bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of a commercial MRI Linac based Monte Carlo dose calculation algorithm with geant 4
Authors: Ahmad Syed Bilal , Sarfehnia Arman , Paudel Moti Raj , Kim Anthony , Hissoiny Sami , Sahgal Arjun , Keller Brian 
Published: January 2016

Purpose:This paper provides a comparison between a fast, commercial, in‐patient Monte Carlo dose calculation algorithm (GPUMCD) and geant4. It also evaluates the dosimetric impact of the application of an external 1.5 T magnetic field.Methods:A stand‐alone version of the Elekta™ GPUMCD algorithm, to be used within the Monaco treatment planning system to model dose for the Elekta™ magnetic resonance imaging (MRI) Linac, was compared against geant4 (v10.1). This was done in the presence or absence of a 1.5 T static magnetic field directed orthogonally to the radiation beam axis. Phantoms with material compositions of water, ICRU lung, ICRU compact‐bone, and titanium were used for this purpose. Beams with 2 MeV monoenergetic photons as well as a 7 MV histogrammed spectrum representing the MRI Linac spectrum were emitted from a point source using a nominal source‐to‐surface distance of 142.5 cm. Field sizes ranged from 1.5 × 1.5 to 10 × 10 cm2. Dose scoring was performed using a 3D grid comprising 1 mm3 voxels. The production thresholds were equivalent for both codes. Results were analyzed based upon a voxel by voxel dose difference between the two codes and also using a volumetric gamma analysis.Results:Comparisons were drawn from central axis depth doses, cross beam profiles, and isodose contours. Both in the presence and absence of a 1.5 T static magnetic field the relative differences in doses scored along the beam central axis were less than 1% for the homogeneous water phantom and all results matched within a maximum of ±2% for heterogeneous phantoms. Volumetric gamma analysis indicated that more than 99% of the examined volume passed gamma criteria of 2%—2 mm (dose difference and distance to agreement, respectively). These criteria were chosen because the minimum primary statistical uncertainty in dose scoring voxels was 0.5%. The presence of the magnetic field affects the dose at the interface depending upon the density of the material on either sides of the interface. This effect varies with the field size. For example, at the water‐lung interface a 33.94% increase in dose was observed (relative to the Dmax), by both GPUMCD and geant4 for the field size of 2 × 2 cm2 (compared to no B‐field case), which increased to 47.83% for the field size of 5 × 5 cm2 in the presence of the magnetic field. Similarly, at the lung‐water interface, the dose decreased by 19.21% (relative to Dmax) for a field size of 2 × 2 cm2 and by 30.01% for 5 × 5 cm2 field size. For more complex combinations of materials the dose deposition also becomes more complex.Conclusions:The GPUMCD algorithm showed good agreement against geant4 both in the presence and absence of a 1.5 T external magnetic field. The application of 1.5 T magnetic field significantly alters the dose at the interfaces by either increasing or decreasing the dose depending upon the density of the material on either side of the interfaces.
Patterns and Determinants of Physical Inactivity in Rural and Urban Areas in Peru: A Population-Based Study
Authors: Miranda J. Jaime , Carrillo-Larco Rodrigo M. , Gilman Robert H , Avilez Jose L. , Smeeth Liam , Checkley William , Bernabe-Ortiz Antonio , _ _ 
Published: January 2016

Background:Physical inactivity and sedentary behaviors have been linked with impaired health outcomes. Establishing the physical inactivity profiles of a given population is needed to establish program targets and to contribute to international monitoring efforts. We report the prevalence of, and explore sociodemographical and built environment factors associated with physical inactivity in 4 resource-limited settings in Peru: rural Puno, urban Puno, Pampas de San Juan de Miraflores (urban), and Tumbes (semiurban).Methods:Cross-sectional analysis of the CRONICAS Cohort Study’s baseline assessment. Outcomes of interest were physical inactivity of leisure time (<600 MET-min/week) and transport-related physical activity (not reporting walking or cycling trips) domains of the IPAQ, as well as watching TV, as a proxy of sedentarism (≥2 hours per day). Exposures included demographic factors and perceptions about neighborhood’s safety. Associations were explored using Poisson regression models with robust standard errors. Prevalence ratios (PR) and 95% confidence intervals (95% CI) are presented.Results:Data from 3593 individuals were included: 48.5% males, mean age 55.1 (SD: 12.7) years. Physical inactivity was present at rates of 93.7% (95% CI 93.0%–94.5%) and 9.3% (95% CI 8.3%–10.2%) within the leisure time and transport domains, respectively. In addition, 41.7% (95% CI 40.1%–43.3%) of participants reported watching TV for more than 2 hours per day. Rates varied according to study settings (P < .001). In multivariable analysis, being from rural settings was associated with 3% higher prevalence of leisure time physical inactivity relative to highly urban Lima. The pattern was different for transport-related physical inactivity: both Puno sites had around 75% to 50% lower prevalence of physical inactivity. Too much traffic was associated with higher levels of transport-related physical inactivity (PR = 1.24; 95% CI 1.01–1.54).Conclusions:Our study showed high levels of inactivity and marked contrasting patterns by rural/urban sites. These findings highlight the need to generate synergies to expand nationwide physical activity surveillance systems.
Complete Genome Sequence of Serratia marcescens SmUNAM836, a Nonpigmented Multidrug-Resistant Strain Isolated from a Mexican Patient with Obstructive Pulmonary Disease
Authors: Sandner-Miranda Luisa , Vinuesa Pablo , Soberón-Chávez Gloria , Morales-Espinosa Rosario 
Published: January 2016

ABSTRACT

Serratia marcescens
SmUNAM836 is a multidrug-resistant clinical strain isolated in Mexico City from a patient with chronic obstructive pulmonary disease. Its complete genome sequence was determined using PacBio RS II SMRT technology, consisting of a 5.2-Mb chromosome and a 26.3-kb plasmid, encoding multiple resistance determinants and virulence factors.
Genome Sequence of a
Clostridium neonatale
Strain Isolated in a Canadian Neonatal Intensive Care Unit
Authors: Benamar Samia , Cassir Nadim , La Scola Bernard 
Published: January 2016

ABSTRACT

Clostridium neonatale
is a Gram-positive endospore-forming obligate anaerobe first isolated from the feces of premature neonates during an intensive care unit outbreak of necrotizing enterocolitis (NEC) in a Canadian neonatal intensive care unit. Here, we announce the genome draft sequence of this bacterium. It is composed of 4,710,818 bp and contains 4,169 protein-coding genes and 80 RNA genes, including 11 rRNA genes.
Revised Genome Sequence of the Purple Photosynthetic Bacterium
Blastochloris viridis
Authors: Liu Lu-Ning , Faulkner Matthew , Liu Xuan , Huang Fang , Darby Alistair C. , Hall Neil 
Published: January 2016

ABSTRACT

Blastochloris viridis
is a unique anaerobic, phototrophic purple bacterium that produces bacteriochlorophyll
b
. Here we report an improved genome sequence of
Blastochloris viridis
DSM133, which is instrumental to the studies of photosynthesis, metabolic versatility, and genetic engineering of this microorganism.
Genome Sequences of Murine Pneumotropic Virus (
Polyomaviridae
) Detected in Wild House Mice (Mus musculus)
Authors: Ben Salem Nicole , Moens Ugo , Ehlers Bernhard 
Published: January 2016

ABSTRACT

Using generic PCR, we identified a variant of murine pneumotropic virus (MptV) (family
Polyomaviridae
) in 3 wild house mice (
Mus musculus
). The fully amplified and sequenced genomes display considerable differences from the MptV genomes published previously and enlighten us on the natural diversity of rodent polyomaviruses.
Complete Genome Sequence of the Highly Virulent Aeromonas schubertii Strain WL1483, Isolated from Diseased Snakehead Fish (
Channa argus
) in China
Authors: Liu Lihui , Li Ningqiu , Zhang Defeng , Fu Xiaozhe , Shi Cunbin , Lin Qiang , Hao Guijie 
Published: January 2016

ABSTRACT

We sequenced the complete genome of the highly virulent
Aeromonas schubertii
strain WL1483, which was isolated from diseased snakehead fish (
Channa argus
) in China. The full genome sequence of
A. schubertii
WL1483 is 4,400,034 bp, which encodes 4,376 proteins and contains 195 predicted RNA genes.
Draft Genome Sequence of a 94-Year-Old Listeria monocytogenes Isolate, SLCC208
Authors: Hyden Patrick , Pietzka Ariane , Allerberger Franz , Springer Burkhard , Sensen Christoph , Ruppitsch Werner 
Published: January 2016

ABSTRACT

We report here the draft genome sequence of
Listeria monocytogenes
strain SLCC208 from Seeliger's historical Special
Listeria
Culture Collection, initially cultured from a human case in France in 1921. This is, to our knowledge, the oldest
L. monocytogenes
isolate available and may be useful for comparative genomic studies of
L. monocytogenes
.
Draft Genome Sequence of
Halomonas
sp. HG01, a Polyhydroxyalkanoate-Accumulating Strain Isolated from Peru
Authors: Cardinali-Rezende Juliana , Nahat Rafael Augusto Teodoro Pereira de Souza , Guzmán Moreno César Wilber , Carreño Farfán Carmen Rosa , Silva Luiziana Ferreira , Taciro Marilda Keico , Gomez José Gregório Cabrera 
Published: January 2016

ABSTRACT

Halomonas
sp. strain HG01, isolated from a salt mine in Peru, is a halophilic aerobic heterotrophic bacterium accumulating poly-3-hydroxybutyrate and poly(3-hydroxybutyrate-
co
-3-hydroxyvalerate) from different carbon sources. Here, we report the draft genome sequence of this isolate, which was found to be 3,665,487 bp long, with a G+C content of 68%.
Draft Genome Sequence of Mycobacterium tuberculosis KT-0192, Isolated in South Korea
Authors: Lee Sanghyun , Han Seung Jung , Kwon Taesoo , Yoo Won Gi , Yun Mi-ran , Lee Jong Seok , Kim Dae-Won 
Published: January 2016

ABSTRACT

We report the draft genome sequence of totally drug-resistant (XDR)
Mycobacterium tuberculosis
KT-0192. This sequence will provide new insights into the main cause and evolution of drug resistance in
M. tuberculosis
KT-0192.
Whole-Genome Sequence of Francisella noatunensis subsp.
orientalis
Strain FNO01 Isolated from Diseased Nile Tilapia in Brazil
Authors: Figueiredo H. C. P. , Leal C. A. G. , Pereira F. L. , Soares S. C. , Gonçalves L. A. , Dorella F. A. , Carvalho A. F. , Azevedo V. A. C. 
Published: January 2016

ABSTRACT

This paper describes the complete genome sequence of
Francisella noatunensis
subsp.
orientalis
strain FNO01, which was isolated during the first outbreak of francisellosis in cultured Nile tilapia in Brazil. The genome is composed of a circular chromosome with 1,859,830 bp and a G+C content of ~32%.
Draft Genome Sequence of Erythromycin- and Oxytetracycline-Sensitive Nocardia seriolae Strain U-1 (NBRC 110359)
Authors: Imajoh Masayuki , Sukeda Masaki , Shimizu Masato , Yamane Jin , Ohnishi Kouhei , Oshima Syun-ichirou 
Published: January 2016

ABSTRACT

In Japan, the emergence of macrolide- and oxytetracycline-resistant strains of
Nocardia seriolae
has previously been reported. Here, we describe the draft genome sequence of
N. seriolae
strain U-1, isolated in 2011 from a diseased yellowtail in Kagoshima Prefecture. The draft genome does not have any genes responsible for macrolide and tetracycline resistance.
Draft Genome Sequence of
Marinobacter
sp. Strain P4B1, an Electrogenic Perchlorate-Reducing Strain Isolated from a Long-Term Mixed Enrichment Culture of Marine Bacteria
Authors: Stepanov Victor G. , Xiao Yeyuan , Lopez April J. , Roberts Deborah J. , Fox George E. 
Published: January 2016

ABSTRACT

The perchlorate-reducing strain
Marinobacter
sp. strain P4B1 was isolated from a long-term perchlorate-degrading enrichment culture seeded with marine sediment. The draft genome of
Marinobacter
sp. P4B1 is comprised of the bacterial chromosome (3.60 Mbp, G+C 58.51%, 3,269 predicted genes) and its associated plasmid pMARS01 (0.14 Mbp, G+C 52.95%, 165 predicted genes).
Whole-Genome Sequencing of Salmonella enterica subsp.
enterica
Serovar Ouakam Isolated from Ground Turkey
Authors: Marasini Daya , Abo-Shama Usama H. , Fakhr Mohamed K. 
Published: January 2016

ABSTRACT

In this report, we announce the first whole-genome sequencing of
Salmonella enterica
subsp.
enterica
serovar Ouakam strain GNT-01, isolated from ground turkey retail meat. The strain has a chromosome of 5,088,451 bp long, with a G+C content of 52.3%, and a plasmid of 109,715 bp.
Genome Sequences of Two Pseudorabies Virus Strains Isolated in Greece
Authors: Papageorgiou Konstantinos V. , Suárez Nicolás M. , Wilkie Gavin S. , Filioussis George , Papaioannou Nikolaos , Nauwynck Hans J. , Davison Andrew J. , Kritas Spyridon K. 
Published: January 2016

ABSTRACT

Pseudorabies virus (species
Suid herpesvirus 1
) belongs to the genus
Varicellovirus
, subfamily
Alphaherpesvirinae
, family
Herpesviridae
, and is the causative agent of an acute and frequently fatal disease that affects mainly pigs. Here, we report the genome sequences of two strains of this virus isolated in Greece in 2010.
Two Populations of Viral Minichromosomes Are Present in a Geminivirus-Infected Plant Showing Symptom Remission (Recovery)
Authors: Ceniceros-Ojeda Esther Adriana , Rodríguez-Negrete Edgar Antonio , Rivera-Bustamante Rafael Francisco 
Published: January 2016

ABSTRACT
Geminiviruses are important plant pathogens characterized by circular, single-stranded DNA (ssDNA) genomes. However, in the nuclei of infected cells, viral double-stranded DNA (dsDNA) associates with host histones to form a minichromosome. In phloem-limited geminiviruses, the characterization of viral minichromosomes is hindered by the low concentration of recovered complexes due to the small number of infected cells. Nevertheless, geminiviruses are both inducers and targets of the host posttranscriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) machinery. We have previously characterized a “recovery” phenomenon observed in pepper plants infected with pepper golden mosaic virus (PepGMV) that is associated with a reduction of viral DNA and RNA levels, the presence of virus-related siRNAs, and an increase in the levels of viral DNA methylation. Initial micrococcal nuclease-based assays pinpointed the presence of different viral chromatin complexes in symptomatic and recovered tissues. Using the pepper-PepGMV system, we developed a methodology to obtain a viral minichromosome-enriched fraction that does not disturb the basic chromatin structural integrity, as evaluated by the detection of core histones. Using this procedure, we have further characterized two populations of viral minichromosomes in PepGMV-infected plants. After further purification using sucrose gradient sedimentation, we also observed that minichromosomes isolated from symptomatic tissue showed a relaxed conformation (based on their sedimentation rate), are associated with a chromatin activation marker (H3K4me3), and present a low level of DNA methylation. The minichromosome population obtained from recovered tissue, on the other hand, sedimented as a compact structure, is associated with a chromatin-repressive marker (H3K9me2), and presents a high level of DNA methylation.

IMPORTANCE
Viral minichromosomes have been reported in several animal and plant models. However, in the case of geminiviruses, there has been some recent discussion about the importance of this structure and the significance of the epigenetic modifications that it can undergo during the infective cycle. Major problems in this type of studies are the low concentration of these complexes in an infected plant and the asynchronicity of infected cells along the process; therefore, the complexes isolated in a given moment usually represent a mixture of cells at different infection stages. The recovery process observed in PepGMV-infected plants and the isolation procedure described here provide two distinct populations of minichromosomes that will allow a more precise characterization of the modifications of viral DNA and its host proteins associated along the infective cycle. This structure could be also an interesting model to study several processes involving plant chromatin.
Role of Mitochondrial Membrane Spherules in Flock House Virus Replication
Authors: Short James R. , Speir Jeffrey A. , Gopal Radhika , Pankratz Logan M. , Lanman Jason , Schneemann Anette 
Published: January 2016

ABSTRACT

Viruses that generate double-stranded RNA (dsRNA) during replication must overcome host defense systems designed to detect this infection intermediate. All positive-sense RNA viruses studied to date modify host membranes to help facilitate the sequestration of dsRNA from host defenses and concentrate replication factors to enhance RNA production. Flock House virus (FHV) is an attractive model for the study of these processes since it is well characterized and infects
Drosophila
cells, which are known to have a highly effective RNA silencing system. During infection, FHV modifies the outer membrane of host mitochondria to form numerous membrane invaginations, called spherules, that are ∼50 nm in diameter and known to be the site of viral RNA replication. While previous studies have outlined basic structural features of these invaginations, very little is known about the mechanism underlying their formation. Here we describe the optimization of an experimental system for the analysis of FHV host membrane modifications using crude mitochondrial preparations from infected
Drosophila
cells. These preparations can be programmed to synthesize both single- and double-stranded FHV RNA. The system was used to demonstrate that dsRNA is protected from nuclease digestion by virus-induced membrane invaginations and that spherules play an important role in stimulating RNA replication. Finally, we show that spherules generated during FHV infection appear to be dynamic as evidenced by their ability to form or disperse based on the presence or absence of RNA synthesis.

IMPORTANCE
It is well established that positive-sense RNA viruses induce significant membrane rearrangements in infected cells. However, the molecular mechanisms underlying these rearrangements, particularly membrane invagination and spherule formation, remain essentially unknown. How the formation of spherules enhances viral RNA synthesis is also not understood, although it is assumed to be partly a result of evading host defense pathways. To help interrogate some of these issues, we optimized a cell-free replication system consisting of mitochondria isolated from Flock House virus-infected
Drosophila
cells for use in biochemical and structural studies. Our data suggest that spherules generated during Flock House virus replication are dynamic, protect double-stranded RNA, and enhance RNA replication in general. Cryo-electron microscopy suggests that the samples are amenable to detailed structural analyses of spherules engaged in RNA synthesis. This system thus provides a foundation for understanding the molecular mechanisms underlying spherule formation, maintenance, and function during positive-sense viral RNA replication.
Codon Deletions in the Influenza A Virus PA Gene Generate Temperature-Sensitive Viruses
Authors: Meyer Léa , Sausset Alix , Sedano Laura , Da Costa Bruno , Le Goffic Ronan , Delmas Bernard 
Published: January 2016

ABSTRACT

The influenza virus RNA-dependent RNA polymerase, which is composed of three subunits, PB1, PB2, and PA, catalyzes genome replication and transcription within the cell nucleus. The PA linker (residues 197 to 256) can be altered by nucleotide substitutions to engineer temperature-sensitive (
ts
), attenuated mutants that display a defect in the transport of the PA–PB1 complex to the nucleus at a restrictive temperature. In this study, we investigated the ability of the PA linker to tolerate deletion mutations for further
in vitro
and
in vivo
characterization. Four viable mutants with single-codon deletions were generated; all of them exhibited a
ts
phenotype that was associated with the reduced efficiency of replication/transcription of a pseudoviral reporter RNA in a minireplicon assay. Using fluorescently tagged PB1, we observed that the deletion mutants did not efficiently recruit PB1 to reach the nucleus at a restrictive temperature (39.5°C). Mouse infections showed that the four mutants were attenuated and induced antibodies that were able to protect mice from challenge with a lethal homologous wild-type virus. Serial
in vitro
passages of two deletion mutants at 39.5°C and 37°C did not allow the restoration of a wild-type phenotype among virus progeny. Thus, our results identify codons that can be deleted in the PA gene to engineer genetically stable
ts
mutants that could be used to design novel attenuated vaccines.

IMPORTANCE
In order to generate genetically stable live influenza A virus vaccines, we constructed viruses with single-codon deletions in a discrete domain of the RNA polymerase PA gene. The four rescued viruses exhibited a temperature-sensitive phenotype that we found was associated with a defect in the transport of the PA–PB1 dimer to the nucleus, where viral replication occurs. These
ts
deletion mutants were shown to be attenuated and to be able to produce antibodies in mice and to protect them from a lethal challenge. Assays to select revertants that were able to grow efficiently at a restrictive temperature failed, showing that these deletion mutants are genetically more stable than conventional substitution mutants. These results are of interest for the design of genetically stable live influenza virus vaccines.
ReducedCD300LGmRNA tissue expression, increased intramyocellular lipid content and impaired glucose metabolism in healthy male carriers of Arg82Cys inCD300LG: a novel genometabolic cross-link betweenCD300LGand common metabolic phenotypes
Authors: Støy Julie , Kampmann Ulla , Mengel Annette , Magnusson Nils E , Jessen Niels , Grarup Niels , Rungby Jørgen , Stødkilde-Jørgensen Hans , Brandslund Ivan , Christensen Cramer , Hansen Torben , Pedersen Oluf , Møller Niels 
Published: January 2016

BackgroundCD300LGrs72836561 (c.313C>T, p.Arg82Cys) has in genetic-epidemiological studies been associated with the lipoprotein abnormalities of the metabolic syndrome.CD300LGbelongs to the CD300-family of membrane-bound molecules which have the ability to recognize and interact with extracellular lipids. We tested whether this specific polymorphism results in abnormal lipid accumulation in skeletal muscle and liver and other indices of metabolic dysfunction.Methods40 healthy men with a mean age of 55 years were characterized metabolically including assessment of insulin sensitivity by the hyperinsulinemic euglycemic clamp, intrahepatic lipid content (IHLC) and intramyocellular lipid content (IMCL) by MR spectroscopy, and β-cell function by an intravenous glucose tolerance test. Changes in insulin signaling andCD300LGmRNA expression were determined by western blotting and quantitative PCR in muscle and adipose tissue.ResultsCompared with the 20 controls (CC carriers), the 20 CT carriers (polymorphism carriers) had higher IMCL (p=0.045), a reduced fasting forearm glucose uptake (p=0.011), a trend toward lower M-values during the clamp; 6.0 mg/kg/min vs 7.1 (p=0.10), and higher IHLC (p=0.10). CT carriers had lowerCD300LGmRNA expression andCD300LGexpression in muscle correlated with IMCL (β=−0.35, p=0.046), forearm glucose uptake (β=0.37, p=0.03), and tended to correlate with the M-value (β=0.33, p=0.06), independently ofCD300LGgenotype. β-cell function was unaffected.ConclusionsTheCD300LGpolymorphism was associated with decreasedCD300LGmRNA expression in muscle and adipose tissue, increased IMCL, and abnormalities of glucose metabolism.CD300LGmRNA levels correlated with IMCL and forearm glucose uptake. These findings link a specificCD300LGpolymorphism with features of the metabolic syndrome suggesting a role forCD300LGin the regulation of common metabolic traits.Trial registration numberNCT01571609.