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Charles, Jermilia, Chandra S. Tangudu, and Bradley J. Blitvich. "Complete nucleotide sequences of the large RNA genome segments of Main Drain and Northway viruses (family Peribunyaviridae)." Archives of Virology 163, no. 8 (April 3, 2018): 2253–55. http://dx.doi.org/10.1007/s00705-018-3826-6.
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Chaudhary, Anita, Sheridan Kidd Haack, Joseph W. Duris, and Terence L. Marsh. "Bacterial and Archaeal Phylogenetic Diversity of a Cold Sulfur-Rich Spring on the Shoreline of Lake Erie, Michigan." Applied and Environmental Microbiology 75, no. 15 (June 19, 2009): 5025–36. http://dx.doi.org/10.1128/aem.00112-09.
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ABSTRACT Studies of sulfidic springs have provided new insights into microbial metabolism, groundwater biogeochemistry, and geologic processes. We investigated Great Sulphur Spring on the western shore of Lake Erie and evaluated the phylogenetic affiliations of 189 bacterial and 77 archaeal 16S rRNA gene sequences from three habitats: the spring origin (11-m depth), bacterial-algal mats on the spring pond surface, and whitish filamentous materials from the spring drain. Water from the spring origin water was cold, pH 6.3, and anoxic (H2, 5.4 nM; CH4, 2.70 μM) with concentrations of S2− (0.03 mM), SO4 2− (14.8 mM), Ca2+ (15.7 mM), and HCO3 − (4.1 mM) similar to those in groundwater from the local aquifer. No archaeal and few bacterial sequences were >95% similar to sequences of cultivated organisms. Bacterial sequences were largely affiliated with sulfur-metabolizing or chemolithotrophic taxa in Beta-, Gamma-, Delta-, and Epsilonproteobacteria. Epsilonproteobacteria sequences similar to those obtained from other sulfidic environments and a new clade of Cyanobacteria sequences were particularly abundant (16% and 40%, respectively) in the spring origin clone library. Crenarchaeota sequences associated with archaeal-bacterial consortia in whitish filaments at a German sulfidic spring were detected only in a similar habitat at Great Sulphur Spring. This study expands the geographic distribution of many uncultured Archaea and Bacteria sequences to the Laurentian Great Lakes, indicates possible roles for epsilonproteobacteria in local aquifer chemistry and karst formation, documents new oscillatorioid Cyanobacteria lineages, and shows that uncultured, cold-adapted Crenarchaeota sequences may comprise a significant part of the microbial community of some sulfidic environments.
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Smith, B. Y., S. J. Turner, and K. A. Rodgers. "Opal-A and associated microbes from Wairakei, New Zealand: the first 300 days." Mineralogical Magazine 67, no. 3 (June 2003): 563–79. http://dx.doi.org/10.1180/0026461036730118.
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AbstractAll samples of silica sinter, <2 y old taken from the discharge drain of the Wairakei geothermal power station and the Rainbow Terrace of Orakei Korako, consist of non-crystalline opal-A. This silica phase deposits directly upon the concrete drain wall and filamentous templets, extending from this wall, afforded by the microbial community present in the drain, whose nature was determined by a culture- independent strategy that entailed construction, fingerprinting and sequencing of a 16S clone library. The bacterial community is dominated by five major groups of organisms, present in approximately equal proportions, and which account for ∼50% of the community. None of the 16S sequences from these dominant groups yielded a perfect match with 16S sequences for named organisms in the international databases. However one dominant group clusters withHydrogenophilus thermoluteus,a thermophilic filamentous bacterium, and two cluster with putatively thermophilic members of theCyanobacteriaand green non-sulphur bacteria respectively. Initial opal-A deposits rapidly as agglomerations of silica nanospheres that, in turn, form chains of coalesced, oblate, microspheres <0.4 x 0.2 mm about the barbicel-like filaments, to produce a mat of fine woven strands. The majority of individual filaments are <8 μm long and 0.8 mm wide but may be up to 55 mm long by 1 mm wide. Where laminar flow dominates, most strands develop parallel to the drain current but some strands crisscross while others protrude above the mat surface. Where flow is turbulent, strands lack preferred orientation and some adopt a helical form. In general, following deposition, the values of the scattering broadband at half (FWHM) and three quarters (FWTM) of the maximum intensity decrease with increasing sample age. The behaviour of the band at one quarter maximum intensity (FWQM) is less consistent, but, in general, the youngest sinters possess the highest FWQM, FWHM and FWTM values that prove independent of fabric type. Opal-A silica matures following its removal from the parent fluid, especially where the sinter surface is filmed by water. A continual movement of silica is shown by a second generation of microspheres formed on the silica mat surface, by an increase in size of the initial microspheres, and by an increase in maximum intensity of the X-ray scattering broadbands. Similar silica aging behaviour occurs among young sinters developed upon microbial mats at Orakei Korako. The deposition and aging processes accord with the known behaviour of juvenile opaline silica in both natural and artificial systems whose pH, temperature and dissolved salt content are similar to Wairakei and Rainbow terrace: gelling of silica is favoured by the high pH (∼8.3) and temperature (∼60°C) of the Wairakei discharge fluid but the high dissolved salt content of the water (Na+= 930 μg/g, Ca2+= 12 μg/g, Cl = 1500 μg/g) and abundant microbial community facilitate rapid and copious flocculation of solid silica within the drain, in contrast to the slower accumulation on the natural sinter terrace at lower temperature (30—45°C) from less saline dilute bicarbonate-chloride waters (Na+= 180 μg/g, Ca2+= 0.2 μg/g, Cl = 400 μg/g, pH = 8.1).
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Harris, R. H., G. J. Scammell, W. J. Müller, and J. F. Angus. "Crop productivity in relation to species of previous crops and management of previous pasture." Australian Journal of Agricultural Research 53, no. 11 (2002): 1271. http://dx.doi.org/10.1071/ar02021.
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An experiment at Rutherglen in north-eastern Victoria compared 5 grass-removal methods in subterranean clover-based pastures that were grown before cropping sequences of canola–wheat–lupin–wheat or wheat–wheat–lupin–wheat. The cropping sequences were started in 3 successive years to provide replication in time. Grass removal from the pasture was more effective in winter than in spring and led to yield increases by the first and second crops. The largest increase (80%) was by the first canola crop after winter-cleaned pasture. The yield increase by the equivalent wheat crop was 42%. Since annual grasses and canola do not host the same root pathogens, we conclude that the yield responses were not due to root-disease control but probably to increased N supply. Assays of wheat roots confirmed that root disease was negligible throughout the experiment. Wheat growing in the year after canola yielded 11% more than wheat growing after wheat. The most surprising result was a 17% increase in the yield of wheat growing 3 years after canola compared with wheat growing 3 years after wheat, with wheat–lupin sequences in the intervening years for both systems. We suggest that canola and lupin, both of which are non-hosts of arbuscular mycorrhizal fungi, reduced mycorrhizal root colonisation in the fourth-year wheat crop, leading to less drain on assimilates.
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Liu, Sheng, Shuang Song, Ning Xie, Hai Chen, Xiaobo Wu, and Menglian Zhao. "Miller Plateau Corrected with Displacement Currents and Its Use in Analyzing the Switching Process and Switching Loss." Electronics 10, no. 16 (August 20, 2021): 2013. http://dx.doi.org/10.3390/electronics10162013.
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This paper reveals the relationship between the Miller plateau voltage and the displacement currents through the gate–drain capacitance (CGD) and the drain–source capacitance (CDS) in the switching process of a power transistor. The corrected turn-on Miller plateau voltage and turn-off Miller plateau voltage are different even with a constant current load. Using the proposed new Miller plateau, the turn-on and turn-off sequences can be more accurately analyzed, and the switching power loss can be more accurately predicted accordingly. Switching loss models based on the new Miller plateau have also been proposed. The experimental test result of the power MOSFET (NCE2030K) verified the relationship between the Miller plateau voltage and the displacement currents through CGD and CDS. A carefully designed verification test bench featuring a power MOSFET written in Verilog-A proved the prediction accuracy of the switching waveform and switching loss with the new proposed Miller plateau. The average relative error of the loss model using the new plateau is reduced to 1/2∼1/4 of the average relative error of the loss model using the old plateau; the proposed loss model using the new plateau, which also takes the gate current’s variation into account, further reduces the error to around 5%.
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Gaboury, M. N., R. A. Janusz, and K. E. Broughton. "Stream Channel and Riparian Zone Rehabilitation in the Dauphin Lake Watershed, Manitoba." Water Quality Research Journal 32, no. 2 (May 1, 1997): 257–72. http://dx.doi.org/10.2166/wqrj.1997.019.
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Abstract An extensive program of drain construction, stream channelization and diversion, begun in the early 1900s, expanded the area of cultivated, arable land within the Dauphin Lake basin. The developed drainage network altered flows, shortened natural streams, eliminated aquatic habitats, and caused channel erosion. The Stream Rehabilitation Program was developed in 1992 to rehabilitate riparian zones and unstable stream reaches within the seven major tributaries of the watershed. The rehabilitation strategy included stream condition assessments, improvement of the channel stability and aquatic habitats by reintroducing pool and riffle sequences, and involvement of landowners in the design and implementation of their on-farm riparian rehabilitation plans. Between 1993 and 1996, 36 km of straightened channels were rehabilitated using pool and riffle sequences, and 14 cooperating livestock producers implemented new farm layouts and practices. Under a signed stewardship agreement, landowners committed to maintain the project works and a minimum 10-m riparian corridor for at least 10 years. The Stream Rehabilitation Program has been adopted as a model for other watershed level management programs throughout Manitoba. The program has raised public awareness of fisheries, wildlife, recreation, agriculture and land stewardship issues.
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Schwalbe, E., R. Koschitzki, and H. G. Maas. "RECOGNITION OF DRAINAGE TUNNELS DURING GLACIER LAKE OUTBURST EVENTS FROM TERRESTRIAL IMAGE SEQUENCES." ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLI-B8 (June 23, 2016): 537–43. http://dx.doi.org/10.5194/isprsarchives-xli-b8-537-2016.
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In recent years, many glaciers all over the world have been distinctly retreating and thinning. One of the consequences of this is the increase of so called glacier lake outburst flood events (GLOFs). The mechanisms ruling such GLOF events are still not yet fully understood by glaciologists. Thus, there is a demand for data and measurements that can help to understand and model the phenomena. Thereby, a main issue is to obtain information about the location and formation of subglacial channels through which some lakes, dammed by a glacier, start to drain. The paper will show how photogrammetric image sequence analysis can be used to collect such data. <br><br> For the purpose of detecting a subglacial tunnel, a camera has been installed in a pilot study to observe the area of the Colonia Glacier (Northern Patagonian Ice Field) where it dams the Lake Cachet II. To verify the hypothesis, that the course of the subglacial tunnel is indicated by irregular surface motion patterns during its collapse, the camera acquired image sequences of the glacier surface during several GLOF events. Applying tracking techniques to these image sequences, surface feature motion trajectories could be obtained for a dense raster of glacier points. Since only a single camera has been used for image sequence acquisition, depth information is required to scale the trajectories. Thus, for scaling and georeferencing of the measurements a GPS-supported photogrammetric network has been measured. <br><br> The obtained motion fields of the Colonia Glacier deliver information about the glacier’s behaviour before during and after a GLOF event. If the daily vertical glacier motion of the glacier is integrated over a period of several days and projected into a satellite image, the location and shape of the drainage channel underneath the glacier becomes visible. The high temporal resolution of the motion fields may also allows for an analysis of the tunnels dynamic in comparison to the changing water level of the lake.
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Schwalbe, E., R. Koschitzki, and H. G. Maas. "RECOGNITION OF DRAINAGE TUNNELS DURING GLACIER LAKE OUTBURST EVENTS FROM TERRESTRIAL IMAGE SEQUENCES." ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLI-B8 (June 23, 2016): 537–43. http://dx.doi.org/10.5194/isprs-archives-xli-b8-537-2016.
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In recent years, many glaciers all over the world have been distinctly retreating and thinning. One of the consequences of this is the increase of so called glacier lake outburst flood events (GLOFs). The mechanisms ruling such GLOF events are still not yet fully understood by glaciologists. Thus, there is a demand for data and measurements that can help to understand and model the phenomena. Thereby, a main issue is to obtain information about the location and formation of subglacial channels through which some lakes, dammed by a glacier, start to drain. The paper will show how photogrammetric image sequence analysis can be used to collect such data. <br><br> For the purpose of detecting a subglacial tunnel, a camera has been installed in a pilot study to observe the area of the Colonia Glacier (Northern Patagonian Ice Field) where it dams the Lake Cachet II. To verify the hypothesis, that the course of the subglacial tunnel is indicated by irregular surface motion patterns during its collapse, the camera acquired image sequences of the glacier surface during several GLOF events. Applying tracking techniques to these image sequences, surface feature motion trajectories could be obtained for a dense raster of glacier points. Since only a single camera has been used for image sequence acquisition, depth information is required to scale the trajectories. Thus, for scaling and georeferencing of the measurements a GPS-supported photogrammetric network has been measured. <br><br> The obtained motion fields of the Colonia Glacier deliver information about the glacier’s behaviour before during and after a GLOF event. If the daily vertical glacier motion of the glacier is integrated over a period of several days and projected into a satellite image, the location and shape of the drainage channel underneath the glacier becomes visible. The high temporal resolution of the motion fields may also allows for an analysis of the tunnels dynamic in comparison to the changing water level of the lake.
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Armstrong, William H., and Robert S. Anderson. "Ice-marginal lake hydrology and the seasonal dynamical evolution of Kennicott Glacier, Alaska." Journal of Glaciology 66, no. 259 (June 11, 2020): 699–713. http://dx.doi.org/10.1017/jog.2020.41.
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AbstractGlacier basal motion is responsible for the majority of ice flux on fast-flowing glaciers, enables rapid changes in glacier motion and provides the means by which glaciers shape alpine landscapes. In an effort to enhance our understanding of basal motion, we investigate the evolution of glacier velocity and ice-marginal lake stage on Kennicott Glacier, Alaska, during the spring–summer transition, a time when subglacial drainage is undergoing rapid change. A complicated record of > 50 m fill-and-drain sequences on a hydraulically-connected ice-marginal lake likely reflects the punctuated establishment of efficient subglacial drainage as the melt season begins. The rate of change of lake stage generally correlates with diurnal velocity maxima, both in timing and magnitude. At the seasonal scale, the up-glacier progression of enhanced summer basal motion promotes uniformity of daily glacier velocity fluctuations throughout the 10 km study reach, and results in diurnal velocity patterns suggesting increasingly efficient meltwater delivery to and drainage from the subglacial channel system. Our findings suggest the potential of using an ice-marginal lake as a proxy for subglacial water pressure, and show how widespread basal motion affects bulk glacier behavior.
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Yumoto, Isao, Kikue Hirota, Hideyuki Kimoto, Yoshinobu Nodasaka, Hidetoshi Matsuyama, and Kazuaki Yoshimune. "Psychrobacter piscatorii sp. nov., a psychrotolerant bacterium exhibiting high catalase activity isolated from an oxidative environment." International Journal of Systematic and Evolutionary Microbiology 60, no. 1 (January 1, 2010): 205–8. http://dx.doi.org/10.1099/ijs.0.010959-0.
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A Gram-negative, non-motile, psychrotolerant bacterium exhibiting high catalase activity, designated strain T-3-2T, was isolated from a drain of a fish-processing plant. Its catalase activity was 12 000 U (mg protein)−1, much higher than the activity of the other Psychrobacter strains tested. The strain grew at 0–30 °C and in the presence of 0–12 % NaCl. The predominant isoprenoid quinone was ubiquinone-8 (Q-8), and C16 : 1 ω9c and C18 : 1 ω9c were the predominant cellular fatty acids. The DNA G+C content of strain T-3-2T was 43.9 mol%. 16S rRNA gene sequence phylogeny suggested that strain T-3-2T is a member of the genus Psychrobacter, with the closest relatives being the type strains of Psychrobacter nivimaris (99.2 % similarity), P. aquimaris (98.7 %) and P. proteolyticus (98.5 %). DNA–DNA hybridization showed less than 65 % relatedness with these strains. A phylogenetic tree based on gyrB gene sequences was more reliable, with higher bootstrap values than the 16S rRNA gene sequence-based tree. The result also differentiated the isolate from previously reported Psychrobacter species. Owing to the significant differences in phenotypic and chemotaxonomic characteristics and the phylogenetic and DNA–DNA relatedness data, the isolate merits classification within a novel species, for which the name Psychrobacter piscatorii sp. nov. is proposed. The type strain is T-3-2T (=JCM 15603T =NCIMB 14510T).
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Bourdin, Thibault, Emilie Bedard, Marie-Ève Benoit, Michèle Prévost, Etienne Robert, Caroline Quach, Eric Déziel, and Philippe Constant. "Development of a New High-Throughput Multilocus Sequence Typing Method to Monitor Causative Agents of Nosocomial Infections." Infection Control & Hospital Epidemiology 41, S1 (October 2020): s187. http://dx.doi.org/10.1017/ice.2020.726.
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Background: Nosocomial infections cause 4%–56% mortality in newborns. Several epidemiological studies have shown that transmission of opportunistic pathogens from the sink to the patient, including Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Serratia marcescens are associated with nosocomial infections in neonatal intensive care units (NICUs). In this project, we aimed to develop fast, accurate, and high-throughput multilocus sequence typing assays (HiMLST-Illumina) to detect opportunistic pathogens to assess their distribution in the sink environment of NICUs and their transfer to patients. Methods: Genome sequences of P. aeruginosa (n = 45), S. maltophilia (n = 23) and S. marcescens (n = 34) strains were retrieved from public genome databases to build their pangenomes, using the open-source PGAdb-builder server. The core genome was identified for each opportunistic pathogen and was searched for genes displaying the highest polymorphism. The minimal number of loci to include in a HiMLST-Illumina assay was determined by comparing topology of phylogenetic trees of concatenated loci based on genome similarity, computed as the average nucleotide identity (ANI) score. The primers used for HiMLST-Illumina schemes were designed in silico on a conserved domain and were tested on reference strains of each species. Results: Bioinformatics analyses showed that 3–4 loci (<300 base pairs per locus) distinguished strains with the same performances than ANI scores. The assays were tested using opportunistic pathogen isolates and environmental DNA originating from NICU sinks. The HiMLST-Illumina analysis of environmental DNA revealed the presence of at least 1 of the 3 studied opportunistic pathogens in 50% of sampled drains (n = 20). In a previous sampling, P. aeruginosa was isolated on selective culture media before and 48 hours after disinfection of a sink drain with chlorine. S. marcescens was also isolated from another sink 2 weeks after disinfection. Identification of the isolates was confirmed by HiMLST-Illumina analyses and will be typed to compare with clinical isolates. Conclusions: Initial in silico tests predict a high discriminating power of the HiMLST-Illumina method, suggesting that it would be possible to quickly identify strains of interest in a large number of samples. The power of this method is also in the possibility for molecular typing without a need for cultivation. Preliminary results suggest that sinks are readily colonized by opportunistic pathogens. This HiMLST-Illumina scheme will be applied in a 2-year intensive survey of NICUs in 3 hospitals in Montreal to evaluate the performance of new sink designs in limiting bioaerosol production and transmission of opportunistic pathogens to patients.Funding: NoneDisclosures: None
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Xiao, Xiao Qiu, Kevin L. Grove, See Yan Lau, Shannon McWeeney, and M. Susan Smith. "Deoxyribonucleic Acid Microarray Analysis of Gene Expression Pattern in the Arcuate Nucleus/Ventromedial Nucleus of Hypothalamus during Lactation." Endocrinology 146, no. 10 (October 1, 2005): 4391–98. http://dx.doi.org/10.1210/en.2005-0561.
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Lactation is characterized by extreme hyperphagia and negative energy balance resulting from a large energy drain due to milk production and by a suppression of cyclic ovarian function. Increases in neuropeptide Y and agouti-related protein and a decrease in proopiomelanocortin expression in the arcuate nucleus of hypothalamus (ARH) may contribute to the hyperphagia to maintain energy balance and to the suppression of LH secretion associated with lactation. However, little is known about the full extent of neuroendocrine changes in the ARH that may contribute to the various adaptations occurring during lactation. To address this issue, we used Affymetrix microarray to acquire a reliable profile of the lactation-induced transcriptional changes in micropunches containing the ARH and a portion of the ventromedial nucleus of the hypothalamus. Using high stringency criteria, 12 genes were identified as being differentially regulated during lactation, and an additional 10 genes and three transcribed sequences were identified using moderate stringency criteria. Changes in neuropeptide Y, enkephalin, tyrosine hydroxylase, and dynorphin, genes previously shown to be differentially regulated during lactation, provide validation for the microarray analysis. New genes identified as being differentially expressed include those related to neurotransmission, growth factors, signal transduction, and structure remodeling. These data identify new genes in ARH/ventromedial nucleus of the hypothalamus that may play an important role in the adaptations of lactation related to hyperphagia, milk production, and the suppression of cyclic reproductive function and may contribute to elucidating a framework for integrating changes in energy intake with the regulation of reproductive function during lactation.
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Spennato, Pietro, Carmela Chiaramonte, Domenico Cicala, Vittoria Donofrio, Manlio Barbarisi, Anna Nastro, Giuseppe Mirone, Vincenzo Trischitta, and Giuseppe Cinalli. "Acute triventricular hydrocephalus caused by choroid plexus cysts: a diagnostic and neurosurgical challenge." Neurosurgical Focus 41, no. 5 (November 2016): E9. http://dx.doi.org/10.3171/2016.8.focus16269.
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OBJECTIVE Intraventricular choroid plexus cysts are unusual causes of acute hydrocephalus in children. Radiological diagnosis of intraventricular choroid plexus cysts is difficult because they have very thin walls and fluid contents similar to CSF and can go undetected on routine CT studies. METHODS This study reports the authors' experience with 5 patients affected by intraventricular cysts originating from the choroid plexus. All patients experienced acute presentation with rapid neurological deterioration, sometimes associated with hypothalamic dysfunction, and required urgent surgery. In 2 cases the symptoms were intermittent, with spontaneous remission and sudden clinical deteriorations, reflecting an intermittent obstruction of the CSF pathway. RESULTS Radiological diagnosis was difficult in these cases because a nonenhanced CT scan revealed only triventricular hydrocephalus, with slight lateral ventricle asymmetry in all cases. MRI with driven-equilibrium sequences and CT ventriculography (in 1 case) allowed the authors to accurately diagnose the intraventricular cysts that typically occupied the posterior part of the third ventricle, occluding the aqueduct and at least 1 foramen of Monro. The patients were managed by urgent implantation of an external ventricular drain in 1 case (followed by endoscopic surgery, after completing a diagnostic workup) and by urgent endoscopic surgery in 4 cases. Endoscopic surgery allowed the shrinkage and near-complete removal of the cysts in all cases. Use of neuronavigation and a laser were indispensable. All procedures were uneventful, resulting in restoration of normal neurological conditions. Long-term follow-up (> 2 years) was available for 2 patients, and no complications or recurrences occurred. CONCLUSIONS This case series emphasizes the necessity of an accurate and precise identification of the possible causes of triventricular hydrocephalus. Endoscopic surgery can be considered the ideal treatment of choroid plexus cysts in children.
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Aydanian, Antonina, Li Tang, J. Glenn Morris, Judith A. Johnson, and O. Colin Stine. "Genetic Diversity of O-Antigen Biosynthesis Regions inVibrio cholerae." Applied and Environmental Microbiology 77, no. 7 (February 11, 2011): 2247–53. http://dx.doi.org/10.1128/aem.01663-10.
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ABSTRACTO-antigen biosynthetic (wbf) regions forVibrio choleraeserogroups O5, O8, and O108 were isolated and sequenced. Sequences were compared to those of other publishedV. choleraeO-antigen regions. Thesewbfregions showed a high degree of heterogeneity both in gene content and in gene order. Genes identified frequently showed greater similarities to polysaccharide biosynthesis genes from species other thanV. cholerae. Our results demonstrate the plasticity of O-antigen genes inV. cholerae, the diversity of the genetic pool from which they are drawn, and the likelihood that new pandemic serogroups will emerge.
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Byun, Roy, Liam D. H. Elbourne, Ruiting Lan, and Peter R. Reeves. "Evolutionary Relationships of Pathogenic Clones of Vibrio cholerae by Sequence Analysis of Four Housekeeping Genes." Infection and Immunity 67, no. 3 (March 1, 1999): 1116–24. http://dx.doi.org/10.1128/iai.67.3.1116-1124.1999.
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ABSTRACT Studies of the Vibrio cholerae population, using molecular typing techniques, have shown the existence of several pathogenic clones, mainly sixth-pandemic, seventh-pandemic, and U.S. Gulf Coast clones. However, the relationship of the pathogenic clones to environmental V. cholerae isolates remains unclear. A previous study to determine the phylogeny of V. cholerae by sequencing the asd (aspartate semialdehyde dehydrogenase) gene of V. cholerae showed that the sixth-pandemic, seventh-pandemic, and U.S. Gulf Coast clones had very differentasd sequences which fell into separate lineages in theV. cholerae population. As gene trees drawn from a single gene may not reflect the true topology of the population, we sequenced the mdh (malate dehydrogenase) and hlyA(hemolysin A) genes from representatives of environmental and clinical isolates of V. cholerae and found that the mdhand hlyA sequences from the three pathogenic clones were identical, except for the previously reported 11-bp deletion inhlyA in the sixth-pandemic clone. Identical sequences were obtained, despite average nucleotide differences in the mdhand hlyA genes of 1.52 and 3.25%, respectively, among all the isolates, suggesting that the three pathogenic clones are closely related. To extend these observations, segments of the recAand dnaE genes were sequenced from a selection of the pathogenic isolates, where the sequences were either identical or substantially different between the clones. The results show that the three pathogenic clones are very closely related and that there has been a high level of recombination in their evolution.
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Timofeev, E. A. "Unbiased Entropy Estimator for Binary Sequences." Modeling and Analysis of Information Systems 20, no. 1 (March 18, 2015): 107–15. http://dx.doi.org/10.18255/1818-1015-2013-1-107-115.
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Zhang, Hong-ying, Meng-kai Qiao, Xuan Wang, Min He, Li-min Shi, Guo-xiang Xie, and Hei-ying Jin. "Molecular Diversity of Sapovirus Infection in Outpatients Living in Nanjing, China (2011–2013)." Gastroenterology Research and Practice 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/4210462.
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Aim. To gain insight into the molecular diversity of sapovirus in outpatients with acute gastroenteritis in Nanjing, China.Methods. The specimens from outpatients clinically diagnosed as acute gastroenteritis were detected by real-time PCR; RT-PCR was then performed to amplify part of VP1 sequences. The PCR products were cloned into pGEM-T Easy vector and bidirectionally sequenced. All sequences were edited and analyzed. A phylogenetic tree was drawn with the MEGA 5.0 software.Results. Between 2011 and 2013, 16 sapovirus positive cases were confirmed by real-time PCR. The infected cases increased from two in 2011 and six in 2012 to eight in 2013. The majority was children and the elderly (15, 93.75%) and single infections (15, 93.75%). Of the 16 real-time positive specimens, 14 specimens had PCR products and the analysis data of the 14 nucleic sequences showed that there was one GI genogroup with four genotypes, two GI.2 in 2011, three GI.2, and one GI.1 in 2012 and one GI.2, three GI.1, two GI.3, and two GI.5 in 2013.Conclusion. Our data confirmed continuous existing of GI genogroup and GI.2 genotype from 2011 to 2013 in Nanjing and the successive appearance of different genotypes from outpatients with gastroenteritis.
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HARE, KEVIN G., IAN D. MORRIS, and NIKITA SIDOROV. "Extremal sequences of polynomial complexity." Mathematical Proceedings of the Cambridge Philosophical Society 155, no. 2 (May 2, 2013): 191–205. http://dx.doi.org/10.1017/s0305004113000157.
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AbstractThe joint spectral radius of a bounded set of d × d real matrices is defined to be the maximum possible exponential growth rate of products of matrices drawn from that set. For a fixed set of matrices, a sequence of matrices drawn from that set is called extremal if the associated sequence of partial products achieves this maximal rate of growth. An influential conjecture of J. Lagarias and Y. Wang asked whether every finite set of matrices admits an extremal sequence which is periodic. This is equivalent to the assertion that every finite set of matrices admits an extremal sequence with bounded subword complexity. Counterexamples were subsequently constructed which have the property that every extremal sequence has at least linear subword complexity. In this paper we extend this result to show that for each integer p ≥ 1, there exists a pair of square matrices of dimension 2p(2p+1 − 1) for which every extremal sequence has subword complexity at least 2−p2np.
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Amaral, Paulo de Paiva Rosa, Paulo César Martins Alves, Natália Florêncio Martins, Felipe Rodrigues da Silva, Guy de Capdeville, and Manoel Teixeira Souza Júnior. "Identification and characterization of a resistance gene analog (RGA) from the Caricaceae Dumort family." Revista Brasileira de Fruticultura 28, no. 3 (December 2006): 458–62. http://dx.doi.org/10.1590/s0100-29452006000300026.
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The majority of cloned resistance (R) genes characterized so far contain a nucleotide-binding site (NBS) and a leucine-rich repeat (LRR) domain, where highly conserved motifs are found. Resistance genes analogs (RGAs) are genetic markers obtained by a PCR-based strategy using degenerated oligonucleotide primers drawn from these highly conserved "motifs". This strategy has the advantage of the high degree of structural and amino acid sequence conservation that is observed in R genes. The objective of the present study was to search for RGAs in Carica papaya L. and Vasconcellea cauliflora Jacq. A. DC. Out of three combinations of primers tested, only one resulted in amplification. The amplified product was cloned in pCR2.1TOPO and than sequenced using M13 forward and reverse primers. Forty-eight clones were sequenced from each species. The 96 sequences generated for each species were cleaned of vector sequences and clustered using CAP3 assembler. From the GENEBANK, one RGA was identified in C. papaya showing a BlastX e-value of 2x10-61 to the gb|AAP45165.1| putative disease resistant protein RGA3 (Solanum bulbocastanum). To the extent of our knowledge this is the first report of a RGA in the Caricaceae Dumort family. Preliminary structural studies were performed to further characterize this putative NBS-LRR type protein. Efforts to search for other RGAs in papaya should continue, mostly to provide basis for the development of transgenic papaya with resistance to diseases.
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Kapili, Bennett J., and Anne E. Dekas. "PPIT: an R package for inferring microbial taxonomy from nifH sequences." Bioinformatics 37, no. 16 (February 13, 2021): 2289–98. http://dx.doi.org/10.1093/bioinformatics/btab100.
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Abstract Motivation Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale. Results We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset, we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. Availability and implementation PPIT is freely available to noncommercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL and DDBJ databases under BioProject number PRJEB37167. Supplementary information Supplementary data are available at Bioinformatics online.
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Sun, L., Y. Wang, C. Yu, Y. Zhao, and Y. Gan. "Genome Sequence of Clostridium tunisiense TJ, Isolated from Drain Sediment from a Pesticide Factory." Journal of Bacteriology 194, no. 24 (December 3, 2012): 6950–51. http://dx.doi.org/10.1128/jb.01873-12.
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Foster, D. P., R. A. Stine, and A. J. Wyner. "Universal codes for finite sequences of integers drawn from a monotone distribution." IEEE Transactions on Information Theory 48, no. 6 (June 2002): 1713–20. http://dx.doi.org/10.1109/tit.2002.1003851.
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KOTOB, S. I., S. M. McLAUGHLIN, P. Van BERKUM, and M. FAISAL. "Discrimination between two Perkinsus spp. isolated from the softshell clam, Mya arenaria, by sequence analysis of two internal transcribed spacer regions and the 5·8S ribosomal RNA gene." Parasitology 119, no. 4 (October 1999): 363–68. http://dx.doi.org/10.1017/s0031182099004801.
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The internal transcribed spacer (ITS-1 and ITS-2) regions and the 5·8S ribosomal RNA gene of 2 Perkinsus spp. (G117 and H49) originating from the softshell clam, Mya arenaria, of the Chesapeake Bay were cloned and sequenced to obtain evidence for their genetic divergence. A high level of heterogeneity in both regions, probably resulting from deletions, insertions, and base substitutions, was evident from alignments of the sequences of the 2 isolates with published sequences of other Perkinsus spp. The isolate G117 and other Perkinsus spp. were highly divergent (13–26% and 19–20% sequence divergence in ITS-1 and ITS-2, respectively). These regions in the isolate H49 and Perkinsus marinus were similar (99·07% and 99% for ITS-1 and ITS-2, respectively). Evidence obtained from a phylogenetic analysis using the aligned sequences suggests that G117 and H49 belong to 2 distinct species of Perkinsus. The isolate G117 possibly belongs to an as yet undescribed species of Perkinsus, and H49 belongs to the species P. marinus. The conclusions drawn from the genetic analysis of H49 and G117 are supported by previously reported morphological characteristics (McLaughlin & Faisal, 1998b). Isolates H49 and G117 originated from the same molluscan species demonstrating that at least 2 different species of Perkinsus can co-exist in 1 host.
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Adegoke, Kunle, Robert Frontczak, and Taras Goy. "Partial sum of the products of the Horadam numbers with subscripts in arithmetic progression." Notes on Number Theory and Discrete Mathematics 27, no. 2 (June 2021): 54–63. http://dx.doi.org/10.7546/nntdm.2021.27.2.54-63.
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Breaker, Jeanine. "The Complexion of Two Bodies. Part One: Nuance Drawn Out." Leonardo 46, no. 5 (October 2013): 425–31. http://dx.doi.org/10.1162/leon_a_00636.
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Motion capture, eye-tracking and digital image capture technologies are rapidly replacing traditional life drawing practice. We are led to believe that such technologies provide high-quality movement-analysis resources, yet these new tools are only in the early developmental stages. The author employed cutting-edge movement-analysis technologies and traditional drawing practice to create a series of “transparent” key-frame drawings based on Muybridge-style movement sequences, depicting specificity of the skeleton and musculature at key anatomical landmarks as though seen through the skin to stimulate perception of both movement and structure simultaneously.
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Slatkin, Montgomery. "The average number of sites separating DNA sequences drawn from a subdivided population." Theoretical Population Biology 32, no. 1 (August 1987): 42–49. http://dx.doi.org/10.1016/0040-5809(87)90038-4.
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SOBOL’, ILYA M., and BORIS V. SHUKHMAN. "INTEGRATION WITH QUASIRANDOM SEQUENCES: NUMERICAL EXPERIENCE." International Journal of Modern Physics C 06, no. 02 (April 1995): 263–75. http://dx.doi.org/10.1142/s0129183195000204.
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Numerical experiments with two multivariable integrands and various quasirandom sequences are described. The integrands were introduced as models of Monte Carlo algorithms for particle tracking with or without statistical weights. Though analytically both integrands are very similar, the corresponding integration errors behave quite differently. From these experiments together with earlier ones (that are briefly summarized in the paper) several non-standard conclusions are drawn both on quasirandom sequences and on types of integrands.
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Baker, Ishraq Mohammed, and Hayder Badri Ali. "Taxonomical Study of Spiders (Order, Araneae) from Different Localities of Iraq." Iraq Natural History Museum Publication -, no. 38 (November 30, 2020): 1–51. http://dx.doi.org/10.26842/inhmp.7.2020.2.38.0051.
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This study represents the first molecular and morphological work on spiders of Iraq. Specimens were collected from different localities in seven provinces during June 2018-July 2019 in different climate conditions. Using both molecular and morphological approaches, eight families representing 17 genera and nine species were identified. Eight genera: Cryptachaea Archer, 1946; Micaria Western, 1851; Ozyptila Simon, 1864; Paramicromerys Millot, 1946; Tegenaria Latreille, 1804; Trachyzelotes Lohmander, 1944; Uroctea Dufour, 1820 and Zelotes Gistel, 1848; and five species: Cryptachaea riparia (Blackwall, 1834); Tegenaria pagana C. L. Koch, 1840; Trachyzelotes jaxartensis (Kroneberg, 1875); Pardosa amentata (Clerck, 1757) and Oecobius putus O. Pickard-Cambridge, 1876 were first recorded for the Iraqi spider fauna. Identification keys for distinguishing families and genera based on the main characteristics were constructed. Molecular-identification was performed for specimens that were difficult to identify by morphological methods, and to confirm the results of the morphological identification. DNA was extracted from 28 spiders’ specimens; PCR-amplified the mtDNA fragment of 710bp of the Cytochrome C Oxidase Subunit I (COI) gene using the primers LCO 1490 Forward / HCO-700ME Reverse. The results of DNA sequences showed 16 samples successful in sequencing. Sixteen local sequenced specimens were submitted to GenBank and edited and combined with COI gene sequences that are associated in GenBank using the neighbor-joining method and the phylogenetic tree was drawn. Eight species of 16 genera belonging to eight families were confirmed by molecular barcoding. The DNA sequences and associated information about the specimens (collection and locality date) deposited in GenBank.
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Lilburn, Timothy G., and George M. Garrity. "Exploring prokaryotic taxonomy." International Journal of Systematic and Evolutionary Microbiology 54, no. 1 (January 1, 2004): 7–13. http://dx.doi.org/10.1099/ijs.0.02749-0.
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Techniques drawn from exploratory data analysis, using tools found in the S-Plus statistical software package, have been used to inspect and maintain the Bergey's Taxonomic Outline and to move towards an automated and community-based means of working on the outline. These techniques can be used to classify sequences from unnamed and uncultured organisms, to visualize errors in the taxonomy or in the curation of the sequences, to suggest emendations to the taxonomy or to the classification of extant species and to complement the visualization of phylogenies based on treeing methods. A dataset of more than 9200 aligned small-subunit rRNA sequences was analysed in the context of the current taxonomic outline. The use of the algorithm in exploring and modifying the taxonomy is illustrated with an example drawn from the family Comamonadaceae.
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Hino, Yutaro, Muraosa Yasunori, Akira Watanabe, Kyoko Yarita, Maki Yahiro, Emiko Sakaida, Koutaro Yokote, and Katsuhiko Kamei. "Indoor Plumbing Drains Are Important Sources for Invasive Fusariosis in Patients with Hematological Disorders: Culture-Based and Metagenomic Analysis." Blood 134, Supplement_1 (November 13, 2019): 4875. http://dx.doi.org/10.1182/blood-2019-121391.
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Despite the advances in antifungal drugs, the number of invasive fusariosis (IF) has been increasing in patients with hematological disorders, especially hematopoietic stem cell transplantation (HSCT) patients. IF is still a severe infection and refractory to treat because Fusarium is naturally resistant to most of the antifungal drugs. Therefore, prior to infection, avoidance of contact with Fusarium would be critical in immunocompromised patients. However, little is known about the source of Fusarium infection. The purpose of this study is to investigate the epidemiology of IF in patients with hematological disorders in Japan and to find out the infectious source of Fusarium and the relationship between Fusarium species isolated from clinical samples and the ones from environment using culture-based and metagenomic methods. In our center, a total of 99 clinically isolated Fusarium were stored and maintained. They were obtained from hospitals in 33 prefectures in Japan. 50 and 49 strains were recovered from IF patients and superficial fusariosis (SF) patients, respectively. In this study, we analyzed 42 IF cases which developed in patients with hematological disorders. The most common underlying disease was AML (35.7%), followed by ALL (23.8%). About 60% of the patients received HSCT, and most of them became infected with Fusarium in the early phase after HSCT (within eight weeks). This result indicated that IF infection mostly occurred in indoor environments. As the next step, we performed the surveys in indoor environments such as air and plumbing drains in medical institutions and residences to figure out the source of infection. Few Fusarium species were collected from air samples. From the indoor air, we collected 142 filamentous fungi isolates. Only 2/142 strains (1.4%) were Fusarium species (Fusarium fujikuroi species complex 1, F. nisikadoi 1). In contrast, among the 72 drain port samples collected from 6 medical institutions (hematology wards, including bone marrow transplantation units, and ICU/NICU) and 15 residences, Fusarium species were positive at 26 (36.1%) sampling points. One hundred and eight filamentous fungi were isolated from the drain samples, and 29/108 isolates (27%) were Fusarium species. In details, 20 strains were Fusarium solani species complex (F. petroliphilum 7, F. keratoplasticum 4, F. sensu stricto 4, F. falciforme 1, others 4) and nine strains were Fusarium oxysporum species complex. Interestingly, the FSSC compositions of drain port samples were similar to those of IF samples from patients with hematological disorders and different from those of SF samples. In contrast, no Fusarium strains were detected in the places where the regular sink-cleaning was performed. Likewise, the samples for the metagenomic analysis were obtained in the places where the culture samples were collected. DNA extraction from samples was performed by the PowerLyzer Powersoil Kit (QIAGEN, Hilden, Germany). Fungal ITS regions were amplified with modified ITS1F and ITS2 primer set and sequenced with Illumina Miseq platform. After filtering and denoising, we were able to analyze 8 air samples and 23 drain samples (10 culture-positive samples and 13 culture-negative samples). It is also revealed that a lot of Fusarium live indoor plumbing drains but few Fusarium spp. inhabit indoor air (less than 0.1%). In summary, we investigate the epidemiology of IF in patients with hematological disorders in Japan and the distribution of Fusarium species in indoor environments. Our survey has demonstrated that a lot of Fusarium inhabits the indoor plumbing drains, not the indoor air using the culture-based and metagenomic methods. The similarity of FSSC distribution between the drain samples and causative species of IF cases indicated that the indoor plumbing drains would be potential sources of IF infection. We suggested that regular sink-cleaning was critical to prevent patients with hematological disorders from Fusarium infection. Disclosures No relevant conflicts of interest to declare.
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Dugas, Edwige. "[non-Adj] sequences in French." Morphology and its interfaces 37, no. 2 (December 31, 2014): 194–208. http://dx.doi.org/10.1075/li.37.2.01dug.
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This paper addresses the status and formation of [non-Adj] sequences in French, such as non occupé ‘non-occupied’, non effaçable ‘non-erasable’. These sequences can be compared to two other types of negative constructions which are built in morphology, namely [non-N]N (e.g. non occupation, non violence) and [in-Adj] (e.g. inoccupé ‘unoccupied’, ineffaçable ‘unerasable’). Taking as a starting point the observation made by Gaatone (1971, 1987) that [non-Adj] have syntactic properties which differ from that of [in-Adj], I use authentic data drawn from different corpora to determine whether [non-Adj] are formed in morphology or in syntax, and I attempt to provide a constructional account (Goldberg, 1995; Croft, 2001; Booij, 2010) of these sequences.
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Baum, B. R., T. Edwards, M. Mamuti, and D. A. Johnson. "Phylogenetic relationships among the polyploid and diploid Aegilops species inferred from the nuclear 5S rDNA sequences (Poaceae: Triticeae)." Genome 55, no. 3 (March 2012): 177–93. http://dx.doi.org/10.1139/g2012-006.
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Phylogenetic inferences of the polyploid Aegilops taxa were drawn based upon the analysis of 909 nuclear 5S rDNA sequences obtained from 15 Aegilops polyploid taxa (531 sequences new to this paper) and 378 sequences from our previous study on the diploid taxa. The 531 sequences can be split into two orthologous groups (unit classes), the long AE1 and short AE1 previously identified in the diploid set. An examination of the relationships between unit classes and their associated haplomes suggests that U haplome sequences found in Ae. umbellulata are the closest to the T sequences found in Amblyopyrum muticum and that sequences of the polyploid species expected to be the M type found in Ae. comos are more similar to the T haplome sequences, except in the three hexaploids Ae. glumiaristata, Ae. juvenalis, and Ae. vavilovii and the tetraploid Ae. crassa where they are found to be similar to the M haplome sequences. These three hexaploid taxa likely originated from the tetraploid Ae. crassa (DM), while the closest taxon to the fourth hexaploid, Ae. recta, is the tetraploid Ae. neglecta (UM). Based upon the distribution of the unit classes, several reticulate phylogenies depicting evolutionary relationships among diploid, tetraploid, and hexaploid taxa were constructed; however, none of these widely used methods could depict the expected reticulate relationship as previously drawn from cytogenetic analyses in this group of allopolyploid species. These results suggest that evolutionary relationships derived from models based upon the assumption of bifurcating species require careful interpretation when these same models are applied to species with reticulate evolution.
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Tang, Bei-Sha. "Attention Should be Drawn to Rare Diseases and Interpretation of Sequence Variants." Chinese Medical Journal 129, no. 9 (May 2016): 1009–10. http://dx.doi.org/10.4103/0366-6999.180531.
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CHANG, CHANG-HENG, LI-CHING HSIEH, TA-YUAN CHEN, HONG-DA CHEN, LIAOFU LUO, and HOONG-CHIEN LEE. "SHANNON INFORMATION IN COMPLETE GENOMES." Journal of Bioinformatics and Computational Biology 03, no. 03 (June 2005): 587–608. http://dx.doi.org/10.1142/s0219720005001181.
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Shannon information in the genomes of all completely sequenced prokaryotes and eukaryotes are measured in word lengths of two to ten letters. It is found that in a scale-dependent way, the Shannon information in complete genomes are much greater than that in matching random sequences — thousands of times greater in the case of short words. Furthermore, with the exception of the 14 chromosomes of Plasmodium falciparum, the Shannon information in all available complete genomes belong to a universality class given by an extremely simple formula. The data are consistent with a model for genome growth composed of two main ingredients: random segmental duplications that increase the Shannon information in a scale-independent way, and random point mutations that preferentially reduces the larger-scale Shannon information. The inference drawn from the present study is that the large-scale and coarse-grained growth of genomes was selectively neutral and this suggests an independent corroboration of Kimura's neutral theory of evolution.
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Hope, RM, S. Cooper, and B. Wainwright. "Globin Macromolecular Sequences in Marsupials and Monotremes." Australian Journal of Zoology 37, no. 3 (1989): 289. http://dx.doi.org/10.1071/zo9890289.
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We have reviewed published data on haemoglobin and myoglobin DNA and protein sequences from marsupial and monotreme mammals, and drawn attention to the difficulties that have been encountered in using these data to estimate dates of evolutionary divergence. We argue that continuing studies of marsupial and monotreme globins, particularly molecular studies on gene organisation and regulation, are likely to contribute significantly to our understanding of gene and organismal evolution. In this context we suggest that studies on the globin genes of a monotreme and a South American marsupial would be especially rewarding.
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Edlind, Tom. "678. Polymorphic Locus Sequence Typing for Pseudomonas aeruginosa Outbreak Detection and Investigation." Open Forum Infectious Diseases 7, Supplement_1 (October 1, 2020): S392. http://dx.doi.org/10.1093/ofid/ofaa439.870.
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Abstract Background Pseudomonas aeruginosa is a common agent of healthcare-associated infection (HAI), which can be challenging to treat due to intrinsic or acquired antibiotic resistance. In contrast to most HAI, the source of P. aeruginosa infection is typically environmental; e.g., from the faucets, drains, and showers in patient rooms. To unambiguously identify the source, strain typing of patient and environmental isolates is required. Typing methods include sequence-based MLST and WGS which resolve strains based on relatively rare SNPs, and length-based MLVA which resolves strains based on relatively frequent insertions/deletions within tandem repeats. These and other methods previously applied to P. aeruginosa have one or more limitations relating to cost, technical complexity, reproducibility, and turnaround time that preclude their routine use. Polymorphic locus sequence typing (PLST) is a hybrid approach that employs sequence analysis of the one or two most phylogenetically informative tandem repeat-containing loci within the genome of a microbial species. Strain resolution equals or exceeds MLST and MLVA and approaches that of WGS. Here, the identification and evaluation of candidate PLST loci for P. aeruginosa epidemiology are described. Methods Tandem repeats were bioinformatically identified in representative genome sequences, and screened by BLASTN queries of GenBank genome databases followed by clustal alignments and phylogenetic analysis. Candidate loci were amplified from heat-treated colony lysates and Sanger sequenced. Results PLST locus PaMT1 (Mbp 2.568-2.569 in the PA01 genome) resolved 99 alleles from 144 epidemiologically unrelated isolates with GenBank genome sequences, yielding diversity index = 0.991. Nineteen sets of isolates shared healthcare facility and PaMT1 allele, consistent with nosocomial transmission. Examples, confirmed by WGS-SNP analysis, include isolates from 8 VAP patients, 2 sets of cancer patient isolates, and a pair of isolates from patient and hospital sewage. In the laboratory, locus PaMT1 was readily amplified and sequenced from colony lysates, yielding typing data with 1-2 day turnaround. Conclusion PaMT1 PLST provides an affordable, user-friendly, and timely tool for P. aeruginosa outbreak detection and investigaton. Disclosures Tom Edlind, PhD, MicrobiType LLC (Employee, Scientific Research Study Investigator)
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Horwitz, Marshall S. Z., Dipak K. Dube, and Lawrence A. Loeb. "Selection of new biological activities from random nucleotide sequences: evolutionary and practical considerations." Genome 31, no. 1 (January 1, 1989): 112–17. http://dx.doi.org/10.1139/g89-021.
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Recent advances in the selection of biologically active DNA sequences from random populations are reviewed. Within the framework of evolution, forces are considered that have precluded the testing of all possible DNA sequences, purely with regard to their functionality as genetic regulatory elements or protein coding sequences. Examples are drawn from cassette mutagenesis of enzyme active sites, protein domain replacement by fusion with random genomic digests, and the selection of bacterial promoters from random DNA. Efforts to derive new activities are examined, and the likelihood of future success is evaluated.Key words: active DNA, nucleotide permutation, DNA evolution.
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Shin, Hyun Soo, Byung Du Ahn, Kyung Ho Kim, Jin-Seong Park, and Hyun Jae Kim. "The effect of thermal annealing sequence on amorphous InGaZnO thin film transistor with a plasma-treated source–drain structure." Thin Solid Films 517, no. 23 (October 2009): 6349–52. http://dx.doi.org/10.1016/j.tsf.2009.02.071.
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Vershinin, A. V., E. A. Salina, V. V. Solovyov, and L. L. Timofeyeva. "Genomic organization, evolution, and structural peculiarities of highly repetitive DNA of Hordeum vulgare." Genome 33, no. 3 (June 1, 1990): 441–49. http://dx.doi.org/10.1139/g90-066.
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A fraction of highly repeated DNA sequences of Hordeum vulgare has been investigated by cloning 19 separate highly repetitive sequences in the plasmid pBR327. Characteristics studied included genus specificity of isolated sequences, their prevalence, and genome organization. Sequences (pHv7161, pHv7191, pHv7179) have been identified that are the most widespread in the H. vulgare genome and have a complicated arrangement. A tandemly arranged sequence, pHv7141, was also identified. The primary structure of a 999 bp long, BamHI fragment of one of the most widespread sequences, pHv7161, as well as the adjacent pHv7302 and pHv7245 sequences was determined. The fragment abounds in inverted repeats, of which two are flanked by direct repeats, and contains short subrepeats, A, B, and C, and a great variety of potential protein-binding sites. A comparison is drawn between the content and genome organization of highly repeated DNA sequences of H. vulgare and those of the wild barley species Hordeum bulbosum, Hordeum jubatum, Hordeum geniculatum, Hordeum brevisubulatum, Hordeum turkestanicum, and Hordeum murinum. According to the above characters (close copy number and genome organization similarity of highly repetitive sequences) the species under discussion have been classified into four groups. This division is in good agreement with other data on interspecific crossing in Hordeum and on chromosome pairing in hybrid meiosis.Key words: Hordeum, highly repeated DNA sequences, copy number.
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Lendzion, K. "Sedimentation of the Vendian–Cambrian marine sequence, Poland." Geological Magazine 123, no. 4 (July 1986): 361–65. http://dx.doi.org/10.1017/s0016756800033458.
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AnbstractIn the Lublin area of the East European Platform (southeast Poland) sedimentation of the Vendian–Cambrian marine sequence began in Late Vendian times. Vendian and Cambrian strata occur in sedimentary continuity and their features indicate sedimentation in the tidal zone of a shallow epicontinental sea. The Vendian–Cambrian boundary, drawn on the basis of mainly palaeontological data, passes between theVendotaeniaandSabellidites zones.
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Beyers, W. B., and D. P. Lindahl. "Strategic Behavior and Development Sequences in Producer Service Businesses." Environment and Planning A: Economy and Space 29, no. 5 (May 1997): 887–912. http://dx.doi.org/10.1068/a290887.
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Though it is widely recognized that the producer services are among the fastest growing industries in advanced economies, there is little research documenting development experiences of establishments within these industries. In this paper we address this topic by illustrating types of strategic behaviors exhibited by producer service firms and the effectiveness of these behaviors, developing a taxonomy of firm segments, and relating types of strategic behavior to this taxonomy. The paper is based on results from 444 in-depth interviews. Key variables addressed in the analysis are drawn from the industrial sociology and business strategy literature and include organizational structure, age, dynamics of client and geographic markets, and changes in services supplied.
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Adu-Sackey, Albert, Francis T. Oduro, and Gabriel Obed Fosu. "Inequalities approach in determination of convergence of recurrence sequences." Open Journal of Mathematical Sciences 5, no. 1 (February 5, 2021): 65–72. http://dx.doi.org/10.30538/oms2021.0145.
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The paper proves convergence for three uniquely defined recursive sequences, namely, arithmetico-geometric sequence, the Newton-Raphson recursive sequence, and the nested/composite recursive sequence. The three main hurdles for this prove processes are boundedness, monotonicity, and convergence. Oftentimes, these processes lie in the predominant use of prove by mathematical induction and also require some bit of creativity and inspiration drawn from the convergence monotone theorem. However, these techniques are not adopted here, rather, as a novelty, extensive use of basic manipulation of inequalities and useful equations are applied in illustrating convergence for these sequences. Moreover, we established a mathematical expression for the limit of the nested recurrence sequence in terms of its leading term which yields favorable results.
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Allison, Donald E., and David C. Thomas. "Item-Difficulty Sequence in Achievement Examinations: Examinees' Preferences and Test-Taking Strategies." Psychological Reports 59, no. 2 (October 1986): 867–70. http://dx.doi.org/10.2466/pr0.1986.59.2.867.
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Elementary, secondary school, and university students were asked for the test-taking strategy usually used in taking an achievement test and for the sequence of difficulty preferred for achievement test items. The majority preferred an easy-to-hard strategy with items in order-presented as second choice, and the hard-to-easy strategy chosen least often. No conclusions were drawn as to the effect of students' usual test-taking strategies on research with various item-difficulty sequences. The data on students' preferences for item sequences support the use of the easy-to-hard or random arrangement over the hard-to-easy.
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Garrity, George M. "A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?" Journal of Clinical Microbiology 54, no. 8 (May 18, 2016): 1956–63. http://dx.doi.org/10.1128/jcm.00200-16.
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Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins contemporary microbiology and serves as a principal means of shaping and referencing knowledge. Using methods drawn from the field of exploratory data analysis, this minireview examines the current state of the field as it transitions from a taxonomy based on 16S rRNA gene sequences to one based on whole-genome sequences and tests the validity of some commonly held beliefs.
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BERNASCONI, NICLA, KONSTANTINOS PANAGIOTOU, and ANGELIKA STEGER. "The Degree Sequence of Random Graphs from Subcritical Classes." Combinatorics, Probability and Computing 18, no. 5 (September 2009): 647–81. http://dx.doi.org/10.1017/s0963548309990368.
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In this work we determine the expected number of vertices of degreek=k(n) in a graph withnvertices that is drawn uniformly at random from asubcritical graph class. Examples of such classes are outerplanar, series-parallel, cactus and clique graphs. Moreover, we provide exponentially small bounds for the probability that the quantities in question deviate from their expected values.
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Xu, Qi. "Formulaic Sequences and the Implications for Second Language Learning." English Language Teaching 9, no. 8 (June 2, 2016): 39. http://dx.doi.org/10.5539/elt.v9n8p39.
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<p>The present paper is a review of literature in relation to formulaic sequences and the implications for second language learning. The formulaic sequence is a significant part of our language, and plays an essential role in both first and second language learning. The paper first introduces the definition, classifications, and major features of formulaic sequences. Then relevant studies on second language learning are reviewed, and pedagogical implications will be drawn from previous research. It is suggested that more emphasis should be put on prefabs in foreign language teaching, but at the same time, there is also danger of overemphasizing the role of prefabs in SLA research, given limited exposure to the target language in a foreign language learning environment.</p>
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Garulli, Torquato, Anita Catapano, Daniele Fanteria, Julien Jumel, and Eric Martin. "Design and finite element assessment of fully uncoupled multi-directional layups for delamination tests." Journal of Composite Materials 54, no. 6 (August 14, 2019): 773–90. http://dx.doi.org/10.1177/0021998319868293.
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In this paper, a procedure to obtain fully uncoupled multi-directional stacking sequences for delamination specimens is outlined. For such sequences, in-plane, membrane-bending and torsion–bending coupling terms are null (in closed-form solution in the framework of classical laminated plate theory) for the entire stack and for both its halves, which form two arms in the pre-cracked region of a typical delamination specimen. This is achieved exploiting the superposition of quasi-trivial quasi-homogeneous stacking sequences, according to appropriate rules. Any pair of orientations of the plies embedding the delamination plane can be obtained. To assess the effectiveness of the proposed approach, a fully uncoupled multi-directional sequence is designed and compared to other relevant sequences proposed in the literature. Finite element simulations of double cantilever beam test are performed using classic virtual crack closure technique and a revised state-of-the-art virtual crack closure technique formulation too. Some interesting conclusions regarding proper design of multidirectional stacks for delamination tests are drawn. Moreover, the results confirm the suitability of fully uncoupled multi-directional sequences for delamination tests. Thanks to their properties, these sequences might lay the foundations for the development of standard test procedures for delamination in angle-ply interfaces.
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Mohie El-Din, Mostafa, and Walid Emam. "Nonparametric Prediction Intervals of generalized order statistics from two independent sequences." International Journal of Advanced Statistics and Probability 4, no. 1 (March 31, 2016): 36. http://dx.doi.org/10.14419/ijasp.v4i1.5896.
Full textAbstract:
<p>This paper, discusses the problem of predicting future a generalized order statistic of an iid sequence sample was drawn from an arbitrary unknown distribution, based on observed also generalized order statistics from the same population. The coverage probabilities of these prediction intervals are exact and free of the parent distribution F(). Prediction formulas of ordinary order statistics and upper record values are extracted as special cases from the productive results. Finally, numerical computations on several models of ordered random variables are given to illustrate the proposed procedures.</p>
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Herman, David. "Scripts, Sequences, and Stories: Elements of a Postclassical Narratology." PMLA/Publications of the Modern Language Association of America 112, no. 5 (October 1997): 1046–59. http://dx.doi.org/10.2307/463482.
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This essay begins by differentiating between narratively organized sequences of events and nonnarrative sequences associated with deductive reasoning, conversational exchanges, descriptions, and recipes. After reviewing classical accounts of narrative sequences, the essay sketches developments in language theory and cognitive science that have occurred after the heyday of structuralist narrative poetics and that throw further light on two interlinked questions: what is necessary to make a sequence of events a narrative, and what makes some narrative sequences more readily processed as stories than others? Both questions can be addressed by the concept, drawn from artificial-intelligence research, of “scripts”—knowledge representations storing finite, sequentially ordered groups of actions required for the accomplishment of particular tasks. Exploring some literary applications of a theoretical model based on scripts, the final section of the text outlines research strategies for a postclassical narratology that encompasses cognitive approaches to stories. By examining different modalities of the script-story interface, theorists of narrative may be able to rethink the historical development of narrative techniques and to understand better the differences among narrative genres at any given time.
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Southwell, Rosy, Anna Baumann, Cécile Gal, Nicolas Barascud, Karl Friston, and Maria Chait. "Is predictability salient? A study of attentional capture by auditory patterns." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1714 (February 19, 2017): 20160105. http://dx.doi.org/10.1098/rstb.2016.0105.
Full textAbstract:
In this series of behavioural and electroencephalography (EEG) experiments, we investigate the extent to which repeating patterns of sounds capture attention. Work in the visual domain has revealed attentional capture by statistically predictable stimuli, consistent with predictive coding accounts which suggest that attention is drawn to sensory regularities. Here, stimuli comprised rapid sequences of tone pips, arranged in regular (REG) or random (RAND) patterns. EEG data demonstrate that the brain rapidly recognizes predictable patterns manifested as a rapid increase in responses to REG relative to RAND sequences. This increase is reminiscent of the increase in gain on neural responses to attended stimuli often seen in the neuroimaging literature, and thus consistent with the hypothesis that predictable sequences draw attention. To study potential attentional capture by auditory regularities, we used REG and RAND sequences in two different behavioural tasks designed to reveal effects of attentional capture by regularity. Overall, the pattern of results suggests that regularity does not capture attention. This article is part of the themed issue ‘Auditory and visual scene analysis’.