2013. The daptomycin MICs of the DNSE isolates ranged from 6 to >256 μg/ml. Three major clones of E. faecium (ST18, ST412, and ST736) were identified among these clinical isolates by MLST and whole-genome sequence-based analysis. A newly recognized clone, ST736, was seen in 32 of 42 (76.2%) DNSE isolates and in only 14 of 43 (32.6%) daptomycin-susceptible E. faecium isolates (P clone ST736 and daptomycin nonsusceptibility. The identification and potential spread of this novel E. faecium clone and its association with daptomycin nonsusceptibility constitute a challenge for patient management and infection control at our medical center. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Two-year Randomized Clinical Trial of Self-etching Adhesives and Selective Enamel Etching.

Science.gov (United States)

Pena, C E; Rodrigues, J A; Ely, C; Giannini, M; Reis, A F

2016-01-01

The aim of this randomized, controlled prospective clinical trial was to evaluate the clinical effectiveness of restoring noncarious cervical lesions with two self-etching adhesive systems applied with or without selective enamel etching. A one-step self-etching adhesive (Xeno V(+)) and a two-step self-etching system (Clearfil SE Bond) were used. The effectiveness of phosphoric acid selective etching of enamel margins was also evaluated. Fifty-six cavities were restored with each adhesive system and divided into two subgroups (n=28; etch and non-etch). All 112 cavities were restored with the nanohybrid composite Esthet.X HD. The clinical effectiveness of restorations was recorded in terms of retention, marginal integrity, marginal staining, caries recurrence, and postoperative sensitivity after 3, 6, 12, 18, and 24 months (modified United States Public Health Service). The Friedman test detected significant differences only after 18 months for marginal staining in the groups Clearfil SE non-etch (p=0.009) and Xeno V(+) etch (p=0.004). One restoration was lost during the trial (Xeno V(+) etch; p>0.05). Although an increase in marginal staining was recorded for groups Clearfil SE non-etch and Xeno V(+) etch, the clinical effectiveness of restorations was considered acceptable for the single-step and two-step self-etching systems with or without selective enamel etching in this 24-month clinical trial.

A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data

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Himmelreich Uwe

2009-07-01

Full Text Available Abstract Background Regularized regression methods such as principal component or partial least squares regression perform well in learning tasks on high dimensional spectral data, but cannot explicitly eliminate irrelevant features. The random forest classifier with its associated Gini feature importance, on the other hand, allows for an explicit feature elimination, but may not be optimally adapted to spectral data due to the topology of its constituent classification trees which are based on orthogonal splits in feature space. Results We propose to combine the best of both approaches, and evaluated the joint use of a feature selection based on a recursive feature elimination using the Gini importance of random forests' together with regularized classification methods on spectral data sets from medical diagnostics, chemotaxonomy, biomedical analytics, food science, and synthetically modified spectral data. Here, a feature selection using the Gini feature importance with a regularized classification by discriminant partial least squares regression performed as well as or better than a filtering according to different univariate statistical tests, or using regression coefficients in a backward feature elimination. It outperformed the direct application of the random forest classifier, or the direct application of the regularized classifiers on the full set of features. Conclusion The Gini importance of the random forest provided superior means for measuring feature relevance on spectral data, but – on an optimal subset of features – the regularized classifiers might be preferable over the random forest classifier, in spite of their limitation to model linear dependencies only. A feature selection based on Gini importance, however, may precede a regularized linear classification to identify this optimal subset of features, and to earn a double benefit of both dimensionality reduction and the elimination of noise from the classification task.

Selective isolation of potentially phosphate-mobilizing, biosurfactant-producing and biodegradative bacteria associated with a sub-Arctic, terricolous lichen, Peltigera membranacea.

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Sigurbjörnsdóttir, Margrét Auður; Vilhelmsson, Oddur

2016-06-01

Lichens are the symbiotic association of fungi and a photosynthetic partner. However, non-phototrophic bacteria are also present and thought to comprise an essential part of the lichen symbiosis, although their roles in the symbiosis are still poorly understood. In this study, we isolated and characterized 110 non-phototrophic bacterial lichen associates from thalli of the terricolous lichen Peltigera membranacea The biodegradative and other nutrient-scavenging properties studied among selected isolates were phosphate mobilization, biosurfactant production and degradation of napthalene and several biopolymers, suggesting organic and inorganic nutrient scavenging as roles for bacteria in the lichen symbiotic association. Identification by partial 16S rRNA gene sequencing revealed that the isolates comprised 18 genera within the Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes, many with high similarities with bacteria typically associated with the plant and rhizosphere environments, could suggest that plants may be important sources of terricolous lichen-associated bacteria, or vice versa. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Random effect selection in generalised linear models

DEFF Research Database (Denmark)

Denwood, Matt; Houe, Hans; Forkman, Björn

We analysed abattoir recordings of meat inspection codes with possible relevance to onfarm animal welfare in cattle. Random effects logistic regression models were used to describe individual-level data obtained from 461,406 cattle slaughtered in Denmark. Our results demonstrate that the largest...

Molecular characterization and evaluation of mycorrhizal capacity of Suillus isolates from central Spain for the selection of fungal inoculants.

Science.gov (United States)

Ruiz-Díez, Beatriz; Rincón, Ana M; de Felipe, María R; Fernández-Pascual, Mercedes

2006-10-01

Suillus fungal specimens of pine forests from a Mediterranean area of central Spain (Madrid region) were studied based on molecular and physiological analysis of sporocarps to obtain fungal native inocula to produce mycorrhizal Pinus halepensis Miller in nursery. Variation within the internal transcribed spacer (ITS) region of the ribosomal RNA genes of Suillus was examined by restriction fragment length polymorphism (RFLP) and direct sequencing of polymerase chain reaction products. Ribosomal DNA (rDNA) spacers were amplified from pure cultures obtained from fruit bodies of a range of Suillus species: Suillus bellinii (Inzenga) Watling, Suillus bovinus (Pers.) Kuntze, Suillus collinitus (Fr.) Kuntze, Suillus granulatus (L.) Snell, Suillus mediterraneensis (Jacquet. & Blum) Redeuil, Suillus luteus L. (Gray), and Suillus variegatus (Sw.) Kuntze. Interspecific variation in the length and number of restriction sites of the amplified ITS region was observed. This variation was confirmed by sequencing, which allowed us to identify some isolates. This is the first time that the ITS sequence of S. mediterraneensis is completely described. No intraspecific rDNA variation was observed within isolates of S. collinitus, S. mediterraneensis, and S. luteus. The phylogenetic analysis established the close relationship among these Mediterranean fungal species. As a further step to characterize the different isolates and to understand the relation between genetic and functional diversity, some physiological variables were evaluated. Intraspecific variation in axenic fungal growth and in mycorrhizal capacities was detected, especially within S. collinitus isolates. The fungal isolates stimulated the growth of P. halepensis in different rates. These studies indicated that ITS analysis, in conjunction with mycorrhizal tests, provides suitable combined tools for the analysis of Suillus spp. in a small geographic area for selecting isolates with final afforestation purposes.

Genomic relations among 31 species of Mammillaria haworth (Cactaceae) using random amplified polymorphic DNA.

Science.gov (United States)

Mattagajasingh, Ilwola; Mukherjee, Arup Kumar; Das, Premananda

2006-01-01

Thirty-one species of Mammillaria were selected to study the molecular phylogeny using random amplified polymorphic DNA (RAPD) markers. High amount of mucilage (gelling polysaccharides) present in Mammillaria was a major obstacle in isolating good quality genomic DNA. The CTAB (cetyl trimethyl ammonium bromide) method was modified to obtain good quality genomic DNA. Twenty-two random decamer primers resulted in 621 bands, all of which were polymorphic. The similarity matrix value varied from 0.109 to 0.622 indicating wide variability among the studied species. The dendrogram obtained from the unweighted pair group method using arithmetic averages (UPGMA) analysis revealed that some of the species did not follow the conventional classification. The present work shows the usefulness of RAPD markers for genetic characterization to establish phylogenetic relations among Mammillaria species.

Quincke random walkers

Science.gov (United States)

Pradillo, Gerardo; Heintz, Aneesh; Vlahovska, Petia

2017-11-01

The spontaneous rotation of a sphere in an applied uniform DC electric field (Quincke effect) has been utilized to engineer self-propelled particles: if the sphere is initially resting on a surface, it rolls. The Quincke rollers have been widely used as a model system to study collective behavior in ``active'' suspensions. If the applied field is DC, an isolated Quincke roller follows a straight line trajectory. In this talk, we discuss the design of a Quincke roller that executes a random-walk-like behavior. We utilize AC field - upon reversal of the field direction a fluctuation in the axis of rotation (which is degenerate in the plane perpendicular to the field and parallel to the surface) introduces randomness in the direction of motion. The MSD of an isolated Quincke walker depends on frequency, amplitude, and waveform of the electric field. Experiment and theory are compared. We also investigate the collective behavior of Quincke walkers,the transport of inert particles in a bath of Quincke walkers, and the spontaneous motion of a drop containing Quincke active particle. supported by NSF Grant CBET 1437545.

RAPD-PCR characterization of lactobacilli isolated from artisanal meat plants and traditional fermented sausages of Veneto region (Italy).

Science.gov (United States)

Andrighetto, C; Zampese, L; Lombardi, A

2001-07-01

The study was carried out to evaluate the use of randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) as a method for the identification of lactobacilli isolated from meat products. RAPD-PCR with primers M13 and D8635 was applied to the identification and intraspecific differentiation of 53 lactobacilli isolates originating from traditional fermented sausages and artisanal meat plants of the Veneto region (Italy). Most of the isolates were assigned to the species Lactobacillus sakei and Lact. curvatus; differentiation of groups of strains within the species was also possible. RAPD-PCR could be applied to the identification of lactobacilli species most commonly found in meat products. The method, which is easy and rapid to perform, could be useful for the study of the lactobacilli populations present in fermented sausages, and could help in the selection of candidate strains to use as starter cultures in meat fermentation.

Schizosaccharomyces isolation method

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Benito Santiago

2014-01-01

Full Text Available This study discusses the optimization of a selective and differential medium which would facilitate the isolation of Schizosaccharomyces (a genus with a low incidence compared to other microorganisms to select individuals from this genus for industrial purposes, especially in light of the recent recommendation of the use of yeasts from this genus in the wine industry by the International Organisation of Vine and Wine, or to detect the presence of such yeasts, for those many authors who consider them food spoilers. To this end, we studied various selective differential agents based on the main physiological characteristics of these species, such as their high resistances to high concentrations of sugar, sulfur dioxide, sorbic acid, benzoic acid, acetic acid or malo ethanolic fermentation. This selective medium is based on the genus resistance to the antibiotic actidione and its high resistance to inhibitory agents such as benzoic acid. Malic acid was used as a differential factor due to the ability of this genus to metabolise it to ethanol, which allows detecting of the degradation of this compound. Lastly, the medium was successfully used to isolate strains of Schizosaccharomyces pombe from honey and honeycombs.

Selection of Rhizobium strain from Wonogiri, Central Java on the growth of soybean (Glycine max L. on the sand sterile medium in greenhouse

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SRI PURWANINGSIH

2005-07-01

Full Text Available An experiment on the selection of Rhizobium strain from Wonogiri, Central Java on the growth of soybean (Glycine max L. on the sand sterile medium in green house. The aim of the experiment the selection and potency of the Rhizobium strain to increase the growth of soybean. The experiment was carried out in green house condition in Microbiology Division, Research Center for Biology-LIPI with sterile sand medium. The research design was Completely Randomized Design with three replications for each treatment. The Rhizobium strains used were 1 W (isolated from bean, Vigna radiata, 2 W (isolated from soybean, 3 W (isolated from bean, 4 W (isolated from soybean, 5 W (isolated from soybean, 6 W (isolated from peanut, Arachis hypogaea, 7 W (isolated from peanut, 8 W (isolated from peanut, the controls were uninoculated with Rhizobium strain and without urea fertilizer (K1, uninoculated and with urea fertilizer equal 100 kg/ha (K2. The plants were harvested after 50 days, the variable of investigation were the dry weight of canopy, roots, nodules root, total plants, number of nodules and ‘symbiotic capacity”. The results showed that all of experiment plant which be inoculated with Rhizobium able to form nodule. Strain of 2 W (isolated from soybean has given the best effects on the growth of soybean.

Comparison of phenotypic and virulence genes characteristics in human and chicken isolates of Proteus mirabilis.

Science.gov (United States)

Barbour, Elie K; Hajj, Zahi G; Hamadeh, Shadi; Shaib, Houssam A; Farran, Mohamad T; Araj, George; Faroon, Obaid; Barbour, Kamil E; Jirjis, Faris; Azhar, Esam; Kumosani, Taha; Harakeh, Steve

2012-10-01

The objective of this work is to compare the phenotypic and virulence genes characteristics in human and chicken isolates of Proteus mirabilis. The bacterial examination of 50 livers of individual broilers, marketed by four major outlets, revealed a high recovery of P. mirabilis (66%), and a low recovery frequency of Salmonella spp. (4%), Serratia odorifera (2%), Citrobacter brakii (2%), and Providencia stuartii (2%). The phenotypic biochemical characterization of the recovered 33 chicken isolates of P. mirabilis were compared to 30 human isolates (23 urinary and six respiratory isolates). The comparison revealed significant differences in the presence of gelatinase enzyme (100% presence in chicken isolates versus 91.3 and 83.3% presence in human urinary and respiratory isolates, respectively, P,0.05). The H(2)S production occurred in 100% of chicken isolates versus 95.6 and 66.7% presence in human urinary and respiratory isolates, respectively, P,0.05). The other 17 biochemical characteristics did not differ significantly among the three groups of isolates (P.0.05). Two virulence genes, the mrpA and FliL, were having a typical 100% presence in randomly selected isolates of P. mirabilis recovered from chicken livers (N510) versus isolates recovered from urinary (N55) and respiratory specimens of humans (N55) (P.0.05). The average percentage similarity of mrpA gene nucleotide sequence of poultry isolates to human urinary and respiratory isolates was 93.2 and 97.5-%, respectively. The high similarity in phenotypic characteristics, associated with typical frequency of presence of two virulence genes, and high similarity in sequences of mrpA gene among poultry versus human P. mirabilis isolates justifies future investigations targeting the evaluation of adaptable pathogenicity of avian Proteus mirabilis isolates to mammalian hosts.

Prevalence of Listeria species in camel sausages from retail markets in Aydin province in Turkey and RAPD analysis of Listeria monocytogenes Isolates

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Ozbey Gokben

2006-06-01

Full Text Available Abstract Samples were taken from 100 camel sausages from the different retail markets in Aydin province in the south-west of Turkey and they were tested for the presence of Listeria spp by biochemical methods. Samples were enriched using Listeria Enrichment Broth and they were inoculated onto Listeria Selective Agar. Listeria monocytogenes was isolated from nine samples (9%, Listeria innocua from 14 samples (14% and Listeria welshimeri from two samples(2%. A 701 bp fragment of listeriolysin O sequence for L. monocytogenes was amplified using specific primers by polymerase chain reaction (PCR for confirmation of the identification. A random primer (OPA-11 was used in a random amplified polymorphic DNA (RAPD assay. This detected five different band profiles amongst the L. monocytogenes isolates, indicating a relatively large amount of genetic heterogeneity amongst the nine isolates. The study has highlighted the need for improved strategies for food safety, in particular appropriate hygienic precautions to avoid contamination of sausage during the manufacturing process and appropriate preservation techniques during storage and transport, to prevent transmission of Listeria spp to consumers at home and abroad.

Random forest variable selection in spatial malaria transmission modelling in Mpumalanga Province, South Africa

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Thandi Kapwata

2016-11-01

Full Text Available Malaria is an environmentally driven disease. In order to quantify the spatial variability of malaria transmission, it is imperative to understand the interactions between environmental variables and malaria epidemiology at a micro-geographic level using a novel statistical approach. The random forest (RF statistical learning method, a relatively new variable-importance ranking method, measures the variable importance of potentially influential parameters through the percent increase of the mean squared error. As this value increases, so does the relative importance of the associated variable. The principal aim of this study was to create predictive malaria maps generated using the selected variables based on the RF algorithm in the Ehlanzeni District of Mpumalanga Province, South Africa. From the seven environmental variables used [temperature, lag temperature, rainfall, lag rainfall, humidity, altitude, and the normalized difference vegetation index (NDVI], altitude was identified as the most influential predictor variable due its high selection frequency. It was selected as the top predictor for 4 out of 12 months of the year, followed by NDVI, temperature and lag rainfall, which were each selected twice. The combination of climatic variables that produced the highest prediction accuracy was altitude, NDVI, and temperature. This suggests that these three variables have high predictive capabilities in relation to malaria transmission. Furthermore, it is anticipated that the predictive maps generated from predictions made by the RF algorithm could be used to monitor the progression of malaria and assist in intervention and prevention efforts with respect to malaria.

Clonality Analysis of Helicobacter pylori in Patients Isolated from Several Biopsy Specimens and Gastric Juice in a Japanese Urban Population by Random Amplified Polymorphic DNA Fingerprinting

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Nariaki Toita

2013-01-01

Full Text Available Background. The number of Helicobacter pylori clones infecting a single host has been discussed in numerous reports. The number has been suggested to vary depending on the regions in the world. Aim. The purpose of this study was to examine the number of clones infecting a single host in a Japanese urban population. Materials and Methods. Thirty-one Japanese patients undergoing upper gastrointestinal endoscopy were enrolled in this study. H. pylori isolates (total 104 strains were obtained from biopsy specimens (antrum, corpus, and duodenum and gastric juice. Clonal diversity was examined by the random amplified polymorphic DNA (RAPD fingerprinting method. Results. The RAPD fingerprinting patterns of isolates from each patient were identical or very similar. And the isolates obtained from several patients with 5- to 9-year intervals showed identical or very similar RAPD patterns. Conclusion. Each Japanese individual of an urban population is predominantly infected with a single H. pylori clone.

Selecting Optimal Parameters of Random Linear Network Coding for Wireless Sensor Networks

DEFF Research Database (Denmark)

Heide, J; Zhang, Qi; Fitzek, F H P

2013-01-01

This work studies how to select optimal code parameters of Random Linear Network Coding (RLNC) in Wireless Sensor Networks (WSNs). With Rateless Deluge [1] the authors proposed to apply Network Coding (NC) for Over-the-Air Programming (OAP) in WSNs, and demonstrated that with NC a significant...... reduction in the number of transmitted packets can be achieved. However, NC introduces additional computations and potentially a non-negligible transmission overhead, both of which depend on the chosen coding parameters. Therefore it is necessary to consider the trade-off that these coding parameters...... present in order to obtain the lowest energy consumption per transmitted bit. This problem is analyzed and suitable coding parameters are determined for the popular Tmote Sky platform. Compared to the use of traditional RLNC, these parameters enable a reduction in the energy spent per bit which grows...

Application of random coherence order selection in gradient-enhanced multidimensional NMR

International Nuclear Information System (INIS)

Bostock, Mark J.; Nietlispach, Daniel

2016-01-01

Development of multidimensional NMR is essential to many applications, for example in high resolution structural studies of biomolecules. Multidimensional techniques enable separation of NMR signals over several dimensions, improving signal resolution, whilst also allowing identification of new connectivities. However, these advantages come at a significant cost. The Fourier transform theorem requires acquisition of a grid of regularly spaced points to satisfy the Nyquist criterion, while frequency discrimination and acquisition of a pure phase spectrum require acquisition of both quadrature components for each time point in every indirect (non-acquisition) dimension, adding a factor of 2 N -1 to the number of free- induction decays which must be acquired, where N is the number of dimensions. Compressed sensing (CS) ℓ 1 -norm minimisation in combination with non-uniform sampling (NUS) has been shown to be extremely successful in overcoming the Nyquist criterion. Previously, maximum entropy reconstruction has also been used to overcome the limitation of frequency discrimination, processing data acquired with only one quadrature component at a given time interval, known as random phase detection (RPD), allowing a factor of two reduction in the number of points for each indirect dimension (Maciejewski et al. 2011 PNAS 108 16640). However, whilst this approach can be easily applied in situations where the quadrature components are acquired as amplitude modulated data, the same principle is not easily extended to phase modulated (P-/N-type) experiments where data is acquired in the form exp (iωt) or exp (-iωt), and which make up many of the multidimensional experiments used in modern NMR. Here we demonstrate a modification of the CS ℓ 1 -norm approach to allow random coherence order selection (RCS) for phase modulated experiments; we generalise the nomenclature for RCS and RPD as random quadrature detection (RQD). With this method, the power of RQD can be extended

Approaches for enhancing in situ detection of enterocin genes in thermized milk, and selective isolation of enterocin-producing Enterococcus faecium from Baird-Parker agar.

Science.gov (United States)

Vandera, Elpiniki; Tsirka, Georgia; Kakouri, Athanasia; Koukkou, Anna-Irini; Samelis, John

2018-05-21

Enterococci are naturally selected for growth in thermized ewes'/goats' milk mixtures used for traditional cooked hard cheese processing in Greece. A culture-independent PCR-based approach was applied to detect the presence of enterocin-encoding genes in naturally culture-enriched thermized milk (TM). Portions of TM (63 °C, 30 s) collected from a commercial cheese plant before addition of starters were fermented at 37 °C for 48 h to facilitate growth of indigenous enterococci. The multiple enterocin-producing (m-Ent+) Enterococcus faecium KE82 and the nisin A-producing Lactococcus lactis subsp. cremoris M104 served as bacteriocin-positive inocula in separate TM treatments. The PCR results revealed a constant presence of the enterocin A, B and P genes in TM fermented naturally at 37 °C. Eleven out of 42 (26.2%) lactic isolates from the enriched TM cultures without inoculation were Ent+ E. faecium assigned to three biotypes. Biotype I (4 isolates) included single entA possessors, whereas biotype II (5 isolates) and biotype III (2 isolates) were m-Ent+ variants profiling entA-entB-entP and entA-entB genes, respectively. Biotype II displayed the strongest antilisterial activity in vitro. Surprisingly, 85.7% (6/7) of the m-Ent+ E. faecium were selectively isolated from Baird-Parker agar, reflecting their natural resistance to 0.01% tellurite contained in the egg yolk supplement. No cytolysin-positive E. faecalis or other Ent+ Enterococcus spp. were isolated. In conclusion, commercially thermized Greek milk is a natural pool or 'reservoir' of antagonistic Ent+ or m-Ent+ E. faecium strains that can be easily detected and recovered by applying this PCR-based approach to naturally fermented milks or cheese products. Copyright © 2018 Elsevier B.V. All rights reserved.

Pepino mosaic virus isolates and differential symptomatology in tomato

NARCIS (Netherlands)

Hanssen, I.M.; Paeleman, A.; Vandewoestijne, E.; Bergen, Van L.; Bragard, C.; Lievens, B.; Vanachter, A.C.R.C.; Thomma, B.P.H.J.

2009-01-01

Based on a survey conducted in commercial tomato production in Belgium in 2006, four Pepino mosaic virus (PepMV) isolates that differed in symptom expression in the crop of origin were selected for greenhouse trials. The selected isolates were inoculated onto tomato plants grown in four separate

Antibiotic content of selective culture media for isolation of Capnocytophaga species from oral polymicrobial samples.

Science.gov (United States)

Ehrmann, E; Jolivet-Gougeon, A; Bonnaure-Mallet, M; Fosse, T

2013-10-01

In oral microbiome, because of the abundance of commensal competitive flora, selective media with antibiotics are necessary for the recovery of fastidious Capnocytophaga species. The performances of six culture media (blood agar, chocolate blood agar, VCAT medium, CAPE medium, bacitracin chocolate blood agar and VK medium) were compared with literature data concerning five other media (FAA, LB, TSBV, CapR and TBBP media). To understand variable growth on selective media, the MICs of each antimicrobial agent contained in this different media (colistin, kanamycin, trimethoprim, trimethoprim-sulfamethoxazole, vancomycin, aztreonam and bacitracin) were determined for all Capnocytophaga species. Overall, VCAT medium (Columbia, 10% cooked horse blood, polyvitaminic supplement, 3·75 mg l(-1) of colistin, 1·5 mg l(-1) of trimethoprim, 1 mg l(-1) of vancomycin and 0·5 mg l(-1) of amphotericin B, Oxoid, France) was the more efficient selective medium, with regard to the detection of Capnocytophaga species from oral samples (P culture, a simple blood agar allowed the growth of all Capnocytophaga species. Nonetheless, in oral samples, because of the abundance of commensal competitive flora, selective media with antibiotics are necessary for the recovery of Capnocytophaga species. The demonstrated superiority of VCAT medium made its use essential for the optimal detection of this bacterial genus. This work showed that extreme caution should be exercised when reporting the isolation of Capnocytophaga species from oral polymicrobial samples, because the culture medium is a determining factor. © 2013 The Society for Applied Microbiology.

The supply solutions for isolated rural consumers

International Nuclear Information System (INIS)

Hazi, Gheorghe; Solomon, Petre; Hazi, Aneta

2004-01-01

This paper establishes the supply optimal solutions for isolated rural consumers. A complex technical-economical calculation method is developed for selection of the best solutions. This analysis is based on the minimization of the net present value, NPV, criterion. Using the results of this calculation, one can select easily the supply solution for a given active power and for a given distance separating the power source and the isolated consumer. (authors)

On Random Numbers and Design

Science.gov (United States)

Ben-Ari, Morechai

2004-01-01

The term "random" is frequently used in discussion of the theory of evolution, even though the mathematical concept of randomness is problematic and of little relevance in the theory. Therefore, since the core concept of the theory of evolution is the non-random process of natural selection, the term random should not be used in teaching the…

Comparison of seismic isolation concepts for FBR

International Nuclear Information System (INIS)

Shiojiri, H.; Mazda, T.; Kasai, H.; Kanda, J.N.; Kubo, T.; Madokoro, M.; Shimomura, T.; Nojima, O.

1989-01-01

This paper seeks to verify the reliability and effectiveness of seismic isolation for FBR. Some results of the preliminary study of the program are described. Seismic isolation concepts and corresponding seismic isolation devices were selected. Three kinds of seismically-isolated FBR plant concepts were developed by applying promising seismic isolation concepts to the non-isolated FBR plant, and by developing plant component layout plans and building structural designs. Each plant was subjected to seismic response analysis and reduction in the amount of material of components and buildings were estimated for each seismic isolation concepts. Research and development items were evaluated

Antimicrobial susceptibility survey of pathogens isolated from selected patients in Northern Italy

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Elisabetta Maioli

2005-03-01

Full Text Available The Clinical Microbiology Laboratory of the University of Genoa participated, during the year 2003, in an international antimicrobial surveillance program.The collection of isolates was done according to the site of infection and/or type of patient. Four hundred twenty (420 clinical isolates were analyzed during this year and the frequencies of the different pathogens were investigated. A reference centre carried out susceptibility tests. Oxacillin-resistant Staphylococcus aureus represented 47.6% of all S. aureus isolates from blood stream infections and 33.3% of all S. aureus isolated from skin and soft tissue infections in hospitalised patients.These strains showed resistance to most of the antimicrobial agents evaluated, except vancomycin, teicoplanin, quinupristin/dalfopristin and linezolid which registered 100% of susceptibility. Some isolates from blood stream infections such as E. coli demonstrated resistance to ciprofloxacin (23.3%, levofloxacin (20%, and gatifloxacin (16.6%, and Klebsiella pneumoniae was resistant (18% to all fluoroquinolones tested. Pseudomonas aeruginosa manifested resistance to ciprofloxacin (16.6%, while 27.7% of these strains were resistant both to levofloxacin and gatifloxacin. All the Enterobacter cloacae isolated from blood were susceptible to ciprofloxacin, levofloxacin and gatifloxacin. Haemophilus influenzae and Moraxella catarrhalis collected from community-acquired respiratory tract infections were all inhibited by ciprofloxacin, levofloxacin and gatifloxacin. E. coli isolated from urinary tract infections in hospitalised patients were resistant to ciprofloxacin, levofloxacin and gatifloxacin (2.7%. All Salmonella spp. collected from samples of patients affected by infections of the gastro-intestinal tract were susceptible to all fluoroquinolones. Penicillin resistance in Streptococcus pneumoniae was found in 21.4% of isolates from patients with respiratory tract infections. Fluoroquinolone resistance was

Selecting for Fast Protein-Protein Association As Demonstrated on a Random TEM1 Yeast Library Binding BLIP.

Science.gov (United States)

Cohen-Khait, Ruth; Schreiber, Gideon

2018-04-27

Protein-protein interactions mediate the vast majority of cellular processes. Though protein interactions obey basic chemical principles also within the cell, the in vivo physiological environment may not allow for equilibrium to be reached. Thus, in vitro measured thermodynamic affinity may not provide a complete picture of protein interactions in the biological context. Binding kinetics composed of the association and dissociation rate constants are relevant and important in the cell. Therefore, changes in protein-protein interaction kinetics have a significant impact on the in vivo activity of the proteins. The common protocol for the selection of tighter binders from a mutant library selects for protein complexes with slower dissociation rate constants. Here we describe a method to specifically select for variants with faster association rate constants by using pre-equilibrium selection, starting from a large random library. Toward this end, we refine the selection conditions of a TEM1-β-lactamase library against its natural nanomolar affinity binder β-lactamase inhibitor protein (BLIP). The optimal selection conditions depend on the ligand concentration and on the incubation time. In addition, we show that a second sort of the library helps to separate signal from noise, resulting in a higher percent of faster binders in the selected library. Fast associating protein variants are of particular interest for drug development and other biotechnological applications.

Selected fault testing of electronic isolation devices used in nuclear power plant operation

International Nuclear Information System (INIS)

Villaran, M.; Hillman, K.; Taylor, J.; Lara, J.; Wilhelm, W.

1994-05-01

Electronic isolation devices are used in nuclear power plants to provide electrical separation between safety and non-safety circuits and systems. Major fault testing in an earlier program indicated that some energy may pass through an isolation device when a fault at the maximum credible potential is applied in the transverse mode to its output terminals. During subsequent field qualification testing of isolators, concerns were raised that the worst case fault, that is, the maximum credible fault (MCF), may not occur with a fault at the maximum credible potential, but rather at some lower potential. The present test program investigates whether problems can arise when fault levels up to the MCF potential are applied to the output terminals of an isolator. The fault energy passed through an isolated device during a fault was measured to determine whether the levels are great enough to potentially damage or degrade performance of equipment on the input (Class 1E) side of the isolator

MOX Fabrication Isolation Considerations

Energy Technology Data Exchange (ETDEWEB)

Eric L. Shaber; Bradley J Schrader

2005-08-01

This document provides a technical position on the preferred level of isolation to fabricate demonstration quantities of mixed oxide transmutation fuels. The Advanced Fuel Cycle Initiative should design and construct automated glovebox fabrication lines for this purpose. This level of isolation adequately protects the health and safety of workers and the general public for all mixed oxide (and other transmutation fuel) manufacturing efforts while retaining flexibility, allowing parallel development and setup, and minimizing capital expense. The basis regulations, issues, and advantages/disadvantages of five potential forms of isolation are summarized here as justification for selection of the preferred technical position.

A Permutation Importance-Based Feature Selection Method for Short-Term Electricity Load Forecasting Using Random Forest

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Nantian Huang

2016-09-01

Full Text Available The prediction accuracy of short-term load forecast (STLF depends on prediction model choice and feature selection result. In this paper, a novel random forest (RF-based feature selection method for STLF is proposed. First, 243 related features were extracted from historical load data and the time information of prediction points to form the original feature set. Subsequently, the original feature set was used to train an RF as the original model. After the training process, the prediction error of the original model on the test set was recorded and the permutation importance (PI value of each feature was obtained. Then, an improved sequential backward search method was used to select the optimal forecasting feature subset based on the PI value of each feature. Finally, the optimal forecasting feature subset was used to train a new RF model as the final prediction model. Experiments showed that the prediction accuracy of RF trained by the optimal forecasting feature subset was higher than that of the original model and comparative models based on support vector regression and artificial neural network.

Topical antibiotics as a major contextual hazard toward bacteremia within selective digestive decontamination studies: a meta-analysis.

Science.gov (United States)

Hurley, James C

2014-12-31

Among methods for preventing pneumonia and possibly also bacteremia in intensive care unit (ICU) patients, Selective Digestive Decontamination (SDD) appears most effective within randomized concurrent controlled trials (RCCT's) although more recent trials have been cluster randomized. However, of the SDD components, whether protocolized parenteral antibiotic prophylaxis (PPAP) is required, and whether the topical antibiotic actually presents a contextual hazard, remain unresolved. The objective here is to compare the bacteremia rates and patterns of isolates in SDD-RCCT's versus the broader evidence base. Bacteremia incidence proportion data were extracted from component (control and intervention) groups decanted from studies investigating antibiotic (SDD) or non-antibiotic methods of VAP prevention and summarized using random effects meta-analysis of study and group level data. A reference category of groups derived from purely observational studies without any prevention method under study provided a benchmark incidence. Within SDD RCCTs, the mean bacteremia incidence among concurrent component groups not exposed to PPAP (27 control; 17.1%; 13.1-22.1% and 12 intervention groups; 16.2%; 9.1-27.3%) is double that of the benchmark bacteremia incidence derived from 39 benchmark groups (8.3; 6.8-10.2%) and also 20 control groups from studies of non-antibiotic methods (7.1%; 4.8 - 10.5). There is a selective increase in coagulase negative staphylococci (CNS) but not in Pseudomonas aeruginosa among bacteremia isolates within control groups of SDD-RCCT's versus benchmark groups with data available. The topical antibiotic component of SDD presents a major contextual hazard toward bacteremia against which the PPAP component partially mitigates.

Direct random insertion mutagenesis of Helicobacter pylori

NARCIS (Netherlands)

de Jonge, Ramon; Bakker, Dennis; van Vliet, Arnoud H. M.; Kuipers, Ernst J.; Vandenbroucke-Grauls, Christina M. J. E.; Kusters, Johannes G.

2003-01-01

Random insertion mutagenesis is a widely used technique for the identification of bacterial virulence genes. Most strategies for random mutagenesis involve cloning in Escherichia coli for passage of plasmids or for phenotypic selection. This can result in biased selection due to restriction or

Direct random insertion mutagenesis of Helicobacter pylori.

NARCIS (Netherlands)

Jonge, de R.; Bakker, D.; Vliet, van AH; Kuipers, E.J.; Vandenbroucke-Grauls, C.M.J.E.; Kusters, J.G.

2003-01-01

Random insertion mutagenesis is a widely used technique for the identification of bacterial virulence genes. Most strategies for random mutagenesis involve cloning in Escherichia coli for passage of plasmids or for phenotypic selection. This can result in biased selection due to restriction or

Enterotoxigenicity of Staphylococcus aureus isolated from traditional and commercial dairy products marketed in Iran

Directory of Open Access Journals (Sweden)

Ebrahim Rahimi

2013-01-01

Full Text Available This study was conducted to determine the prevalence rate, enterotoxigenecity, and antimicrobial resistance of S. aureus isolated from dairy products in Iran. From September 2010 to July 2011, a total of 347 samples from various dairy products, traditional and commercial, were collected from randomly selected retail stores. Overall, 20 samples (5.8% were found to be contaminated with S. aureus. The highest prevalence of S. aureus was found in traditional cheese (11.1%, followed by traditional ice-cream (5.9%, cream (5.6%, and butter (5.3%. The ability to synthesize classical staphylococcal enterotoxins (SEA-E was determined in 7 of 20 (35% isolates by using ELISA. SE type C was the most common enterotoxin found in the isolated S. aureus (42.9%, followed by SE type A (28.6%, SEA+SEC and SE type D (14.3%. Of the 20 isolates, 16 (80.0% were positive for one or more entrotoxin genes and 8 different genotypes were observed. Susceptibilities of the isolates were determined for 14 antimicrobial drugs using the disk diffusion assay. Most of the isolates (95.0% were resistant to one or more two antimicrobial agent and 45.0% of the isolates were resistant to three or more of drugs. Resistance to ampicillin was the most common finding (55.0%, followed by tetracycline (40.0% and penicillin G (30.0%. The results of this study showed the wide spread of enterotoxigenic and multidrug-resistant S. aureus strains in traditional dairy products in Iran and highlighted their public health hazards.

Isolation of saprophytic Leptospira spp. from a selected environmental water source of Argentina.

Science.gov (United States)

Scialfa, Exequiel; Grune, Sylvia; Brihuega, Bibiana; Aguirre, Pablo; Rivero, Marina

2017-11-29

Ten Leptospira spp. strains were isolated from water samples from Nievas stream, Olavarría, Buenos Aires province (Argentina). The isolates showed the typical motility and morphology of the genus Leptospira under dark field microscopy, developing in liquid EMJH medium after eight days of incubation at 13°C and 30°C. All isolates were negative by the Multiple Locus Variable Number Tandem Repeat Analysis (MLVA). Molecular identification by 16S rRNA gene sequencing identified all isolates as nonpathogenic leptospires. Four isolates showed a genetic profile identical to that of the reference strain Leptospira biflexa serovar Patoc, and six isolates revealed sequence similarities within the 97-98% range, closely related to Leptospira yanagawae and Leptospira meyeri, respectively. Strains ScialfaASA42, ScialfaASA45, ScialfaASA44, ScialfaASA47, ScialfaASA49, ScialfaASA50 and ScialfaASA51 possibly represent a novel species of the genus Leptospira. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Random mutagenesis of the hyperthermophilic archaeon Pyrococcus furiosus using in vitro mariner transposition and natural transformation.

Science.gov (United States)

Guschinskaya, Natalia; Brunel, Romain; Tourte, Maxime; Lipscomb, Gina L; Adams, Michael W W; Oger, Philippe; Charpentier, Xavier

2016-11-08

Transposition mutagenesis is a powerful tool to identify the function of genes, reveal essential genes and generally to unravel the genetic basis of living organisms. However, transposon-mediated mutagenesis has only been successfully applied to a limited number of archaeal species and has never been reported in Thermococcales. Here, we report random insertion mutagenesis in the hyperthermophilic archaeon Pyrococcus furiosus. The strategy takes advantage of the natural transformability of derivatives of the P. furiosus COM1 strain and of in vitro Mariner-based transposition. A transposon bearing a genetic marker is randomly transposed in vitro in genomic DNA that is then used for natural transformation of P. furiosus. A small-scale transposition reaction routinely generates several hundred and up to two thousands transformants. Southern analysis and sequencing showed that the obtained mutants contain a single and random genomic insertion. Polyploidy has been reported in Thermococcales and P. furiosus is suspected of being polyploid. Yet, about half of the mutants obtained on the first selection are homozygous for the transposon insertion. Two rounds of isolation on selective medium were sufficient to obtain gene conversion in initially heterozygous mutants. This transposition mutagenesis strategy will greatly facilitate functional exploration of the Thermococcales genomes.

Selective oropharyngeal decontamination versus selective digestive decontamination in critically ill patients: a meta-analysis of randomized controlled trials

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Zhao D

2015-07-01

Full Text Available Di Zhao,1,* Jian Song,2,* Xuan Gao,3 Fei Gao,4 Yupeng Wu,2 Yingying Lu,5 Kai Hou1 1Department of Neurosurgery, The First Hospital of Hebei Medical University, 2Department of Neurosurgery, 3Department of Neurology, The Second Hospital of Hebei Medical University, 4Hebei Provincial Procurement Centers for Medical Drugs and Devices, 5Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang People’s Republic of China *These authors contributed equally to this work Background: Selective digestive decontamination (SDD and selective oropharyngeal decontamination (SOD are associated with reduced mortality and infection rates among patients in intensive care units (ICUs; however, whether SOD has a superior effect than SDD remains uncertain. Hence, we conducted a meta-analysis of randomized controlled trials (RCTs to compare SOD with SDD in terms of clinical outcomes and antimicrobial resistance rates in patients who were critically ill. Methods: RCTs published in PubMed, Embase, and Web of Science were systematically reviewed to compare the effects of SOD and SDD in patients who were critically ill. Outcomes included day-28 mortality, length of ICU stay, length of hospital stay, duration of mechanical ventilation, ICU-acquired bacteremia, and prevalence of antibiotic-resistant Gram-negative bacteria. Results were expressed as risk ratio (RR with 95% confidence intervals (CIs, and weighted mean differences (WMDs with 95% CIs. Pooled estimates were performed using a fixed-effects model or random-effects model, depending on the heterogeneity among studies. Results: A total of four RCTs involving 23,822 patients met the inclusion criteria and were included in this meta-analysis. Among patients whose admitting specialty was surgery, cardiothoracic surgery (57.3% and neurosurgery (29.7% were the two main types of surgery being performed. Pooled results showed that SOD had similar effects as SDD in day-28 mortality (RR =1

Isolation of peat swamp forest foliar endophyte fungi as biofertilizer

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Safinah Surya Hakim

2017-01-01

Full Text Available Peatland restoration activity is facing many obstacles, particularly in planting techniques and poor nutrient in peat soil. Naturally, endophytic fungi are abundant and have great potential as biofertilizer. This research investigates the potential endophytic fungi isolated from leaves of peat swamp tree species for biofertilizer. Research activities include: exploration, in vitro test to examine the phosphate solubilization and identification. Result showed that there were 360 leave segments collected from 4 sampling locations. The colonization percentage of 222 isolates ranged from 52.17% - 60.17%. Fifty seven morphospecies were selected from 222 isolates. Twelve isolates demonstrated ability to produce clear zones and ten isolates were selected for identification. It is concluded that twelve isolated demonstrated potential ability to produce clear zone and Penicillum citrinum isolate P3.10 was identified as an isolate that show the highest potential ability as a biofertilizer

Comparação da eficiência dos caldos de enriquecimento seletivo no isolamento de Salmonella Dublin Comparison of the efficiency of selective enrichment broths for Salmonella Dublin isolation

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D.G. Silva

2008-06-01

Full Text Available The aim of this study was to compare three different selective enrichment broths: Rappaport-Vassiliadis (RV, selenite cystine (SC and Muller-Kauffmann tetrathionate (MKT for Salmonella Dublin isolation from faecal samples of calf experimentally infected. The bacteriological procedure involved pre-enrichment stages in Hajna-GN broth (only for the samples inoculated in RV broth, selective enrichment, culture in modified brilliant green agar (BGA, presumptive biochemistry tests (using triple-sugar-iron agar and lysine-agar and slide agglutination test with poli-O and poli-H Salmonella antiserum. The effects of enrichment temperatures using RV broth were also evaluated (37ºC and 42ºC. SC broth was significantly more efficient in the isolation of Salmonella Dublin (P<0,05, whereas RV broth incubated at 42ºC had a lower efficiency in the microbiological isolation.

Antibacterial Activities of Lactic Acid Bacteria Isolated from Selected ...

African Journals Online (AJOL)

Members of lactic acid bacteria (LAB) are known probiotics and have been reported to have antimicrobial properties. Although various researchers have documented the isolation of these bacteria from fruits and vegetables, studies on LAB associated with lettuce, cucumber and cabbage are limited and non-existing in ...

Strategyproof Peer Selection using Randomization, Partitioning, and Apportionment

OpenAIRE

Aziz, Haris; Lev, Omer; Mattei, Nicholas; Rosenschein, Jeffrey S.; Walsh, Toby

2016-01-01

Peer review, evaluation, and selection is a fundamental aspect of modern science. Funding bodies the world over employ experts to review and select the best proposals of those submitted for funding. The problem of peer selection, however, is much more general: a professional society may want to give a subset of its members awards based on the opinions of all members; an instructor for a MOOC or online course may want to crowdsource grading; or a marketing company may select ideas from group b...

Isolation and characterization of iron chelators from turmeric (Curcuma longa): selective metal binding by curcuminoids.

Science.gov (United States)

Messner, Donald J; Surrago, Christine; Fiordalisi, Celia; Chung, Wing Yin; Kowdley, Kris V

2017-10-01

Iron overload disorders may be treated by chelation therapy. This study describes a novel method for isolating iron chelators from complex mixtures including plant extracts. We demonstrate the one-step isolation of curcuminoids from turmeric, the medicinal food spice derived from Curcuma longa. The method uses iron-nitrilotriacetic acid (NTA)-agarose, to which curcumin binds rapidly, specifically, and reversibly. Curcumin, demethoxycurcumin, and bisdemethoxycurcumin each bound iron-NTA-agarose with comparable affinities and a stoichiometry near 1. Analyses of binding efficiencies and purity demonstrated that curcuminoids comprise the primary iron binding compounds recovered from a crude turmeric extract. Competition of curcuminoid binding to the iron resin was used to characterize the metal binding site on curcumin and to detect iron binding by added chelators. Curcumin-Iron-NTA-agarose binding was inhibited by other metals with relative potency: (>90% inhibition) Cu 2+  ~ Al 3+  > Zn 2+  ≥ Ca 2+  ~ Mg 2+  ~ Mn 2+ (80% by addition of iron to the media; uptake was completely restored by desferoxamine. Ranking of metals by relative potencies for blocking curcumin uptake agreed with their relative potencies in blocking curcumin binding to iron-NTA-agarose. We conclude that curcumin can selectively bind toxic metals including iron in a physiological setting, and propose inhibition of curcumin binding to iron-NTA-agarose for iron chelator screening.

Evaluation of isolation methods for pathogenic Yersinia enterocolitica from pig intestinal content.

Science.gov (United States)

Laukkanen, R; Hakkinen, M; Lundén, J; Fredriksson-Ahomaa, M; Johansson, T; Korkeala, H

2010-03-01

The aim of this study was to evaluate the efficiency of four isolation methods for the detection of pathogenic Yersinia enterocolitica from pig intestinal content. The four methods comprised of 15 isolation steps using selective enrichments (irgasan-ticarcillin-potassium chlorate and modified Rappaport broth) and mildly selective enrichments at 4 or 25 degrees C. Salmonella-Shigella-desoxycholate-calcium chloride agar, cefsulodin-irgasan-novobiocin agar were used as plating media. The most sensitive method detected 78% (53/68) of the positive samples. Individual isolation steps using cold enrichment as the only enrichment or as a pre-enrichment step with further selective enrichment showed the highest sensitivities (55-66%). All isolation methods resulted in high numbers of suspected colonies not confirmed as pathogenic Y. enterocolitica. Cold enrichment should be used in the detection of pathogenic Y. enterocolitica from pig intestinal contents. In addition, more than one parallel isolation step is needed. The study shows that depending on the isolation method used for Y. enterocolitica, the detected prevalence of Y. enterocolitica in pig intestinal contents varies greatly. More selective and sensitive isolation methods need to be developed for pathogenic Y. enterocolitica.

Impact of cell lines included in enterovirus isolation protocol on perception of nonpolio enterovirus species C diversity.

Science.gov (United States)

Adeniji, Johnson Adekunle; Faleye, Temitope Oluwasegun Cephas

2014-10-01

There has been under-reporting of nonpolio enterovirus species Cs (NPESCs) in Nigeria despite the fact that most isolates recovered from the Nigerian vaccine derived poliovirus serotype 2 (VDPV2) outbreak were recombinants with nonstructural region of NPESC origin. It has been suggested that cell lines included in enterovirus isolation protocols might account for this phenomenon and this study examined this suggestion. Fifteen environmental samples concentrated previously and analysed using L20B and RD cell lines as part of the poliovirus environmental surveillance (ES) program in Nigeria were randomly selected and inoculated into two cell lines (MCF-7 and LLC-MK2). Isolates were identified as enteroviruses and species C members using different RT-PCR assays, culture in L20B cell line and sequencing of partial VP1. Forty-eight (48) isolates were recovered from the 15 samples, 47 (97.9%) of which were enteroviruses. Of the enteroviruses, 32 (68.1%) belonged to enterovirus species C (EC) of which 19 (40.4%) were polioviruses and 13 (27.7%) were NPESC members. All 13 NPESC isolates were recovered on MCF-7. Results of the study show that NPESCs are circulating in Nigeria and their under-reporting was due to the combination of cell lines used for enterovirus isolation in previous reports. Copyright © 2014 Elsevier B.V. All rights reserved.

Selection of Beauveria bassiana sensu lato and Metarhizium anisopliae sensu lato isolates as microbial control agents against the boll weevil (Anthonomus grandis) in Argentina.

Science.gov (United States)

Nussenbaum, A L; Lecuona, R E

2012-05-01

The boll weevil (Anthonomus grandis) is the main pest of cotton in the Americas. The aim of this work was to evaluate isolates of the entomopathogenic fungi Beauveria bassiana sensu lato and Metarhizium anisopliae sensu lato virulent against A. grandis. Screening was performed to evaluate the pathogenicity of 28 isolates of M. anisopliae s.l. and 66 isolates of B. bassiana s.l. against boll weevil adults. To select the isolates, LC(50) values of the most virulent isolates were calculated, and compatibility between the fungi and insecticides was studied. In addition, the effects of these isolates on the feeding behavior of the adults were evaluated. Isolates Ma 50 and Ma 20 were the most virulent against A. grandis and their LC(50) values were 1.13×10(7) and 1.20×10(7) conidia/ml, respectively. In addition, these isolates were compatible with pyrethroid insecticides, but none with endosulfan. On the other hand, infected females reduced the damage caused by feeding on the cotton squares and their weight gain. This shows that entomopathogenic fungi cause mortality in the insects, but also these fungi could influence the feeding behavior of the females. In summary, these results indicate the possibility of the use of M. anisopliae s.l. as a microbiological control agent against boll weevils. Also, this species could be included in an Integrated Pest Management program. Copyright © 2012 Elsevier Inc. All rights reserved.

Isolated trochlear nerve palsy with midbrain hemorrhage

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Raghavendra S

2010-01-01

Full Text Available Midbrain hemorrhage causing isolated fourth nerve palsy is extremely rare. Idiopathic, traumatic and congenital abnormalities are the most common causes of fourth nerve palsy. We report acute isolated fourth nerve palsy in an 18-year-old lady due to a midbrain hemorrhage probably due to a midbrain cavernoma. The case highlights the need for neuroimaging in selected cases of isolated trochlear nerve palsy.

47 CFR 1.1604 - Post-selection hearings.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 1 2010-10-01 2010-10-01 false Post-selection hearings. 1.1604 Section 1.1604 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Random Selection Procedures for Mass Media Services General Procedures § 1.1604 Post-selection hearings. (a) Following the random...

Molecular detection of genes encoding AcrAB , Qep A efflux pumps in Klebsiella pneumoniae strains isolated from hospitalized patients in selected hospitals in Tehran

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Mohsen Heidary

2017-03-01

Full Text Available Abstract Background and Objectives: Increasing emergence of fluoroquinolone resistance among clinical isolates of Klebsiella pneumoniae  (K. pneumoniae, has limited the treatment options for treatment of infections caused by these bacteria. The aim of this study was to investigate the dissemination of genes encoding AcrAB and QepA efflux pumps among K. pneumoniae strains. Methods: This study was carried out on 117 K. pneumoniae strains isolated from patients hospitalized in selected hospitals in Tehran city, 2015-2016, Iran. Antimicrobial susceptibility tests were performed using disk diffusion method (based on CLSI guidelines and identification of acr A, acr B and qep A genes using PCR assay. Results: In this study, colistin and tigecycline had the best effect against clinical isolates of K. pneumoniae. According to PCR results, 110 (94% isolates had acrA gene and 102 (87% isolates had acrB gene, respectively. The qepA gene was not found in any of the K. pneumoniae strains. Conclusion: According to the results of the present study, dissemination of the genes encoding AcrAB efflux pumps among K. pneumoniae strains, which cause resistance to fluoroquinolones, is a matter of concern. Therefore, infection control and prevention of the spread of drug-resistant bacteria requires careful management in drug prescription and identification of resistant isolates.

Random genetic drift, natural selection, and noise in human cranial evolution.

Science.gov (United States)

Roseman, Charles C

2016-08-01

This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

HIV-1 isolation from infected peripheral blood mononuclear cells

NARCIS (Netherlands)

Dispinseri, Stefania; Saba, Elisa; Vicenzi, Elisa; Kootstra, Neeltje A.; Schuitemaker, Hanneke; Scarlatti, Gabriella

2014-01-01

Human immunodeficiency virus 1 (HIV-1) isolation from peripheral blood mononuclear cells (PBMCs) allows retrieval of replication-competent viral variants. In order to impose the smallest possible selective pressure on the viral isolates, isolation must be carried out in primary cultures of cells and

Patterns of reproductive isolation in the Drosophila subquinaria complex: can reinforced premating isolation cascade to other species?

Science.gov (United States)

Humphreys, Devon P.; Rundle, Howard D.; Dyer, Kelly A.

2016-01-01

Abstract The reinforcement of premating barriers due to reduced hybrid fitness in sympatry may cause secondary sexual isolation within a species as a by-product. Consistent with this, in the fly Drosophila subquinaria, females that are sympatric with D. recens mate at very low rates not only with D. recens, but also with conspecific D. subquinaria males from allopatry. Here, we ask if these effects of reinforcement cascade more broadly to affect sexual isolation with other closely related species. We assay reproductive isolation of these species with D. transversa and find that choosy D. subquinaria females from the region sympatric with D. recens discriminate strongly against male D. transversa, whereas D. subquinaria from the allopatric region do not. This increased sexual isolation cannot be explained by natural selection to avoid mating with this species, as they are allopatric in geographic range and we do not identify any intrinsic postzygotic isolation between D. subquinaria and D. transversa. Variation in epicuticular hydrocarbons, which are used as mating signals in D. subquinaria, follow patterns of premating isolation: D. transversa and allopatric D. subquinaria are most similar to each other and differ from sympatric D. subquinaria, and those of D. recens are distinct from the other two species. We suggest that the secondary effects of reinforcement may cascade to strengthen reproductive isolation with other species that were not a target of selection. These effects may enhance the divergence that occurs in allopatry to help explain why some species are already sexually isolated upon secondary contact. PMID:29491905

Development of novel agar media for isolating guaiacol producing Alicyclobacillus spp.

Science.gov (United States)

Chang, S S; Park, S H; Kang, D H

2013-06-03

The purpose of this study is to develop a selective and differential medium (SK2 agar) for isolating guaiacol producing Alicyclobacillus. Forty-one selected dyes and vanillic acid were incorporated in SK agar for screening selective and differential agents. Two guaiacol producing (1016, 1101) and two non-guaiacol producing (19220, C-GD 1-1) Alicyclobacillus isolates were streaked onto media and color differentiation of the isolates was assessed. Among 41 tested dyes, Chrome Azurol S (CAS) allowed color differentiation of the two types of Alicyclobacillus. Colonies of guaiacol producing Alicyclobacillus isolates appeared as dark purple to royal blue color with yellow background, whereas non-guaiacol producing Alicyclobacillus isolates produced cream colored colonies with yellow background. Vanillic acid not only served as a precursor for guaiacol formation but also inhibited non-guaiacol producing Alicyclobacillus. Non-guaiacol producing isolates did not grow on SK agar containing more than 70 ppm vanillic acid, whereas the recovery of guaiacol producing isolates was unaffected. When compared with other Alicyclobacillus isolation media, not only was SK2 agar capable of selectively recovering guaiacol-producing Alicyclobacillus, the degree of growth was also approximately equal if not better than orange serum agar, potato dextrose agar, and K agar. The development of SK2 agar provides the fruit juice industry with an inexpensive, simple to use alternative for the detection of guaiacol producing Alicyclobacillus. Copyright © 2013 Elsevier B.V. All rights reserved.

Diversity of Geotrichum candidum strains isolated from traditional cheesemaking fabrications in France.

Science.gov (United States)

Marcellino, N; Beuvier, E; Grappin, R; Guéguen, M; Benson, D R

2001-10-01

The diversity of French fungus-ripened cheeses is due partly to the succession of fungi that colonize the cheese during ripening. Geotrichum candidum appears in the early stages of ripening on soft cheeses such as Camembert and semihard cheeses such as St. Nectaire and Reblochon. Its lipases and proteases promote flavor development, and its aminopeptidases reduce bitterness imparted by low-molecular-weight peptides in cheese. We assessed the genetic diversity of G. candidum strains by using random amplification of polymorphic DNA (RAPD)-PCR correlated with phenotypic tests for carbon assimilation and salt tolerance. Strains were isolated from milk, curd, and cheese collected in seven major cheesemaking regions of France. Sixty-four isolates were characterized. We found high genetic diversity of G. candidum even within the same cheesemaking regions. Strains did not group according to region. All of the strains from the Haute-Savoie were able to assimilate lactate as the sole source of carbon, while lactate assimilation varied among strains from the Auvergne. Strains varied in D-mannitol assimilation, and none used citrate as the sole source of carbon. Yeast-like colony morphology predominated in Reblochon, while all of the strains isolated from St. Nectaire were filamentous. The RAPD-PCR technique readily differentiated Geotrichum fragrans isolated from milk and curd in a St. Nectaire cheesemaking facility. This study reveals an enormous diversity of G. candidum that has been empirically selected through the centuries by the cheesemakers of France.

Assessing the accuracy and stability of variable selection methods for random forest modeling in ecology.

Science.gov (United States)

Fox, Eric W; Hill, Ryan A; Leibowitz, Scott G; Olsen, Anthony R; Thornbrugh, Darren J; Weber, Marc H

2017-07-01

Random forest (RF) modeling has emerged as an important statistical learning method in ecology due to its exceptional predictive performance. However, for large and complex ecological data sets, there is limited guidance on variable selection methods for RF modeling. Typically, either a preselected set of predictor variables are used or stepwise procedures are employed which iteratively remove variables according to their importance measures. This paper investigates the application of variable selection methods to RF models for predicting probable biological stream condition. Our motivating data set consists of the good/poor condition of n = 1365 stream survey sites from the 2008/2009 National Rivers and Stream Assessment, and a large set (p = 212) of landscape features from the StreamCat data set as potential predictors. We compare two types of RF models: a full variable set model with all 212 predictors and a reduced variable set model selected using a backward elimination approach. We assess model accuracy using RF's internal out-of-bag estimate, and a cross-validation procedure with validation folds external to the variable selection process. We also assess the stability of the spatial predictions generated by the RF models to changes in the number of predictors and argue that model selection needs to consider both accuracy and stability. The results suggest that RF modeling is robust to the inclusion of many variables of moderate to low importance. We found no substantial improvement in cross-validated accuracy as a result of variable reduction. Moreover, the backward elimination procedure tended to select too few variables and exhibited numerous issues such as upwardly biased out-of-bag accuracy estimates and instabilities in the spatial predictions. We use simulations to further support and generalize results from the analysis of real data. A main purpose of this work is to elucidate issues of model selection bias and instability to ecologists interested in

Frequency of isolation and antibiotic resistance patterns of bacterial isolates from wound infections

Directory of Open Access Journals (Sweden)

Stojanović-Radić, Z.

2016-12-01

Full Text Available Six hundred and thirteen bacterial strains were isolated from wound swabs and the isolates were identified on the basis of growth on differential and selective media. In order to test the sensitivity of isolated strains to different antibiotics, the disc diffusion method, according to EUCAST protocol v 5.0 was used. The most common species isolated from wound swabs was Staphylococcus epidermidis (18.4%, followed by Staphylococcus aureus, Pseudomonas aeruginosa and Enterococcus faecalis (16.8%, 12.7% and 10.4%, respectively. The maximum resistance of Gram-positive cocci was observed to penicillin and the lowest to linezolid. Gram-negative bacteria showed the highest resistance to tetracyclines, while the same strains demonstrated the highest sensitivity to polypeptide antibiotics. Comparison of the resistance patterns of Gramnegative and Gram-positive bacterial strains showed significant difference in the tetracycline efficiency.

Emerging moxifloxacin resistance in Pseudomonas aeruginosa keratitis isolates in South India.

Science.gov (United States)

Oldenburg, Catherine E; Lalitha, Prajna; Srinivasan, Muthiah; Rajaraman, Revathi; Ravindran, Meenakshi; Mascarenhas, Jeena; Borkar, Durga S; Ray, Kathryn J; Zegans, Michael E; McLeod, Stephen D; Porco, Travis C; Lietman, Thomas M; Acharya, Nisha R

2013-06-01

To describe temporal trends in Pseudomonas aeruginosa resistance to moxifloxacin in keratitis isolates from South India. The Steroids for Corneal Ulcers Trial (SCUT) was a randomized, double-masked, placebo-controlled trial assessing outcomes in patients with culture positive bacterial corneal ulcers randomized to receive prednisolone phosphate or placebo. All patients received moxifloxacin, and susceptibility to moxifloxacin was measured at baseline using Etest. We investigated trends in moxifloxacin susceptibility of P. aeruginosa during 2007, 2008, and 2009 isolated in SCUT in South India. There were 89 P. aeruginosa isolates during 2007, 2008, and 2009 in SCUT that were eligible for this study. There was an increase in the proportion of resistant isolates from 19% in 2007 to 52% in 2009 (p = 0.02, χ(2) test for trend). Logistic regression showed that there was a 2-fold increase in odds of resistance per 1 year increase during the study period (odds ratio 2.16, 95% confidence interval 1.09-4.26, p = 0.027). We found a sharp increase in the proportion of isolates that were resistant to moxifloxacin from 2007 to 2009. Further work needs to be done to characterize the nature of this increase.

Selection of rhizosphere local microbial as bioactive inoculant based on irradiated compost

International Nuclear Information System (INIS)

Dadang Sudrajat; Nana Mulyana; Arief Adhari

2014-01-01

One of the main components of carrier based on irradiation compost for bio organic fertilizer is a potential microbial isolates role in nutrient supply and growth hormone. This research was conducted to obtain microbial isolates from plant root zone (rhizosphere), further isolation and selection in order to obtain potential isolates capable of nitrogen fixation (N 2 ), resulting in growth hormone (Indole Acetic Acid), and phosphate solubilizing. Selected potential isolates used as bioactive microbial inoculants formulation in irradiation compost based. Forty eight (48) rhizosphere samples were collected from different areas of West and Central Java. One hundred sixteen (116) isolates have been characterized for their morphological, cultural, staining and biochemical characteristics. Isolates have been selected for further screening of PGPR traits. Parameters assessed were Indole Acetic Acid (IAA) content analysis with colorimetric methods, dinitrogen fixation using gas chromatography, phosphate solubility test qualitatively (in the media pikovskaya) and quantitative assay of dissolved phosphate (spectrophotometry). Evaluation of the ability of selected isolates on the growth of corn plants were done in pots. The isolates will be used as inoculant consortium base on compost irradiation. The selection obtained eight (8) bacterial isolates identified as Bacillus circulans (3 isolates), Bacillus stearothermophilus (1 isolate), Azotobacter sp (3 isolates), Pseudomonas diminuta (1 isolate). The highest phosphate released (91,21 mg/l) was by BD2 isolate (Bacillus circulan) with a holo zone size (1.32 cm) on Pikovskaya agar medium. Isolate of Pseudomonas diminuta (KACI) was capable to produce the highest IAA hormone (74.34 μg/ml). The highest nitrogen (N 2 ) fixation activity was shown by Azotobacter sp isolates (KDB2) at a rate of 235.05 nmol/hour. The viability test showed that all selected isolates in compost irradiation carrier slightly decreased after 3 months of

Characterization of Trypanosoma brucei gambiense stocks isolated ...

African Journals Online (AJOL)

Trypanosoma brucei gambiense was isolated twice from each of 23 patients in Côte d'Ivoire. Genetic characterization using RAPD (Random Primed Amplified Polymorphic DNA) showed additional variability within a given isoenzyme profile (zymodeme), confirming that this fingerprinting method has a higher discriminative ...

Isolated hepatic perfusion as a treatment for uveal melanoma liver metastases (the SCANDIUM trial)

DEFF Research Database (Denmark)

Olofsson, Roger; Ny, Lars; Eilard, Malin Sternby

2014-01-01

for patients with liver metastases is between 6 and 12 months, and no treatment has in randomized trials ever been shown to prolong survival. A previous phase II trial using isolated hepatic perfusion (IHP) has suggested a 14-month increase in overall survival compared with a historic control group consisting...... of the longest surviving patients in Sweden during the same time period (26 versus 12 months). METHODS/DESIGN: This is the protocol for a multicenter phase III trial randomizing patients with isolated liver metastases of uveal melanoma to IHP or best alternative care (BAC). Inclusion criteria include liver....... The planned sample size is 78 patients throughout five years. DISCUSSION: Patients with isolated liver metastases of uveal melanoma origin have a short expected survival and no standard treatment option exists. This is the first randomized clinical trial to evaluate IHP as a treatment option with overall...

Cryotherapy is preferable to ablative CO2 laser for the treatment of isolated actinic keratoses of the face and scalp: a randomized clinical trial.

Science.gov (United States)

Zane, C; Facchinetti, E; Rossi, M T; Specchia, C; Ortel, B; Calzavara-Pinton, P

2014-05-01

Actinic keratosis (AK) may progress to squamous cell carcinoma. In the case of normal or mildly photodamaged skin, lesion-directed treatments are considered valuable options despite poor published evidence of their therapeutic activity. The aim of this single-centre, open-label, prospective, nonsponsored, randomized, controlled clinical trial was to compare CO2 laser ablation with cryotherapy in the treatment of isolated AKs of the face and scalp. Patients with isolated (≤ 4) AKs of the face and scalp were randomized to receive CO2 laser ablation or cryotherapy. After 90 days, the overall complete remission (CR) rates of patients and lesions were assessed and correlated with thickness grade. Two hundred patients with a total number of 543 AKs were enrolled. The CR rates of lesions after 3 months were 78·2% with cryotherapy and 72·4% with CO2 laser ablation. Thicker lesions were significantly more responsive to cryotherapy (P = 0·034). Seventy-three patients (71·6%) had CR of all lesions 3 months after cryotherapy and 64 (65·3%) after laser ablation. At 12 months after treatment the number of patients with CR was reduced to 53 with cryotherapy and 14 with laser ablation. The rate of patients and lesions with CR is similar after 3 months, but more patients remain in stable remission for 12 months after cryotherapy. Cryotherapy is more effective for thick lesions. The cosmetic outcome was good or excellent in almost all patients. © 2014 British Association of Dermatologists.

Divergent Selection and Then What Not: The Conundrum of Missing Reproductive Isolation in Misty Lake and Stream Stickleback

Directory of Open Access Journals (Sweden)

Katja Räsänen

2012-01-01

Full Text Available In ecological speciation, reproductive isolation evolves as a consequence of adaptation to different selective environments. A frequent contributor to this process is the evolution of positive assortative mate choice between ecotypes. We tested this expectation for lake and inlet stream threespine stickleback (Gasterosteus aculeatus from the Misty system (Vancouver Island, Canada, which show strong genetically based adaptive divergence and little genetic exchange in nature. This, and work on other stickleback systems, led us to expect positive assortative mating. Yet, our standard “no-choice” laboratory experiment on common-garden fish revealed no evidence for this—despite divergence in traits typically mediating assortative mating in stickleback. These results remind us that divergent natural selection may not inevitably lead to the evolution of positive assortative mate choice. The apparent lack of strong and symmetric reproductive barriers in this system presents a conundrum: why are such barriers not evident despite strong adaptive divergence and low gene flow in nature?

Blind Measurement Selection: A Random Matrix Theory Approach

KAUST Repository

Elkhalil, Khalil; Kammoun, Abla; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim

2016-01-01

-aware fashions. We present two potential applications where the proposed algorithms can be used, namely antenna selection for uplink transmissions in large scale multi-user systems and sensor selection for wireless sensor networks. Numerical results are also

Fermentation of Apple Juice with a Selected Yeast Strain Isolated from the Fermented Foods of Himalayan Regions and Its Organoleptic Properties

OpenAIRE

Kanwar, S. S.; Keshani,

2016-01-01

Twenty-three Saccharomyces cerevisiae strains isolated from different fermented foods of Western Himalayas have been studied for strain level and functional diversity in our department. Among these 23 strains, 10 S. cerevisiae strains on the basis of variation in their brewing traits were selected to study their organoleptic effect at gene level by targeting ATF1 gene, which is responsible for ester synthesis during fermentation. Significant variation was observed in ATF1 gene sequences, sugg...

Teaching basic lung isolation skills on human anatomy simulator: attainment and retention of lung isolation skills.

Science.gov (United States)

Latif, Rana K; VanHorne, Edgar M; Kandadai, Sunitha Kanchi; Bautista, Alexander F; Neamtu, Aurel; Wadhwa, Anupama; Carter, Mary B; Ziegler, Craig H; Memon, Mohammed Faisal; Akça, Ozan

2016-01-20

Lung isolation skills, such as correct insertion of double lumen endobronchial tube and bronchial blocker, are essential in anesthesia training; however, how to teach novices these skills is underexplored. Our aims were to determine (1) if novices can be trained to a basic proficiency level of lung isolation skills, (2) whether video-didactic and simulation-based trainings are comparable in teaching lung isolation basic skills, and (3) whether novice learners' lung isolation skills decay over time without practice. First, five board certified anesthesiologist with experience of more than 100 successful lung isolations were tested on Human Airway Anatomy Simulator (HAAS) to establish Expert proficiency skill level. Thirty senior medical students, who were naive to bronchoscopy and lung isolation techniques (Novice) were randomized to video-didactic and simulation-based trainings to learn lung isolation skills. Before and after training, Novices' performances were scored for correct placement using pass/fail scoring and a 5-point Global Rating Scale (GRS); and time of insertion was recorded. Fourteen novices were retested 2 months later to assess skill decay. Experts' and novices' double lumen endobronchial tube and bronchial blocker passing rates showed similar success rates after training (P >0.99). There were no differences between the video-didactic and simulation-based methods. Novices' time of insertion decayed within 2 months without practice. Novices could be trained to basic skill proficiency level of lung isolation. Video-didactic and simulation-based methods we utilized were found equally successful in training novices for lung isolation skills. Acquired skills partially decayed without practice.

Genetic homogeneity among Ugandan isolates of Xanthomonas ...

African Journals Online (AJOL)

Seven random primers were used because of their ability to amplify reproducible and reliable fingerprints generated between 6 - 12 amplicons each from the Xcm isolates obtained from central core of pseudostems, peduncles, fruit peelings, sap, nectar, insects' bodies and bacterial oozes. Regardless of the source and ...

Isolation of Salmonella and Shigella species from house flies ...

African Journals Online (AJOL)

Salmonella and Shigella species were isolated from House flies (Musca domestica L.) from various sampling sites using selective media. Out of 34 pooled samples Shigella species were isolated in all (100%) of the samples while Salmonella species were isolated in 21 (61.7%) of the samples. The flies pooled from the ...

A select bibliography with abstracts of reports related to Waste Isolation Pilot Plant geotechnical studies (1972--1990)

Energy Technology Data Exchange (ETDEWEB)

Powers, D.W. [Powers (Dennis W.), Anthony, TX (United States); Martin, M.L. [International Technology, Inc., Las Vegas, NV (United States)

1993-08-01

This select bibliography contains 941 entries. Each bibliographic entry contains the citation of a report, conference paper, or journal article containing geotechnical information about the Waste Isolation Pilot Plant (WIPP). The entries cover the period from 1972, when investigation began for a WIPP Site in southeastern New Mexico, through December 1990. Each entry is followed by an abstract. If an abstract or suitable summary existed, it has been included; 316 abstracts were written for other documents. For some entries, an annotation has been provided to clarify the abstract, comment on the setting and significance of the document, or guide the reader to related reports. An index of key words/phrases is included for all entries.

A select bibliography with abstracts of reports related to Waste Isolation Pilot Plant geotechnical studies (1972--1990)

International Nuclear Information System (INIS)

Powers, D.W.; Martin, M.L.

1993-08-01

This select bibliography contains 941 entries. Each bibliographic entry contains the citation of a report, conference paper, or journal article containing geotechnical information about the Waste Isolation Pilot Plant (WIPP). The entries cover the period from 1972, when investigation began for a WIPP Site in southeastern New Mexico, through December 1990. Each entry is followed by an abstract. If an abstract or suitable summary existed, it has been included; 316 abstracts were written for other documents. For some entries, an annotation has been provided to clarify the abstract, comment on the setting and significance of the document, or guide the reader to related reports. An index of key words/phrases is included for all entries

Effects of choice architecture and chef-enhanced meals on the selection and consumption of healthier school foods: a randomized clinical trial.

Science.gov (United States)

Cohen, Juliana F W; Richardson, Scott A; Cluggish, Sarah A; Parker, Ellen; Catalano, Paul J; Rimm, Eric B

2015-05-01

Little is known about the long-term effect of a chef-enhanced menu on healthier food selection and consumption in school lunchrooms. In addition, it remains unclear if extended exposure to other strategies to promote healthier foods (eg, choice architecture) also improves food selection or consumption. To evaluate the short- and long-term effects of chef-enhanced meals and extended exposure to choice architecture on healthier school food selection and consumption. A school-based randomized clinical trial was conducted during the 2011-2012 school year among 14 elementary and middle schools in 2 urban, low-income school districts (intent-to-treat analysis). Included in the study were 2638 students in grades 3 through 8 attending participating schools (38.4% of eligible participants). Schools were first randomized to receive a professional chef to improve school meal palatability (chef schools) or to a delayed intervention (control group). To assess the effect of choice architecture (smart café), all schools after 3 months were then randomized to the smart café intervention or to the control group. School food selection was recorded, and consumption was measured using plate waste methods. After 3 months, vegetable selection increased in chef vs control schools (odds ratio [OR], 1.75; 95% CI, 1.36-2.24), but there was no effect on the selection of other components or on meal consumption. After long-term or extended exposure to the chef or smart café intervention, fruit selection increased in the chef (OR, 3.08; 95% CI, 2.23-4.25), smart café (OR, 1.45; 95% CI, 1.13-1.87), and chef plus smart café (OR, 3.10; 95% CI, 2.26-4.25) schools compared with the control schools, and consumption increased in the chef schools (OR, 0.17; 95% CI, 0.03-0.30 cups/d). Vegetable selection increased in the chef (OR, 2.54; 95% CI, 1.83-3.54), smart café (OR, 1.91; 95% CI, 1.46-2.50), and chef plus smart café schools (OR, 7.38, 95% CI, 5.26-10.35) compared with the control schools

Modified random hinge transport mechanics and multiple scattering step-size selection in EGS5

International Nuclear Information System (INIS)

Wilderman, S.J.; Bielajew, A.F.

2005-01-01

The new transport mechanics in EGS5 allows for significantly longer electron transport step sizes and hence shorter computation times than required for identical problems in EGS4. But as with all Monte Carlo electron transport algorithms, certain classes of problems exhibit step-size dependencies even when operating within recommended ranges, sometimes making selection of step-sizes a daunting task for novice users. Further contributing to this problem, because of the decoupling of multiple scattering and continuous energy loss in the dual random hinge transport mechanics of EGS5, there are two independent step sizes in EGS5, one for multiple scattering and one for continuous energy loss, each of which influences speed and accuracy in a different manner. Further, whereas EGS4 used a single value of fractional energy loss (ESTEPE) to determine step sizes at all energies, to increase performance by decreasing the amount of effort expended simulating lower energy particles, EGS5 permits the fractional energy loss values which are used to determine both the multiple scattering and continuous energy loss step sizes to vary with energy. This results in requiring the user to specify four fractional energy loss values when optimizing computations for speed. Thus, in order to simplify step-size selection and to mitigate step-size dependencies, a method has been devised to automatically optimize step-size selection based on a single material dependent input related to the size of problem tally region. In this paper we discuss the new transport mechanics in EGS5 and describe the automatic step-size optimization algorithm. (author)

Social isolation, drunkenness, and cigarette use among adolescents.

Science.gov (United States)

Niño, Michael D; Cai, Tianji; Ignatow, Gabe

2016-02-01

This study compares isolated to sociable youth to investigate the relations between different network types of social isolation and alcohol and cigarette use. Using data from the National Longitudinal Study of Adolescent to Adult Health we developed a network measure that includes various types of social isolation. Types of social isolation were operationalized as socially avoidant, actively isolated, and socially disinterested, with sociable youth as the reference category. Random effects ordinal logit models were fit to estimate the association between different types of social isolation and drunkenness and cigarette use. Different types of social isolation had varying effects on drunkenness and cigarette use. On the one hand, socially disinterested youth were at an increased risk for drunkenness and cigarette use. On the other hand, socially avoidant youth had lower odds of drunkenness and no significant differences in cigarette use when compared to sociable youth. Actively isolated youth showed no differences in drunkenness and cigarette use. The role played by marginalized social positions in youth substance use is an important yet overlooked problem. This study can contribute to better targeted and more effective health behavior prevention efforts for vulnerable adolescents. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Genetic isolates and inbreeding customs in three rural municipalities from Honduras].

Science.gov (United States)

Herrera-Paz, Edwin Francisco

2016-01-01

The isonymic method has been amply used to assess the approximate genetic structure of human communities. The objective of the study was to evaluate the magnitude of genetic isolation and inbreeding customs in 57 communities from three rural municipalities of Honduras using isonymy techniques. The list of 408 different surnames from 20712 voters registered in the national electoral organism, residing in the 57 Honduran communities, was used for this study. For each community, random (IR), non-random (IN), and total (IT) isonymy values were calculated in order to assess inbreeding coefficients FST, FIS and FIT. High consanguinity due to isolation and to endogamous customs was unveiled in many communities. Significant deviation from the exogamous behavior typical of many human populations was observed in the three studied municipalities, when compared to other Honduran populations. The studied communities present high consanguinity due to isolation, ethnic segregation and/or endogamous customs.

Invitro Evaluation Of Antibacterial Activity Of Lactic Acid Bacteria Isolated From Ergo And Qotchqotcha Ethiopian Traditional Fermented Foods Against Some Selected Food Borne Pathogens

Directory of Open Access Journals (Sweden)

Lamenew Fenta

2017-09-01

Full Text Available The prevention of pathogenic bacteria by lactic acid bacteria LAB isolated directly from foods is an innovative approach. With the aim of determining the anti-bacterial activity of Lactic acid bacteria isolated from ergo and qotchqotcha Ethiopian fermented food 12 samples of each were taken from the 4 different kebeles of Assosa town. Isolation of LAB from the selected samples were carried out using MRS media. The different set of isolates were characterized using primary biochemical tests. Isolates which were gram positive catalase negative and KOH negative were considered to be presumptive LAB and further characterized by using different biochemical tests for further identification. 16 isolates from ergo samples were isolated. Based on Bergeys manual of determinative bacteriology the 16 isolates belonged to four 4 LAB species namely Lactobacillus acidophilus 18.75 Lactobacillus casei 31.25 Streptococcus thermophiles 25 and Lactobacillus bulgaricus 25. Likewise 5 isolates were isolated from Qotchqotcha and the five isolates were found to be Lactobacillus acidophilus 80 and Pediococcus acidilactici 20. Cell free solution from MRS broth culture of theses LAB was prepared and tested against Escherichia coli O157H7 and Staphylococcus aureus using agar-well diffusion method. Of the 16 isolates isolated from ergo 9 of them show antimicrobial activity against E. coli O157H7 with a largest inhibition zone measured about 7.331.20mm by EK0101 and 12 of them show antimicrobial activity against S. aureus with a largest inhibition zone measured about 11.66 0.88mm by EK0201. On the basis of morphological and biochemical test done EK0101 was found to be presumptive Lactobacillus acidophilus and EK0201 to be Streptococcus thermophiles. All of the isolates isolated from Qotchqotcha showed antimicrobial activity against the tested organisms though there was a significant difference in their activity P0.05. The isolate QK0201 showed an inhibition zone of about 6

Selected lactic acid-producing bacterial isolates with the capacity to reduce Salmonella translocation and virulence gene expression in chickens.

Directory of Open Access Journals (Sweden)

Xiaojian Yang

Full Text Available BACKGROUND: Probiotics have been used to control Salmonella colonization/infection in chickens. Yet the mechanisms of probiotic effects are not fully understood. This study has characterized our previously-selected lactic acid-producing bacterial (LAB isolates for controlling Salmonella infection in chickens, particularly the mechanism underlying the control. METHODOLOGY/PRINCIPAL FINDINGS: In vitro studies were conducted to characterize 14 LAB isolates for their tolerance to low pH (2.0 and high bile salt (0.3-1.5% and susceptibility to antibiotics. Three chicken infection trials were subsequently carried out to evaluate four of the isolates for reducing the burden of Salmonella enterica serovar Typhimurium in the broiler cecum. Chicks were gavaged with LAB cultures (10(6-7 CFU/chick or phosphate-buffered saline (PBS at 1 day of age followed by Salmonella challenge (10(4 CFU/chick next day. Samples of cecal digesta, spleen, and liver were examined for Salmonella counts on days 1, 3, or 4 post-challenge. Salmonella in the cecum from Trial 3 was also assessed for the expression of ten virulence genes located in its pathogenicity island-1 (SPI-1. These genes play a role in Salmonella intestinal invasion. Tested LAB isolates (individuals or mixed cultures were unable to lower Salmonella burden in the chicken cecum, but able to attenuate Salmonella infection in the spleen and liver. The LAB treatments also reduced almost all SPI-1 virulence gene expression (9 out of 10 in the chicken cecum, particularly at the low dose. In vitro treatment with the extracellular culture fluid from a LAB culture also down-regulated most SPI-1 virulence gene expression. CONCLUSIONS/SIGNIFICANCE: The possible correlation between attenuation of Salmonella infection in the chicken spleen and liver and reduction of Salmonella SPI-1 virulence gene expression in the chicken cecum by LAB isolates is a new observation. Suppression of Salmonella virulence gene expression in

Evolving artificial metalloenzymes via random mutagenesis

Science.gov (United States)

Yang, Hao; Swartz, Alan M.; Park, Hyun June; Srivastava, Poonam; Ellis-Guardiola, Ken; Upp, David M.; Lee, Gihoon; Belsare, Ketaki; Gu, Yifan; Zhang, Chen; Moellering, Raymond E.; Lewis, Jared C.

2018-03-01

Random mutagenesis has the potential to optimize the efficiency and selectivity of protein catalysts without requiring detailed knowledge of protein structure; however, introducing synthetic metal cofactors complicates the expression and screening of enzyme libraries, and activity arising from free cofactor must be eliminated. Here we report an efficient platform to create and screen libraries of artificial metalloenzymes (ArMs) via random mutagenesis, which we use to evolve highly selective dirhodium cyclopropanases. Error-prone PCR and combinatorial codon mutagenesis enabled multiplexed analysis of random mutations, including at sites distal to the putative ArM active site that are difficult to identify using targeted mutagenesis approaches. Variants that exhibited significantly improved selectivity for each of the cyclopropane product enantiomers were identified, and higher activity than previously reported ArM cyclopropanases obtained via targeted mutagenesis was also observed. This improved selectivity carried over to other dirhodium-catalysed transformations, including N-H, S-H and Si-H insertion, demonstrating that ArMs evolved for one reaction can serve as starting points to evolve catalysts for others.

Incidence and Antibiotic Susceptibility Pattern of Bacterial Isolates ...

African Journals Online (AJOL)

bacterial isolates. The isolates were characterized and identified by standard microbiological methods. Antibiotic susceptibility testing was carried out ... Pure cultures were characterized using morphological appearances on selective and .... J Nepal Health Res Council. 2007; 5(1): 22-26. 4. Taiwo SS, Okesina AB, Onile BA.

Ecological Divergence and the Origins of Intrinsic Postmating Isolation with Gene Flow

Directory of Open Access Journals (Sweden)

Aneil F. Agrawal

2011-01-01

Full Text Available The evolution of intrinsic postmating isolation has received much attention, both historically and in recent studies of speciation genes. Intrinsic isolation often stems from between-locus genetic incompatibilities, where alleles that function well within species are incompatible with one another when brought together in the genome of a hybrid. It can be difficult for such incompatibilities to originate when populations diverge with gene flow, because deleterious genotypic combinations will be created and then purged by selection. However, it has been argued that if genes underlying incompatibilities are themselves subject to divergent selection, then they might overcome gene flow to diverge between populations, resulting in the origin of incompatibilities. Nonetheless, there has been little explicit mathematical exploration of such scenarios for the origin of intrinsic incompatibilities during ecological speciation with gene flow. Here we explore theoretical models for the origin of intrinsic isolation where genes subject to divergent natural selection also affect intrinsic isolation, either directly or via linkage disequilibrium with other loci. Such genes indeed overcome gene flow, diverge between populations, and thus result in the evolution of intrinsic isolation. We also examine barriers to neutral gene flow. Surprisingly, we find that intrinsic isolation sometimes weakens this barrier, by impeding differentiation via ecologically based divergent selection.

Isolasi, Seleksi Dan Opttmasi Produksi Protease Daribeberapaisolat Bakteri*(isolation, Selection and Optimalization of Protease Production of Some Bacterial Isolates)

OpenAIRE

Naiola, Elidar; Widhyastuti, Nunuk

2002-01-01

Thirty-seven out of sixty-one bacterial isolates from various sources of samples were screened for protease production. The isolate of ISO PL3 could produce the highest enzyme activity, and it was used as a standard bacterial strain in this observation. For any reason,we implemented ISO PL2 to study the optimum condition for producing bacterial protease. Result shows that the maximum protease activity was obtained in a medium containing 100 gram of rice brand in a liter tofu liquid waste. The...

Batesian mimicry promotes pre- and postmating isolation in a snake mimicry complex.

Science.gov (United States)

Pfennig, David W; Akcali, Christopher K; Kikuchi, David W

2015-04-01

We evaluated whether Batesian mimicry promotes early-stage reproductive isolation. Many Batesian mimics occur not only in sympatry with their model (as expected), but also in allopatry. As a consequence of local adaptation within both sympatry (where mimetic traits are favored) and allopatry (where nonmimetic traits are favored), divergent, predator-mediated natural selection should disfavor immigrants between these selective environments as well as any between-environment hybrids. This selection might form the basis for both pre- and postmating isolation, respectively. We tested for such selection in a snake mimicry complex by placing clay replicas of sympatric, allopatric, or hybrid phenotypes in both sympatry and allopatry and measuring predation attempts. As predicted, replicas with immigrant phenotypes were disfavored in both selective environments. Replicas with hybrid phenotypes were also disfavored, but only in a region of sympatry where previous studies have detected strong selection favoring precise mimicry. By fostering immigrant inviability and ecologically dependent selection against hybrids (at least in some habitats), Batesian mimicry might therefore promote reproductive isolation. Thus, although Batesian mimicry has long been viewed as a mechanism for convergent evolution, it might play an underappreciated role in fueling divergent evolution and possibly even the evolution of reproductive isolation and speciation. © 2015 The Author(s).

Microbiological and molecular identification of bacterial species isolated from nasal and oropharyngeal mucosa of fuel workers in Riyadh, Saudi Arabia.

Science.gov (United States)

AlWakeel, Suaad S

2017-09-01

This study aimed to determine the bacterial species colonizing the nasal and oropharyngeal mucosa of fuel workers in Central Riyadh, Saudi Arabia on a microbiological and molecular level. Throat and nasal swab samples were obtained from 29 fuel station attendants in the period of time extending from March to May 2014 in Riyadh, Saudi Arabia. Microbiological identification techniques were utilized to identify the bacterial species isolated. Antibiotic sensitivity was assessed for each of the bacterial isolates. Molecular identification techniques based on PCR analysis of specific genomic sequences was conducted and was the basis on which phylogeny representation was done for 10 randomly selected samples of the isolates. Blood was drawn and a complete blood count was conducted to note the hematological indices for each of the study participants. Nineteen bacterial species were isolated from both the nasal cavity and the oropharynx including Streptococcus thoraltensis , alpha-hemolytic streptococci, Staphylococcus hominis , coagulase-negative staphylococci, Leuconostoc mesenteroides , Erysipelothrix rhusiopathiae and several others. We found 100% sensitivity of the isolates to ciprofloxacin, cefuroxime and gentamicin. Whereas cefotaxime and azithromycin posted sensitivities of 85.7% and 91.4%, respectively. Low sensitivities (fuel products may be a contributing factor to bacterial colonization of the respiratory tract in fuel workers.

The Study of Isolated Bacteria Application for Bioremediation Agent of Uranium Radionuclide in the Environment

International Nuclear Information System (INIS)

Yazid, Mochd

2007-01-01

Application of the isolated bacteria on the Low Level Uranium Waste as uranium bioremediation agent in the environment has been studied. The objective of this research is to study the possibility of isolated bacteria to be used on uranium remediation process. The isolation of uranium resistance bacteria was carried out on the selective medium SBS containing 10 mg/l uranium, incubated at 37°C until the growth was visible. Selection of binding uranium bacteria was carried out based on their ability to grow on liquid medium containing various concentration of uranium that shacked on 120 rpm speed. The isolated bacteria with the highest specific growth rate constant (μ) were selected for biochemical characterization and identification by matching profile method. The result of this research showed that three selected isolate bacteria were able to grow well on liquid SBS medium until 100 mg/l uranium concentration. The identification results showed that two of them were suspected belong to the genus Pseudomonas and one isolates belong to the genus of Bacillus. The uranium reduction studied was performed by growing up the isolated bacteria on the SBS liquid medium that containing 40 mg/l uranium. Bacterial growth were measured by weighted of bacterial biomass and uranium concentration were measured by spectrophotometer. The research result showed that the selected isolates bacteria may applicable for bioremediation agent because of their ability to grow well on liquid SBS medium and their ability on uranium concentration reduction. The efficiency of reduction by Pseudomonas in the isolated bacteria one were 78.51 % and in the isolated bacteria three were 91.47 % , and Bacillus in the isolate bacteria six were 52.73%. (author)

Lactobacillus hammesii sp. nov., isolated from French sourdough.

Science.gov (United States)

Valcheva, Rosica; Korakli, Maher; Onno, Bernard; Prévost, Hervé; Ivanova, Iskra; Ehrmann, Matthias A; Dousset, Xavier; Gänzle, Michael G; Vogel, Rudi F

2005-03-01

Twenty morphologically different strains were chosen from French wheat sourdough isolates. Cells were Gram-positive, non-spore-forming, non-motile rods. The isolates were identified using amplified-fragment length polymorphism, randomly amplified polymorphic DNA and 16S rRNA gene sequence analysis. All isolates were members of the genus Lactobacillus. They were identified as representing Lactobacillus plantarum, Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus spicheri and Lactobacillus sakei. However, two isolates (LP38(T) and LP39) could be clearly discriminated from recognized Lactobacillus species on the basis of genotyping methods. 16S rRNA gene sequence similarity and DNA-DNA relatedness data indicate that the two strains belong to a novel Lactobacillus species, for which the name Lactobacillus hammesii is proposed. The type strain is LP38(T) (=DSM 16381(T)=CIP 108387(T)=TMW 1.1236(T)).

Antimicrobial Susceptibilities of Geographically Diverse Clinical Human Isolates of Leptospira▿

OpenAIRE

Ressner, Roseanne A.; Griffith, Matthew E.; Beckius, Miriam L.; Pimentel, Guillermo; Miller, R. Scott; Mende, Katrin; Fraser, Susan L.; Galloway, Renee L.; Hospenthal, Duane R.; Murray, Clinton K.

2008-01-01

Although antimicrobial therapy of leptospirosis has been studied in a few randomized controlled clinical studies, those studies were limited to specific regions of the world and few have characterized infecting strains. A broth microdilution technique for the assessment of antibiotic susceptibility has been developed at Brooke Army Medical Center. In the present study, we assessed the susceptibilities of 13 Leptospira isolates (including recent clinical isolates) from Egypt, Thailand, Nicarag...

Isolation of gallic acid-producing microorganisms and their use in ...

African Journals Online (AJOL)

A total number of eighty gallic acid producing strains were isolated from forest soil or plant samples. Among these strains, thirteen isolates were selected for gallic acid production and these isolates were Aspergillus niger 1, A. niger 2, A. niger 3, Penicillium canescens (3), P. frequentans (2), P. spinulosum (2), ...

Critical node lifetimes in random networks via the Chen-Stein method

NARCIS (Netherlands)

Franceschetti, M.; Meester, R.W.J.

2006-01-01

This correspondence considers networks where nodes are connected randomly and can fail at random times. It provides scaling laws that allow to find the critical time at which isolated nodes begin to appear in the system as its size tends to infinity. Applications are in the areas of sensor and

WIPP: Waste Isolation Pilot Plant

International Nuclear Information System (INIS)

1984-01-01

The following aspects of the Waste Isolation Pilot Plant are discussed briefly: history and site selection; salt as a disposal medium; transporting waste materials; early key events; impacts on New Mexico; project organization; and site certification profile

O-naphthoquinone isolated from Capraria biflora L. induces selective cytotoxicity in tumor cell lines.

Science.gov (United States)

de S Wisintainer, G G N; Scola, G; Moura, S; Lemos, T L G; Pessoa, C; de Moraes, M O; Souza, L G S; Roesch-Ely, M; Henriques, J A P

2015-12-21

Biflorin is an o-naphthoquinone isolated from the roots of the plant Capraria biflora L. (Scrophulariaceae). In this study, the cytotoxic effects of biflorin were verified, and late apoptosis was detected in various cancer cell lines by in situ analysis. The cytotoxicity was further evaluated exclusively for 48 h of treatment in different tumor and non-tumor cell lines (Hep-2, HeLa, HT-29, A-375, and A-549, and HEK-293, respectively). The results indicated that biflorin induced selective cytotoxicity in tumor cells. HeLa cells were more susceptible to biflorin, followed by HT-29, A-549, A-375, and Hep-2 at all concentrations (range 5-50 μg/mL), and the highest half-maximal inhibitory concentration IC50 (56.01 ± 1.17 μg/mL) was observed in HEK-293 cells. Late apoptotic/necrotic events, observed by in situ immunostaining with Annexin V, varied with each cell line; an increase in late apoptotic events was observed corresponding to the increase in biflorin dosage. Hep-2 cells showed a greater percentage of late apoptotic events among the tumor cell lines when treated with higher concentrations of biflorin (69.63 ± 2.28%). The non-tumor HEK-293 line showed greater resistance to late apoptotic events, as well as a lower level of cytotoxicity (77.69 ± 6.68%) than the tested tumor lines. The data presented indicate that biflorin showed an important, possibly selective, cytotoxicity against tumor cell lines, thereby revealing a promising novel substance with potential anticancer activity for tumor therapy.

Determining the source of Bacillus cereus and Bacillus licheniformis isolated from raw milk, pasteurized milk and yoghurt.

Science.gov (United States)

Banykó, J; Vyletelová, M

2009-03-01

Strain-specific detection of Bacillus cereus and Bacillus licheniformis in raw and pasteurized milk, and yoghurt during processing. Randomly selected isolates of Bacillus spp. were subjected to PCR analysis, where single primer targeting to the repetitive sequence Box elements was used to fingerprint the species. The isolates were separated into six different fingerprint patterns. The results show that isolates clustered together at about the 57% similarity level with two main groups at the 82% and 83% similarity levels, respectively. Contamination with identical strains both of B. cereus and B. licheniformis in raw and pasteurized milk was found as well as contaminated with different strains (in the case of raw milk and yoghurt/pasteurized milk and yoghurt). Several BOX types traced in processed milk samples were not discovered in the original raw milk. BOX-PCR fingerprinting is useful for characterizing Bacillus populations in a dairy environment. It can be used to confirm environmental contamination, eventually clonal transfer of Bacillus strains during the technological processing of milk. Despite the limited number of strains analysed, the two Bacillus species yielded adequately detectable banding profiles, permitting differentiation of bacteria at the strain level and showing their diversity throughout dairy processing.

Mass-selective isolation of ions stored in a quadrupole ion trap. A simulation study

Science.gov (United States)

March, Raymond E.; Londry, Frank A.; Alfred, Roland L.; Franklin, Anthony M.; Todd, John F. J.

1992-01-01

Trajectories of single ions stored in the quadrupole ion trap have been calculated using a simulation program described as the specific program for quadrupolar resonance (SPQR). Previously, the program has been used for the investigation of quadrupolar resonance excitation of ions with a static working point (or co-ordinates) in the stability diagram. The program has been modified to accommodate continuous d.c. and/or r.f. voltage ramps so as to permit calculation of ion trajectories while the working point is being changed. The modified program has been applied to the calculation of ion trajectories during ion isolation, or mass-selective storage, in the ion trap. The quadrupolar resonance excitation aspect of SPQR was not used in this study. Trajectories are displayed as temporal variations of ion kinetic energy, and axial and radial excursions from the centre of the ion trap. The working points of three ion species (m/z 144, 146 and 148), located initially on the qz, axis with qz [approximate] 0.12, were moved to the vicinity of the upper apex by a combination of r.f. and d.c. voltages applied in succession. Stable trajectories were maintained only for the ion species of m/z 146 for which the working point lay within this apex; the other ion species were ejected either radially or axially. The d.c. voltage was then reduced to zero so as to restore the working point of the isolated ion species to the qz axis. The amplitude of the r.f voltage was reduced to its initial value so as to retrieve the initial working point for m/z 146. The process extended over a real time of 2.9 ms, and was collision-free. The trajectory of the isolated ion was stable during this process; the ion species with m/z value lower than that of the target ion, that is, m/z 144, was ejected axially at the [beta]z = 1 boundary, while that with higher m/z value, that is, m/z 148, was ejected radially at the [beta]r = 0 boundary, as expected. The moderating effects of buffer gas were not taken

Isolation of putative probionts from cod rearing environment

DEFF Research Database (Denmark)

Lauzon, H.L.; Gudmundsdottir, S.; Pedersen, M.H.

2008-01-01

, metabolite production and adhesion to fish cell lines. Our study demonstrated that 14% of screened bacteria (n = 188) had antagonistic properties towards fish pathogens. The majority of these isolates were Gram-positive (81%), belonging to Firmicutes (69.2%) and Actinobacteria (11.5%) phyla based on 16S r...... was designed to search for new probiotics to target this critical period in cod rearing. Potential probionts were selected from the naturalmicrobiota of cod aquacultural environment. The selection was based on several criteria: pathogen inhibition potential, growth characteristics, strain identification......RNA gene sequencing. Only 6 (3.2%) of 188 isolates could inhibit all three pathogens tested: Vibrio anguillarum, Aeromonas salmonicida subsp. achromogenes and Vibrio salmonicida. Differences observed in activity intensity and spectrum among inhibitory isolates emphasise the need to develop probiotic...

Selected, annotated bibliography of studies relevant to the isolation of nuclear wastes

International Nuclear Information System (INIS)

Hyder, L.K.; Fore, C.S.; Vaughan, N.D.; Faust, R.A.

1980-09-01

This annotated bibliography of 705 references represents the first in a series to be published by the Ecological Sciences Information Center containing scientific, technical, economic, and regulatory information relevant to nuclear waste isolation. Most references discuss deep geologic disposal, with fewer studies of deep seabed disposal; space disposal is also included. The publication covers both domestic and foreign literature for the period 1954 to 1980. Major chapters selected are Chemical and Physical Aspects; Container Design and Performance; Disposal Site; Envirnmental Transport; General Studies and Reviews; Geology, Hydrology and Site Resources; Regulatory and Economic Aspects; Repository Design and Engineering; Transportation Technology; Waste Production; and Waste Treatment. Specialized data fields have been incorporated to improve the ease and accuracy of locating pertinent references. Specific radionuclides for which data are presented are listed in the Measured Radionuclides field, and specific parameters which affect the migration of these radionuclides are presented in the Measured Parameters field. The references within each chapter are arranged alphabetically by leading author, corporate affiliation, or title of the document. When the author is not given, the corporate affiliation appears first. If these two levels of authorship are not given, the title of the document is used as the identifying level. Indexes are provided for author(s), keywords, subject category, title, geographic location, measured parameters, measured radionuclides, and publication description

Diagnostic properties of three conventional selective plating media for selection of Bacillus cereus, B. thuringiensis and B. weihenstephanensis

DEFF Research Database (Denmark)

Hendriksen, Niels Bohse; Hansen, Bjarne Munk

2011-01-01

The aim of this study was to assess the diagnostic properties of the two selective plating media and a chromogenic medium for identification of Bacillus cereus. The 324 isolates were B. cereus (37%), Bacillus weihenstephanensis (45%) or Bacillus thuringiensis (18%), as identified by a new...... combination of techniques. All isolates were growing on mannitol–egg yolk–polymyxin agar (MYP), and they did not form acid from mannitol. However, a significant lower number of B. thuringiensis isolates did not show lecithinase activity. All isolates were also growing on polymyxin–egg yolk...... recommended selective plating media MYP and PEMBA for detection of B. cereus group bacteria both have their limitations for identification of some B. cereus, B. weihenstephanensis or B. thuringiensis. However, MYP is preferable compared to PEMBA. The chromogenic medium has its own advantages and limitations...

Isolation and characterization of a cellulolytic actinomycete Microbispora bispora

Energy Technology Data Exchange (ETDEWEB)

Waldron, Jr, C R; Becker-Vallone, C A; Eveleigh, D E

1986-09-01

Protocols for the isolation of cellulolytic actinomycetes are described, and their use illustrated in the selection of thermophilic bacteria from soil. One isolate, Microbispora bispora, was selected for further study. It grew readily at 55/sup 0/C, produced an extracellular cellulase in good yield (endoglucanase, 5.9 U/ml) that had a broad pH range (pH 5.5 - 7.2) and was thermally stable. Its aryl-..beta..-glucosidase was cell-associated and was relatively resistant to end-product inhibition.

Antibiotic resistant Salmonella and Escherichia coli isolated from ...

African Journals Online (AJOL)

Objective: To characterise and investigate antimicrobial resistance of Esherichia coli and salmonella strains isolated from indigenous Gallus gallus in a leading slaughterhouse/market outlet in Nairobi-Kenya. Design: A repeated cross sectional study and based on random sampling was used. Setting: The study was carried ...

Isolation and identification of radiation resistant yeasts from sea water

International Nuclear Information System (INIS)

Park, Jong Cheon; Jeong, Yong Uk; Kim, Du Hong; Jo, Eun A

2011-12-01

This study was conducted to isolate radiation-resistant yeasts from sea water for development of application technology of radiation-resistant microorganism. · Isolation of 656 yeasts from sea water and selection of 2 radiation-resistant yeasts (D 10 value >3) · Identification of isolated yeasts as Filobasidium elegans sharing 99% sequence similarity · Characterization of isolated yeast with ability to repair of the DNA damage and membrane integrity to irradiation

ISOLATION AND LIGNOCELLULOLYTIC ACTIVITIES OF FIBER-DIGESTING BACTERIA FROM DIGESTIVE TRACT OF TERMITE (Cryptothermes sp.

Directory of Open Access Journals (Sweden)

B.I.M. Tampoebolon

2015-09-01

Full Text Available The objectives of this study were to obtain the fiber-digesting bacteria isolates from termitedigestive tract and to determine the optimum conditions of growth and production of cellulase, xylanaseand ligninase enzyme of isolate. The first study was conducted to isolate and select the fiber-digestingbacteria from the digestive tract of termites based on the highest activity of cellulolytic (S, xylanolytic(X and lignolytic (L. The second study was optimation of the growth conditions of bacteria and theenzyme production due to effect of rice straw substrate and nitrogen. The material used were dry woodtermites, rice straw, and culture medium. The design used was a completely randomized factorial design,in which the first factor was rice straw substrate (1, 2, and 3% W/V, while the second factor wasnitrogen (0.1, 0.2 and 0.3% W/V. Variables measured were cellulase, xylanase and ligninase activities.Results of the first sudy showed that the isolates obtained consisted of 3 types, those were cellulolyticbacteria (S1, S2, and S3, 3 types of bacteria xylanolytic (X1, X2, and X3 and 3 types of bacteria lignolytic(L1, L2, and L3. Meanwhile, results of the second study showed that isolates of S2, X3, and L1 had thehighest activity, those were 1.894 U/mL, 1.722 U/mL and 0.314 U/mL, respectively. In conclusion, the addition of 1% level of rice straw substrate and 0.3% of nitrogen showed the highest enzyme activity oncellulase, xylanase and ligninase.

Comparison of confirmed inactive and randomly selected compounds as negative training examples in support vector machine-based virtual screening.

Science.gov (United States)

Heikamp, Kathrin; Bajorath, Jürgen

2013-07-22

The choice of negative training data for machine learning is a little explored issue in chemoinformatics. In this study, the influence of alternative sets of negative training data and different background databases on support vector machine (SVM) modeling and virtual screening has been investigated. Target-directed SVM models have been derived on the basis of differently composed training sets containing confirmed inactive molecules or randomly selected database compounds as negative training instances. These models were then applied to search background databases consisting of biological screening data or randomly assembled compounds for available hits. Negative training data were found to systematically influence compound recall in virtual screening. In addition, different background databases had a strong influence on the search results. Our findings also indicated that typical benchmark settings lead to an overestimation of SVM-based virtual screening performance compared to search conditions that are more relevant for practical applications.

Variable Selection in Time Series Forecasting Using Random Forests

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Hristos Tyralis

2017-10-01

Full Text Available Time series forecasting using machine learning algorithms has gained popularity recently. Random forest is a machine learning algorithm implemented in time series forecasting; however, most of its forecasting properties have remained unexplored. Here we focus on assessing the performance of random forests in one-step forecasting using two large datasets of short time series with the aim to suggest an optimal set of predictor variables. Furthermore, we compare its performance to benchmarking methods. The first dataset is composed by 16,000 simulated time series from a variety of Autoregressive Fractionally Integrated Moving Average (ARFIMA models. The second dataset consists of 135 mean annual temperature time series. The highest predictive performance of RF is observed when using a low number of recent lagged predictor variables. This outcome could be useful in relevant future applications, with the prospect to achieve higher predictive accuracy.

Effect of isolates of fibre degrading bacteria on body weight changes ...

African Journals Online (AJOL)

tc

2013-05-22

May 22, 2013 ... evaluate the effect of supplementation of fibrolytic bac- terial isolate on body weight changes, milk production, nutrient intake and nutrient utilization in lactating Murrah buffaloes. This study was conducted to evaluate the digestibility of lignocellulosic feeds by some selected bacterial isolates isolated from ...

The Long-Term Effectiveness of a Selective, Personality-Targeted Prevention Program in Reducing Alcohol Use and Related Harms: A Cluster Randomized Controlled Trial

Science.gov (United States)

Newton, Nicola C.; Conrod, Patricia J.; Slade, Tim; Carragher, Natacha; Champion, Katrina E.; Barrett, Emma L.; Kelly, Erin V.; Nair, Natasha K.; Stapinski, Lexine; Teesson, Maree

2016-01-01

Background: This study investigated the long-term effectiveness of Preventure, a selective personality-targeted prevention program, in reducing the uptake of alcohol, harmful use of alcohol, and alcohol-related harms over a 3-year period. Methods: A cluster randomized controlled trial was conducted to assess the effectiveness of Preventure.…

Identification at Biovar Level of Brucella Isolates Causing Abortion in Small Ruminants of Iran

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Ali Mohammad Behroozikhah

2012-01-01

Full Text Available To determine the most prevalent biovar responsible for brucellosis in sheep and goat populations of Iran, a cross-sectional study was carried out over 2 years in six provinces selected based on geography and disease prevalence. Specimens obtained from referred aborted sheep and goat fetuses were cultured on Brucella selective media for microbiological isolation. Brucellae were isolated from 265 fetuses and examined for biovar identification using standard microbiological methods. Results showed that 246 isolates (92.8% were B. melitensis biovar 1, 18 isolates (6.8% were B. melitensis biovar 2, and, interestingly, one isolate (0.4% obtained from Mazandaran province was B. abortus biovar 3. In this study, B. melitensis biovar 3 was isolated in none of the selected provinces, and all isolates from 3 provinces (i.e., Chehar-mahal Bakhtiari, Markazi, and Ilam were identified only as B. melitensis biovar 1. In conclusion, we found that B. melitensis biovar 1 remains the most prevalent cause of small ruminant brucellosis in various provinces of Iran.

Isolation, selection and evaluation of yeasts for use in fermentation of coffee beans by the wet process.

Science.gov (United States)

de Melo Pereira, Gilberto Vinícius; Soccol, Vanete Thomaz; Pandey, Ashok; Medeiros, Adriane Bianchi Pedroni; Andrade Lara, João Marcos Rodrigues; Gollo, André Luiz; Soccol, Carlos Ricardo

2014-10-01

During wet processing of coffee, the ripe cherries are pulped, then fermented and dried. This study reports an experimental approach for target identification and selection of indigenous coffee yeasts and their potential use as starter cultures during the fermentation step of wet processing. A total of 144 yeast isolates originating from spontaneously fermenting coffee beans were identified by molecular approaches and screened for their capacity to grow under coffee-associated stress conditions. According to ITS-rRNA gene sequencing, Pichia fermentans and Pichia kluyveri were the most frequent isolates, followed by Candida Candida glabrata, quercitrusa, Saccharomyces sp., Pichia guilliermondii, Pichia caribbica and Hanseniaspora opuntiae. Nine stress-tolerant yeast strains were evaluated for their ability to produce aromatic compounds in a coffee pulp simulation medium and for their pectinolytic activity. P. fermentans YC5.2 produced the highest concentrations of flavor-active ester compounds (viz., ethyl acetate and isoamyl acetate), while Saccharomyces sp. YC9.15 was the best pectinase-producing strain. The potential impact of these selected yeast strains to promote flavor development in coffee beverages was investigated for inoculating coffee beans during wet fermentation trials at laboratory scale. Inoculation of a single culture of P. fermentans YC5.2 and co-culture of P. fermentans YC5.2 and Saccharomyces sp. YC9.15 enhanced significantly the formation of volatile aroma compounds during the fermentation process compared to un-inoculated control. The sensory analysis indicated that the flavor of coffee beverages was influenced by the starter cultures, being rated as having the higher sensory scores for fruity, buttery and fermented aroma. This demonstrates a complementary role of yeasts associated with coffee quality through the synthesis of yeast-specific volatile constituents. The yeast strains P. fermentans YC5.2 and Saccharomyces sp. YC9.15 have a great

Isolation, Identification, and Evaluation of Novel Probiotic Strains Isolated from Feces of Breast-Fed Infants.

Science.gov (United States)

Panya, Marutpong; Lulitanond, Viraphong; Rattanachaikunsopon, Pongsak; Srivoramas, Thanyakarn; Chaiwong, Tarinee

2016-01-01

To isolate, identify, and evaluate the probiotic properties of lactic acid bacteria (LAB) isolated from the feces of breast-fed infants. The probiotic tests included investigation of hemolysis activity, survival in simulated gastrointestinal tract conditions (acid and bile salt tolerance), susceptibility to antibiotics, and ability to inhibit selected bacterial pathogens (Escherichia coli O157:H7, Vibrio cholerae and Salmonella enterica subsp enterica serovar Typhimurium). The bacterial species identification was performed by both carbohydrate utilization and partial 16S ribosomal RNA sequencing. Five of fifty LAB isolates (UBU-03, UBU-06, UBU-09, UBU-34, and UBU-37) showed good probiotic properties. These five isolates showed non-hemolysis type (gamma-hemolysis), susceptibility to all antibiotics tested except for vancomycin, ability to survive in the simulated gastrointestinal conditions of both acid and bile salt solution, and ability to inhibit growth of E. coli O157: H7 and V. cholerae. Bacterial species identification revealed that all five isolates were firmly identified as Lactobacillus rhamnosus species. The L. rhamnosus strains that were isolated and characterized in this study could be considered as probiotic strains, and then used for further probiotic characterization in human cell cultures or animal models.

Protein Pattern and Plasmid Profile of Lactic Acid Bacteria Isolated from Dahi, A Traditional Fermented Milk Product of Pakistan

Directory of Open Access Journals (Sweden)

Tariq Masud

2007-01-01

Full Text Available A total of 116 isolates were identified from randomly collected market dahi samples from Rawalpindi, Pakistan. Lactic acid bacteria dominated the microbial population of dahi and were identified according to their morphological and physiological characteristics. Among these lactobacilli were frequently occurring organisms. The phenotypic and biochemical analyses gave a diversity of species (8 presumptive species. The most abundant species were Lactobacillus delbrueckii subsp. bulgaricus (28 isolates and Streptococcus thermophilus (25 isolates. Some contaminants such as Staphylococcus, Micrococcus and Saccharomyces spp. were also observed. The whole cell protein profiles of selected strains of lactic acid bacteria were examined by SDS-PAGE. It was observed that each species yielded a different electrophoretic pattern. It was further observed that among the strains investigated for the analysis of plasmid DNA 22 strains were found positive, 8 strains of L. delbrueckii subsp. bulgaricus followed by 5 of L. acidophilus, 4 of L. casei, 3 of L. helveticus and one of each L. delbrueckii subsp. delbrueckii and L. delbrueckii subsp. lactis, whereas no plasmid was observed in S. thermophilus and L. lactis strains investigated during the study. All the plasmids isolated were mostly large size plasmids and ranged from 20 to 25 kb in size.

Generating equilateral random polygons in confinement III

International Nuclear Information System (INIS)

Diao, Y; Ernst, C; Montemayor, A; Ziegler, U

2012-01-01

In this paper we continue our earlier studies (Diao et al 2011 J. Phys. A: Math. Theor. 44 405202, Diao et al J. Phys. A: Math. Theor. 45 275203) on the generation methods of random equilateral polygons confined in a sphere. The first half of this paper is concerned with the generation of confined equilateral random walks. We show that if the selection of a vertex is uniform subject to the position of its previous vertex and the confining condition, then the distributions of the vertices are not uniform, although there exists a distribution such that if the initial vertex is selected following this distribution, then all vertices of the random walk follow this same distribution. Thus in order to generate a confined equilateral random walk, the selection of a vertex cannot be uniform subject to the position of its previous vertex and the confining condition. We provide a simple algorithm capable of generating confined equilateral random walks whose vertex distribution is almost uniform in the confinement sphere. In the second half of this paper we show that any process generating confined equilateral random walks can be turned into a process generating confined equilateral random polygons with the property that the vertex distribution of the polygons approaches the vertex distribution of the walks as the polygons get longer and longer. In our earlier studies, the starting point of the confined polygon is fixed at the center of the sphere. The new approach here allows us to move the starting point of the confined polygon off the center of the sphere. (paper)

Feather wastes digestion by new isolated strains Bacillus sp. in ...

African Journals Online (AJOL)

Feather wastes digestion by new isolated strains Bacillus sp. in Morocco. ... The most efficient isolated strain selected was compared with Bacillus subtilis ATCC 6633. Results showed ... African Journal of Biotechnology Vol.3(1) 2004: 67-70 ...

Characterization of bacterial strains isolated from a beef-processing plant following cleaning and disinfection - Influence of isolated strains on biofilm formation by Sakaï and EDL 933 E. coli O157:H7.

Science.gov (United States)

Marouani-Gadri, Nesrine; Augier, Gladys; Carpentier, Brigitte

2009-07-31

The objective of this study was to investigate the effects on Escherichia coli O157:H7 biofilm formation of bacteria isolated from meat site surfaces following cleaning and disinfection. We first isolated and identified, to the genus level, strains of the latter organisms. Samples were obtained by swabbing the surfaces of equipment or floors over areas ranging from 315 to 3200 cm(2) in a slaughter hall, a meat cutting room and a meat boning room of a meat-processing plant. The number of bacteria recovered from these surfaces ranged from 10(5) CFU/cm(2). In the slaughter hall, stainless steel was in one case one of the most contaminated materials and in other cases one of the less contaminated. The same observation was made for conveyor belts made of polyvinyl chloride in the boning room. Dominant genera in the meat plant were Staphylococcus and Bacillus which were both 34% of the isolates from the slaughter hall and 14 and 4% respectively of the isolates from the cutting room. Randomly selected isolates of each of the genera recovered from the slaughter hall were cultured with E. coli O157:H7 in meat exudate at 15 degrees C to form dual-organism biofilms on polyurethane. In all cases but one, the isolates increased the numbers of attached E. coli O157:H7. The effects ranged from 0.37 to 1.11 for EDL 933 strain and from 0.19 to 1.38 log (CFU/cm(2)) for Sakaï strain. This is the first time that a resident microbiota of a meat-processing plant has been shown to have a favourable effect on E. coli O157:H7 colonization of a solid surface, which is of great interest from a food safety standpoint.

Affinity selection of Nipah and Hendra virus-related vaccine candidates from a complex random peptide library displayed on bacteriophage virus-like particles

Energy Technology Data Exchange (ETDEWEB)

Peabody, David S.; Chackerian, Bryce; Ashley, Carlee; Carnes, Eric; Negrete, Oscar

2017-01-24

The invention relates to virus-like particles of bacteriophage MS2 (MS2 VLPs) displaying peptide epitopes or peptide mimics of epitopes of Nipah Virus envelope glycoprotein that elicit an immune response against Nipah Virus upon vaccination of humans or animals. Affinity selection on Nipah Virus-neutralizing monoclonal antibodies using random sequence peptide libraries on MS2 VLPs selected peptides with sequence similarity to peptide sequences found within the envelope glycoprotein of Nipah itself, thus identifying the epitopes the antibodies recognize. The selected peptide sequences themselves are not necessarily identical in all respects to a sequence within Nipah Virus glycoprotein, and therefore may be referred to as epitope mimics VLPs displaying these epitope mimics can serve as vaccine. On the other hand, display of the corresponding wild-type sequence derived from Nipah Virus and corresponding to the epitope mapped by affinity selection, may also be used as a vaccine.

Study of Relationship between Genetic Pattern and Susceptibility to Terbinafine in Clinical Isolated of Trichophyton rubrum

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Fatemeh Hadadi

2014-06-01

Full Text Available Background & objectives: Trichophyton rubrum is one of the most common pathogeniccause of dermatophytosis. One of the drugs which have been prescribed widely for fungal infections is terbinafine which belongs to allylamines group of antifungal agents. Recently molecular typing methods have been developed for answering the epidemiological questions and disease recurrence problems. Current study has been conducted on 22 isolates of Trichophyton rubrum obtained from patients randomly. Our aim was the investigation of correlation between genetic pattern and sensitivity to Terbinafine in clinical isolates of Trichophyton rubrum.   Methods: Firstly the genus and species of isolated fungi from patients have been confirmed by macroscopic and microscopic methods, then, the resistance and sensitivity of isolates against drug have been determined using culture medium containing defined amount of drug. In next step fungal DNA has been extracted by RAPD-PCR (random amplified polymorphic DNA with random sequences of 3 primers.   Results: Each primer produced different amplified pattern, and using each 3 primers differences have been observed in genetic pattern of resistant and sensitive samples using each 3 primers, but there was no bond with 100% specificity.   Conclusion: The 12 sensitive isolates which didn’t grow in 0.1 mg concentration of drug, also had limited growth at the low concentration of drug. Ten resistant isolates which grew in 0.1mg/ml of drug, in lower concentration of drug were resisted. RAPD analysis for molecular typing of Trichophyton rubrum seems to be completely suitable.

Target selection biases from recent experience transfer across effectors.

Science.gov (United States)

Moher, Jeff; Song, Joo-Hyun

2016-02-01

Target selection is often biased by an observer's recent experiences. However, not much is known about whether these selection biases influence behavior across different effectors. For example, does looking at a red object make it easier to subsequently reach towards another red object? In the current study, we asked observers to find the uniquely colored target object on each trial. Randomly intermixed pre-trial cues indicated the mode of action: either an eye movement or a visually guided reach movement to the target. In Experiment 1, we found that priming of popout, reflected in faster responses following repetition of the target color on consecutive trials, occurred regardless of whether the effector was repeated from the previous trial or not. In Experiment 2, we examined whether an inhibitory selection bias away from a feature could transfer across effectors. While priming of popout reflects both enhancement of the repeated target features and suppression of the repeated distractor features, the distractor previewing effect isolates a purely inhibitory component of target selection in which a previewed color is presented in a homogenous display and subsequently inhibited. Much like priming of popout, intertrial suppression biases in the distractor previewing effect transferred across effectors. Together, these results suggest that biases for target selection driven by recent trial history transfer across effectors. This indicates that representations in memory that bias attention towards or away from specific features are largely independent from their associated actions.

Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences.

Science.gov (United States)

Warris, Sven; Boymans, Sander; Muiser, Iwe; Noback, Michiel; Krijnen, Wim; Nap, Jan-Peter

2014-01-13

Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification.

Radioactive waste isolation in salt: peer review of Office of Nuclear Waste Isolation's Socioeconomic Program Plan

International Nuclear Information System (INIS)

Winter, R.; Fenster, D.; O'Hare, M.; Zillman, D.; Harrison, W.; Tisue, M.

1984-07-01

The following recommendations have been abstracted from the body of this report. The Office of Nuclear Waste Isolation's Socioeconomic Program Plan for the Establishment of Mined Geologic Repositories to Isolate Nuclear Waste should be modified to: (1) encourage active public participation in the decision-making processes leading to repository site selection; (2) clearly define mechanisms for incorporating the concerns of local residents, state and local governments, and other potentially interested parties into the early stages of the site selection process. In addition, the Office of Nuclear Waste Isolation should carefully review the overall role that these persons and groups, including local pressure groups organized in the face of potential repository development, will play in the siting process; (3) place significantly greater emphasis on using primary socioeconomic data during the site selection process, reversing the current overemphasis on secondary data collection, description of socioeconomic conditions at potential locations, and development of analytical methodologies; (4) include additional approaches to solving socioeconomic problems. For example, a reluctance to acknowledge that solutions to socioeconomic problems need to be found jointly with interested parties is evident in the plan; (5) recognize that mitigation mechanisms other than compensation and incentives may be effective; (6) as soon as potential sites are identified, the US Department of Energy (DOE) should begin discussing impact mitigation agreements with local officials and other interested parties; and (7) comply fully with the pertinent provisions of NWPA

Microbiological and molecular identification of bacterial species isolated from nasal and oropharyngeal mucosa of fuel workers in Riyadh,

Directory of Open Access Journals (Sweden)

Suaad S. AlWakeel

2017-09-01

Full Text Available This study aimed to determine the bacterial species colonizing the nasal and oropharyngeal mucosa of fuel workers in Central Riyadh, Saudi Arabia on a microbiological and molecular level. Throat and nasal swab samples were obtained from 29 fuel station attendants in the period of time extending from March to May 2014 in Riyadh, Saudi Arabia. Microbiological identification techniques were utilized to identify the bacterial species isolated. Antibiotic sensitivity was assessed for each of the bacterial isolates. Molecular identification techniques based on PCR analysis of specific genomic sequences was conducted and was the basis on which phylogeny representation was done for 10 randomly selected samples of the isolates. Blood was drawn and a complete blood count was conducted to note the hematological indices for each of the study participants. Nineteen bacterial species were isolated from both the nasal cavity and the oropharynx including Streptococcus thoraltensis, alpha-hemolytic streptococci, Staphylococcus hominis, coagulase-negative staphylococci, Leuconostoc mesenteroides, Erysipelothrix rhusiopathiae and several others. We found 100% sensitivity of the isolates to ciprofloxacin, cefuroxime and gentamicin. Whereas cefotaxime and azithromycin posted sensitivities of 85.7% and 91.4%, respectively. Low sensitivities (<60% sensitivity to the antibiotics ampicillin, erythromycin, clarithromycin and norfloxacin were observed. Ninety-seven percent similarity to the microbial bank species was noted when the isolates were compared to it. Most hematological indices recorded were within the normal range. In conclusion, exposure to toxic fumes and compounds within fuel products may be a contributing factor to bacterial colonization of the respiratory tract in fuel workers.

Prevalence and antimicrobial resistance of Campylobacter species isolated from raw camel, beef, lamb, and goat meat in Iran.

Science.gov (United States)

Rahimi, Ebrahim; Ameri, Mehrdad; Kazemeini, Hamid Reza

2010-04-01

Campylobacter spp. are one of the most common causes of acute bacterial gastroenteritis in human beings which are transmitted mostly via food originating from animals. This study was conducted to determine the prevalence and antimicrobial resistance of Campylobacter spp. isolated from retail raw meats in Iran. From June 2008 to June 2009, a total of 722 raw meat samples from camel (n = 107), beef (n = 190), lamb (n = 225), and goat (n = 180) were purchased from randomly selected retail outlets in Isfahan and Yazd, Iran, and were evaluated for the presence of Campylobacter spp. In this study, 50 of the 722 meat samples (6.9%) were contaminated with Campylobacter spp. The highest prevalence of Campylobacter spp. was found in lamb meat (12.0%), followed by goat meat (9.4%), beef meat (2.4%), and camel meat (0.9%). The most prevalent Campylobacter spp. isolated from the meat samples was Campylobacter jejuni (84.0%); the remaining isolates were Campylobacter coli (16.0%). Susceptibilities of 50 Campylobacter isolates were determined for 10 antimicrobial drugs using the disk-diffusion assay. Resistance to tetracycline was the most common finding (68.0%), followed by resistance to ciprofloxacin (46.0%) and nalidixic acid (40.0%). All of the isolates were susceptible to erythromycin, gentamicin, and chloramphenicol. Significantly higher prevalence rates of Campylobacter spp. (p meat samples taken in spring (20.0%) and summer (18.9%). To our knowledge, this study is the first report of the isolation of Campylobacter spp. from raw camel, lamb, and goat meat in Iran.

RAPD cluster analysis and chlorate sensitivity of some Indian isolates of Macrophomina phaseolina from sorghum and their relationships with pathogenicity.

Science.gov (United States)

Das, I K; Fakrudin, B; Arora, D K

2008-01-01

Charcoal rot caused by Macrophomina phaseolina is an economically important disease in sorghum grown during the post rainy season in India. Variations in random amplified polymorphic DNA (RAPD) polymorphisms, chlorate sensitivity and pathogenicity were studied among sorghum isolates of M. phaseolina collected from different parts of India. RAPD data based on 14 random primers of Kit A and C (OPA and OPC) on 20 isolates showed a high degree of polymorphism (98.1%) in different isolates. UPGMA dendrogram on RAPD data produced 7 clusters at the level of 37% similarity. Isolates from the same locations showed a tendency to group closer, substantiating closer genetic relatedness. Sorghum infecting Macrophomina isolates showed a mixed response for sensitivity to potassium chlorate (120 mM). Chlorate-resistant isolates were predominant (>65% of the isolates) over sensitive isolates. Chlorate-sensitive isolates were found to be genetically closer among them than the resistant ones. For the first time it was shown that chlorate sensitivity in Macrophomina had some relations with charcoal rot severity in sorghum.

Isolation of thermotolerant, halotolerant, facultative biosurfactant-producing bacteria.

Science.gov (United States)

Ghojavand, H; Vahabzadeh, F; Mehranian, M; Radmehr, M; Shahraki, Kh A; Zolfagharian, F; Emadi, M A; Roayaei, E

2008-10-01

Several facultative bacterial strains tolerant to high temperature and salinity were isolated from the oil reservoir brines of an Iranian oil field (Masjed-I Soleyman). Some of these isolates were able to grow up to 60 degrees C and at high concentration of NaCl (15% w/v). One of the isolates grew at 40 degrees C, while it was able to grow at 15% w/v NaCl. Tolerances to NaCl levels decreased as the growth temperatures were increased. Surfactant production ability was detected in some of these isolates. The use of biosurfactant is considered as an effective mechanism in microbial-enhanced oil recovery processes detected in some of these isolates. The surfactant producers were able to grow at high temperatures and salinities to about 55 degrees C and 10% w/v, respectively. These isolates exhibited morphological and physiological characteristics of the Bacillus genus. The partial sequencing of the 16S ribosomal deoxyribonucleic acid gene of the selected isolates was assigned them to Bacillus subtilis group. The biosurfactant produced by these isolates caused a substantial decrease in the surface tension of the culture media to 26.7 mN/m. By the use of thin-layer chromatography technique, the presence of the three compounds was detected in the tested biosurfactant. Infrared spectroscopy and (1)H nuclear magnetic resonance analysis were used, and the partial structural characterization of the biosurfactant mixture of the three compounds was found to be lipopeptidic in nature. The possibility of use of the selected bacterial strains reported, in the present study, in different sectors of the petroleum industry has been addressed.

COMPARATIVE EVALUATION OF CULTURE MEDIA FOR PATHOGEN ISOLATION OF PURULENT BACTERIAL MENINGITIS

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Ya. V. Podkopaev

2016-01-01

Full Text Available The State Research Center for Applied Microbiology and Biotechnology has designed two nutrient media — chocolate agar and PBM-agar to isolate pathogens of purulent bacterial meningitis (PBM. In our previous research using collected microbial strains the media were shown to be highly susceptible and to provide the growth of Neisseria meningiti-dis, Streptococcus pneumoniae and Haemophilus influenzae strains, when inoculated with microbial suspensions containing single cells. When isolating Haemophilus influenzae, meningococci, and pneumococci the use of selective additives in both media assures selective isolation of required microorganisms, inhibiting contaminants. The objective of this research was to assess the media in bacteriological tests of clinical samples collected from the upper and lower respiratory tract in humans. The bacteriological plating of throat smear specimens (n = 90 from children and adults at the age of 0 to 66 with disorder of the upper respiratory tract on chocolate agar, PBM-agar and on a control medium in the absence of selective additives resulted in the equal amount of microbial cultures isolated. Of 154 isolated cultures 2, 23 and 9 were attributed to Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae, respectively. The plating of throat smears (n = 10 from healthy people at the age of 30 to 55 on the analyzable and control media in the presence of additives allowed us to selectively isolate Haemophilus influenzae and Streptococcus pneumoniae cultures without a quantitative loss, with contaminants inhibited. By their growth characteristics chocolate agar and PBM-agar were highly competitive with reference media being used in clinical practice for isolating main causative agents of purulent bacterial meningitis.

Using selective chromogenic plates to optimize isolation of group B Streptococcus in pregnant women

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Romano Mattei

2014-03-01

Full Text Available Group B Streptococcus (GBS remains the leading cause of severe bacterial infections (sepsis, meningitis, pneumonia in neonates. We compared the detection of GBS from recto-vaginal swabs on blood agar and two chromogenic media and evaluated their antibiotic susceptibility. A total of 1351 swabs were taken from pregnant women at 35-37 weeks of gestation. Following enrichment in Todd Hewitt broth + nalidixic acid and colistin, the samples were plated on Columbia CNA agar (CNA, chromID Strepto B agar (STRB and Granada Agar (GRAN, respectively. GBS were found in 22.4% of recto-vaginal swabs from pregnant women. Sensitivity, specificity, positive and negative predictive values of GBS detection were 88%, 88%, 81% and 96% for CNA, 99%, 97%, 90% and 99% for STRB and 94%, 99%, 98% e 99% for GRAN; Cohen’s k index concordances for CNA, STREB and GRAN were 0.68, 0.92 and 0.96, respectively. All isolates were susceptible to penicillin, whereas resistances of erythromycin and clindamycin were 40% and 42%, respectively. To conclude, selective broth enrichment combined with chromogenic plates is recommended for GBS screening in pregnant women.

Virulence properties and random amplification of polymorphic DNA ...

African Journals Online (AJOL)

Genotypic and phenotypic characterization as well as studies on the virulence factors of Candida albicans isolates obtained from oral cavity of patients was carried out using random amplified polymorphic DNA (RAPD) fingerprinting and epithelial cells adherence assay, respectively. RAPD patterns revealed the presence of ...

Probiotic features of two oral Lactobacillus isolates

OpenAIRE

Zavisic, Gordana; Petricevic, Sasa; Radulovic, Zeljka; Begovic, Jelena; Golic, Natasa; Topisirovic, Ljubisa; Strahinic, Ivana

2012-01-01

In this study, we checked lactobacilli strains of human origin for their potential as probiotic. Samples were collected from oral mucosa of 16 healthy individuals, out of which twenty isolates were obtained and two of them were selected and identified as Lactobacillus plantarum (G1) and L. casei (G3). Both isolates exhibited antagonistic action towards pathogenic microorganisms such as Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Salmonella abony, and Clostridium sporogene...

Heat resistance of thermoduric enterococci isolated from milk.

Science.gov (United States)

McAuley, Catherine M; Gobius, Kari S; Britz, Margaret L; Craven, Heather M

2012-03-15

Enterococci are reported to survive pasteurisation but the extent of their survival is unclear. Sixty-one thermoduric enterococci isolates were selected from laboratory pasteurised milk obtained from silos in six dairy factories. The isolates were screened to determine log(10) reductions incurred after pasteurisation (63°C/30 min) and ranked from highest to lowest log(10) reduction. Two isolates each of Enterococcus faecalis, Enterococcus faecium, Enterococcus durans and Enterococcus hirae, exhibiting the median and the greatest heat resistance, as well as E. faecalis ATCC 19433, were selected for further heat resistance determinations using an immersed coil apparatus. D values were calculated from survival curves plotted from viable counts obtained after heating isolates in Brain Heart Infusion Broth at 63, 69, 72, 75 and 78°C followed by rapid cooling. At 72°C, the temperature employed for High Temperature Short Time (HTST) pasteurisation (72°C/15s), the D values extended from 0.3 min to 5.1 min, depending on the isolate and species. These data were used to calculate z values, which ranged from 5.0 to 9.8°C. The most heat sensitive isolates were E. faecalis (z values 5.0, 5.7 and 7.5°C), while the most heat resistant isolates were E. durans (z values 8.7 and 8.8°C), E. faecium (z value 9.0°C) and E. hirae (z values 8.5 and 9.8°C). The data show that heat resistance in enterococci is highly variable. Copyright © 2011 Elsevier B.V. All rights reserved.

Varying levels of difficulty index of skills-test items randomly selected by examinees on the Korean emergency medical technician licensing examination.

Science.gov (United States)

Koh, Bongyeun; Hong, Sunggi; Kim, Soon-Sim; Hyun, Jin-Sook; Baek, Milye; Moon, Jundong; Kwon, Hayran; Kim, Gyoungyong; Min, Seonggi; Kang, Gu-Hyun

2016-01-01

The goal of this study was to characterize the difficulty index of the items in the skills test components of the class I and II Korean emergency medical technician licensing examination (KEMTLE), which requires examinees to select items randomly. The results of 1,309 class I KEMTLE examinations and 1,801 class II KEMTLE examinations in 2013 were subjected to analysis. Items from the basic and advanced skills test sections of the KEMTLE were compared to determine whether some were significantly more difficult than others. In the class I KEMTLE, all 4 of the items on the basic skills test showed significant variation in difficulty index (P<0.01), as well as 4 of the 5 items on the advanced skills test (P<0.05). In the class II KEMTLE, 4 of the 5 items on the basic skills test showed significantly different difficulty index (P<0.01), as well as all 3 of the advanced skills test items (P<0.01). In the skills test components of the class I and II KEMTLE, the procedure in which examinees randomly select questions should be revised to require examinees to respond to a set of fixed items in order to improve the reliability of the national licensing examination.

Varying levels of difficulty index of skills-test items randomly selected by examinees on the Korean emergency medical technician licensing examination

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Bongyeun Koh

2016-01-01

Full Text Available Purpose: The goal of this study was to characterize the difficulty index of the items in the skills test components of the class I and II Korean emergency medical technician licensing examination (KEMTLE, which requires examinees to select items randomly. Methods: The results of 1,309 class I KEMTLE examinations and 1,801 class II KEMTLE examinations in 2013 were subjected to analysis. Items from the basic and advanced skills test sections of the KEMTLE were compared to determine whether some were significantly more difficult than others. Results: In the class I KEMTLE, all 4 of the items on the basic skills test showed significant variation in difficulty index (P<0.01, as well as 4 of the 5 items on the advanced skills test (P<0.05. In the class II KEMTLE, 4 of the 5 items on the basic skills test showed significantly different difficulty index (P<0.01, as well as all 3 of the advanced skills test items (P<0.01. Conclusion: In the skills test components of the class I and II KEMTLE, the procedure in which examinees randomly select questions should be revised to require examinees to respond to a set of fixed items in order to improve the reliability of the national licensing examination.

Evidence for mating between isolates of Colletotrichum gloeosporioides with different host specificities.

Science.gov (United States)

Cisar, C R; Spiegel, F W; TeBeest, D O; Trout, C

1994-04-01

Individual isolates of the ubiquitous plant pathogen Colletotrichum gloeosporioides (teleomorph Glomerella cingulata) can have very restricted host ranges. Isolates that share the same host range are considered to be genetically discrete units, and sexual compatibility has been reported to be limited to individuals that share the same host range. However, we have recently observed that some isolates of C. gloeosporioides that are specifically pathogenic to different, distantly-related hosts are sexually compatible. Ascospore progeny from one such cross were randomly isolated and outcrossing was verified by the reassortment of several RFLP markers among the progeny. In addition, the progeny were analyzed for pathogenicity to parental hosts. The implications of sexual compatibility between C. gloeosporioides isolates with different host specificities on the evolution of Colletotrichum species are discussed.

Genetic Variability of Macrophomina phaseolina Isolates from Dry Beans in Turkey

OpenAIRE

Serkan Yeşil; Kubilay Kurtuluş Baştaş

2016-01-01

Charcoal rot is a soil and seed borne, economically important fungal disease on dry bean in Turkey. Twenty bean isolates of M. phaseolina collected from different locations in Turkey during 2008 and 2012 years were studied for genetic variability using random amplified polymorphic DNA (RAPD) assay, chlorate sensitivity on medium supplemented with 120mM of potassium, phenotype of colony, and pathogenicity. Isolates were identified as M. phaseolina based on morhological features and PCR assays ...

Isolation and identification of a bacterium from marine shrimp digestive tract: A new degrader of starch and protein

Science.gov (United States)

Li, Jiqiu; Tan, Beiping; Mai, Kangsen

2011-09-01

It is a practical approach to select candidate probiotic bacterial stains on the basis of their special traits. Production of digestive enzyme was used as a trait to select a candidate probiotic bacterial strain in this study. In order to select a bacterium with the ability to degrade both starch and protein, an ideal bacterial strain STE was isolated from marine shrimp ( Litopenaeus vannamei) intestines by using multiple selective media. The selected isolate STE was identified on the basis of its morphological, physiological, and biochemical characteristics as well as molecular analyses. Results of degradation experiments confirmed the ability of the selected isolate to degrade both starch and casein. The isolate STE was aerobic, Gram-negative, rod-shaped, motile and non-spore-forming, and had catalase and oxidase activities but no glucose fermentation activity. Among the tested carbon/nitrogen sources, only Tween40, alanyl-glycine, aspartyl-glycine, and glycyl-l-glutamic acid were utilized by the isolate STE. Results of homology comparison analyses of the 16S rDNA sequences showed that the isolate STE had a high similarity to several Pseudoalteromonas species and, in the phylogenetic tree, grouped with P. ruthenica with maximum bootstrap support (100%). In conclusion, the isolate STE was characterized as a novel strain belonging to the genus Pseudoalteromonas. This study provides a further example of a probiotic bacterial strain with specific characteristics isolated from the host gastrointestinal tract.

Study of Relationship between Genetic Pattern and Susceptibility to Fluconazole in Clinical Isolated of Trichophyton rubrum

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F Hadadi

2015-06-01

Full Text Available Background & objectives: Trichophyton rubrum is one of the most common pathogenic causes of dermatophytosis. One of the drugs prescribed for fungal infections is fluconazole which belongs to Azoles group of antifungal agents. Recently molecular typing methods have been developed for answering the epidemiological questions and disease recurrence problems. Current study has been conducted on 22 isolates of Trichophyton rubrum obtained from patients randomly. Our aim was the investigation of correlation between genetic pattern and sensitivity to Fluconazole in clinical isolates of Trichophyton rubrum .   Methods: Firstly the genus and species of isolated fungi from patients have been confirmed by macroscopic and microscopic methods. Then, the resistance and sensitivity of isolates against drug have been determined using culture medium containing defined amount of drug. In next step fungal DNA has been extracted by RAPD-PCR (random amplified polymorphic DNA with random sequences of 3 primers.   Results: Each primer produced different amplified pattern, and differences have been observed in genetic pattern of resistant and sensitive samples using each 3 primers, but there was no bond with 100% specificity.   Conclusion: The 12 sensitive isolates which didn’t grow in 50µg/ml concentration of drug, also had limited growth at the lower concentration of drug. Ten resistant isolates which grew in 50µg/ml of drug, also showed resistant to lower concentration of drug. There are differences in genetic pattern of resistant and sensitive samples. RAPD analysis for molecular typing of Trichophyton rubrum seems to be completely suitable.

Effect of probiotic microorganisms isolated from Hypostomus plecostomus in Oreochromis sp juveniles

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Yuri Vela-Gutiérrez

2017-01-01

Full Text Available Objective. The aim of this study was to assess the behavior of red tilapia juveniles (Oreochromis sp. in presence of the possible probiotic microorganisms isolated from the gastrointestinal tract of panche fish (Hypostomus plecostomus. Materials and methods. During the phase of assessment of probiotics, 120 red tilapia (Oreochromis sp juveniles were selected, with average weight of 1.28±0.22 g and average length of 2.99±0.27 cm. Three experimental treatments were formulated taking into account the nourishment needs of red tilapia (Oreochromis sp.. The statistical method employed was a completely random design. Results. The three strains of Lactobacillus genus (Lactobacillus plantarum, Lactobacillus pentosus, Lactobacillus rhamnosus isolated from the digestive tract of H. plecostomus, yielded diverse results in the biometrical variables considered, as well as in the SGR, PER, AE, AC. Conclusions. The best rapports regarding the gain in length were for the treatment with native probiotics, and it is deduced that they were easily settled in the intestines of the fish (Oreochromis sp.. It is also determined that there are significant differences in the results or gain in length for the Control Concentrate feed (CC against Concentrate feed plus Native Probiotic (CNP for red tilapia (Oreochromis sp. in the juvenile stag for a 30 day time span.

Fermentation of Apple Juice with a Selected Yeast Strain Isolated from the Fermented Foods of Himalayan Regions and Its Organoleptic Properties.

Science.gov (United States)

Kanwar, S S; Keshani

2016-01-01

Twenty-three Saccharomyces cerevisiae strains isolated from different fermented foods of Western Himalayas have been studied for strain level and functional diversity in our department. Among these 23 strains, 10 S. cerevisiae strains on the basis of variation in their brewing traits were selected to study their organoleptic effect at gene level by targeting ATF1 gene, which is responsible for ester synthesis during fermentation. Significant variation was observed in ATF1 gene sequences, suggesting differences in aroma and flavor of their brewing products. Apple is a predominant fruit in Himachal Pradesh and apple cider is one of the most popular drinks all around the world hence, it was chosen for sensory evaluation of six selected yeast strains. Organoleptic studies and sensory analysis suggested Sc21 and Sc01 as best indigenous strains for soft and hard cider, respectively, indicating their potential in enriching the local products with enhanced quality.

Genotyping and study of the pauA and sua genes of Streptococcus uberis isolates from bovine mastitis.

Science.gov (United States)

Perrig, Melina S; Ambroggio, María B; Buzzola, Fernanda R; Marcipar, Iván S; Calvinho, Luis F; Veaute, Carolina M; Barbagelata, María Sol

2015-01-01

This study aimed to determine the clonal relationship among 137 Streptococcus uberis isolates from bovine milk with subclinical or clinical mastitis in Argentina and to assess the prevalence and conservation of pauA and sua genes. This information is critical for the rational design of a vaccine for the prevention of bovine mastitis caused by S. uberis. The isolates were typed by random amplified polymorphic DNA (RAPD) analysis and by pulsed-field gel electrophoresis (PFGE). The 137 isolates exhibited 61 different PFGE types and 25 distinct RAPD profiles. Simpson's diversity index was calculated both for PFGE (0.983) and for RAPD (0.941), showing a high discriminatory power in both techniques. The analysis of the relationship between pairs of isolates showed 92.6% concordance between both techniques indicating that any given pair of isolates distinguished by one method tended to be distinguished by the other. The prevalence of the sua and pauA genes was 97.8% (134/137) and 94.9% (130/137), respectively. Nucleotide and amino acid sequences of the sua and pauA genes from 20 S. uberis selected isolates, based on their PFGE and RAPD types and geographical origin, showed an identity between 95% and 100% with respect to all reference sequences registered in GenBank. These results demonstrate that, in spite of S. uberis clonal diversity, the sua and pauA genes are prevalent and highly conserved, showing their importance to be included in future vaccine studies to prevent S. uberis bovine mastitis. Copyright © 2015 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

New approach for isolation of VNTR markers.

OpenAIRE

Nakamura, Y; Carlson, M; Krapcho, K; Kanamori, M; White, R

1988-01-01

Elsewhere we have reported an efficient method for isolating VNTR (Variable Number of Tandem Repeats) markers. Several of the VNTR markers isolated in those experiments were sequenced, and a DNA sequence of 9 bp (GNNGTGGG) emerged as an apparent consensus sequence for VNTR markers. To confirm this result and to develop more VNTR markers, we synthesized nine different 18-base-long oligonucleotides whose sequences each included GNNGTGGG. When 102 cosmid clones selected by these oligonucleotides...

Isolation and characterization of two malathiondegrading ...

African Journals Online (AJOL)

Pseudomonas aeruginosa and Pseudomonas mendocina degrading malathion were studied. Morphological, biochemical and 16S rRNA genes for bacterial identification were selected. Biodegradation of some organophosphorus compounds with the 2 bacterial isolates was determined by high performance liquid ...

Random survival forests for competing risks

DEFF Research Database (Denmark)

Ishwaran, Hemant; Gerds, Thomas A; Kogalur, Udaya B

2014-01-01

We introduce a new approach to competing risks using random forests. Our method is fully non-parametric and can be used for selecting event-specific variables and for estimating the cumulative incidence function. We show that the method is highly effective for both prediction and variable selection...

Isolation of novel microsatellites using FIASCO by dual probe enrichment from Jatropha curcas L. and study on genetic equilibrium and diversity of Indian population revealed by isolated microsatellites

KAUST Repository

Pamidimarri, D. V N N Sudheer

2010-03-11

Jatropha curcas L. belongs to family Euphorbiaceae, native to South America attained significant importance for its seed oil which can be converted to biodiesel, a renewable energy source alternative to conventional petrodiesel. Very few attempts were made to isolate novel microsatellite markers and assessment of the extent of genetic equilibrium and diversity that exists in J. curcas. Therefore, the present investigation was undertaken to isolate the novel microsatellites and access genetic equilibrium, diversity that exists among 44 diverse germplasm collected from distinct geographical areas in India using isolated microsatellites. The overall efficiency of the enrichment of microsatellite by dual probe in the present study found to be 54% and among the sequences obtained the percentage of sequences having suitable flanking regions for the primer designing was found to be 89.58%. The mean co-efficient of genetic similarity (CGS) was found to be 0.97. The overall diversity obtained by microsatellites was found to be low in comparison with the diversity reported by multilocus markers systems observed in earlier studies; however, the good allele polymorphism was observed. The overall dendrogram of microsatellite analysis resulted in random clustering of germplasm and not in accordance to geographical area of collection. The present study, diversity analysis using microsatellite markers concludes the low genetic diversity and genetic disequlibrium of J. curcas in India and will provide pavement for further intra-population studies on narrow geographical areas to understand the population genetic structure, phylogeography and molecular ecological studies. The germplasm characterized, and the microsatellite markers isolated and characterized in the present study can be employed efficiently in breeding programs for genetic improvement of the species through marker assisted selection and QTL analysis, for further genetic resource management and help in making the J

Using Random Numbers in Science Research Activities.

Science.gov (United States)

Schlenker, Richard M.; And Others

1996-01-01

Discusses the importance of science process skills and describes ways to select sets of random numbers for selection of subjects for a research study in an unbiased manner. Presents an activity appropriate for grades 5-12. (JRH)

Search for unknown isotopes using the TIARA-ISOL and the JAERI-ISOL

Energy Technology Data Exchange (ETDEWEB)

Asai, Masato [Nagoya Univ. (Japan). School of Engineering

1997-07-01

The new neutron-deficient isotopes {sup 127}Pr and {sup 125}Pr, and the new neutron-rich isotopes {sup 166}Tb, {sup 165}Gd and {sup 161}Sm were identified using the TIARA-ISOL with {sup 36}Ar + {sup 92,94}Mo reactions, and the gas-jet coupled JAERI-ISOL with a proton-induced fission of {sup 238}U, respectively. The element-selective oxidation technique was used to reduce large contamination from isobars and molecular ions with production cross sections about one or two orders of magnitude as large as those of the new isotopes. The good signal-to-noise ratios achieved in the present measurements were essential to observe and identify weak X/{gamma} rays from the new isotopes. (author)

Selection, isolation and growth kinetic study of a bacterial consortium obtained from the Potengi mangrove in the presence of crude oil

Energy Technology Data Exchange (ETDEWEB)

Costa, C.C.; Vaz, M.R.F.; Santos, E.S.; Macedo, G.R. [Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN (Brazil). Dept. de Engenharia Quimica], E-mail: natcintia@gmail.com; Costa, J.G. da [Universidade Federal do Amazonas (UFAM), Coari, AM (Brazil). Inst. de Saude e Biotecnologia

2011-10-15

The selection, isolation and kinetic study of a bacterial consortium obtained from a sample of soil from the Potengi mangrove, located in the city of Natal, Rio Grande do Norte, Brazil, has been carried out using the enrichment culture technique to observe aspects such as the evaluation of main growth parameters. The kinetic study used a rotary incubator shaker at 150rpm, under 30 deg C. The bacterial consortium isolated from the estuary of the Potengi River showed a good acclimation in minimum mineral medium with 1% (v/v) of oil. The cell concentration reached 2.55 g/L at 16h of cultivation and surface tension dropped. The maximum productivity in cells obtained was of 0.3 g/L.h, the specific velocity of growth was of 0.075h{sup -1}, with a generation time (tg) of 9.24h. This study seeks to demonstrate that the consortium can be used as inoculants in biological treatments, capable of reducing the waste's degradation time. (author)

In vivo selection of resistant E. coli after ingestion of milk with added drug residues.

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Richard Van Vleck Pereira

Full Text Available Antimicrobial resistance represents a major global threat to modern medicine. In vitro studies have shown that very low concentrations of drugs, as frequently identified in the environment, and in foods and water for human and animal consumption, can select for resistant bacteria. However, limited information is currently available on the in vivo impact of ingested drug residues. The objective of our study was to evaluate the effect of feeding preweaned calves milk containing antimicrobial drug residues (below the minimum inhibitory concentration, similar to concentrations detected in milk commonly fed to dairy calves, on selection of resistant fecal E. coli in calves from birth to weaning. At birth, thirty calves were randomly assigned to a controlled feeding trial where: 15 calves were fed raw milk with no drug residues (NR, and 15 calves were fed raw milk with drug residues (DR by adding ceftiofur, penicillin, ampicillin, and oxytetracycline at final concentrations in the milk of 0.1, 0.005, 0.01, and 0.3 µg/ml, respectively. Fecal samples were rectally collected from each calf once a week starting at birth prior to the first feeding in the trial (pre-treatment until 6 weeks of age. A significantly greater proportion of E. coli resistant to ampicillin, cefoxitin, ceftiofur, streptomycin and tetracycline was observed in DR calves when compared to NR calves. Additionally, isolates from DR calves had a significant decrease in susceptibility to ceftriaxone and ceftiofur when compared to isolates from NR calves. A greater proportion of E. coli isolates from calves in the DR group were resistant to 3 or more antimicrobial drugs when compared to calves in the ND group. These findings highlight the role that low concentrations of antimicrobial drugs have on the evolution and selection of resistance to multiple antimicrobial drugs in vivo.

Poly-γ-Glutamic Acids Contribute to Biofilm Formation and Plant Root Colonization in Selected Environmental Isolates of Bacillus subtilis

Science.gov (United States)

Yu, Yiyang; Yan, Fang; Chen, Yun; Jin, Christopher; Guo, Jian-Hua; Chai, Yunrong

2016-01-01

Bacillus subtilis is long known to produce poly-γ-glutamic acids (γ-PGA) as one of the major secreted polymeric substances. In B. subtilis, the regulation of γ-PGA production and its physiological role are still unclear. B. subtilis is also capable of forming structurally complex multicellular communities, or biofilms, in which an extracellular matrix consisting of secreted proteins and polysaccharides holds individual cells together. Biofilms were shown to facilitate B. subtilis–plant interactions. In this study, we show that different environmental isolates of B. subtilis, all capable of forming biofilms, vary significantly in γ-PGA production. This is possibly due to differential regulation of γ-PGA biosynthesis genes. In many of those environmental isolates, γ-PGA seems to contribute to robustness and complex morphology of the colony biofilms, suggesting a role of γ-PGA in biofilm formation. Our evidence further shows that in selected B. subtilis strains, γ-PGA also plays a role in root colonization by the bacteria, pinpointing a possible function of γ-PGA in B. subtilis–plant interactions. Finally, we found that several pathways co-regulate both γ-PGA biosynthesis genes and genes for the biofilm matrix in B. subtilis, but in an opposing fashion. We discussed potential biological significance of that. PMID:27891125

Biodegradation of propargite by Pseudomonas putida, isolated from tea rhizosphere.

Science.gov (United States)

Sarkar, Soumik; Seenivasan, Subbiah; Asir, Robert Premkumar Samuel

2010-02-15

Biodegradation of miticide propargite was carried out in vitro by selected Pseudomonas strains isolated from tea rhizosphere. A total number of 13 strains were isolated and further screened based on their tolerance level to different concentrations of propargite. Five best strains were selected and further tested for their nutritional requirements. Among the different carbon sources tested glucose exhibited the highest growth promoting capacity and among nitrogen sources ammonium nitrate supported the growth to the maximum. The five selected Pseudomonas strain exhibited a range of degradation capabilities. Mineral salts medium (MSM) amended with glucose provided better environment for degradation with the highest degradation potential in strain SPR 13 followed by SPR 8 (71.9% and 69.0% respectively).

Comparative study of Microsporum canis isolates by DNA fingerprinting.

Science.gov (United States)

Shafiee, Shabnam; Khosravi, Ali Reza; Ashrafi Tamai, Iradj

2014-08-01

Microsporum canis is a zoophilic fungus and it is an important agent of dermatophytosis. Cats act as important reservoirs. Clinically, it is too difficult to differentiate dermatophytosis caused by various species, also this fungus loses its morphological characteristics easily because of subculture; so using of rapid and accurate laboratory techniques for identifying the dermatophytes is important, therefore, RAPD-PCR was applied for the differentiation of the isolates. In this study, 10 M. canis isolates were detected in cats, dog, human, fox and rabbit at the Mycology Research Center, Faculty of Veterinary Medicine, University of Tehran. For running the RAPD-PCR, PCR set system and three random primers OPU 15, OPU 13 and OPA 04 were used. Then phylogenetic tree and similarity coefficient table were drawn. The results showed that there were some common bands between M. canis isolates. There were some specific bands for each isolates, as well. Our study showed, despite the typical morphology of the whole isolates, they were placed in different branches in molecular typing. © 2014 Blackwell Verlag GmbH.

Isolation of monoclonal antibodies with predetermined conformational epitope specificity.

Directory of Open Access Journals (Sweden)

Anton M Sholukh

Full Text Available Existing technologies allow isolating antigen-specific monoclonal antibodies (mAbs from B cells. We devised a direct approach to isolate mAbs with predetermined conformational epitope specificity, using epitope mimetics (mimotopes that reflect the three-dimensional structure of given antigen subdomains. We performed differential biopanning using bacteriophages encoding random peptide libraries and polyclonal antibodies (Abs that had been affinity-purified with either native or denatured antigen. This strategy yielded conformational mimotopes. We then generated mimotope-fluorescent protein fusions, which were used as baits to isolate single memory B cells from rhesus monkeys (RMs. To amplify RM immunoglobulin variable regions, we developed RM-specific PCR primers and generated chimeric simian-human mAbs with predicted epitope specificity. We established proof-of-concept of our strategy by isolating mAbs targeting the conformational V3 loop crown of HIV Env; the new mAbs cross-neutralized viruses of different clades. The novel technology allows isolating mAbs from RMs or other hosts given experimental immunogens or infectious agents.

Characterization of Petroleum Hydrocarbon Decomposing Fungi Isolated from Mangrove Rhizosphere

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Nuni Gofar

2011-01-01

Full Text Available The research was done to obtain the isolates of soil borne fungi isolated from mangrove rhizosphere which were capable of degrading petroleum hydrocarbon compounds. The soil samples were collected from South Sumatra mangrove forest which was contaminated by petroleum. The isolates obtained were selected based on their ability to survive, to grow and to degrade polycyclic aromatic hydrocarbons in medium containing petroleum residue. There were 3 isolates of soil borne hydrocarbonoclastic fungi which were able to degrade petroleum in vitro. The 3 isolates were identified as Aspergillus fumigates, A. parasiticus, and Chrysonilia sitophila. C. sitophila was the best isolate to decrease total petroleum hydrocarbon (TPH from medium containing 5-20% petroleum residue.

Prevalence and antibiogram profiles of Escherichia coli O157:H7 isolates recovered from three selected dairy farms in the Eastern Cape Province, South Africa

Directory of Open Access Journals (Sweden)

Luyanda Msolo

2016-12-01

Full Text Available Objective: To investigate the occurrence and antibiotics susceptibility of Escherichia coli (E. coli O157:H7 isolates from raw milk, cattle udder, milking machines and worker’s hand swabs from three selected commercial dairy farms in the Amathole District Municipality, Eastern Cape Province, South Africa. Methods: Raw milk samples were collected from bulk storage tanks and swab samples were collected from milking machines, cattle udders and worker’s hands fortnightly over a sixmonth sampling regime between June and November 2014. A standard culture-based method was used for the enumeration and isolation of E. coli O157:H7, presumptive identification using sorbitol MacConkey agar (supplemented with cefixime (50 µg/L and potassium tellurite (25 mg/L. A serological confirmation of the presumptive E. coli O157:H7 isolates was conducted using the O157 latex agglutination test kit. Results: A total of 252 E. coli O157:H7 isolates were further subjected to PCR amplification of rfbEO157 and flCH7 genes of which 27(11% of the isolates were confirmed positive E. coli O157:H7. The percentage antibiotic resistance of the 27 E. coli O157:H7 isolates from the dairy farms revealed penicillin [23 (85%], tetracycline [22 (81%], erythromycin [19 (70%], streptomycin [14 (52%] and chloramphenicol [12 (45%]. The highest resistances were penicillin [23 (85%] and tetracycline [22 (81%]. Conclusions: These findings revealed that the dairy farms are potential reservoirs of E. coli O157:H7 serotype, and harbor antibiotic-resistant determinants, a concern to public and environmental health.

Observations on biofilm bacteria isolated from aluminium panels immersed in estuarine waters

Digital Repository Service at National Institute of Oceanography (India)

Sonak, S.; Bhosle, N.B.

Microfouling biomass generally increased on aluminium panels immersed in the surface waters of a tropical estuary over a period of 30 d. A hundred bacterial colonies were randomly isolated, purified and morphologically, physiologically...

Recurrence of pulmonary vein conduction and atrial fibrillation after pulmonary vein isolation for atrial fibrillation

DEFF Research Database (Denmark)

Nilsson, Brian; Chen, Xu; Pehrson, Steen

2006-01-01

BACKGROUND: Both segmental ostial and circumferential extraostial pulmonary vein (PV) isolation have been proven effective in the treatment of atrial fibrillation (AF). However, the recurrence of AF and PV conduction after the 2 ablation strategies has never been compared in a randomized study...... isolation. Extraostial PV isolation was performed by encircling the paired left and right PVs, respectively, guided by an electroanatomic mapping system. RESULTS: A total of 84% of the patients had recurrent AF after the first PV isolation procedure, showing 72% with AF and 12% with organized left atrial...

Antibiotic resistance of Verotoxigenic Escherichia coli isolated from vegetables

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mojtaba boniadian

2017-01-01

Full Text Available Introduction: Human gastrointestinal disease caused by verotoxigenic Escherichia coli has been diagnosed for recent decades. Escherichia coli O157:H7 is the most important serotype of verotoxigenic Escherichia coli that cause hemolytic uremic syndrome and hemorrhagic colitis in humans. This study was conducted to determine the occurrence of verotoxigenic E. coli and antibiotic resistance of the isolates from vegetables. Materials and methods: A total of 500 fresh vegetable samples were collected randomly from retail shops in Shahrekord, Iran. E. coli was isolated and identified using bacteriological and biochemical tests. PCR method was used to identify the rbfE, stx1, stx2 and eae genes. Also, antibiotic resistance of the isolates was determined by disk diffusion method. Results: The results represented that among 25 isolates possess virulence genes, 40, 12 and 4% of the isolates contained eaeA, STx2, and both genes, respectively. But none of them contained H7, STx1, and rfbE genes. The antibiotic resistance pattern demonstrated that the isolates were highly resistant to Gentamycin and cefotoxime. Discussion and conclusion: The results of this study showed that the presence of verotoxigenic E.coli in vegetables; and high resistance of the isolates to antibiotics could be hazardous for public health.

Ohcratoxin producing Aspergillus spp. Isolated from tropical soils in Sarawak, Malaysia

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J.S.S. Seelan

2010-03-01

Full Text Available Aspergillus strains isolated from tropical soils were selected for additional characterization and for ochratoxin analysis, which was determined by ELISA method and high performance liquid chromatography (HPLC profiles. Because of its great morphological variability and mycotoxin production availability, 18 isolates of Aspergillus species were selected for this study. Only two isolates of these tropical soils, A. sulphureus and A. carbonarius, showed positive results for ohcratoxin (OA in lower concentration (0.05-0.10 µg/ml. Ochratoxin production by these species was confirmed by high performance liquid chromatography. HPLC analysis for ochratoxin producing A. sulphureus and A. carbonarius showed retention time, Rt value = 4.417 and Rt value = 4.081 respectively.

Acute effects of active isolated stretching on vertical jump ...

African Journals Online (AJOL)

The purpose of the study was to determine the acute effects of active isolated stretching on muscular peak power production. Sixty healthy, physically active volunteers (aged 18-28) participated as subjects in this study. Subjects were randomly assigned to two groups; the control group and the experimental group. Subjects ...

Effectively designed molecularly imprinted polymers for selective isolation of the antidiabetic drug metformin and its transformation product guanylurea from aqueous media

Energy Technology Data Exchange (ETDEWEB)

Kyzas, George Z.; Nanaki, Stavroula G. [Laboratory of Polymer Chemistry and Technology, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24 Thessaloniki (Greece); Koltsakidou, Anastasia; Papageorgiou, Myrsini; Kechagia, Maria [Laboratory of Environmental Pollution Control, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24 Thessaloniki (Greece); Bikiaris, Dimitrios N. [Laboratory of Polymer Chemistry and Technology, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24 Thessaloniki (Greece); Lambropoulou, Dimitra A., E-mail: dlambro@chem.auth.gr [Laboratory of Environmental Pollution Control, Department of Chemistry, Aristotle University of Thessaloniki, GR-541 24 Thessaloniki (Greece)

2015-03-25

Highlights: • Preparation of novel MIPs with remarkable recognition properties. • Selective isolation and removal of metformin and guanylurea from aqueous media. • Detailed adsorbent characterization and adsorption studies. • Successful application of synthesized MIPs as dispersive SPE sorbents. • Estimation of expanded uncertainty following a bottom-up approach. - Abstract: In the present study, two novel molecularly imprinted polymers (MIPs) with remarkable recognition properties for metformin and its transformation product, guanylurea, have been prepared for their selective, enrichment, isolation and removal from aqueous media. The prepared adsorbents were characterized by Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and swelling experiments. The performance of the prepared MIPs was evaluated by various parameters including the influence of pH, contact time, temperature and initial compound concentration. The effects on the adsorption behavior of the removal process parameters were studied and the equilibrium data were fitted by the Langmuir and Freundlich models. Due to the imprinting effect, adsorption performance of MIPs was always superior to its corresponding NIP (non-imprinted polymer), with maximum adsorption capacity ∼80 mg g{sup −1} for both MIPs. Stability and reusability of the MIPs up to the 5th cycle meant that they could be applied repeatedly without losing substantial removal ability. In the next step, the prepared MIP nanoparticles were evaluated as sorbents in a dispersive solid phase extraction (D-SPE) configuration for selective enrichment and determination of metformin and guanylurea in different aqueous matrices. Under the working extraction conditions, the D-SPE method showed good linearity in the range of 50–1000 ng L{sup −1}, repeatability of the extractions (RSD 2.1–5.1%, n = 3), and low limits of detection (1.5–3.4 ng L{sup −1}). The expanded uncertainty of the data obtained

Antibiogram of bacteria isolated from automated teller machines in Hamadan, West Iran

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Mahmoudi, Hassan

2017-02-01

Full Text Available Aim: Bacteria are ubiquitous in the environment. In keeping with the continued expansion of urbanization and the growing population, an increasing number of people use automated banking, i.e. automated teller machines (ATMs. The aim of this study was to investigate the bacterial contamination and its antibiotic sensitivity on computer keyboards located at ATMs in Hamadan province, Iran. Method: Out of 360 ATMs at four locations in Hamadan, 96 were randomly selected for this study. The antibiotic susceptibility pattern of all isolates was determined by the agar disk diffusion method using gentamicin (10 µg, vancomycin (30 µg, trimethoprim/sulfamethoxazole (25 µg, amikacin (30 µg, tobramycin (10 µg, cephalotin (30 µg, norfloxacin (5 µg, and ceftizoxim (30 µg disks. Results: Melli and Saderat Banks had the most frequently contaminated ATMS, with 18 (27.7% and 12 (18.5%, respectively. The most frequently isolated bacteria were in 12 (18.5% ATMs, in in 11 (16.9%, in 6 (9.2%, spp. in 8 (12.3%, spp. in 2 (3.1%, in 6 (9.2%, in 3 (4.6%, and spp. in 5 (7.69% cases. All isolated bacteria were susceptible to gentamicin, cephalotin, tobramycin, amikacin, norfloxacin, and vancomycin. The resistance rate to trimethoprim/sulfamole was 50%. Conclusion: All tested ATM keyboards were contaminated with at least one species of bacteria. Based on these findings, it is recommendable to disinfect the hands after entering one’s own apartment, work area or a hospital, in order to hinder the spread of critical pathogens in the personal environment or in the hospital.

Transcription of the var genes from a freshly-obtained field isolate of Plasmodium falciparum shows more variable switching patterns than long laboratory-adapted isolates.

Science.gov (United States)

Ye, Run; Zhang, Dongmei; Chen, Biaobang; Zhu, Yongqiang; Zhang, Yilong; Wang, Shengyue; Pan, Weiqing

2015-02-07

Antigenic variation in Plasmodium falciparum involves switching among multicopy var gene family and is responsible for immune evasion and the maintenance of chronic infections. Current understanding of var gene expression and switching patterns comes from experiments conducted on long laboratory-adapted strains, with little known about their wild counterparts. Genome sequencing was used to obtain 50 var genes from a parasite isolated from the China-Myanmar border. Four clones with different dominant var genes were cultured in vitro in replicates for 50 generations. Transcription of the individual var gene was detected by real-time PCR and then the switching process was analysed. The expression of multicopy var genes is mutually exclusive in clones of a wild P. falciparum isolate. The activation of distinct primary dominant var genes leads to different and favoured switching patterns in the four clones. The on/off rates of individual var genes are variable and the choice of subsequent dominant var genes are random, which results in the different switching patterns among replicates of each clonal wild P. falciparum isolate with near identical initial transcription profiles. This study suggests that the switching patterns of var genes are abundant, which consist of both conserved and random parts.

Correlates of smoking with socioeconomic status, leisure time physical activity and alcohol consumption among Polish adults from randomly selected regions.

Science.gov (United States)

Woitas-Slubowska, Donata; Hurnik, Elzbieta; Skarpańska-Stejnborn, Anna

2010-12-01

To determine the association between smoking status and leisure time physical activity (LTPA), alcohol consumption, and socioeconomic status (SES) among Polish adults. 466 randomly selected men and women (aged 18-66 years) responded to an anonymous questionnaire regarding smoking, alcohol consumption, LTPA, and SES. Multiple logistic regression was used to examine the association of smoking status with six socioeconomic measures, level of LTPA, and frequency and type of alcohol consumed. Smokers were defined as individuals smoking occasionally or daily. The odds of being smoker were 9 times (men) and 27 times (women) higher among respondents who drink alcohol several times/ week or everyday in comparison to non-drinkers (p times higher compared to those with the high educational attainment (p = 0.007). Among women we observed that students were the most frequent smokers. Female students were almost three times more likely to smoke than non-professional women, and two times more likely than physical workers (p = 0.018). The findings of this study indicated that among randomly selected Polish man and women aged 18-66 smoking and alcohol consumption tended to cluster. These results imply that intervention strategies need to target multiple risk factors simultaneously. The highest risk of smoking was observed among low educated men, female students, and both men and women drinking alcohol several times a week or every day. Information on subgroups with the high risk of smoking will help in planning future preventive strategies.

Monoterpene biosynthesis in lemon (Citrus limon) cDNA isolation and functional analysis of four monoterpene synthases

NARCIS (Netherlands)

Lücker, J.; Tamer, El M.K.; Schwab, W.; Verstappen, F.W.A.; Plas, van der L.H.W.; Bouwmeester, H.J.; Verhoeven, H.A.

2002-01-01

Citrus limon possesses a high content and large variety of monoterpenoids, especially in the glands of the fruit flavedo. The genes responsible for the production of these monoterpenes have never been isolated. By applying a random sequencing approach to a cDNA library from mRNA isolated from the

cDNA fingerprinting of osteoprogenitor cells to isolate differentiation stage-specific genes.

OpenAIRE

Candeliere, G A; Rao, Y; Floh, A; Sandler, S D; Aubin, J E

1999-01-01

A cDNA fingerprinting strategy was developed to identify genes based on their differential expression pattern during osteoblast development. Preliminary biological and molecular staging of cDNA pools prepared by global amplification PCR allowed discrim-inating choices to be made in selection of expressed sequence tags (ESTs) to be isolated. Sequencing of selected ESTs confirmed that both known and novel genes can be isolated from any developmental stage of interest, e.g. from primitive progen...

Isolation and characterization of mutated alcohol oxidases from the yeast Hansenula polymorpha with decreased affinity toward substrates and their use as selective elements of an amperometric biosensor

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Schuhmann Wolfgang

2007-06-01

Full Text Available Abstract Background Accurate, rapid, and economic on-line analysis of ethanol is very desirable. However, available biosensors achieve saturation at very low ethanol concentrations and thus demand the time and labour consuming procedure of sample dilution. Results Hansenula polymorpha (Pichia angusta mutant strains resistant to allyl alcohol in methanol medium were selected. Such strains possessed decreased affinity of alcohol oxidase (AOX towards methanol: the KM values for AOX of wild type and mutant strains CA2 and CA4 are shown to be 0.62, 2.48 and 1.10 mM, respectively, whereas Vmax values are increased or remain unaffected. The mutant AOX alleles from H. polymorpha mutants CA2 and CA4 were isolated and sequenced. Several point mutations in the AOX gene, mostly different between the two mutant alleles, have been identified. Mutant AOX forms were isolated and purified, and some of their biochemical properties were studied. An amperometric biosensor based on the mutated form of AOX from the strain CA2 was constructed and revealed an extended linear response to the target analytes, ethanol and formaldehyde, as compared to the sensor based on the native AOX. Conclusion The described selection methodology opens up the possibility of isolating modified forms of AOX with further decreased affinity toward substrates without reduction of the maximal velocity of reaction. It can help in creation of improved ethanol biosensors with a prolonged linear response towards ethanol in real samples of wines, beers or fermentation liquids.

IDENTIFICATION AND BIOLOGICAL ACTIVITY OF POTENTIAL PROBIOTIC BACTERIA ISOLATED FROM POECILIA RETICULATA (GUPPY

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Aparna Balakrishna

2014-08-01

Full Text Available Antagonistic activities against candidate indicator strains, adhesion to mucus and biofilm formation of potential probiotic strains isolated from Poecilia reticulata were evaluated. Four isolated strains (MBTU_PB1, MBTU_PB2, MBTU_PB3 and MBTU_PB4 showed moderate to strong antagonistic activities against the tested five indicator strains (Aeromonas hydrophila1739, Vibrio cholera 3906, Flavobacterium 2495, Acinetobacter 1271 and Alcaligenes 1424 and these isolates were further identified using biochemical tests and 16S rDNA gene sequence analysis. Except the whole cell product, the other three cellular components, namely, heat-killed whole cell product, intracellular product and extracellular product of all the four selected isolates were equally effective, as revealed by the zone of inhibitions to the tested indicator strains. The in vitro adhesion property or the ability of colonization is often considered as a selection criteria for probiotics. All the selected four strains had higher adhesion abilities than the indicator strains. Further, these four strains had the ability to form biofilms on polystyrene surfaces. The in vitro characterization of these four strains suggests possibility of using the isolates, as individual strain or in combination, for probiotic therapy in aquaculture.

Resistance pattern of clinical isolates of staphylococcus aureus against five groups of antibiotics

International Nuclear Information System (INIS)

Farzana, K.; Hameed, A.

2006-01-01

Among the samples received in pathology laboratory, Pakistan institute of Medical Science, Islamabad, 5069 samples had bacterial growth, among these 2580 (51%) samples were Gram-positive cocci and 1688 were Staphylococcus aureus during a period of two years. Out of these Gram-positive cocci 56% were resistant to penicillin group, 27% were resistant to cephalosporin group, 22% were resistant to aminoglycoside group 15% were resistant to quinolone group and 31% were resistant to other antibiotics (cotrimaxazole, erythromycin, aztreonam, vancomycin, nitrofurantion and meropenam). Antibio-grams of Gram-positive cocci were determined against various antibiotics by disc diffusion method. The rate of resistance to most of the antibiotics such as ampicillin, piperacillin, carbenicillin, penicillin, cephradine, cefotaxime, erythromycin, ceclor, ofloxacin, pefloxacin, ciprofloxacin, cotrimexazole (septran), gentamicin, meropenem, ceftazidime, erythromycin, tobramycin, enoxacin was higher when tested against the isolates collected from pus as compared to those from blood and urine. Antibiotic resistant strains were more prevalent in pus samples than other clinical isolates (blood and urine). The randomly selected 155 strains of Staphylococcus aureus when tested against five groups of antibiotics showed resistance rate against ampicillin (92%), cephradine (92%), cephradine (60%), and gentamicin (58%). However intermediate resistance was found in case of vancomicin (38%), in hospitalized and non-hospitalized patients. (author)

Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast.

Science.gov (United States)

Herrera, C M; Pozo, M I; Bazaga, P

2011-11-01

Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights into the ecological and genetic correlates of clonality, and into the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using amplified fragment length polymorphism (AFLP) markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by amova (Φ(st)  = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparts to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality. © 2011 Blackwell Publishing Ltd.

Diversity of Antifungal Compounds-Producing Bacillus spp. Isolated from Rhizosphere of Soybean Plant Based on ARDRA and 16S rRNA

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ARIS TRI WAHYUDI

2010-09-01

Full Text Available Plant growth promoting rhizobacteria (PGPR play an important role in improvement of seed germination, root development, and water utilization by plants. These rhizobacteria can stimulate plant growth directly by producing growth hormones or indirectly by producing antifungal compounds/antibiotics to suppress phytopathogenic fungi. The objective of this research was to analyze the diversity of 22 antifungal-producing rhizobacteria of Bacillus sp. isolated from rhizosphere of soybean plant based on Amplified rDNA Restriction Analysis (ARDRA and 16S rRNA Sequence. Restriction enzymes in ARDRA analysis, HinfI, HaeIII, and RsaI were used to digest 22 16S rDNA amplified from Bacillus sp. genomes. Based on this analysis, genetic diversity of 22 Bacillus sp. producing antifungal compounds were classified into eight different groups. Moreover, six selected isolates randomly from each ARDRA group that have strong activity to suppress fungal growth were analyzed for their 16S rDNA sequences compared with reference strains. The distributions of these isolates were genetically diverse on several species of Bacillus sp. such as B. subtilis, B. cereus, and B. fusiformis. ARDRA is a reliable technique to analyze genetic diversity of Bacillus sp. community in the rhizosphere.

Characterization of Italian isolates of Inonotus rickii

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Tiziana ANNESI

2011-01-01

Full Text Available Thirty-seven isolates of Inonotus rickii, a pathogenic fungus causing white rot and cankers, were collected from diseased boxelder trees lining boulevards in Rome and from other hosts in Rome and Sicily. During the survey, it was observed that this fungus occasionally produced basidiomes, but more frequently it had anamorphic structures that released a brown powdery mass of chlamydospores, presumably acting as asexual propagules. All isolates were characterized using random amplified microsatellite analysis and somatic incompatibility tests in order to investigate the diversity of genotypes within and between the different disease centers surveyed in Italy. The results suggest that both sexual and asexual reproduction play an important role in the spread of this disease, with important epidemiological implications. .

Effects of one versus two bouts of moderate intensity physical activity on selective attention during a school morning in Dutch primary schoolchildren: A randomized controlled trial.

Science.gov (United States)

Altenburg, Teatske M; Chinapaw, Mai J M; Singh, Amika S

2016-10-01

Evidence suggests that physical activity is positively related to several aspects of cognitive functioning in children, among which is selective attention. To date, no information is available on the optimal frequency of physical activity on cognitive functioning in children. The current study examined the acute effects of one and two bouts of moderate-intensity physical activity on children's selective attention. Randomized controlled trial (ISRCTN97975679). Thirty boys and twenty-six girls, aged 10-13 years, were randomly assigned to three conditions: (A) sitting all morning working on simulated school tasks; (B) one 20-min physical activity bout after 90min; and (C) two 20-min physical activity bouts, i.e. at the start and after 90min. Selective attention was assessed at five time points during the morning (i.e. at baseline and after 20, 110, 130 and 220min), using the 'Sky Search' subtest of the 'Test of Selective Attention in Children'. We used GEE analysis to examine differences in Sky Search scores between the three experimental conditions, adjusting for school, baseline scores, self-reported screen time and time spent in sports. Children who performed two 20-min bouts of moderate-intensity physical activity had significantly better Sky Search scores compared to children who performed one physical activity bout or remained seated the whole morning (B=-0.26; 95% CI=[-0.52; -0.00]). Our findings support the importance of repeated physical activity during the school day for beneficial effects on selective attention in children. Copyright © 2015 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Mites as selective fungal carriers in stored grain habitats.

Science.gov (United States)

Hubert, Jan; Stejskal, Václav; Kubátová, Alena; Munzbergová, Zuzana; Vánová, Marie; Zd'árková, Eva

2003-01-01

Mites are well documented as vectors of micromycetes in stored products. Since their vectoring capacity is low due to their small size, they can be serious vectors only where there is selective transfer of a high load of specific fungal species. Therefore the aim of our work was to find out whether the transfer of fungi is selective. Four kinds of stored seeds (wheat, poppy, lettuce, mustard) infested by storage mites were subjected to mycological analysis. We compared the spectrum of micromycete species isolated from different species of mites (Acarus siro, Lepidoglyphus destructor, Tyrophagus putrescentiae, Caloglyphus rhizoglyphoides and Cheyletus malaccensis) and various kinds of stored seeds. Fungi were separately isolated from (a) the surface of mites, (b) the mites' digestive tract (= faeces), and (c) stored seeds and were then cultivated and determined. The fungal transport via mites is selective. This conclusion is supported by (i) lower numbers of isolated fungal species from mites than from seeds; (ii) lower Shannon-Weaver diversity index in the fungal communities isolated from mites than from seeds; (iii) significant effect of mites/seeds as environmental variables on fungal presence in a redundancy analysis (RDA); (iv) differences in composition of isolated fungi between mite species shown by RDA. The results of our work support the hypothesis that mite-fungal interactions are dependent on mite species. The fungi attractive to mites seem to be dispersed more than others. The selectivity of fungal transport via mites enhances their pest importance.

Antimicrobial resistence of Shigella species isolated during 2004 and 2005 from selected sites in Zimbabwe.

Science.gov (United States)

Ndlovu, N; Tarupiwa, A; Mudzori, J T

2006-01-01

To determine the predominant serotype and antibiotic sensitivity pattern of Shigella isolates during 2004 and 2005 in Zimbabwe. Cross sectional study. National Microbiology Reference Laboratory (NMRL), Harare, Zimbabwe. 259 clinical isolates of Shigella species isolated during 2004 and 2005 in Zimbabwe were studied. These samples had been referred to the NMRL for further testing. Serotype and antibiotic sensitivity pattern of Shigella species. Of the 259 clinical isolates of Shigella tested the following species were serotyped; 141 (54.4%) were S. flexneri; 70 (27%) S. sonnei; 38 (14.7%) S. dysenteriae and 10 (3.9%) S. boydii. About 4% of all Shigella isolates tested showed full sensitivity to commonly used antibiotics, 20.8% were resistant to one antibiotic only while 75.3% were resistant to at least two antibiotics. The most common resistance among Shigella species was to cotrimoxazole (89%), tetracycline (73%), ampicillin (49%) and chloramphenicol (41%). High susceptibility among Shigella species was observed to nalidixic acid (86%), ciprofloxacin (99%) and ceftazidine (99%). There was a low drug resistance of Shigella species to nalidixic acid, a drug of choice in Zimbabwe, except among Shigella dysenteriae type 1 strains. Continuous monitoring of the susceptibility patterns of Shigella species is important in order to detect the emergence of drug resistance and to update guidelines for antibiotic treatment in shigellosis.

HYPOVIRULENT ISOLATES OF FUSARIUM COLLECTED FROM CHILI CROPS IN BOYOLALI REGENCY, CENTRAL JAVA, INDONESIA

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Supyani

2015-02-01

Full Text Available Fusarium, a genus of filamentous fungi, has many species which serving as important pathogens to many diseases in crops. Till today, there have not been effective and efficient control methods for such fungi. Recently, scientists agree that application of biological agents is a tactful choice. Development of hypovirulent strains of fungus as biocontrol agents is very limited. This research was aimed to find hypovirulent isolates of Fusarium from field as biological agents. A hundred isolates of Fusarium from chili were collected in Boyolali, Central Java. Morphological characterization revealed that isolates performed varied colony phenotypes. Based on colony phenotype pattern, isolates were classified into five groups. From each group, one hypovirulent isolate was selected based on colony growth rate on potato dextrose agar media. The selected hypovirulent isolates were used for virulence assay in apple. The result showed that there were four hypovirulent isolates i.e.: B6, C15, D19, and E20 isolates. Total RNA extraction of the identified hypovirulent isolates revealed the existence of viral RNA in C15 isolate. Based on the existence of viral RNA in C15 isolate, the hypovirulent traits were due to mycoviral infection, whereas the hypovirulent traits performed by the other three were due to genetic factors.

Isolation and characterization of promoter regions from Streptococcus gordonii CH1

NARCIS (Netherlands)

Vriesema, A.J.M.; Dankert, J.; Zaat, S.A.J.

1999-01-01

We aimed to identify transcription signal sequences from Streptococcus gordonii strain CH1 by random chromosomal cloning. Five genomic fragments from a Sau3A digest, which constitutively activated transcription of a promoterless spectinomycin resistance gene in this strain, were isolated and

Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction.

Science.gov (United States)

Marques, Yuri Bento; de Paiva Oliveira, Alcione; Ribeiro Vasconcelos, Ana Tereza; Cerqueira, Fabio Ribeiro

2016-12-15

MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs). The current ab initio approaches, however, have selectivity issues, i.e., a high number of false positives is reported, which can lead to laborious and costly attempts to provide biological validation. This study presents an extension of the ab initio method miRNAFold, with the aim of improving selectivity through machine learning techniques, namely, random forest combined with the SMOTE procedure that copes with imbalance datasets. By comparing our method, termed Mirnacle, with other important approaches in the literature, we demonstrate that Mirnacle substantially improves selectivity without compromising sensitivity. For the three datasets used in our experiments, our method achieved at least 97% of sensitivity and could deliver a two-fold, 20-fold, and 6-fold increase in selectivity, respectively, compared with the best results of current computational tools. The extension of miRNAFold by the introduction of machine learning techniques, significantly increases selectivity in pre-miRNA ab initio prediction, which optimally contributes to advanced studies on miRNAs, as the need of biological validations is diminished. Hopefully, new research, such as studies of severe diseases caused by miRNA malfunction, will benefit from the proposed computational tool.

A new approach to isolating siderophore-producing actinobacteria.

Science.gov (United States)

Nakouti, I; Sihanonth, P; Hobbs, G

2012-07-01

This study was conducted to investigate the application of 2,2'-dipyridyl as a new approach to isolating siderophore-producing actinobacteria. Isolation of actinobacteria from soil was conducted by a soil dilution plate technique using starch-casein agar. Iron starvation was fostered by the incorporation of the iron chelator 2,2'-dipyridyl in the isolation medium. Pretreatment of the samples at an elevated temperature (40°C) ensured that the majority of nonsporulating bacteria were excluded. The survivors of this treatment were largely actinobacteria. Of the viable cultures grown in the presence of 2,2'-dipyridyl, more than 78-88% (average of three separate studies) were reported to produce siderophore-like compounds compared to 13-18% (average of three separate studies) when grown on the basic media in the absence of the chelating agent. The most prolific producers as assessed by the chrome azurol sulphate (CAS) assay were further characterized and found to belong to the genus Streptomyces. Selective pressure using 2,2'-dipyridyl as an iron-chelating agent in starch-casein media increased the isolation of siderophore-producing actinobacteria compared to the unamended medium. The study described represents a new approach to the isolation of siderophore-producing actinobacteria using a novel procedure that places a selection on cell population based upon the incorporation of a chelating agent in the medium. © 2012 The Authors. Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

Imperfect isolation: factors and filters shaping Madagascar's extant vertebrate fauna.

Science.gov (United States)

Samonds, Karen E; Godfrey, Laurie R; Ali, Jason R; Goodman, Steven M; Vences, Miguel; Sutherland, Michael R; Irwin, Mitchell T; Krause, David W

2013-01-01

Analyses of phylogenetic topology and estimates of divergence timing have facilitated a reconstruction of Madagascar's colonization events by vertebrate animals, but that information alone does not reveal the major factors shaping the island's biogeographic history. Here, we examine profiles of Malagasy vertebrate clades through time within the context of the island's paleogeographical evolution to determine how particular events influenced the arrival of the island's extant groups. First we compare vertebrate profiles on Madagascar before and after selected events; then we compare tetrapod profiles on Madagascar to contemporary tetrapod compositions globally. We show that changes from the Mesozoic to the Cenozoic in the proportions of Madagascar's tetrapod clades (particularly its increase in the representation of birds and mammals) are tied to changes in their relative proportions elsewhere on the globe. Differences in the representation of vertebrate classes from the Mesozoic to the Cenozoic reflect the effects of extinction (i.e., the non-random susceptibility of the different vertebrate clades to purported catastrophic global events 65 million years ago), and new evolutionary opportunities for a subset of vertebrates with the relatively high potential for transoceanic dispersal potential. In comparison, changes in vertebrate class representation during the Cenozoic are minor. Despite the fact that the island's isolation has resulted in high vertebrate endemism and a unique and taxonomically imbalanced extant vertebrate assemblage (both hailed as testimony to its long isolation), that isolation was never complete. Indeed, Madagascar's extant tetrapod fauna owes more to colonization during the Cenozoic than to earlier arrivals. Madagascar's unusual vertebrate assemblage needs to be understood with reference to the basal character of clades originating prior to the K-T extinction, as well as to the differential transoceanic dispersal advantage of other, more

High In Vitro Activity of the Novel Spiropyrimidinetrione AZD0914, a DNA Gyrase Inhibitor, against Multidrug-Resistant Neisseria gonorrhoeae Isolates Suggests a New Effective Option for Oral Treatment of Gonorrhea

Science.gov (United States)

Jacobsson, Susanne; Golparian, Daniel; Alm, Richard A.; Huband, Michael; Mueller, John; Jensen, Jorgen Skov; Ohnishi, Makoto

2014-01-01

We evaluated the activity of the novel spiropyrimidinetrione AZD0914 (DNA gyrase inhibitor) against clinical gonococcal isolates and international reference strains (n = 250), including strains with diverse multidrug resistance and extensive drug resistance. The AZD0914 MICs were substantially lower than those of most other currently or previously recommended antimicrobials. AZD0914 should be further evaluated, including in vitro selection, in vivo emergence and mechanisms of resistance, pharmacokinetics/pharmacodynamics in humans, optimal dosing, and performance, in appropriate randomized and controlled clinical trials. PMID:24982070

Synthesis of Optimal Isolation Systems of Hand-Transmitted Vibration

Directory of Open Access Journals (Sweden)

Marek Książek

1997-01-01

Full Text Available In this article a procedure is presented for the analytical synthesis of optimal vibration isolation for a hand-arm system subjected to stochastic excitation. A general approach is discussed for a selected vibration isolation criterion. The general procedure is illustrated by analytical examples for different hand-arm systems described by their driving-point impedances. The influence of particular forms of excitation and the structure of the vibroisolated hand-arm systems on the resultant vibration isolation is then discussed. Some numerical examples illustrating the procedure have also been included.

Differences among incarcerated women with assaultive offenses: isolated versus patterned use of violence.

Science.gov (United States)

Kubiak, Sheryl Pimlott; Kim, Woo Jong; Fedock, Gina; Bybee, Deborah

2013-08-01

A majority of the existing research on women's use of violence focuses on intimate partner violence, often excluding other types of violence for which women may be incarcerated. The current study expands this area of research by assessing between and within-group differences among a randomly selected group of incarcerated women (n = 543). Comparisons between violent and nonviolent offense types among women found few differences, but significant differences among women with an assaultive offense, based on the presence or absence of a self-reported uncaught violence, were found. Differences in women with isolated (i.e., single incident of violence perpetration through a review of formal and self-report data) and patterned uses of violence were present in relation to issues of mental health, substance abuse, criminogenic risk, and expressions of anger and personality factors. These findings have important implications for intervention as well as future research.

Prevalence and antimicrobial resistance of listeria species isolated from different types of raw meat in Iran.

Science.gov (United States)

Rahimi, Ebrahim; Yazdi, Farzad; Farzinezhadizadeh, Hussein

2012-12-01

Listeria and particularly Listeria monocytogenes are important foodborne pathogens that can cause listeriosis and severe complications in immunocompromised individuals, children, pregnant women, and the elderly. The objective of this study was to determine the prevalence of Listeria spp. in raw meat in Iran. From July 2010 to November 2011, a total of 1,107 samples of various raw meats were obtained from randomly selected retail butcher shops. The results of conventional bacteriologic and PCR methods revealed that 141 samples (12.7%) were positive for Listeria spp. The highest prevalence of Listeria was found in raw buffalo meat samples (7 of 24 samples; 29.2%) followed by quail meat (26 of 116 samples; 22.4%), partridge meat (13 of 74 samples; 17.6%), and chicken meat (27 of 160 samples; 16.9%). The most common species recovered was Listeria innocua (98 of 141 strains; 75.9 % ); the remaining isolates were L. monocytogenes (19.1% of strains), Listeria welshimeri (6.4% of strains), Listeria seeligeri (3.5% of strains), and Listeria grayi (1.4% of strains). Susceptibilities of the 141 strains to 11 antimicrobial drugs were determined using the disk diffusion assay. Overall, 104 (73.8%) of the Listeria isolates were resistant to one or more antimicrobials, and 17.0% of the isolates were resistant to three or more antimicrobials. The present study provides the first baseline data on the prevalence of Listeria in raw meat derived from sheep, goat, buffalo, quail, partridge, chicken, and ostrich in Iran and the susceptibility of these isolates to antimicrobials.

Development of a forward genetic screen to isolate oil mutants in the green microalga Chlamydomonas reinhardtii.

Science.gov (United States)

Cagnon, Caroline; Mirabella, Boris; Nguyen, Hoa Mai; Beyly-Adriano, Audrey; Bouvet, Séverine; Cuiné, Stéphan; Beisson, Fred; Peltier, Gilles; Li-Beisson, Yonghua

2013-12-02

Oils produced by microalgae are precursors to biodiesel. To achieve a profitable production of biodiesel from microalgae, identification of factors governing oil synthesis and turnover is desirable. The green microalga Chlamydomonas reinhardtii is amenable to genetic analyses and has recently emerged as a model to study oil metabolism. However, a detailed method to isolate various types of oil mutants that is adapted to Chlamydomonas has not been reported. We describe here a forward genetic approach to isolate mutants altered in oil synthesis and turnover from C. reinhardtii. It consists of a three-step screening procedure: a primary screen by flow cytometry of Nile red stained transformants grown in 96-deep-well plates under three sequential conditions (presence of nitrogen, then absence of nitrogen, followed by oil remobilization); a confirmation step using Nile red stained biological triplicates; and a validation step consisting of the quantification by thin layer chromatography of oil content of selected strains. Thirty-one mutants were isolated by screening 1,800 transformants generated by random insertional mutagenesis (1.7%). Five showed increased oil accumulation under the nitrogen-replete condition and 13 had altered oil content under nitrogen-depletion. All mutants were affected in oil remobilization. This study demonstrates that various types of oil mutants can be isolated in Chlamydomonas based on the method set-up here, including mutants accumulating oil under optimal biomass growth. The strategy conceived and the protocol set-up should be applicable to other microalgal species such as Nannochloropsis and Chlorella, thus serving as a useful tool in Chlamydomonas oil research and algal biotechnology.

Randomized algorithms in automatic control and data mining

CERN Document Server

Granichin, Oleg; Toledano-Kitai, Dvora

2015-01-01

In the fields of data mining and control, the huge amount of unstructured data and the presence of uncertainty in system descriptions have always been critical issues. The book Randomized Algorithms in Automatic Control and Data Mining introduces the readers to the fundamentals of randomized algorithm applications in data mining (especially clustering) and in automatic control synthesis. The methods proposed in this book guarantee that the computational complexity of classical algorithms and the conservativeness of standard robust control techniques will be reduced. It is shown that when a problem requires "brute force" in selecting among options, algorithms based on random selection of alternatives offer good results with certain probability for a restricted time and significantly reduce the volume of operations.

The basic science and mathematics of random mutation and natural selection.

Science.gov (United States)

Kleinman, Alan

2014-12-20

The mutation and natural selection phenomenon can and often does cause the failure of antimicrobial, herbicidal, pesticide and cancer treatments selection pressures. This phenomenon operates in a mathematically predictable behavior, which when understood leads to approaches to reduce and prevent the failure of the use of these selection pressures. The mathematical behavior of mutation and selection is derived using the principles given by probability theory. The derivation of the equations describing the mutation and selection phenomenon is carried out in the context of an empirical example. Copyright © 2014 John Wiley & Sons, Ltd.

Isolation of Individual Egg Cells and Zygotes in Alstroemeria Followed by Manual Selection with a Microcapillary-connected Micropump

Science.gov (United States)

HOSHINO, YOICHIRO; MURATA, NAHO; SHINODA, KOICHI

2006-01-01

• Aims To develop a procedure for isolating living egg cells and zygotes from Alstroemeria ovules. • Scope An attempt was made to isolate egg cells and zygotes from the ovules of Alstroemeria aurea. The ovules were histologically observed using a clearing procedure which revealed the localization and sizes of the embryo sacs and egg apparatus within the ovules. For the isolation of egg cells, ovules were cut into sections with a surgical blade and treated with an enzyme solution. Subsequently, these ovule sections were dissected using a glass needle under an inverted microscope. Egg cells successfully isolated by this procedure were collected using microcapillaries connected to a micropump. For zygote isolation, ovules were excised from ovaries 24 h after self-pollination. By treating excised ovules with an enzyme solution and subsequently dissecting them using a glass needle, zygotes were successfully isolated from the ovules and collected with a microcapillary. The isolated zygotes were associated with pollen tubes and one of the synergids. Egg cells and zygotes were viable for up to 2 h following isolation, as determined by fluorescein diacetate staining. • Conclusions The procedures for isolating egg cells and zygotes in Alstroemeria were established, and each egg cell and zygote was captured with a microcapillary. PMID:16621859

Selecting Optimal Random Forest Predictive Models: A Case Study on Predicting the Spatial Distribution of Seabed Hardness

Science.gov (United States)

Li, Jin; Tran, Maggie; Siwabessy, Justy

2016-01-01

Spatially continuous predictions of seabed hardness are important baseline environmental information for sustainable management of Australia’s marine jurisdiction. Seabed hardness is often inferred from multibeam backscatter data with unknown accuracy and can be inferred from underwater video footage at limited locations. In this study, we classified the seabed into four classes based on two new seabed hardness classification schemes (i.e., hard90 and hard70). We developed optimal predictive models to predict seabed hardness using random forest (RF) based on the point data of hardness classes and spatially continuous multibeam data. Five feature selection (FS) methods that are variable importance (VI), averaged variable importance (AVI), knowledge informed AVI (KIAVI), Boruta and regularized RF (RRF) were tested based on predictive accuracy. Effects of highly correlated, important and unimportant predictors on the accuracy of RF predictive models were examined. Finally, spatial predictions generated using the most accurate models were visually examined and analysed. This study confirmed that: 1) hard90 and hard70 are effective seabed hardness classification schemes; 2) seabed hardness of four classes can be predicted with a high degree of accuracy; 3) the typical approach used to pre-select predictive variables by excluding highly correlated variables needs to be re-examined; 4) the identification of the important and unimportant predictors provides useful guidelines for further improving predictive models; 5) FS methods select the most accurate predictive model(s) instead of the most parsimonious ones, and AVI and Boruta are recommended for future studies; and 6) RF is an effective modelling method with high predictive accuracy for multi-level categorical data and can be applied to ‘small p and large n’ problems in environmental sciences. Additionally, automated computational programs for AVI need to be developed to increase its computational efficiency and

Comparative genotyping of Clostridium thermocellum strains isolated from biogas plants: genetic markers and characterization of cellulolytic potential.

Science.gov (United States)

Koeck, Daniela E; Zverlov, Vladimir V; Liebl, Wolfgang; Schwarz, Wolfgang H

2014-07-01

Clostridium thermocellum is among the most prevalent of known anaerobic cellulolytic bacteria. In this study, genetic and phenotypic variations among C. thermocellum strains isolated from different biogas plants were determined and different genotyping methods were evaluated on these isolates. At least two C. thermocellum strains were isolated independently from each of nine different biogas plants via enrichment on cellulose. Various DNA-based genotyping methods such as ribotyping, RAPD (Random Amplified Polymorphic DNA) and VNTR (Variable Number of Tandem Repeats) were applied to these isolates. One novel approach - the amplification of unknown target sequences between copies of a previously discovered Random Inserted Mobile Element (RIME) - was also tested. The genotyping method with the highest discriminatory power was found to be the amplification of the sequences between the insertion elements, where isolates from each biogas plant yielded a different band pattern. Cellulolytic potentials, optimal growth conditions and substrate spectra of all isolates were characterized to help identify phenotypic variations. Irrespective of the genotyping method used, the isolates from each individual biogas plant always exhibited identical patterns. This is suggestive of a single C. thermocellum strain exhibiting dominance in each biogas plant. The genotypic groups reflect the results of the physiological characterization of the isolates like substrate diversity and cellulase activity. Conversely, strains isolated across a range of biogas plants differed in their genotyping results and physiological properties. Both strains isolated from one biogas plant had the best specific cellulose-degrading properties and might therefore achieve superior substrate utilization yields in biogas fermenters. Copyright © 2014 Elsevier GmbH. All rights reserved.

Live Cell Genomics: RNA Exon-Specific RNA-Binding Protein Isolation.

Science.gov (United States)

Bell, Thomas J; Eberwine, James

2015-01-01

RNA-binding proteins (RBPs) are essential regulatory proteins that control all modes of RNA processing and regulation. New experimental approaches to isolate these indispensable proteins under in vivo conditions are needed to advance the field of RBP biology. Historically, in vitro biochemical approaches to isolate RBP complexes have been useful and productive, but biological relevance of the identified RBP complexes can be imprecise or erroneous. Here we review an inventive experimental to isolate RBPs under the in vivo conditions. The method is called peptide nucleic acid (PNA)-assisted identification of RBP (PAIR) technology and it uses cell-penetrating peptides (CPPs) to deliver photo-activatible RBP-capture molecule to the cytoplasm of the live cells. The PAIR methodology provides two significant advantages over the most commonly used approaches: (1) it overcomes the in vitro limitation of standard biochemical approaches and (2) the PAIR RBP-capture molecule is highly selective and adaptable which allows investigators to isolate exon-specific RBP complexes. Most importantly, the in vivo capture conditions and selectivity of the RBP-capture molecule yield biologically accurate and relevant RBP data.

Measuring of -1,3 Glucanase Activity in Trichoderma Virens Isolates and Selection of the Best Isolates for Biological Control of Cucumber Root Rot

Directory of Open Access Journals (Sweden)

Fatemeh Zavvari

2013-02-01

Full Text Available In this study four isolates of  Trichoderma virens (T.virens 414, T.virens 414.8, T.virens 304 and  T.virens 404.4 were compared based on extra cellular β-1,3 glucanase production and biological control of root rot cucumber (Phytophthora drerchsleri in laboratory and green house experiments.The in vitro potential of those isolates were evaluated against  P.drechsleri  through production of volatile and dual culture. The pH (3, 5, 7, 8, 9 and temperature effects(5, 15, 20, 25, 30, 40˚C on Trichoderma mycelial growth were also evaluated. Colony growth rate of thease isolates were also studied in water agar culture medium containing carboxy methyle cellulose (CMC and showed direct correlation with β-1,3 glucanase secretion. According to results T. virens 304 and T. virens 414.8  were the best isolates in biocontrol of . drechsleri. Result also showed direct correlation between β-1,3 glucanase secretion and inhibition growth of phytophthora  mycelium and reduction of phytophthora infection.

Identification of Spanish isolates of Rhizoctonia solani from potato by anastomosis grouping, ITS-RFLP and RAMS-fingerprinting

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A.M. Elbakali

2003-08-01

Full Text Available Anastomosis grouping, restriction fragment length polymorphism (RFLP of the ITS regions including the 5.85 rDNA, and random amplified microsatellites (RAMS were used to characterize isolates of Rhizoctonia solani collected from Spain and Finland. There was a high similarity between the results obtained with the three techniques. RAMS markers revealed more genetic variation among isolates of R. solani than RFLP. The anastomosis group (AG–3 isolates were clearly separated from isolates belonging to other AGs by RAMS, RFLPs and anastomosis grouping. Almost all the isolates sampled from potato belonged to AG–3. No differences were observed between Spanish and Finnish AG–3 isolates.

RANDOM WALK HYPOTHESIS IN FINANCIAL MARKETS

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Nicolae-Marius JULA

2017-05-01

Full Text Available Random walk hypothesis states that the stock market prices do not follow a predictable trajectory, but are simply random. If you are trying to predict a random set of data, one should test for randomness, because, despite the power and complexity of the used models, the results cannot be trustworthy. There are several methods for testing these hypotheses and the use of computational power provided by the R environment makes the work of the researcher easier and with a cost-effective approach. The increasing power of computing and the continuous development of econometric tests should give the potential investors new tools in selecting commodities and investing in efficient markets.

Progress in ISOL target-ion source systems

Energy Technology Data Exchange (ETDEWEB)

Koester, U. [Institut Laue Langevin, 6 Rue Jules Horowitz, F-38042 Grenoble Cedex 9 (France); ISOLDE, CERN, CH-1211 Geneve 23 (Switzerland)], E-mail: koester@ill.fr; Arndt, O. [HGF VISTARS and Institut fuer Kernchemie, Johannes-Gutenberg Universitaet Mainz, D-55128 Mainz (Germany); Bouquerel, E.; Fedoseyev, V.N. [ISOLDE, CERN, CH-1211 Geneve 23 (Switzerland); Franberg, H. [ISOLDE, CERN, CH-1211 Geneve 23 (Switzerland); Laboratory for Radio- and Environmental Chemistry, Paul Scherrer Institut, CH-5232 Villigen PSI (Switzerland); Joinet, A. [ISOLDE, CERN, CH-1211 Geneve 23 (Switzerland); Centre d' Etude Spatiale des Rayonnements, 9 Av. du Colonel Roche, F-31028 Toulouse Cedex 4 (France); Jost, C. [HGF VISTARS and Institut fuer Kernchemie, Johannes-Gutenberg Universitaet Mainz, D-55128 Mainz (Germany); Kerkines, I.S.K. [Laboratory of Physical Chemistry, National and Kapodistrian University of Athens, Department of Chemistry, Zografou 157 71, GR (Greece); Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, GA 30322 (United States); Kirchner, R. [Gesellschaft fuer Schwerionenforschung, Planckstr. 1, D-64291 Darmstadt (Germany)

2008-10-15

The heart of every ISOL (isotope separation on-line) facility is its target and ion source system. Its efficiency, selectivity and rapidity is decisive for the production of intense and pure ion beams of short-lived isotopes. Recent progress in ISOL target and ion source technology is discussed at the examples of radioactive ion beams of exotic zinc and tin isotopes that were purified by isothermal chromatography and molecular sideband separation respectively. An outlook is given to which other elements these purification methods are applicable.

Progress in ISOL target-ion source systems

International Nuclear Information System (INIS)

Koester, U.; Arndt, O.; Bouquerel, E.; Fedoseyev, V.N.; Franberg, H.; Joinet, A.; Jost, C.; Kerkines, I.S.K.; Kirchner, R.

2008-01-01

The heart of every ISOL (isotope separation on-line) facility is its target and ion source system. Its efficiency, selectivity and rapidity is decisive for the production of intense and pure ion beams of short-lived isotopes. Recent progress in ISOL target and ion source technology is discussed at the examples of radioactive ion beams of exotic zinc and tin isotopes that were purified by isothermal chromatography and molecular sideband separation respectively. An outlook is given to which other elements these purification methods are applicable.

The Goodness of Covariance Selection Problem from AUC Bounds

OpenAIRE

Khajavi, Navid Tafaghodi; Kuh, Anthony

2016-01-01

We conduct a study of graphical models and discuss the quality of model selection approximation by formulating the problem as a detection problem and examining the area under the curve (AUC). We are specifically looking at the model selection problem for jointly Gaussian random vectors. For Gaussian random vectors, this problem simplifies to the covariance selection problem which is widely discussed in literature by Dempster [1]. In this paper, we give the definition for the correlation appro...

Site selection report basalt waste isolation program near-surface test facility

International Nuclear Information System (INIS)

Sharpe, S.D.

1978-01-01

A site selection committee was established to review the information gathered on potential sites and to select a site for the Near-Surface Test Facility Phase I. A decision was made to use a site on the north face of Gable Mountain located on the Hanford Site. This site provided convenient access to the Pomona Basalt Flow. This flow was selected for use at this site because it exhibited the characteristics established in the primary criteria. These criteria were: the flows thickness; its dryness; its nearness to the surface; and, its similarities to basalt units which are candidates for the repository. After the selection of the Near-Surface Test Facility Phase I Site, the need arose for an additional facility to demonstrate safe handling, storage techniques, and the physical effects of radioactive materials on an in situ basalt formation. The committee reviewed the sites selected for Phase I and chose the same site for locating Phase II of the Near-Surface Test Facility

BanglaLekha-Isolated: A multi-purpose comprehensive dataset of Handwritten Bangla Isolated characters

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Mithun Biswas

2017-06-01

Full Text Available BanglaLekha-Isolated, a Bangla handwritten isolated character dataset is presented in this article. This dataset contains 84 different characters comprising of 50 Bangla basic characters, 10 Bangla numerals and 24 selected compound characters. 2000 handwriting samples for each of the 84 characters were collected, digitized and pre-processed. After discarding mistakes and scribbles, 1,66,105 handwritten character images were included in the final dataset. The dataset also includes labels indicating the age and the gender of the subjects from whom the samples were collected. This dataset could be used not only for optical handwriting recognition research but also to explore the influence of gender and age on handwriting. The dataset is publicly available at https://data.mendeley.com/datasets/hf6sf8zrkc/2.

Organic Ferroelectric-Based 1T1T Random Access Memory Cell Employing a Common Dielectric Layer Overcoming the Half-Selection Problem.

Science.gov (United States)

Zhao, Qiang; Wang, Hanlin; Ni, Zhenjie; Liu, Jie; Zhen, Yonggang; Zhang, Xiaotao; Jiang, Lang; Li, Rongjin; Dong, Huanli; Hu, Wenping

2017-09-01

Organic electronics based on poly(vinylidenefluoride/trifluoroethylene) (P(VDF-TrFE)) dielectric is facing great challenges in flexible circuits. As one indispensable part of integrated circuits, there is an urgent demand for low-cost and easy-fabrication nonvolatile memory devices. A breakthrough is made on a novel ferroelectric random access memory cell (1T1T FeRAM cell) consisting of one selection transistor and one ferroelectric memory transistor in order to overcome the half-selection problem. Unlike complicated manufacturing using multiple dielectrics, this system simplifies 1T1T FeRAM cell fabrication using one common dielectric. To achieve this goal, a strategy for semiconductor/insulator (S/I) interface modulation is put forward and applied to nonhysteretic selection transistors with high performances for driving or addressing purposes. As a result, high hole mobility of 3.81 cm 2 V -1 s -1 (average) for 2,6-diphenylanthracene (DPA) and electron mobility of 0.124 cm 2 V -1 s -1 (average) for N,N'-1H,1H-perfluorobutyl dicyanoperylenecarboxydiimide (PDI-FCN 2 ) are obtained in selection transistors. In this work, we demonstrate this technology's potential for organic ferroelectric-based pixelated memory module fabrication. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selective medium for aerobic incubation of Campylobacter

Science.gov (United States)

Studies were conducted on the formulation of a selective medium that could be used to isolate Campylobacter from mixed bacterial cultures using aerobic incubation. A non-selective, basal broth medium was prepared and supplemented with Bolton, Cefex, or Skirrow antibiotic mixtures. The ability of pur...

Cyrtopodium paludicolum germination with two Tulasnella isolates

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Otieres Cirino de Carvalho

2017-11-01

Full Text Available ABSTRACT Symbiosis between orchid seeds and mycorrhizal fungi has been reported to be a determining factor in the success of germination and protocorm development in vitro. The aim of this study was to isolate and identify by molecular analysis the mycorrhizal fungus associated with Cyrtopodium paludicolum, and to evaluate its efficiency in facilitating seed germination and development. Germination experiments were carried out using a fungus isolated from C. paludicolum (CH01 and Epidendrum secundum (M65, which has been successfully used a number of times in symbiotic germination. The experiments were conducted in a completely randomized design with treatments of CH01, M65 as well as under asymbiotic conditions. The mycobiont CH01 was successfully isolated from Cyrtopodium paludicolum and identified as Tulasnella sp. Treatments with both fungi reached a higher germination percentage than under asymbiotic conditions, indicating no specificity in the relationship between Cyrtopodium paludicolum and the fungi. The results presented have the potential to advance research into the propagation and conservation of C. paludicolum, a native of the Cerrado biome.

Selected, annotated bibliography of studies relevant to the isolation of nuclear wastes. [705 references

Energy Technology Data Exchange (ETDEWEB)

Hyder, L.K.; Fore, C.S.; Vaughan, N.D.; Faust, R.A.

1980-09-01

This annotated bibliography of 705 references represents the first in a series to be published by the Ecological Sciences Information Center containing scientific, technical, economic, and regulatory information relevant to nuclear waste isolation. Most references discuss deep geologic disposal, with fewer studies of deep seabed disposal; space disposal is also included. The publication covers both domestic and foreign literature for the period 1954 to 1980. Major chapters selected are Chemical and Physical Aspects; Container Design and Performance; Disposal Site; Envirnmental Transport; General Studies and Reviews; Geology, Hydrology and Site Resources; Regulatory and Economic Aspects; Repository Design and Engineering; Transportation Technology; Waste Production; and Waste Treatment. Specialized data fields have been incorporated to improve the ease and accuracy of locating pertinent references. Specific radionuclides for which data are presented are listed in the Measured Radionuclides field, and specific parameters which affect the migration of these radionuclides are presented in the Measured Parameters field. The references within each chapter are arranged alphabetically by leading author, corporate affiliation, or title of the document. When the author is not given, the corporate affiliation appears first. If these two levels of authorship are not given, the title of the document is used as the identifying level. Indexes are provided for author(s), keywords, subject category, title, geographic location, measured parameters, measured radionuclides, and publication description.

Genomic characterization of Burkholderia pseudomallei isolates selected for medical countermeasures testing: comparative genomics associated with differential virulence.

Directory of Open Access Journals (Sweden)

Jason W Sahl

Full Text Available Burkholderia pseudomallei is the causative agent of melioidosis and a potential bioterrorism agent. In the development of medical countermeasures against B. pseudomallei infection, the US Food and Drug Administration (FDA animal Rule recommends using well-characterized strains in animal challenge studies. In this study, whole genome sequence data were generated for 6 B. pseudomallei isolates previously identified as candidates for animal challenge studies; an additional 5 isolates were sequenced that were associated with human inhalational melioidosis. A core genome single nucleotide polymorphism (SNP phylogeny inferred from a concatenated SNP alignment from the 11 isolates sequenced in this study and a diverse global collection of isolates demonstrated the diversity of the proposed Animal Rule isolates. To understand the genomic composition of each isolate, a large-scale blast score ratio (LS-BSR analysis was performed on the entire pan-genome; this demonstrated the variable composition of genes across the panel and also helped to identify genes unique to individual isolates. In addition, a set of ~550 genes associated with pathogenesis in B. pseudomallei were screened against the 11 sequenced genomes with LS-BSR. Differential gene distribution for 54 virulence-associated genes was observed between genomes and three of these genes were correlated with differential virulence observed in animal challenge studies using BALB/c mice. Differentially conserved genes and SNPs associated with disease severity were identified and could be the basis for future studies investigating the pathogenesis of B. pseudomallei. Overall, the genetic characterization of the 11 proposed Animal Rule isolates provides context for future studies involving B. pseudomallei pathogenesis, differential virulence, and efficacy to therapeutics.

Antibiogram of bacteria isolated from automated teller machines in Hamadan, West Iran

Science.gov (United States)

Mahmoudi, Hassan; Arabestani, Mohammad Reza; Alikhani, Mohammad Yousef; Sedighi, Iraj; Kohan, Hamed Farhadi; Molavi, Mohammad

2017-01-01

Aim: Bacteria are ubiquitous in the environment. In keeping with the continued expansion of urbanization and the growing population, an increasing number of people use automated banking, i.e. automated teller machines (ATMs). The aim of this study was to investigate the bacterial contamination and its antibiotic sensitivity on computer keyboards located at ATMs in Hamadan province, Iran. Method: Out of 360 ATMs at four locations in Hamadan, 96 were randomly selected for this study. The antibiotic susceptibility pattern of all isolates was determined by the agar disk diffusion method using gentamicin (10 µg), vancomycin (30 µg), trimethoprim/sulfamethoxazole (25 µg), amikacin (30 µg), tobramycin (10 µg), cephalotin (30 µg), norfloxacin (5 µg), and ceftizoxim (30 µg) disks. Results: Melli and Saderat Banks had the most frequently contaminated ATMS, with 18 (27.7%) and 12 (18.5%), respectively. The most frequently isolated bacteria were Staphylococcus epidermidis in 12 (18.5%) ATMs, Pseudomonas aeruginosa in 12 (18.5%), Bacillus subtilis in 11 (16.9%), Escherichia coli in 6 (9.2%), Klebsiella spp. in 8 (12.3%), Enterobacter spp. in 2 (3.1%), Bacillus cereus in 6 (9.2%), Staphylococcus aureus in 3 (4.6%), and Micrococcaceae spp. in 5 (7.69%) cases. All isolated bacteria were susceptible to gentamicin, cephalotin, tobramycin, amikacin, norfloxacin, and vancomycin. The S. aureus resistance rate to trimethoprim/sulfamethoxazole was 50%. Conclusion: All tested ATM keyboards were contaminated with at least one species of bacteria. Based on these findings, it is recommendable to disinfect the hands after entering one’s own apartment, work area or a hospital, in order to hinder the spread of critical pathogens in the personal environment or in the hospital. PMID:28197394

Random-walk simulation of selected aspects of dissipative collisions

International Nuclear Information System (INIS)

Toeke, J.; Gobbi, A.; Matulewicz, T.

1984-11-01

Internuclear thermal equilibrium effects and shell structure effects in dissipative collisions are studied numerically within the framework of the model of stochastic exchanges by applying the random-walk technique. Effective blocking of the drift through the mass flux induced by the temperature difference, while leaving the variances of the mass distributions unaltered is found possible, provided an internuclear potential barrier is present. Presence of the shell structure is found to lead to characteristic correlations between the consecutive exchanges. Experimental evidence for the predicted effects is discussed. (orig.)

Francisella tularensis subsp. novicida isolated from a human in Arizona

Directory of Open Access Journals (Sweden)

Birdsell Dawn N

2009-11-01

Full Text Available Abstract Background Francisella tularensis is the etiologic agent of tularemia and is classified as a select agent by the Centers for Disease Control and Prevention. Currently four known subspecies of F. tularensis that differ in virulence and geographical distribution are recognized:tularensis (type A, holarctica (type B, mediasiatica, and novicida. Because of the Select Agent status and differences in virulence and geographical location, the molecular analysis of any clinical case of tularemia is of particular interest. We analyzed an unusual Francisella clinical isolate from a human infection in Arizona using multiple DNA-based approaches. Findings We report that the isolate is F. tularensis subsp. novicida, a subspecies that is rarely isolated. Conclusion The rarity of this novicida subspecies in clinical settings makes each case study important for our understanding of its role in disease and its genetic relationship with other F. tularensis subspecies.

Isolation and identification of lactic acid bacteria from abalone (Haliotis asinina as a potential candidate of probiotic

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YAYAN SOFYAN

2010-01-01

Full Text Available Sarkono, Faturrahman, Sofyan Y. 2010. Isolation and identification of lactic acid bacteria from abalone (Haliotis asinina as a potential candidate of probiotic. Nusantara Bioscience 2: 38-42. The purpose of this study was to isolate, select and characterize lactic acid bacteria (LAB from abalone as a potential candidate probiotic in abalone cultivation system. Selective isolation of LAB performed using de Man Rogosa Sharpe medium. LAB isolate that potential as probiotics was screened. Selection was based on its ability to suppress the growth of pathogenic bacteria, bacterial resistance to acidic conditions and bacterial resistance to bile salts (bile. Further characterization and identification conducted to determine the species. The results showed that two of the ten isolates potential to be developed as probiotic bacteria that have the ability to inhibit several pathogenic bacteria such as Eschericia coli, Bacillus cereus dan Staphylococus aureus, able to grow at acidic condition and bile tolerance during the incubation for 24 hour. Based on the API test kit, the both of isolate identified as members of the species Lactobacillus paracasei ssp. paracasei.

Isolation, screening and identification of novel isolates of Actinomycetes from India for antimicrobial applications

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Vineeta Singh

2016-12-01

Full Text Available The search for novel bioactive compounds from the natural environment has been rapidly increased with the increase in multi-drug resistant (MDR pathogens. In the present study, the antimicrobial potential of novel actinomycetes has been evaluated by initial screening of six soil samples. Primary and secondary screening was performed against Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Candida albicans, Candida tropicalis, Trichophyton rubrum, and other MDR bacterial and fungal test strains, and at the end thirteen active isolates were selected for further study. Microbial strains were identified on the basis of growth conditions and other biochemical characters. Five most active microbial strains were identified using 16S rRNA sequence homology and designated as Streptomyces xanthophaeus MTCC 11938, Streptomyces variabilis MTCC 12266, Streptomyces xanthochromogenes MTCC 11937, Streptomyces levis EU 124569 and Streptomyces sp. NCIM 5500. Four antibacterial and three antifungal compounds isolated from the above five isolates were purified and partially characterized using UV absorption and IR spectra. Two antibacterial metabolites, belong to chromone and peptide antibiotic, respectively. The antifungal compounds were found to be of non-polyene nature. In conclusion, we study the isolation of novel bacterial strains of actinomycetes for producing novel compounds having antibacterial and antifungal activities from the unexplored agro-ecological niches of India. Also, this study paves the way for further characterization of these isolates of Streptomyces sp. for their optimum utilization for antimicrobial purposes.

Effects of isolated soluble fiber supplementation on body weight, glycemia, and insulinemia in adults with overweight and obesity: a systematic review and meta-analysis of randomized controlled trials.

Science.gov (United States)

Thompson, Sharon V; Hannon, Bridget A; An, Ruopeng; Holscher, Hannah D

2017-12-01

Background: There is strong epidemiologic evidence that dietary fiber intake is protective against overweight and obesity; however, results of intervention studies have been mixed. Soluble fiber beneficially affects metabolism, and fiber supplementation may be a feasible approach to improve body composition and glycemia in adults with overweight and obesity. Objective: We evaluated randomized controlled trials (RCTs) of isolated soluble fiber supplementation in overweight and obese adults on outcomes related to weight management [body mass index (BMI; in kg/m 2 ), body weight, percentage of body fat, and waist circumference] and glucose and insulin metabolism (homeostasis model assessment of insulin resistance and fasting insulin) through a systematic review and meta-analysis. Design: We searched PubMed, Web of Science, Cumulative Index to Nursing and Allied Health Literature and Cochrane Library databases. Eligible studies were RCTs that compared isolated soluble fiber with placebo treatments without energy-restriction protocols. Random-effects models were used to estimate pooled effect sizes and 95% CIs. Meta-regressions were performed to assess outcomes in relation to the intervention duration, fiber dose, and fiber type. Publication bias was assessed via Begg's and Egger's tests and funnel plot inspection. Results: Findings from 12 RCTs ( n = 609 participants) from 2 to 17 wk of duration are summarized in this review. Soluble fiber supplementation reduced BMI by 0.84 (95% CI: -1.35, -0.32; P = 0.001), body weight by 2.52 kg (95% CI: -4.25, -0.79 kg; P = 0.004), body fat by 0.41% (95% CI: -0.58%, -0.24%; P < 0.001), fasting glucose by 0.17 mmol/L (95% CI: -0.28, -0.06 mmol/L; P = 0.002), and fasting insulin by 15.88 pmol/L (95% CI: -29.05, -2.71 pmol/L; P = 0.02) compared with the effects of placebo treatments. No publication bias was identified. Considerable between-study heterogeneity was observed for most outcomes. Conclusions: Isolated soluble fiber

Random number generation and creativity.

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Bains, William

2008-01-01

A previous paper suggested that humans can generate genuinely random numbers. I tested this hypothesis by repeating the experiment with a larger number of highly numerate subjects, asking them to call out a sequence of digits selected from 0 through 9. The resulting sequences were substantially non-random, with an excess of sequential pairs of numbers and a deficit of repeats of the same number, in line with previous literature. However, the previous literature suggests that humans generate random numbers with substantial conscious effort, and distractions which reduce that effort reduce the randomness of the numbers. I reduced my subjects' concentration by asking them to call out in another language, and with alcohol - neither affected the randomness of their responses. This suggests that the ability to generate random numbers is a 'basic' function of the human mind, even if those numbers are not mathematically 'random'. I hypothesise that there is a 'creativity' mechanism, while not truly random, provides novelty as part of the mind's defence against closed programming loops, and that testing for the effects seen here in people more or less familiar with numbers or with spontaneous creativity could identify more features of this process. It is possible that training to perform better at simple random generation tasks could help to increase creativity, through training people to reduce the conscious mind's suppression of the 'spontaneous', creative response to new questions.

An optimized method for mouse liver sinusoidal endothelial cell isolation

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Meyer, Jeremy, E-mail: jeremy.meyer@hcuge.ch [Division of Digestive and Transplantation Surgery, University Hospitals of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14 (Switzerland); Unit of Surgical Research, University of Geneva, Rue Michel-Servet 1, 1206 Genève (Switzerland); Lacotte, Stéphanie, E-mail: stephanie.lacotte@unige.ch [Unit of Surgical Research, University of Geneva, Rue Michel-Servet 1, 1206 Genève (Switzerland); Morel, Philippe, E-mail: philippe.morel@hcuge.ch [Division of Digestive and Transplantation Surgery, University Hospitals of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14 (Switzerland); Unit of Surgical Research, University of Geneva, Rue Michel-Servet 1, 1206 Genève (Switzerland); Gonelle-Gispert, Carmen, E-mail: carmen.gonelle@unige.ch [Unit of Surgical Research, University of Geneva, Rue Michel-Servet 1, 1206 Genève (Switzerland); Bühler, Léo, E-mail: leo.buhler@hcuge.ch [Division of Digestive and Transplantation Surgery, University Hospitals of Geneva, Rue Gabrielle-Perret-Gentil 4, 1211 Genève 14 (Switzerland); Unit of Surgical Research, University of Geneva, Rue Michel-Servet 1, 1206 Genève (Switzerland)

2016-12-10

The objective of the present study was to develop an accurate and reproducible method for liver sinusoidal endothelial cell (LSEC) isolation in mice. Non-parenchymal cells were isolated using a modified two-step collagenase digestion combined with Optiprep density gradient centrifugation. LSEC were further purified using two prevalent methods, short-term selective adherence and CD146+ magnetic-activated cell sorting (MACS), and compared in terms of cell yield, viability and purity to our purification technique using CD11b cell depletion combined with long-term selective adherence. LSEC purification using our technique allowed to obtain 7.07±3.80 million LSEC per liver, while CD146+ MACS and short-term selective adherence yielded 2.94±1.28 and 0.99±0.66 million LSEC, respectively. Purity of the final cell preparation reached 95.10±2.58% when using our method. In contrast, CD146+ MACS and short-term selective adherence gave purities of 86.75±3.26% and 47.95±9.82%, respectively. Similarly, contamination by non-LSEC was the lowest when purification was performed using our technique, with a proportion of contaminating macrophages of only 1.87±0.77%. Further, isolated cells analysed by scanning electron microscopy presented typical LSEC fenestrations organized in sieve plates, demonstrating that the technique allowed to isolate bona fide LSEC. In conclusion, we described a reliable and reproducible technique for the isolation of high yields of pure LSEC in mice. This protocol provides an efficient method to prepare LSEC for studying their biological functions. - Highlights: • This protocol provides an efficient method to prepare primary mouse LSEC for studying their biological functions. • The liver cell dispersion step was improved by performing a retrograde cannulation of the liver. • The cell yield and the purity obtained were higher than comparative techniques in mice. • Contaminating macrophages were removed by introducing a CD11b- magnetic �

An optimized method for mouse liver sinusoidal endothelial cell isolation

International Nuclear Information System (INIS)

Meyer, Jeremy; Lacotte, Stéphanie; Morel, Philippe; Gonelle-Gispert, Carmen; Bühler, Léo

2016-01-01

The objective of the present study was to develop an accurate and reproducible method for liver sinusoidal endothelial cell (LSEC) isolation in mice. Non-parenchymal cells were isolated using a modified two-step collagenase digestion combined with Optiprep density gradient centrifugation. LSEC were further purified using two prevalent methods, short-term selective adherence and CD146+ magnetic-activated cell sorting (MACS), and compared in terms of cell yield, viability and purity to our purification technique using CD11b cell depletion combined with long-term selective adherence. LSEC purification using our technique allowed to obtain 7.07±3.80 million LSEC per liver, while CD146+ MACS and short-term selective adherence yielded 2.94±1.28 and 0.99±0.66 million LSEC, respectively. Purity of the final cell preparation reached 95.10±2.58% when using our method. In contrast, CD146+ MACS and short-term selective adherence gave purities of 86.75±3.26% and 47.95±9.82%, respectively. Similarly, contamination by non-LSEC was the lowest when purification was performed using our technique, with a proportion of contaminating macrophages of only 1.87±0.77%. Further, isolated cells analysed by scanning electron microscopy presented typical LSEC fenestrations organized in sieve plates, demonstrating that the technique allowed to isolate bona fide LSEC. In conclusion, we described a reliable and reproducible technique for the isolation of high yields of pure LSEC in mice. This protocol provides an efficient method to prepare LSEC for studying their biological functions. - Highlights: • This protocol provides an efficient method to prepare primary mouse LSEC for studying their biological functions. • The liver cell dispersion step was improved by performing a retrograde cannulation of the liver. • The cell yield and the purity obtained were higher than comparative techniques in mice. • Contaminating macrophages were removed by introducing a CD11b- magnetic �

Selection and characterization of DNA aptamers

NARCIS (Netherlands)

Ruigrok, V.J.B.

2013-01-01

This thesis focusses on the selection and characterisation of DNA aptamers and the various aspects related to their selection from large pools of randomized oligonucleotides. Aptamers are affinity tools that can specifically recognize and bind predefined target molecules; this ability, however,

Marinobacter subterrani, a genetically tractable neutrophilic Fe(II-oxidizing strain isolated from the Soudan Iron Mine

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Benjamin Michael Bonis

2015-07-01

Full Text Available We report the isolation, characterization, and development of a robust genetic system for a halophilic, Fe(II-oxidizing bacterium isolated from a vertical borehole originating 714 m below the surface located in the Soudan Iron Mine in northern Minnesota, USA. Sequence analysis of the 16S rRNA gene places the isolate in the genus Marinobacter of the Gammaproteobacteria. The genome of the isolate was sequenced using a combination of short- and long-read technologies resulting in 2 contigs representing a 4.4 Mbp genome. Using genomic information, we used a suicide vector for targeted deletion of specific flagellin genes, resulting in a motility-deficient mutant. The motility mutant was successfully complemented by expression of the deleted genes in trans. Random mutagenesis using a transposon was also achieved. Capable of heterotrophic growth, this isolate represents a microaerophilic Fe(II-oxidizing species for which a system for both directed and random mutagenesis has been established. Analysis of 16S rDNA suggests Marinobacter represents a major taxon in the mine, and genetic interrogation of this genus may offer insight into the structure of deep subsurface communities as well as an additional tool for analyzing nutrient and element cycling in the subsurface ecosystem.

Pseudo-Random Number Generators

Science.gov (United States)

Howell, L. W.; Rheinfurth, M. H.

1984-01-01

Package features comprehensive selection of probabilistic distributions. Monte Carlo simulations resorted to whenever systems studied not amenable to deterministic analyses or when direct experimentation not feasible. Random numbers having certain specified distribution characteristic integral part of simulations. Package consists of collector of "pseudorandom" number generators for use in Monte Carlo simulations.

Methicillin-resistant staphylococcus aureus isolates in a hospital of shanghai.

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Wang, Xiaoguang; Ouyang, Lin; Luo, Lingfei; Liu, Jiqian; Song, Chiping; Li, Cuizhen; Yan, Hongjing; Wang, Ping

2017-01-24

Methicillin-resistant Staphylococcus aureus (MRSA) strains are now common both in the health care setting and in the community. Active surveillance is critical for MRSA control and prevention. Specimens of patients (200 patients with 1119 specimens) as well as medical staff and hospital setting (1000 specimens) were randomly sampled in a level 2 hospital in Shanghai from September 2011 to August 2012. Isolation, cultivation and identification of S. aureus were performed. Totally, 67 S. aureus strains were isolated. 32 S. aureus strains were isolated from patient samples; 13 (13/32, 40.6%) of the 32 S. aureus isolates were MRSA; sputum sample and patients in the department of general internal medicine were the most frequent specimen and patient group for S. aureus strains isolation. Remaining 35 S. aureus strains were isolated from the medical staff and hospital setting; 20 (20/35, 57.1%) of the 35 S. aureus isolates were MRSA; specimens sampled from doctors and nurses' hands and nose and hospital facilities were the most frequent samples to isolate S. aureus. Resistant and virulent genes detection showed that, all 33 MRSA strains were mecA positive which accounts for 49.3% of the 67 S. aureus strains; 38 isolates were Panton-Valentine leukocidin (PVL) gene positive which accounts for 56.7% of the 67 S. aureus strains; and 17 (17/67, 25.4%) isolates are mecA and PVL genes dual positive. Multidrug-resistant strains of MRSA and PVL positive S. aureus are common in patients, medical staff and hospital setting, the potential health threat is worthy of our attention.

Isolation of Acremonium species producing cephalosporine C (CPC ...

African Journals Online (AJOL)

SERVER

2007-11-19

Nov 19, 2007 ... selective media and Acremonium sp. were isolated. The presence of CPC antibiotic in the fermentation broths of these species was ... Penicillium sp. 28%. Alternaria sp. .... On-line high performance liquid chromatography for ...

Model Selection with the Linear Mixed Model for Longitudinal Data

Science.gov (United States)

Ryoo, Ji Hoon

2011-01-01

Model building or model selection with linear mixed models (LMMs) is complicated by the presence of both fixed effects and random effects. The fixed effects structure and random effects structure are codependent, so selection of one influences the other. Most presentations of LMM in psychology and education are based on a multilevel or…

Molecular study and nucleotide sequencing of Chlamydia abortus isolated from aborted sheep fetuses ewes of Alborz province

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amirreza ebadi

2015-02-01

Full Text Available Chlamydia is an obligate intracellular and gram negative coccobacilli and one of the most important causes of abortion in ruminants especially in ewes. This investigation was performed with the purpose of molecular study and sequencing of Chlamydia abortus isolated from aborted sheep fetuses of Alborz Province. In this study, DNA extraction was performed on 100 samples from aborted fetuses of 32 sheep flocks from different areas of Alborz province. Then using specific primers of gene IGS-Sr- RNA, polymerase chain reaction was conducted and 10 samples were selected randomly from the positive cases were sent to Macrogene company in Korea for sequencing. In this study, 37 samples from a total of 100 aborted fetuses were positive for Chlamydia abortus. After sequencing, more than 99 percent of the positive samples were similar with sequences in gene bank. The sequencing results indicated that the samples were very similar to isolates LN554882/1, AF051935/1 and CR848038/1 of the gene bank and were in the same cluster. Also, this investigation indicated that Chlamydia abortus is one of the main reasons of ewe abortion in Alborz province.