bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity within and between sulfonylurea‐resistant and susceptible populations of Schoenoplectus juncoides in Japan
Authors: Imaizumi T , Kataoka Y , Ogata S , Uchino A 
Published: May 2013

SummaryTo reveal the effects of herbicide selection on genetic diversity in the outcrossing weed species Schoenoplectus juncoides, six sulfonylurea‐resistant (SU‐R) and eight sulfonylurea‐susceptible (SU‐S) populations were analysed using 40 polymorphic inter‐simple sequence repeat loci. The plants were collected from three widely separated regions: the Tohoku, Kanto and Kyushu districts of Japan. Genetic diversity values (Nei's gene diversity, h) within each SU‐S population ranged from h = 0.125 to h = 0.235. The average genetic diversity within the SU‐S populations was HS = 0.161, and the total genetic diversity was HT = 0.271. Although the HS of the SU‐R populations (0.051) was lower than that of the SU‐S populations, the HT of the SU‐R populations (0.202) was comparable with that of the SU‐S populations. Most of the genetic variation was found within the region for both the SU‐S and SU‐R populations (88% of the genetic variation respectively). Two of the SU‐R populations showed relatively high genetic diversity (h = 0.117 and 0.161), which were comparable with those of the SU‐S populations. In contrast, the genetic diversity within four SU‐R populations was much lower (from h = 0 to 0.018) than in the SU‐S populations. The results suggest that selection by sulfonylurea herbicides has decreased genetic diversity within some SU‐R populations of S. juncoides. The different level of genetic diversity in the SU‐R populations is most likely due to different levels of inbreeding in the populations.
Silicone breast phantoms for elastographic imaging evaluation
Authors: Kashif Amer S. , Lotz Thomas F. , McGarry Matthew D. , Pattison Adam J. , Chase James G. 
Published: May 2013

Purpose:Breast cancer is a major public health issue for women, and early detection significantly increases survival rate. Currently, there is increased research interest in elastographic soft‐tissue imaging techniques based on the correlation between pathology and mechanical stiffness. Anthropomorphic breast phantoms are critical forex vivo validation of emerging elastographic technologies. This research develops heterogeneous breast phantoms for use in testing elastographic imaging modalities.Methods:Mechanical property estimation of eight different elastomers is performed to determine storage moduli (E′) and damping ratios (ζ) using a dynamic mechanical analyzer. Dynamic compression testing was carried out isothermally at room temperature over a range of 4–50 Hz. Silicone compositions with physiologically realistic storage modulus were chosen for mimicking skin adipose, cancerous tumors, and pectoral muscles and 13 anthropomorphic breast phantoms were constructed forex vivo trials of digital image elastotomography (DIET) breast cancer screening system. A simpler fabrication was used to assess the possibility of multiple tumor detection using magnetic resonance elastography (MRE).Results:Silicone materials with ranges of storage moduli (E′) from 2 to 570 kPa and damping ratios (ζ) from 0.03 to 0.56 were identified. The resulting phantoms were tested in two different elastographic breast cancer diagnostic modalities. A significant contrast was successfully identified between healthy tissues and cancerous tumors both in MRE and DIET.Conclusions:The phantoms presented promise aid to researchers in elastographic imaging modalities for breast cancer detection and provide a foundation for silicone based phantom materials for mimicking soft tissues of other human organs.
Biogeography of Burkholderia pseudomallei in the Torres Strait Islands of Northern Australia
Authors: Baker Anthony , Mayo Mark , Owens Leigh , Burgess Graham , Norton Robert , McBride William John Hannan , Currie Bart J. , Warner Jeffrey 
Published: May 2013

ABSTRACT

It has been hypothesized that biogeographical boundaries are a feature of
Burkholderia pseudomallei
ecology, and they impact the epidemiology of melioidosis on a global scale. This study examined the relatedness of
B. pseudomallei
sourced from islands in the Torres Strait of Northern Australia to determine if the geography of isolated island communities is a determinant of the organisms' dispersal. Environmental sampling on Badu Island in the Near Western Island cluster recovered a single clone. An additional 32 clinical isolates from the region were sourced. Isolates were characterized using multilocus sequence typing and a multiplex PCR targeting the flagellum gene cluster. Gene cluster analysis determined that 69% of the isolates from the region encoded the ancestral
Burkholderia thailandensis
-like flagellum and chemotaxis gene cluster, a proportion significantly lower than that reported from mainland Australia and consistent with observations of isolates from southern Papua New Guinea. A goodness-of-fit test indicated that there was geographic localization of sequence types throughout the archipelago, with the exception of Thursday Island, the economic and cultural hub of the region. Sequence types common to mainland Australia and Papua New Guinea were identified. These findings demonstrate for the first time an environmental reservoir for
B. pseudomallei
in the Torres Strait, and multilocus sequence typing suggests that the organism is not randomly distributed throughout this region and that seawater may provide a barrier to dispersal of the organism. Moreover, these findings support an anthropogenic dispersal hypothesis for the spread of
B. pseudomallei
throughout this region.
Development of Poliovirus Extraction Method from Stool Extracts by Using Magnetic Nanoparticles Sensitized with Soluble Poliovirus Receptor
Authors: Arita Minetaro 
Published: May 2013

ABSTRACT
A method for extracting poliovirus (PV) from stool extracts was developed. Magnetic nanoparticles sensitized with soluble PV receptor efficiently extracted PV pseudovirus (>99% extraction) or endogenous infectious PVs (>90% extraction) from stool extracts. This method would be useful for extraction of PV from crude biological samples.
Capnocytophaga sputigena Empyema
Authors: Li Andrew , Tambyah Paul , Chan Douglas , Leong Khoo Kay 
Published: May 2013

ABSTRACT

Empyema is a problem faced by clinicians worldwide. Most cases are caused by Gram-positive organisms, such as streptococci and staphylococci. Empyema caused by
Capnocytophaga
spp. is extremely uncommon (H. Bonatti et al., Clin. Microbiol. Infect. 9:380–387, 2003). We present a unique case of a polymicrobial empyema, with a predominance of
Capnocytophaga sputigena
, in an older patient with no history of animal bite or splenectomy.
Dissemination of Acinetobacter nosocomialis Clone among Critically Ill Patients and the Environment
Authors: Girão Valéria Brígido de Carvalho , Martins Natacha , Cacci Luciana Camila , Coelho-Souza Talita , Nouér Simone Aranha , Riley Lee W. , Moreira Beatriz Meurer 
Published: May 2013

ABSTRACT

We examined the environmental dissemination of
Acinetobacter nosocomialis
multilocus sequence typing clonal complex 260/71 in Rio de Janeiro, Brazil, including water from a dam and food samples. The increasing use of sequence based methods has demonstrated a large, previously unpredicted, dissemination of bacteria that may serve as opportunistic pathogens.
Evaluation of Five Susceptibility Test Methods for Detection of Tobramycin Resistance in a Cluster of Epidemiologically Related Acinetobacter baumannii Isolates
Authors: Moodley V. Mischka , Oliver Stephen P. , Shankland Iva , Elisha B. Gay 
Published: May 2013

ABSTRACT

Acinetobacter baumannii
is a major nosocomial pathogen causing infections in critically ill patients. This organism has acquired the propensity to rapidly develop resistance to most antibiotics. At several hospitals within Cape Town, South Africa, tobramycin and colistin are frequently the only therapeutic options. Vitek2 automated susceptibility testing (AST) is used in the clinical laboratory to determine selected susceptibility profiles. The suspicion of a possible AST-related technical error when testing for susceptibility to tobramycin in
A. baumannii
precipitated this study. Thirty-nine
A. baumannii
strains isolated from clinical specimens (June to December 2006) were included in this prospective study. Tobramycin susceptibility testing results obtained by AST, disc diffusion, the epsilometer test (Etest), and agar dilution were compared to those for broth microdilution (BMD), the reference method. The tobramycin susceptibility results revealed errors in 25/39 (64%) isolates (10 very major and 15 minor errors) when AST was compared to BMD, 12/39 (31%) (2 very major and 10 minor errors) when Etest was compared to BMD, 16/39 (41%) (3 very major and 13 minor errors) when disc diffusion was compared to BMD, and 21/39 (54%) (10 very major and 11 minor errors) when agar dilution was compared to BMD. Using PCR, we detected
aac(3)-IIa
, which is associated with tobramycin resistance, in 21/25 of the discrepant isolates. Molecular typing (using pulsed-field gel electrophoresis and repetitive sequence-based PCR [rep-PCR]) showed that these isolates were genetically related. Clinical laboratories that routinely use the Vitek2 system should consider an alternative testing method for determining susceptibility to tobramycin.
The Structure of the NTPase That Powers DNA Packaging into Sulfolobus Turreted Icosahedral Virus 2
Authors: Happonen Lotta J. , Oksanen Esko , Liljeroos Lassi , Goldman Adrian , Kajander Tommi , Butcher Sarah J. 
Published: May 2013

ABSTRACT

Biochemical reactions powered by ATP hydrolysis are fundamental for the movement of molecules and cellular structures. One such reaction is the encapsidation of the double-stranded DNA (dsDNA) genome of an icosahedrally symmetric virus into a preformed procapsid with the help of a genome-translocating NTPase. Such NTPases have been characterized in detail from both RNA and tailed DNA viruses. We present four crystal structures and the biochemical activity of a thermophilic NTPase, B204, from the nontailed, membrane-containing, hyperthermoacidophilic archaeal dsDNA virus
Sulfolobus
turreted icosahedral virus 2. These are the first structures of a genome-packaging NTPase from a nontailed, dsDNA virus with an archaeal host. The four structures highlight the catalytic cycle of B204, pinpointing the molecular movement between substrate-bound (open) and empty (closed) active sites. The protein is shown to bind both single-stranded and double-stranded nucleic acids and to have an optimum activity at 80°C and pH 4.5. The overall fold of B204 places it in the FtsK-HerA superfamily of P-loop ATPases, whose cellular and viral members have been suggested to share a DNA-translocating mechanism.
Identification of Recombination in the Envelope Gene of Simian Foamy Virus Serotype 2 Isolated from Macaca cyclopis
Authors: Galvin Teresa A. , Ahmed Imran A. , Shahabuddin Muhammad , Bryan Theodore , Khan Arifa S. 
Published: May 2013

ABSTRACTThe full-length sequence of simian foamy virus serotype 2 (SFVmcy-2), isolated from a Taiwanese macaque, was determined. SFVmcy-2 was highly related to SFV serotype 1 (SFVmcy-1), an isolate from the same species, except in the putative receptor binding domain (RBD) inenv, which contained novel sequences related to SFV serotype 3 (SFVagm-3), isolated from an African green monkey. The results identify a potential region of neutralization in SFVs and demonstrate recombination between genetically divergent foamy viruses.
Timing and frequency of chlamydia and gonorrhoea testing in a cross-sectional study of HIV postexposure prophylaxis recipients
Authors: Jamani S , Gulholm T , Poynten I M , Templeton D J 
Published: May 2013

ObjectivesAustralian HIV postexposure prophylaxis (PEP) guidelines recommendChlamydia trachomatis(CT) andNeisseria gonorrheae(NG) testing at both baseline and 2-week postexposure visits. We aimed to determine the diagnostic yield of testing at one or more visits, and predictors of infection.MethodsData were collected from patients prescribed PEP at RPA Sexual Health over a 4-year period from January 2008 to December 2011. Predictors of CT/NG were assessed by logistic regression.Results282 individuals presented for PEP on 319 occasions during the study period. The majority (94.3%) were male and over 90% of presentations followed unprotected anal sexual exposures. Most (279, 87.5%) had CT/NG testing at least once. Almost half (153, 48.0%) of baseline presentations, two-thirds (214, 67.1%) of 2-week presentations and over a quarter (88, 27.6%) of both presentations included CT/NG testing. CT/NG was diagnosed at baseline in eight (5.2%, 95% CI 2.3% to 10.0%) presentations. A new CT/NG diagnosis occurred at the 2-week visit in 18 (8.4%, 95% CI 5.1% to 13.0%) presentations, of whom 7 tested negative and 11 were not tested at baseline. Over one-quarter (28.1%) of PEP recipients reported sexual contact between baseline and 2-week visits. Independent predictors of CT/NG at baseline were recent sex work (OR 48.0, 95% CI 3.77 to 611.94); and at 2 weeks a known HIV-positive PEP exposure source (OR 3.54, 95% CI 1.04 to 12.06) and sex between baseline and 2-week visits (OR 3.63, 95% CI 1.10 to 11.96).ConclusionsOur findings suggest that screening PEP recipients for CT/NG at both baseline and 2 weeks may be warranted.
Morphological and molecular study of Californian species of the genus Aporcelaimellus Heyns, 1965 (Dorylaimida: Aporcelaimidae)
Authors: Álvarez-Ortega Sergio , Subbotin Sergei A. , Peña-Santiago Reyes 
Published: May 2013

Several species of Aporcelaimellus collected in natural areas in California, USA, are characterised on the basis of morphological, morphometric and molecular data. Two new species are identified and described here. Aporcelaimellus californicus sp. n. is characterised by its body length of 2.46-3.42 mm, lip region offset by constriction and 24-26 μm broad, odontostyle 23-24 μm long, neck 611-765 μm long, pharyngeal expansion occupying 50-52% of total neck length, a dorsal cellular mass present at level of cardia, uterus simple and 246-408 μm long, V = 53-58, short conoid tail (43-50 μm, c = 56-71, c′ = 0.8-1.0) with a large hyaline portion occupying more than half of its total length, spicules 98 μm long, and 8-9 spaced ventromedian supplements. Aporcelaimellus salicinus sp. n. is distinguished by its body length of 1.45-1.94 mm, lip region offset by deep constriction and 16-18 μm broad, odontostyle 18-20 μm long, neck 393-521 μm long, pharyngeal expansion occupying 45-51% of total neck length, presence of a dorsal cellular mass at level of cardia, uterus simple and 21-45 μm long, V = 51-57, tail conical to conoid (31-38 μm, c = 39-59, c′ = 1.0-1.4), and male unknown. Measurements, sequences and taxonomic comments are provided for the other three Aporcelaimellus species. Californian Aporcelaimellus display a notable morphological homogeneity but a remarkable molecular diversity, putting into question the monophyly of this group.
Bursaphelenchus masseyi sp. n. (Nematoda: Parasitaphelenchinae) – a nematode associate of the bark beetle, Trypophloeus populi Hopkins (Coleoptera: Curculionidae: Scolytinae), in aspen, Populus tremuloides Michx. affected by sudden aspen decline in Colorado
Authors: Tomalak Marek , Worrall James , Filipiak Anna 
Published: May 2013

Bursaphelenchus masseyi sp. n. is described from trunks of unhealthy trembling aspen, Populus tremuloides, affected by sudden aspen decline (SAD) in Colorado, USA. All propagative stages of the nematode were present in larval galleries of a bark beetle, Trypophloeus populi. The dauer juveniles occupy the haemocoel of older larvae, pupae and adult beetles. The characteristic morphology of the male spicules with small but distinct cucullus, extended anterior vulval lip in female, lateral fields with four incisures, and number and arrangement of male caudal papillae, indicate that B. masseyi sp. n. is closely related to the xylophilus group. This relation has been confirmed by DNA sequencing and phylogenetic analysis of the 28S rDNA region. The new species is characterised by the body length of 958 (765-1203) μm in female and 874 (691-1122) μm in male, moderately slender body (a = 38.2 (33.5-41.1) and 38.0 (33.1-44.1) in female and male, respectively), and spicules 29.2 (26.2-34.7) μm long with a small cucullus (1.3-1.5 μm in diam.) at their tips. Bursaphelenchus masseyi sp. n. can be separated from other species in the xylophilus group by the morphology of spicules which have a short capitulum and unique rostrum that is pointed somewhat anteriorly, relatively thick vulval flap, which is straight, parallel to the body long axis and bent towards the body wall at its distal end, and other morphological and morphometric characters. The new species most closely resembles B. trypophloei, but differs by the morphology of spicules (short but distinct condylus vs condylus in a continuous line with dorsal lamina, and smaller cucullus). The taxonomic separation of the new species is also confirmed by the unique molecular profile of the ITS region (ITS-RFLP). Diallelic cross-breeding in vitro revealed also that B. masseyi sp. n. and B. trypophloei are reproductively incompatible. The new species showed poor ability to develop and reproduce on Botrytis cinerea cultures, although it grew vigorously on laboratory cultures of Polish and Colorado isolates of Cytospora chrysosperma, the fungus naturally associated with galleries of the nematode vector, T. populi.
Rain and Water Symbolism in Southern African Religious Systems: Continuity and Change
Authors: Müller Retief , Kruger Frans 
Published: May 2013

Abstract
This article presents a diachronic perspective on rain and water rituals in southern Africa. The authors claim that contemporary rituals can only be properly understood when cognisance has been taken of their deep roots into the past. The authors indicate how water and rain rituals show signs of continuity between past and present, in spite of the dramatic upheavals created by the arrival of colonialism and missionary Christianity. The authors furthermore argue that such rituals are not only of ‘religious’ importance, but also indicative of the material concerns concerning the environment in the communal consciousness of ordinary people. The popular interest in these types of rituals may indeed be understood as the refusal by ordinary people to submit to a dominant globalisation paradigm which has a vested interest in casting them in the role of permanently helpless victims.
Upscale Effects of Deep Convection during the North American Monsoon
Authors: Stensrud David J. 
Published: May 2013

Abstract
The ability of deep monsoon convection to influence the larger-scale circulation over North America is investigated for a 6-day-long case study during the 2006 North American monsoon. Results from Rossby wave ray tracing and numerical simulations using the Advanced Research Weather Research and Forecasting model indicate that North American monsoon convection provides a source region for stationary Rossby waves. Two wave trains are seen in the numerical model simulations, with behaviors that agree well with expectations from theory and ray tracing. The shorter and faster-moving wave train moves eastward from the source region in Mexico and reaches the western Atlantic within 4 days. The longer and slower-moving wave train travels northeastward and reaches the coastal New England region within 6 days. An upstream tail of anticyclonic vorticity extends westward from the source region into the central Pacific Ocean.
The monsoon convection appears to help cut off the low-level anticyclonic flow by developing low-level southerly flow in the Gulf of Mexico and northerly flow in the eastern Pacific, as suggested in earlier global model studies. However, the stationary Rossby wave trains further alter the location and intensity of deep convection in locations remote from the monsoon. These results suggest that unless a numerical model can correctly predict monsoon convection, the ability of the model to produce accurate forecasts of the large-scale pattern and associated convective activity beyond a few days is in question. This result may be important for global climate modeling, since an inaccurate prediction of monsoon convection would lead to an inaccurate Rossby wave response.
Airborne Observations of a Catalina Eddy
Authors: Parish Thomas R. , Rahn David A. , Leon Dave 
Published: May 2013

Abstract
Summertime low-level winds over the ocean adjacent to the California coast are typically from the north, roughly parallel to the coastline. Past Point Conception the flow often turns eastward, thereby generating cyclonic vorticity in the California Bight. Clouds are frequently present when the cyclonic motion is well developed and at such times the circulation is referred to as a Catalina eddy. Onshore flow south of the California Bight associated with the eddy circulation can result in a thickening of the low-level marine stratus adjacent to the coast. During nighttime hours the marine stratus typically expands over a larger area and moves northward along the coast with the cyclonic circulation. A Catalina eddy was captured during the Precision Atmospheric Marine Boundary Layer Experiment in June of 2012. Measurements were made of the cloud structure in the marine layer and the horizontal pressure field associated with the cyclonic circulation using the University of Wyoming King Air research aircraft. Airborne measurements show that the coastal mountains to the south of Los Angeles block the flow, resulting in enhanced marine stratus heights and a local pressure maximum near the coast. The horizontal pressure field also supports a south–north movement of marine stratus. Little evidence of leeside troughing south of Santa Barbara, California, was observed for this case, implying that the horizontal pressure field is forced primarily through topographic blocking by the coastal terrain south of Los Angeles, California, and the ambient large-scale circulation associated with the mean flow.
Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing
Authors: Morin Ryan D. , Mungall Karen , Pleasance Erin , Mungall Andrew J. , Goya Rodrigo , Huff Ryan D. , Scott David W. , Ding Jiarui , Roth Andrew , Chiu Readman , Corbett Richard D. , Chan Fong Chun , Mendez-Lago Maria , Trinh Diane L. , Bolger-Munro Madison , Taylor Greg , Hadj Khodabakhshi Alireza , Ben-Neriah Susana , Pon Julia , Meissner Barbara , Woolcock Bruce , Farnoud Noushin , Rogic Sanja , Lim Emilia L. , Johnson Nathalie A. , Shah Sohrab , Jones Steven , Steidl Christian , Holt Robert , Birol Inanc , Moore Richard , Connors Joseph M. , Gascoyne Randy D. , Marra Marco A. 
Published: May 2013

Key PointsComplete genome sequence analysis of 40 DLBCL tumors and 13 cell lines reveals novel somatic point mutations, rearrangements, and fusions. Recurrence of mutations in genes involved in B-cell homing were identified in germinal center B-cell DLBCLs.