bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sensitivity of volumetric modulated arc therapy patient specific QA results to multileaf collimator errors and correlation to dose volume histogram based metrics
Authors: Coleman Linda , Skourou Christina 
Published: October 2013

Purpose:This study investigates the impact of systematic multileaf collimator (MLC) positional errors on gamma analysis results used for quality assurance (QA) of Rapidarc treatments. In addition, this study evaluates the relationship of these gamma analysis results and clinical dose volume histogram metrics (DVH) for Rapidarc treatment plans.Methods:Five prostate plans were modified by the introduction of systematic MLC errors. The MLC shifts to each individual active leaf introduced were 0.25, 0.5, 0.75, and 1 mm. All QA verification plans were delivered and estimated 3D patient dose or high density phantom dose were obtained based on the ArcCHECK measurement files. QA gamma analysis of 3%/3 mm and 2%/2 mm were implemented and relationships to dose differences in DVH metrics encountered due to MLC errors were determined. Tolerances of 3% and 5% for DVH metric were implemented to determine the sensitivity of gamma analysis to MLC errors. A calculation of sensitivity was determined from the number of incidences of false negative and false positive cases in gamma analysis results.Results:The sensitivity of global gamma analysis for criteria of 3%/3 mm was 0.78 and for 2%/2 mm was 0.82. A number of instances occurred for an acceptable VMAT QA gamma index which did not indicate a DVH metric dose error greater than 5%. The correlation between global gamma analysis using criteria 3%/3 mm and DVH metric dose error were all <0.8 indicating less than a strong correlation.Conclusions:There is a greater sensitivity for detection of dosimetric errors occurring in a Rapidarc plan using gamma criteria of 2%/2 mm than 3%/3 mm. However, there is lack of consistently strong correlation between global gamma indexes and clinical DVH metrics for PTV and bladder and rectum for Rapidarc plans. It is recommended that the sole use of gamma index for Rapidarc QA plan evaluation could be insufficient and a methodology for evaluation of delivered dose to patient is required.
Analysis of Magnetosome Chains in Magnetotactic Bacteria by Magnetic Measurements and Automated Image Analysis of Electron Micrographs
Authors: Katzmann E. , Eibauer M. , Lin W. , Pan Y. , Plitzko J. M. , Schüler D. 
Published: October 2013

ABSTRACT

Magnetotactic bacteria (MTB) align along the Earth's magnetic field by the activity of intracellular magnetosomes, which are membrane-enveloped magnetite or greigite particles that are assembled into well-ordered chains. Formation of magnetosome chains was found to be controlled by a set of specific proteins in
Magnetospirillum gryphiswaldense
and other MTB. However, the contribution of abiotic factors on magnetosome chain assembly has not been fully explored. Here, we first analyzed the effect of growth conditions on magnetosome chain formation in
M. gryphiswaldense
by electron microscopy. Whereas higher temperatures (30 to 35°C) and high oxygen concentrations caused increasingly disordered chains and smaller magnetite crystals, growth at 20°C and anoxic conditions resulted in long chains with mature cuboctahedron-shaped crystals. In order to analyze the magnetosome chain in electron microscopy data sets in a more quantitative and unbiased manner, we developed a computerized image analysis algorithm. The collected data comprised the cell dimensions and particle size and number as well as the intracellular position and extension of the magnetosome chain. The chain analysis program (CHAP) was used to evaluate the effects of the genetic and growth conditions on magnetosome chain formation. This was compared and correlated to data obtained from bulk magnetic measurements of wild-type (WT) and mutant cells displaying different chain configurations. These techniques were used to differentiate mutants due to magnetosome chain defects on a bulk scale.
Regulation of Dual Glycolytic Pathways for Fructose Metabolism in Heterofermentative Lactobacillus panis PM1
Authors: Kang Tae Sun , Korber Darren R. , Tanaka Takuji 
Published: October 2013

ABSTRACT

Lactobacillus panis
PM1 belongs to the group III heterofermentative lactobacilli that use the 6-phosphogluconate/phosphoketolase (6-PG/PK) pathway as their central metabolic pathway and are reportedly unable to grow on fructose as a sole carbon source. We isolated a variant PM1 strain capable of sporadic growth on fructose medium and observed its distinctive characteristics of fructose metabolism. The end product pattern was different from what is expected in typical group III lactobacilli using the 6-PG/PK pathway (i.e., more lactate, less acetate, and no mannitol). In addition,
in silico
analysis revealed the presence of genes encoding most of critical enzymes in the Embden-Meyerhof (EM) pathway. These observations indicated that fructose was metabolized via two pathways. Fructose metabolism in the PM1 strain was influenced by the activities of two enzymes, triosephosphate isomerase (TPI) and glucose 6-phosphate isomerase (PGI). A lack of TPI resulted in the intracellular accumulation of dihydroxyacetone phosphate (DHAP) in PM1, the toxicity of which caused early growth cessation during fructose fermentation. The activity of PGI was enhanced by the presence of glyceraldehyde 3-phosphate (GAP), which allowed additional fructose to enter into the 6-PG/PK pathway to avoid toxicity by DHAP. Exogenous TPI gene expression shifted fructose metabolism from heterolactic to homolactic fermentation, indicating that TPI enabled the PM1 strain to mainly use the EM pathway for fructose fermentation. These findings clearly demonstrate that the balance in the accumulation of GAP and DHAP determines the fate of fructose metabolism and the activity of TPI plays a critical role during fructose fermentation via the EM pathway in
L. panis
PM1.
Sequence-Based Analysis of the Intestinal Microbiota of Sows and Their Offspring Fed Genetically Modified Maize Expressing a Truncated Form of Bacillus thuringiensis Cry1Ab Protein (Bt Maize)
Authors: Buzoianu Stefan G. , Walsh Maria C. , Rea Mary C. , Quigley Lisa , O'Sullivan Orla , Cotter Paul D. , Ross R. Paul , Gardiner Gillian E. , Lawlor Peadar G. 
Published: October 2013

ABSTRACT

The aim was to investigate transgenerational effects of feeding genetically modified (GM) maize expressing a truncated form of
Bacillus thuringiensis
Cry1Ab protein (Bt maize) to sows and their offspring on maternal and offspring intestinal microbiota. Sows were assigned to either non-GM or GM maize dietary treatments during gestation and lactation. At weaning, offspring were assigned within sow treatment to non-GM or GM maize diets for 115 days, as follows: (i) non-GM maize-fed sow/non-GM maize-fed offspring (non-GM/non-GM), (ii) non-GM maize-fed sow/GM maize-fed offspring (non-GM/GM), (iii) GM maize-fed sow/non-GM maize-fed offspring (GM/non-GM), and (iv) GM maize-fed sow/GM maize-fed offspring (GM/GM). Offspring of GM maize-fed sows had higher counts of fecal total anaerobes and
Enterobacteriaceae
at days 70 and 100 postweaning, respectively. At day 115 postweaning, GM/non-GM offspring had lower ileal
Enterobacteriaceae
counts than non-GM/non-GM or GM/GM offspring and lower ileal total anaerobes than pigs on the other treatments. GM maize-fed offspring also had higher ileal total anaerobe counts than non-GM maize-fed offspring, and cecal total anaerobes were lower in non-GM/GM and GM/non-GM offspring than in those from the non-GM/non-GM treatment. The only differences observed for major bacterial phyla using 16S rRNA gene sequencing were that fecal
Proteobacteria
were less abundant in GM maize-fed sows prior to farrowing and in offspring at weaning, with fecal
Firmicutes
more abundant in offspring. While other differences occurred, they were not observed consistently in offspring, were mostly encountered for low-abundance, low-frequency bacterial taxa, and were not associated with pathology. Therefore, their biological relevance is questionable. This confirms the lack of adverse effects of GM maize on the intestinal microbiota of pigs, even following transgenerational consumption.
Microbial Ecology Dynamics during Rye and Wheat Sourdough Preparation
Authors: Ercolini Danilo , Pontonio Erica , De Filippis Francesca , Minervini Fabio , La Storia Antonietta , Gobbetti Marco , Di Cagno Raffaella 
Published: October 2013

ABSTRACT

The bacterial ecology during rye and wheat sourdough preparation was described by 16S rRNA gene pyrosequencing. Viable plate counts of presumptive lactic acid bacteria, the ratio between lactic acid bacteria and yeasts, the rate of acidification, a permutation analysis based on biochemical and microbial features, the number of operational taxonomic units (OTUs), and diversity indices all together demonstrated the maturity of the sourdoughs during 5 to 7 days of propagation. Flours were mainly contaminated by metabolically active genera (
Acinetobacter
,
Pantoea
,
Pseudomonas
,
Comamonas
,
Enterobacter
,
Erwinia
, and
Sphingomonas
) belonging to the phylum
Proteobacteria
or
Bacteroidetes
(genus
Chryseobacterium
). Their relative abundances varied with the flour. Soon after 1 day of propagation, this population was almost completely inhibited except for the
Enterobacteriaceae
. Although members of the phylum
Firmicutes
were present at very low or intermediate relative abundances in the flours, they became dominant soon after 1 day of propagation. Lactic acid bacteria were almost exclusively representative of the
Firmicutes
by this time.
Weissella
spp. were already dominant in rye flour and stably persisted, though they were later flanked by the
Lactobacillus sakei
group. There was a succession of species during 10 days of propagation of wheat sourdoughs. The fluctuation between dominating and subdominating populations of
L. sakei
group,
Leuconostoc
spp.,
Weissella
spp., and
Lactococcus lactis
was demonstrated. Other subdominant species such as
Lactobacillus plantarum
were detectable throughout propagation. As shown by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis,
Saccharomyces cerevisiae
dominated throughout the sourdough propagation. Notwithstanding variations due to environmental and technology determinants, the results of this study represent a clear example of how the microbial ecology evolves during sourdough preparation.
Draft Genome Sequence of Xylella fastidiosa subsp.
multiplex
Strain Griffin-1 from
Quercus rubra
in Georgia
Authors: Chen Jianchi , Huang Hong , Chang Chung-Jan , Stenger Drake C. 
Published: October 2013

ABSTRACT

The draft genome sequence of
Xylella fastidiosa
subsp.
multiplex
strain Griffin-1, isolated from a red oak tree (
Quercus rubra
) in Georgia, is reported here. The bacterium has a genome size of 2,387,314 bp, with a G+C content of 51.7%. The Griffin-1 strain genome contains 2,903 predicted open reading frames and 50 RNA genes.
Draft Genome Sequence of Bacillus thuringiensis var.
thuringiensis
Strain T01-328, a Brazilian Isolate That Produces a Soluble Pesticide Protein, Cry1Ia
Authors: Varani Alessandro M. , Lemos Manoel V. F. , Fernandes Camila C. , Lemos Eliana G. M. , Alves Eliane C. C. , Desidério Janete A. 
Published: October 2013

ABSTRACT

Bacillus thuringiensis
var.
thuringiensis
strain T01-328, isolated from Cubatão county (São Paulo State, Brazil), produces a soluble pesticide protein, Cry1Ia, during vegetative growth. Here, we report the 7.089-Mbp draft genome sequence, composed of a 5.5-Mb chromosome and 14 plasmids, which is the largest
B. thuringiensis
genome sequenced to date.
Evolutionary Analysis of Burkholderia pseudomallei Identifies Putative Novel Virulence Genes, Including a Microbial Regulator of Host Cell Autophagy
Authors: Singh Arvind Pratap , Lai Shu-chin , Nandi Tannistha , Chua Hui Hoon , Ooi Wen Fong , Ong Catherine , Boyce John D. , Adler Ben , Devenish Rodney J. , Tan Patrick 
Published: October 2013

ABSTRACT

Burkholderia pseudomallei
, the causative agent of melioidosis, contains a large pathogen genome (7.2 Mb) with ∼2,000 genes of putative or unknown function. Interactions with potential hosts and environmental factors may induce rapid adaptations in these
B. pseudomallei
genes, which can be discerned through evolutionary analysis of multiple
B. pseudomallei
genomes. Here we show that several previously uncharacterized
B. pseudomallei
genes bearing genetic signatures of rapid adaptation (positive selection) can induce diverse cellular phenotypes when expressed in mammalian cells. Notably, several of these phenotypes are plausibly related to virulence, including multinuclear giant cell formation, apoptosis, and autophagy induction. Specifically, we show that
BPSS0180
, a type VI cluster-associated gene, is capable of inducing autophagy in both phagocytic and nonphagocytic mammalian cells. Following infection of macrophages, a
B. pseudomallei
mutant disrupted in
BPSS0180
exhibited significantly decreased colocalization with LC3 and impaired intracellular survival; these phenotypes were rescued by introduction of an intact
BPSS0180
gene. The results suggest that
BPSS0180
may be a novel inducer of host cell autophagy that contributes to
B. pseudomallei
intracellular growth. More generally, our study highlights the utility of applying evolutionary principles to microbial genomes to identify novel virulence genes.
Structural and Functional Studies of gpX of Escherichia coli Phage P2 Reveal a Widespread Role for LysM Domains in the Baseplates of Contractile-Tailed Phages
Authors: Maxwell Karen L. , Fatehi Hassanabad Mostafa , Chang Tom , Pirani Nawaz , Bona Diane , Edwards Aled M. , Davidson Alan R. 
Published: October 2013

ABSTRACT

A variety of bacterial pathogenicity determinants, including the type VI secretion system and the virulence cassettes from
Photorhabdus
and
Serratia
, share an evolutionary origin with contractile-tailed myophages. The well-characterized
Escherichia coli
phage P2 provides an excellent system for studies related to these systems, as its protein composition appears to represent the “minimal” myophage tail. In this study, we used nuclear magnetic resonance (NMR) spectroscopy to determine the solution structure of gpX, a 68-residue tail baseplate protein. Although the sequence and structure of gpX are similar to those of LysM domains, which are a large family associated with peptidoglycan binding, we did not detect a peptidoglycan-binding activity for gpX. However, bioinformatic analysis revealed that half of all myophages, including all that possess phage T4-like baseplates, encode a tail protein with a LysM-like domain, emphasizing a widespread role for this domain in baseplate function. While phage P2 gpX comprises only a single LysM domain, many myophages display LysM domain fusions with other tail proteins, such as the DNA circulation protein found in Mu-like phages and gp53 of T4-like phages. Electron microscopy of P2 phage particles with an incorporated gpX-maltose binding protein fusion revealed that gpX is located at the top of the baseplate, near the junction of the baseplate and tail tube. gpW, the orthologue of phage T4 gp25, was also found to localize to this region. A general colocalization of LysM-like domains and gpW homologues in diverse phages is supported by our bioinformatic analysis.
Interactions of NBU1 IntN1 and Orf2x Proteins with Attachment Site DNA
Authors: Wood Margaret M. , Rajeev Lara , Gardner Jeffrey F. 
Published: October 2013

ABSTRACT

NBU1 is a mobilizable transposon found in
Bacteroides
spp. Mobilizable transposons require gene products from coresident conjugative transposons for excision and transfer to recipient cells. The integration of NBU1 requires IntN1, which has been identified as a tyrosine recombinase, as well as
Bacteroides
host factor BHFa. Excision of NBU1 is a more complicated process, involving five element-encoded proteins (IntN1, Orf2, Orf2x, Orf3, and PrmN1) as well as a
Bacteroides
host factor and a
cis
-acting DNA sequence. Little has been known about what role the proteins play in excision, although IntN1 and Orf2x have been shown to be the only proteins absolutely required for detectable excision. To determine where IntN1 and Orf2x bind during the excision of NBU1, both proteins were partially purified and tested in DNase I footprinting experiments with the excisive attachment sites
attL
and
attR
. The results demonstrate that IntN1 binds to four core-type sites that flank the region of cleavage and strand exchange, as well as six arm-type sites. A unique feature of the system is the location of DR2a and DR2b arm-type sites immediately downstream of the
attL
core. The DR1a, DR1b, DR3a, and DR3b arm-type sites were shown to be required for
in vitro
integration of NBU1. In addition, we have identified one Orf2x binding site (O1) on
attL
as well as a dA+dT-rich upstream element that is required for Orf2x interactions with O1.
Identification and Characterization of Novel Helicobacter pylori apo-Fur-Regulated Target Genes
Authors: Carpenter Beth M. , Gilbreath Jeremy J. , Pich Oscar Q. , McKelvey Ann M. , Maynard Ernest L. , Li Zhao-Zhang , Merrell D. Scott 
Published: October 2013

ABSTRACT

In
Helicobacter pylori
, the ferric uptake regulator (Fur) has evolved additional regulatory functions not seen in other bacteria; it can repress and activate different groups of genes in both its iron-bound and
apo
forms. Because little is understood about the process of
apo
-Fur repression and because only two
apo
-Fur-repressed genes (
pfr
and
sodB
) have previously been identified, we sought to expand our understanding of this type of regulation. Utilizing published genomic studies, we selected three potential new
apo
-Fur-regulated gene targets:
serB
,
hydA
, and the cytochrome
c
553
gene. Transcriptional analyses confirmed Fur-dependent repression of these genes in the absence of iron, as well as derepression in the absence of Fur. Binding studies showed that
apo
-Fur directly interacted with the suspected
hydA
and cytochrome
c
553
promoters but not that of
serB
, which was subsequently shown to be cotranscribed with
pfr
;
apo
-Fur-dependent regulation occurred at the
pfr
promoter. Alignments of
apo
-regulated promoter regions revealed a conserved, 6-bp consensus sequence (AAATGA). DNase I footprinting showed that this sequence lies within the protected regions of the
pfr
and
hydA
promoters. Moreover, mutation of the sequence in the
pfr
promoter abrogated Fur binding and DNase protection. Likewise, fluorescence anisotropy studies and binding studies with mutated consensus sequences showed that the sequence was important for
apo
-Fur binding to the
pfr
promoter. Together these studies expand the known
apo
-Fur regulon in
H. pylori
and characterize the first reported
apo
-Fur box sequence.
The effects of a mindfulness-based lifestyle programme for adults with Parkinson’s disease: protocol for a mixed methods, randomised two-group control study
Authors: Advocat Jenny , Russell Grant , Enticott Joanne , Hassed Craig , Hester Jennifer , Vandenberg Brooke 
Published: October 2013

IntroductionParkinson's disease (PD) is the second most common neurodegenerative disorder in developed countries. There is an increasing interest in the use of mindfulness-related interventions in the management of patients with a chronic disease. In addition, interventions that promote personal control, stress-management and other lifestyle factors, such as diet and exercise, assist in reducing disability and improving quality of life in people with chronic illnesses. There has been little research in this area for people with PD.MethodsA prospective mixed-method randomised clinical trial involving community living adults with PD aged <76 years and with moderate disease severity (Hoehn and Yahr stage 2) PD. Participants will be randomised into the ESSENCE 6-week programme or a matched wait list control group. ESSENCE is a multifaceted, healthy lifestyle and mindfulness programme designed to improve quality of life. We aim to determine whether participation in a mindfulness and lifestyle programme could improve PD-related function and explore self-management related experiences and changing attitudes towards self-management. The outcome measures will include 5 self-administered questionnaires: PD function and well-being questionnaire (PDQ39), Health Behaviours, Mental health, Multidimensional locus of control, and Freiburg mindfulness inventory. An embedded qualitative protocol will include in-depth interviews with 12 participants before and after participation in the 6-week programme and a researcher will observe the programme and take notes.AnalysisRepeated measures of Analysis of Variance (ANOVA) will examine the outcome measures for any significant effects from the group allocation, age, sex, adherence score and attendance. Qualitative data will be analysed thematically. We will outline the benefits of, and barriers to, the uptake of the intervention.EthicsThis protocol has received ethics approval from the Monash University Human Research Ethics Committee project number CF11/2662–2011001553.DisseminationThis is the first research of its kind in Australia involving a comprehensive, lifestyle-based programme for people with PD and has the potential to involve a broader range of providers than standard care. The findings will be disseminated through peer reviewed journals, primary care conferences in Australia as well as abroad and through the Parkinson's community.Registration detailsAustralian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12612000440820.
What do Canadians think of advanced care planning? Findings from an online opinion poll
Authors: Teixeira Ana A , Hanvey Louise , Tayler Carolyn , Barwich Doris , Baxter Sharon , Heyland Daren K 
Published: October 2013

BackgroundAdvance care planning (ACP) has the potential to increase patient-centred care, reduce caregiver burden, and reduce healthcare costs at the end of life. Current levels of public participation in ACP activities are unknown. The purpose of this study was to determine the level of engagement of average Canadians in ACP activities.MethodsData come from an on-line opinion poll of a national sample of respondents who were asked five questions on ACP activities along with their sociodemographic characteristics.ResultsRespondents were from all provinces of Canada, 52% were women, and 33% were between 45 years and 54 years of age. Of 1021 national sample respondents, 16% were aware of the term, ACP (95% CI 13% to 18%), 52% had discussions with their family or friends (95% CI 49% to 55%), and 10% had discussions with healthcare providers (95% CI 8% to 12%). Overall, 20% (95% CI 18% to 22%) of respondents had a written ACP and 47% (95% CI 44% to 50%) had designated a substitute decision maker. Being older was associated with significantly more engagement in ACP activities and there were significant differences in ACP engagement across Canada.ConclusionsAlthough only a small proportion of Canadians are aware of the formal term, ACP, a higher percentage of Canadians are actually engaged in ACP, through either having discussions or making decisions about end-of-life care. Older citizens are more likely to be engaged in ACP and there are geographic differences in the level of ACP engagement across Canada.