bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultralow dose computed tomography attenuation correction for pediatric PET CT using adaptive statistical iterative reconstruction
Authors: Brady Samuel L. , Shulkin Barry L.
Published: January 2015

Purpose:

To develop ultralow dose computed tomography (CT) attenuation correction (CTAC) acquisition protocols for pediatric positron emission tomography CT (PET CT).

Methods:

A GE Discovery 690 PET CT hybrid scanner was used to investigate the change to quantitative PET and CT measurements when operated at ultralow doses (10–35 mA s). CT quantitation: noise, low‐contrast resolution, and CT numbers for 11 tissue substitutes were analyzed in‐phantom. CT quantitation was analyzed to a reduction of 90% volume computed tomography dose index (0.39/3.64; mGy) from baseline. To minimize noise infiltration, 100% adaptive statistical iterative reconstruction (ASiR) was used for CT reconstruction. PET images were reconstructed with the lower‐dose CTAC iterations and analyzed for: maximum body weight standardized uptake value (SUVbw) of various diameter targets (range 8–37 mm), background uniformity, and spatial resolution. Radiation dose and CTAC noise magnitude were compared for 140 patient examinations (76 post‐ASiR implementation) to determine relative dose reduction and noise control.

Results:

CT numbers were constant to within 10% from the nondose reduced CTAC image for 90% dose reduction. No change in SUVbw, background percent uniformity, or spatial resolution for PET images reconstructed with CTAC protocols was found down to 90% dose reduction. Patient population effective dose analysis demonstrated relative CTAC dose reductions between 62% and 86% (3.2/8.3–0.9/6.2). Noise magnitude in dose‐reduced patient images increased but was not statistically different from predose‐reduced patient images.

Conclusions:

Using ASiR allowed for aggressive reduction in CT dose with no change in PET reconstructed images while maintaining sufficient image quality for colocalization of hybrid CT anatomy and PET radioisotope uptake.
Ionoacoustic characterization of the proton Bragg peak with submillimeter accuracy
Authors: Assmann W. , Kellnberger S. , Reinhardt S. , Lehrack S. , Edlich A. , Thirolf P. G. , Moser M. , Dollinger G. , Omar M. , Ntziachristos V. , Parodi K.
Published: January 2015

Purpose:

Range verification in ion beam therapy relies to date on nuclear imaging techniques which require complex and costly detector systems. A different approach is the detection of thermoacoustic signals that are generated due to localized energy loss of ion beams in tissue (ionoacoustics). Aim of this work was to study experimentally the achievable position resolution of ionoacoustics under idealized conditions using high frequency ultrasonic transducers and a specifically selected probing beam.

Methods:

A water phantom was irradiated by a pulsed 20 MeV proton beam with varying pulse intensity and length. The acoustic signal of single proton pulses was measured by different PZT‐based ultrasound detectors (3.5 and 10 MHz central frequencies). The proton dose distribution in water was calculated by Geant4 and used as input for simulation of the generated acoustic wave by the matlab toolbox k‐WAVE.

Results:

In measurements from this study, a clear signal of the Bragg peak was observed for an energy deposition as low as 1012 eV. The signal amplitude showed a linear increase with particle number per pulse and thus, dose. Bragg peak position measurements were reproducible within ±30 μm and agreed with Geant4 simulations to better than 100 μm. The ionoacoustic signal pattern allowed for a detailed analysis of the Bragg peak and could be well reproduced by k‐WAVE simulations.

Conclusions:

The authors have studied the ionoacoustic signal of the Bragg peak in experiments using a 20 MeV proton beam with its correspondingly localized energy deposition, demonstrating submillimeter position resolution and providing a deep insight in the correlation between the acoustic signal and Bragg peak shape. These results, together with earlier experiments and new simulations (including the results in this study) at higher energies, suggest ionoacoustics as a technique for range verification in particle therapy at locations, where the tumor can be localized by ultrasound imaging. This acoustic range verification approach could offer the possibility of combining anatomical ultrasound and Bragg peak imaging, but further studies are required for translation of these findings to clinical application.
Characterization of a double‐sided silicon strip detector autoradiography system
Authors: Örbom Anders , Ahlstedt Jonas , Serén Tom , Auterinen Iiro , Kotiluoto Petri , Hauge Håvard , Östlund Karl , Olafsen Tove , Wu Anna M. , Dahlbom Magnus , Strand Sven‐Erik
Published: January 2015

Purpose:

The most commonly used technology currently used for autoradiography is storage phosphor screens, which has many benefits such as a large field of view but lacks particle‐counting detection of the time and energy of each detected radionuclide decay. A number of alternative designs, using either solid state or scintillator detectors, have been developed to address these issues. The aim of this study is to characterize the imaging performance of one such instrument, a double‐sided silicon strip detector (DSSD) system for digital autoradiography. A novel aspect of this work is that the instrument, in contrast to previous prototype systems using the same detector type, provides the ability for user accessible imaging with higher throughput. Studies were performed to compare its spatial resolution to that of storage phosphor screens and test the implementation of multiradionuclide ex vivo imaging in a mouse preclinical animal study.

Methods:

Detector background counts were determined by measuring a nonradioactive sample slide for 52 h. Energy spectra and detection efficiency were measured for seven commonly used radionuclides under representative conditions for tissue imaging. System dead time was measured by imaging 18F samples of at least 5 kBq and studying the changes in count rate over time. A line source of 58Co was manufactured by irradiating a 10 μm nickel wire with fast neutrons in a research reactor. Samples of this wire were imaged in both the DSSD and storage phosphor screen systems and the full width at half maximum (FWHM) measured for the line profiles. Multiradionuclide imaging was employed in a two animal study to examine the intratumoral distribution of a 125I‐labeled monoclonal antibody and a 131I‐labeled engineered fragment (diabody) injected in the same mouse, both targeting carcinoembryonic antigen.

Results:

Detector background was 1.81 × 10−6 counts per second per 50 × 50 μm pixel. Energy spectra and detection efficiency were successfully measured for seven radionuclides. The system dead time was measured to be 59 μs, and FWHM for a 58Co line source was 154 ± 14 μm for the DSSD system and 343 ± 15 μm for the storage phosphor system. Separation of the contributions from 125I and 131I was performed on autoradiography images of tumor sections.

Conclusions:

This study has shown that a DSSD system can be beneficially applied for digital autoradiography with simultaneous multiradionuclide imaging capability. The system has a low background signal, ability to image both low and high activity samples, and a good energy resolution.
Arsenite Oxidase Also Functions as an Antimonite Oxidase
Authors: Wang Qian , Warelow Thomas P. , Kang Yoon-Suk , Romano Christine , Osborne Thomas H. , Lehr Corinne R. , Bothner Brian , McDermott Timothy R. , Santini Joanne M. , Wang Gejiao
Published: January 2015

Arsenic and antimony are toxic metalloids and are considered priority environmental pollutants by the U.S. Environmental Protection Agency. Significant advances have been made in understanding microbe-arsenic interactions and how they influence arsenic redox speciation in the environment. However, even the most basic features of how and why a microorganism detects and reacts to antimony remain poorly understood. Previous work with
Agrobacterium tumefaciens
strain 5A concluded that oxidation of antimonite [Sb(III)] and arsenite [As(III)] required different biochemical pathways. Here, we show with
in vivo
experiments that a mutation in
aioA
[encoding the large subunit of As(III) oxidase] reduces the ability to oxidize Sb(III) by approximately one-third relative to the ability of the wild type. Further,
in vitro
studies with the purified As(III) oxidase from
Rhizobium
sp. strain NT-26 (AioA shares 94% amino acid sequence identity with AioA of
A. tumefaciens
) provide direct evidence of Sb(III) oxidation but also show a significantly decreased
V
max
compared to that of As(III) oxidation. The
aioBA
genes encoding As(III) oxidase are induced by As(III) but not by Sb(III), whereas
arsR
gene expression is induced by both As(III) and Sb(III), suggesting that detection and transcriptional responses for As(III) and Sb(III) differ. While Sb(III) and As(III) are similar with respect to cellular extrusion (ArsB or Acr3) and interaction with ArsR, they differ in the regulatory mechanisms that control the expression of genes encoding the different Ars or Aio activities. In summary, this study documents an enzymatic basis for microbial Sb(III) oxidation, although additional Sb(III) oxidation activity also is apparent in this bacterium.
Metabolism of 2-Methylpropene (Isobutylene) by the Aerobic Bacterium Mycobacterium sp. Strain ELW1
Authors: Kottegoda Samanthi , Waligora Elizabeth , Hyman Michael
Published: January 2015

An aerobic bacterium (
Mycobacterium
sp. strain ELW1) that utilizes 2-methylpropene (isobutylene) as a sole source of carbon and energy was isolated and characterized. Strain ELW1 grew on 2-methylpropene (growth rate = 0.05 h
−1
) with a yield of 0.38 mg (dry weight) mg 2-methylpropene
−1
. Strain ELW1 also grew more slowly on both
cis
- and
trans
-2-butene but did not grow on any other C
2
to C
5
straight-chain, branched, or chlorinated alkenes tested. Resting 2-methylpropene-grown cells consumed ethene, propene, and 1-butene without a lag phase. Epoxyethane accumulated as the only detected product of ethene oxidation. Both alkene consumption and epoxyethane production were fully inhibited in cells exposed to 1-octyne, suggesting that alkene oxidation is initiated by an alkyne-sensitive, epoxide-generating monooxygenase. Kinetic analyses indicated that 1,2-epoxy-2-methylpropane is rapidly consumed during 2-methylpropene degradation, while 2-methyl-2-propen-1-ol is not a significant metabolite of 2-methylpropene catabolism. Degradation of 1,2-epoxy-2-methylpropane by 2-methylpropene-grown cells led to the accumulation and further degradation of 2-methyl-1,2-propanediol and 2-hydroxyisobutyrate, two sequential metabolites previously identified in the aerobic microbial metabolism of methyl
tert
-butyl ether (MTBE) and
tert
-butyl alcohol (TBA). Growth of strain ELW1 on 2-methylpropene, 1,2-epoxy-2-methylpropane, 2-methyl-1,2-propanediol, and 2-hydroxyisobutyrate was fully inhibited when cobalt ions were omitted from the growth medium, while growth on 3-hydroxybutyrate and other substrates was unaffected by the absence of added cobalt ions. Our results suggest that, like aerobic MTBE- and TBA-metabolizing bacteria, strain ELW1 utilizes a cobalt/cobalamin-dependent mutase to transform 2-hydroxyisobutyrate. Our results have been interpreted in terms of their impact on our understanding of the microbial metabolism of alkenes and ether oxygenates.
Metabolic Engineering of an ATP-Neutral Embden-Meyerhof-Parnas Pathway in Corynebacterium glutamicum: Growth Restoration by an Adaptive Point Mutation in NADH Dehydrogenase
Authors: Komati Reddy Gajendar , Lindner Steffen N. , Wendisch Volker F.
Published: January 2015

Corynebacterium glutamicum
uses the Embden-Meyerhof-Parnas pathway of glycolysis and gains 2 mol of ATP per mol of glucose by substrate-level phosphorylation (SLP). To engineer glycolysis without net ATP formation by SLP, endogenous phosphorylating NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was replaced by nonphosphorylating NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (GapN) from
Clostridium acetobutylicum
, which irreversibly converts glyceraldehyde-3-phosphate (GAP) to 3-phosphoglycerate (3-PG) without generating ATP. As shown recently (S. Takeno, R. Murata, R. Kobayashi, S. Mitsuhashi, and M. Ikeda, Appl Environ Microbiol 76:7154–7160, 2010,
http://dx.doi.org/10.1128/AEM.01464-10
), this ATP-neutral, NADPH-generating glycolytic pathway did not allow for the growth of
Corynebacterium glutamicum
with glucose as the sole carbon source unless hitherto unknown suppressor mutations occurred; however, these mutations were not disclosed. In the present study, a suppressor mutation was identified, and it was shown that heterologous expression of
udhA
encoding soluble transhydrogenase from
Escherichia coli
partly restored growth, suggesting that growth was inhibited by NADPH accumulation. Moreover, genome sequence analysis of second-site suppressor mutants that were able to grow faster with glucose revealed a single point mutation in the gene of non-proton-pumping NADH:ubiquinone oxidoreductase (NDH-II) leading to the amino acid change D213G, which was shared by these suppressor mutants. Since related NDH-II enzymes accepting NADPH as the substrate possess asparagine or glutamine residues at this position, D213G, D213N, and D213Q variants of
C. glutamicum
NDH-II were constructed and were shown to oxidize NADPH in addition to NADH. Taking these findings together, ATP-neutral glycolysis by the replacement of endogenous NAD-dependent GAPDH with NADP-dependent GapN became possible via oxidation of NADPH formed in this pathway by mutant NADPH-accepting NDH-II
D213G
and thus by coupling to electron transport phosphorylation (ETP).
Oligopolyphenylenevinylene-Conjugated Oligoelectrolyte Membrane Insertion Molecules Selectively Disrupt Cell Envelopes of Gram-Positive Bacteria
Authors: Hinks Jamie , Poh Wee Han , Chu Justin Jang Hann , Loo Joachim Say Chye , Bazan Guillermo C. , Hancock Lynn E. , Wuertz Stefan
Published: January 2015

The modification of microbial membranes to achieve biotechnological strain improvement with exogenous small molecules, such as oligopolyphenylenevinylene-conjugated oligoelectrolyte (OPV-COE) membrane insertion molecules (MIMs), is an emerging biotechnological field. Little is known about the interactions of OPV-COEs with their target, the bacterial envelope. We studied the toxicity of three previously reported OPV-COEs with a selection of Gram-negative and Gram-positive organisms and demonstrated that Gram-positive bacteria are more sensitive to OPV-COEs than Gram-negative bacteria. Transmission electron microscopy demonstrated that these MIMs disrupt microbial membranes and that this occurred to a much greater degree in Gram-positive organisms. We used a number of mutants to probe the nature of MIM interactions with the microbial envelope but were unable to align the membrane perturbation effects of these compounds to previously reported membrane disruption mechanisms of, for example, cationic antimicrobial peptides. Instead, the data support the notion that OPV-COEs disrupt microbial membranes through a suspected interaction with diphosphatidylglycerol (DPG), a major component of Gram-positive membranes. The integrity of model membranes containing elevated amounts of DPG was disrupted to a greater extent by MIMs than those prepared from
Escherichia coli
total lipid extracts alone.
Distinct Roles for Carbohydrate-Binding Modules of Glycoside Hydrolase 10 (GH10) and GH11 Xylanases from Caldicellulosiruptor sp. Strain F32 in Thermostability and Catalytic Efficiency
Authors: Meng Dong-Dong , Ying Yu , Chen Xiao-Hua , Lu Ming , Ning Kang , Wang Lu-Shan , Li Fu-Li
Published: January 2015

Xylanases are crucial for lignocellulosic biomass deconstruction and generally contain noncatalytic carbohydrate-binding modules (CBMs) accessing recalcitrant polymers. Understanding how multimodular enzymes assemble can benefit protein engineering by aiming at accommodating various environmental conditions. Two multimodular xylanases, XynA and XynB, which belong to glycoside hydrolase families 11 (GH11) and GH10, respectively, have been identified from
Caldicellulosiruptor
sp. strain F32. In this study, both xylanases and their truncated mutants were overexpressed in
Escherichia coli
, purified, and characterized. GH11 XynATM1 lacking CBM exhibited a considerable improvement in specific activity (215.8 U nmol
−1
versus 94.7 U nmol
−1
) and thermal stability (half-life of 48 h versus 5.5 h at 75°C) compared with those of XynA. However, GH10 XynB showed higher enzyme activity and thermostability than its truncated mutant without CBM. Site-directed mutagenesis of N-terminal amino acids resulted in a mutant, XynATM1-M, with 50% residual activity improvement at 75°C for 48 h, revealing that the disordered region influenced protein thermostability negatively. The thermal stability of both xylanases and their truncated mutants were consistent with their melting temperature (

T
m

), which was determined by using differential scanning calorimetry. Through homology modeling and cross-linking analysis, we demonstrated that for XynB, the resistance against thermoinactivation generally was enhanced through improving both domain properties and interdomain interactions, whereas for XynA, no interdomain interactions were observed. Optimized intramolecular interactions can accelerate thermostability, which provided microbes a powerful evolutionary strategy to assemble catalysts that are adapted to various ecological conditions.
Inhibitory Effects of C
2
to C
10
1-Alkynes on Ammonia Oxidation in Two Nitrososphaera Species
Authors: Taylor A. E. , Taylor K. , Tennigkeit B. , Palatinszky M. , Stieglmeier M. , Myrold D. D. , Schleper C. , Wagner M. , Bottomley P. J.
Published: January 2015

A previous study showed that ammonia oxidation by the
Thaumarchaeota
Nitrosopumilus maritimus
(group 1.1a) was resistant to concentrations of the C
8
1-alkyne, octyne, which completely inhibits activity by ammonia-oxidizing bacteria. In this study, the inhibitory effects of octyne and other C
2
to C
10
1-alkynes were evaluated on the nitrite production activity of two pure culture isolates from
Thaumarchaeota
group 1.1b,
Nitrososphaera viennensis
strain EN76 and
Nitrososphaera gargensis
. Both
N. viennensis
and
N. gargensis
were insensitive to concentrations of octyne that cause complete and irreversible inactivation of nitrite production by ammonia-oxidizing bacteria. However, octyne concentrations (≥20 μM) that did not inhibit
N. maritimus
partially inhibited nitrite production in
N. viennensis
and
N. gargensis
in a manner that did not show the characteristics of irreversible inactivation. In contrast to previous studies with an ammonia-oxidizing bacterium,
Nitrosomonas europaea
, octyne inhibition of
N. viennensis
was: (i) fully and immediately reversible, (ii) not competitive with NH
4
+
, and (iii) without effect on the competitive interaction between NH
4
+
and acetylene. Both
N. viennensis
and
N. gargensis
demonstrated the same overall trend in regard to 1-alkyne inhibition as previously observed for
N. maritimus
, being highly sensitive to ≤C
5
alkynes and more resistant to longer-chain length alkynes. Reproducible differences were observed among
N. maritimus
,
N. viennensis
, and
N. gargensis
in regard to the extent of their resistance/sensitivity to C
6
and C
7
1-alkynes, which may indicate differences in the ammonia monooxygenase binding and catalytic site(s) among the
Thaumarchaeota
.
Genetic Determinants of Reutericyclin Biosynthesis in Lactobacillus reuteri
Authors: Lin Xiaoxi B. , Lohans Christopher T. , Duar Rebbeca , Zheng Jinshui , Vederas John C. , Walter Jens , Gänzle Michael
Published: January 2015

Reutericyclin is a unique antimicrobial tetramic acid produced by some strains of
Lactobacillus reuteri
. This study aimed to identify the genetic determinants of reutericyclin biosynthesis. Comparisons of the genomes of reutericyclin-producing
L. reuteri
strains with those of non-reutericyclin-producing strains identified a genomic island of 14 open reading frames (ORFs) including genes coding for a nonribosomal peptide synthetase (NRPS), a polyketide synthase (PKS), homologues of PhlA, PhlB, and PhlC, and putative transport and regulatory proteins. The protein encoded by
rtcN
is composed of a condensation domain, an adenylation domain likely specific for
d
-leucine, and a thiolation domain.
rtcK
codes for a PKS that is composed of a ketosynthase domain, an acyl-carrier protein domain, and a thioesterase domain. The products of
rtcA
,
rtcB
, and
rtcC
are homologous to the diacetylphloroglucinol-biosynthetic proteins PhlABC and may acetylate the tetramic acid moiety produced by RtcN and RtcK, forming reutericyclin. Deletion of
rtcN
or
rtcABC
in
L. reuteri
TMW1.656 abrogated reutericyclin production but did not affect resistance to reutericyclin. Genes coding for transport and regulatory proteins could be deleted only in the reutericyclin-negative
L. reuteri
strain TMW1.656Δ
rtcN
, and these deletions eliminated reutericyclin resistance. The genomic analyses suggest that the reutericyclin genomic island was horizontally acquired from an unknown source during a unique event. The combination of PhlABC homologues with both an NRPS and a PKS has also been identified in the lactic acid bacteria
Streptococcus mutans
and
Lactobacillus plantarum
, suggesting that the genes in these organisms and those in
L. reuteri
share an evolutionary origin.
AmyM, a Novel Maltohexaose-Forming α-Amylase from Corallococcus sp. Strain EGB
Authors: Li Zhoukun , Wu Jiale , Zhang Biying , Wang Fei , Ye Xianfeng , Huang Yan , Huang Qiang , Cui Zhongli
Published: January 2015

A novel α-amylase, AmyM, was purified from the culture supernatant of
Corallococcus
sp. strain EGB. AmyM is a maltohexaose-forming exoamylase with an apparent molecular mass of 43 kDa. Based on the results of matrix-assisted laser desorption ionization–time of flight mass spectrometry and peptide mass fingerprinting of AmyM and by comparison to the genome sequence of
Corallococcus
coralloides
DSM 2259, the AmyM gene was identified and cloned into
Escherichia coli
.
amyM
encodes a secretory amylase with a predicted signal peptide of 23 amino acid residues, which showed no significant identity with known and functionally verified amylases.
amyM
was expressed in
E. coli
BL21(DE3) cells with a hexahistidine tag. The signal peptide efficiently induced the secretion of mature AmyM in
E. coli
. Recombinant AmyM (rAmyM) was purified by Ni-nitrilotriacetic acid (NTA) affinity chromatography, with a specific activity of up to 14,000 U/mg. rAmyM was optimally active at 50°C in Tris-HCl buffer (50 mM; pH 7.0) and stable at temperatures of <50°C. rAmyM was stable over a wide range of pH values (from pH 5.0 to 10.0) and highly tolerant to high concentrations of salts, detergents, and various organic solvents. Its activity toward starch was independent of calcium ions. The

K
m

and
V
max
of recombinant AmyM for soluble starch were 6.61 mg ml
−1
and 44,301.5 μmol min
−1
mg
−1
, respectively. End product analysis showed that maltohexaose accounted for 59.4% of the maltooligosaccharides produced. These characteristics indicate that AmyM has great potential in industrial applications.
DNA Double-Strand Breaks and Telomeres Play Important Roles in Trypanosoma brucei Antigenic Variation
Authors: Li Bibo
Published: January 2015

Human-infecting microbial pathogens all face a serious problem of elimination by the host immune response. Antigenic variation is an effective immune evasion mechanism where the pathogen regularly switches its major surface antigen. In many cases, the major surface antigen is encoded by genes from the same gene family, and its expression is strictly monoallelic. Among pathogens that undergo antigenic variation,
Trypanosoma brucei
(a kinetoplastid), which causes human African trypanosomiasis,
Plasmodium falciparum
(an apicomplexan), which causes malaria,
Pneumocystis jirovecii
(a fungus), which causes pneumonia, and
Borrelia burgdorferi
(a bacterium), which causes Lyme disease, also express their major surface antigens from loci next to the telomere. Except for
Plasmodium
, DNA recombination-mediated gene conversion is a major pathway for surface antigen switching in these pathogens. In the last decade, more sophisticated molecular and genetic tools have been developed in
T. brucei
, and our knowledge of functions of DNA recombination in antigenic variation has been greatly advanced. VSG is the major surface antigen in
T. brucei
. In subtelomeric VSG expression sites (ESs),
VSG
genes invariably are flanked by a long stretch of upstream 70-bp repeats. Recent studies have shown that DNA double-strand breaks (DSBs), particularly those in 70-bp repeats in the active ES, are a natural potent trigger for antigenic variation in
T. brucei
. In addition, telomere proteins can influence VSG switching by reducing the DSB amount at subtelomeric regions. These findings will be summarized and their implications will be discussed in this review.
Pilot test of the Healthy Food Environment Policy Index (Food-EPI) to increase government actions for creating healthy food environments
Authors: Vandevijvere Stefanie , Swinburn Boyd
Published: January 2015

Objectives

Effective government policies are essential to increase the healthiness of food environments. The International Network for Food and Obesity/non-communicable diseases (NCDs) Research, Monitoring and Action Support (INFORMAS) has developed a monitoring tool (the Healthy Food Environment Policy Index (Food-EPI)) and process to rate government policies to create healthy food environments against international best practice. The aims of this study were to pilot test the Food-EPI, and revise the tool and process for international implementation.

Setting

New Zealand.

Participants

Thirty-nine informed, independent public health experts and non-governmental organisation (NGO) representatives.

Primary and secondary outcome measures

Evidence on the extent of government implementation of different policies on food environments and infrastructure support was collected in New Zealand and validated with government officials. Two whole-day workshops were convened of public health experts and NGO representatives who rated performance of their government for seven policy and seven infrastructure support domains against international best practice. In addition, the raters evaluated the level of difficulty of rating, and appropriateness and completeness of the evidence presented for each indicator.

Results

Inter-rater reliability was 0.85 (95% CI 0.81 to 0.88; Gwet’s AC2) using quadratic weights, and increased to 0.89 (95% CI 0.85 to 0.92) after deletion of the problematic indicators. Based on raters’ assessments and comments, major changes to the Food-EPI tool include strengthening the leadership domain, removing the workforce development domain, a stronger focus on equity, and adding community-based programmes and government funding for research on obesity and diet-related NCD prevention, as good practice indicators.

Conclusions

The resulting tool and process will be promoted and offered to countries of varying size and income globally. International benchmarking of the extent of government policy implementation on food environments has the potential to catalyse greater government action to reduce obesity and NCDs, and increase civil society's capacity to advocate for healthy food environments.
Protocol for the surgical and large bore procedures in malignant pleural mesothelioma and radiotherapy trial (SMART Trial): an RCT evaluating whether prophylactic radiotherapy reduces the incidence of procedure tract metastases
Authors: Clive Amelia O , Wilson Paula , Taylor Hazel , Morley Anna J , de Winton Emma , Panakis Niki , Rahman Najib , Pepperell Justin , Howell Timothy , Batchelor Timothy J P , Jordan Nikki , Lee Y C Gary , Dobson Lee , Maskell Nick A
Published: January 2015

Introduction

Patients with malignant pleural mesothelioma (MPM) may develop painful ‘procedure tract metastasis’ (PTM) at the site of previous pleural interventions. Prophylactic radiotherapy has been used to minimise this complication; however, three small randomised trials have shown conflicting results regarding its effectiveness. The surgical and large bore procedures in malignant pleural mesothelioma and radiotherapy trial (SMART Trial) is a suitably powered, multicentre, randomised controlled trial, designed to evaluate the efficacy of prophylactic radiotherapy within 42 days of pleural instrumentation in preventing the development of PTM in MPM.

Methods and analysis

203 patients with a histocytologically proven diagnosis of MPM, who have undergone a large bore pleural intervention (thoracic surgery, large bore chest drain, indwelling pleural catheter or local anaesthetic thoracoscopy) in the previous 35 days, will be recruited from UK hospitals. Patients will be randomised (1:1) to receive immediate radiotherapy (21 Gy in 3 fractions over 3 working days within 42 days of the pleural intervention) or deferred radiotherapy (21 Gy in 3 fractions over 3 working days given if a PTM develops). Patients will be followed up for 12 months. The primary outcome measure is the rate of PTM until death or 12 months (whichever is sooner), as defined by the presence of a clinically palpable nodule of at least 1 cm diameter felt within 7 cm of the margins of the procedure site as confirmed by two assessors. Secondary outcome measures include chest pain, quality of life, analgaesic requirements, healthcare utilisation and safety (including radiotherapy toxicity).

Ethics and dissemination

The trial has received ethical approval from the Southampton B Research Ethics Committee (11/SC/0408). There is a Trial Steering Committee, including independent members and a patient and public representative. The trial results will be published in a peer-reviewed journal and presented at international conferences.

Trial registration number

ISRCTN72767336.
A short-term risk–benefit analysis of occasional and regular use of low-dose aspirin in primary prevention of vascular diseases: a nationwide population-based study
Authors: Wu I-Chen , Hsieh Hui-Min , Wu Ming-Tsang
Published: January 2015

Objective

To calculate the short-term risk–benefit effect of occasional and regular use of low-dose aspirin (≤100 mg/day) in primary prevention.

Study design

Two retrospective cohort studies.

Setting

Taiwan.

Participants

63 788 and 24 910 patients of two nationwide population-based studies were examined.

Methods

Two databases of 1 000 000 patients were randomly sampled from data of Taiwan's National Health Insurance (NHI) for years 1997–2000 (NHI 2000) and 2005 (NHI 2005). In NHI 2000, 63 788 patients 30–95 years of age were found not to have previously been prescribed aspirin before 1 January 2000, but to have first been prescribed low-dose aspirin after that date. They were also found to be at risk of first hospitalisation for any major vascular diseases including haemorrhage (major gastrointestinal haemorrhage or cerebral haemorrhage) and ischaemia (acute myocardial infarction or ischaemic stroke) after their first prescription. We also applied it to NHI 2005, and the number of eligible patients was 24 910. Patients prescribed low-dose aspirin for <20% of the days of a 60-day follow-up period were considered to be occasional users, and those prescribed low-dose aspirin for ≥80% of the days were considered to be regular users. Differences in rate of haemorrhage and ischaemia between these users were used to calculate their net clinical risk.

Primary outcome

Vascular diseases.

Results

In NHI 2000, the overall unadjusted rates of haemorrhage and ischaemia were 0.09% and 0.21%, respectively, for occasional users and 0.32% and 2.30%, respectively, for regular users. Adjusted net clinical risk of low-dose aspirin use between the two groups was 2.24% (95% CI 2.03% to 2.48%; p<0.001). Similar results were also found in NHI 2005.

Conclusions

Short-term regular use of low-dose aspirin might not be better than occasional use for preventing major vascular diseases in primary prevention. Prescribing regular low-dose aspirin for primary prevention should be done with caution. Future studies should explore the risk–benefit effect of long-term low-dose aspirin use in primary prevention.
Antineutrophil cytoplasmic antibody-positive conversion and microscopic polyangiitis development in patients with idiopathic pulmonary fibrosis
Authors: Kagiyama Naho , Takayanagi Noboru , Kanauchi Tetsu , Ishiguro Takashi , Yanagisawa Tsutomu , Sugita Yutaka
Published: January 2015

Background

Increasing evidence indicates that antineutrophil cytoplasmic antibody (ANCA)-positive conversion occurs in patients initially diagnosed with idiopathic pulmonary fibrosis (IPF) and as a result, some of these patients develop microscopic polyangiitis (MPA). However, the incidence density of these patients is not well known.

Objectives

To explore the incidence of ANCA-positive conversion and development of MPA during the disease course in patients with IPF and to evaluate whether corticosteroid therapy reduces MPA development in patients with IPF with myeloperoxidase (MPO)-ANCA positivity at diagnosis or who later acquire MPO-ANCA positivity.

Methods

We retrospectively analysed the medical records of 504 Asian patients with IPF treated at our institution in Saitama, Japan.

Results

Of the 504 patients with IPF, 20 (4.0%) had MPO-ANCA and 16 (3.2%) had PR-3-ANCA when first evaluated. In 264 of 504 patients with IPF, ANCA was measured repeatedly and seroconversion to MPO-ANCA and PR3-ANCA occurred in 15 (5.7%) and 14 (5.3%) patients, respectively, and 9 of 35 patients who were either MPO-ANCA positive at IPF diagnosis or who subsequently seroconverted developed MPA. None of the nine patients who developed MPA had been previously treated with steroids. The incidence of MPA tended to be lower in patients treated than not treated with corticosteroids although this was not statistically significant.

Conclusions

Some patients with IPF with MPO-ANCA positivity at IPF diagnosis or with MPO-ANCA-positive conversion during follow-up developed MPA. Clinical trials to determine whether corticosteroid therapy can reduce MPA development and prolong survival in MPO-ANCA-positive patients with IPF should be considered.
Rapid fluorescence in situ hybridisation (FISH) forHER2 (ERBB2)assessment in breast and gastro-oesophageal cancer
Authors: Tafe Laura J , Steinmetz Heather B , Allen Samantha F , Dokus Betty J , Tsongalis Gregory J
Published: January 2015

Evaluation ofHER2(ERBB2) gene amplification or protein expression is standard of care in breast (BR) and advanced stage gastro-oesophageal cancers to identify patients eligible for anti-HER2 therapies. Here, we evaluate a rapid fluorescence in situ hybridisation (FISH) technology (HER2instant quality (IQ) FISH pharmDx Kit) for detection ofHER2in patients with BR and gastro-oesophageal cancer using 30 FFPE samples that had been previously evaluated with the PathVysionHER2DNA Probe Kit. Cases were scored as positive (HER2:CEN-17 ≥2.0), negative (HER2:CEN-17 <2.0) or equivocal according to the ASCO/CAP 2013 BR cancer guidelines. Ten samples were positive forHER2amplification while 20 were negative; none were equivocal. The IQ FISH was able to detect low level amplification (HER2:CEN-17 ratio 2.4). TheHER2IQ FISH pharmDx Kit is a FDA approved kit that offers a rapid turnaround time (approximately 3.5 h) and in our laboratory was 100% concordant with prior PathVysion results.
Health service use, out-of-pocket payments and catastrophic health expenditure among older people in India: The WHO Study on global AGEing and adult health (SAGE)
Authors: Brinda Ethel Mary , Kowal Paul , Attermann Jørn , Enemark Ulrika
Published: January 2015

Background

Healthcare financing through out-of-pocket payments and inequities in healthcare utilisation are common in low and middle income countries (LMICs). Given the dearth of pertinent studies on these issues among older people in LMICs, we investigated the determinants of health service use, out-of-pocket and catastrophic health expenditures among older people in one LMIC, India.

Methods

We accessed data from a nationally representative, multistage sample of 2414 people aged 65 years and older from the WHO's Study on global Ageing and adult health in India. Sociodemographic characteristics, health profiles, health service utilisation and out-of-pocket health expenditure were assessed using standard instruments. Multivariate zero-inflated negative binomial regression models were used to evaluate the determinants of health service visits. Multivariate Heckman sample selection regression models were used to assess the determinants of out-of-pocket and catastrophic health expenditures.

Results

Out-of-pocket health expenditures were higher among participants with disability and lower income. Diabetes, hypertension, chronic pulmonary disease, heart disease and tuberculosis increased the number of health visits and out-of-pocket health expenditures. The prevalence of catastrophic health expenditure among older people in India was 7% (95% CI 6% to 8%). Older men and individuals with chronic diseases were at higher risk of catastrophic health expenditure, while access to health insurance lowered the risk.

Conclusions

Reducing out-of-pocket health expenditure among older people is an important public health issue, in which social as well as medical determinants should be prioritised. Enhanced public health sector performance and provision of publicly funded insurance may protect against catastrophic health expenses and healthcare inequities in India.
Performance characteristics of methods for quantifying spontaneous intracerebral haemorrhage: data from the Efficacy of Nitric Oxide in Stroke (ENOS) trial
Authors: Krishnan Kailash , Mukhtar Siti F , Lingard James , Houlton Aimee , Walker Elizabeth , Jones Tanya , Sprigg Nikola , Cala Lesley A , Becker Jennifer L , Dineen Robert A , Koumellis Panos , Adami Alessandro , Casado Ana M , Bath Philip M W , Wardlaw Joanna M
Published: January 2015

Background

Poor prognosis after intracerebral haemorrhage (ICH) is related to haemorrhage characteristics. Along with developing therapeutic interventions, we sought to understand the performance of haemorrhage descriptors in large clinical trials.

Methods

Clinical and neuroimaging data were obtained for 548 participants with ICH from the Efficacy of Nitric Oxide in Stroke (ENOS) trial. Independent observers performed visual categorisation of the largest diameter, measured volume using ABC/2, modified ABC/2, semiautomated segmentation (SAS), fully automatic measurement methods; shape, density and intraventricular haemorrhage were also assessed. Intraobserver and interobserver reliability were determined for these measures.

Results

ICH volume was significantly different among standard ABC/2, modified ABC/2 and SAS: (mean) 12.8 (SD 16.3), 8.9 (9.2), 12.8 (13.1) cm3, respectively (p<0.0001). There was excellent agreement for haemorrhage volume (n=193): ABC/2 intraobserver intraclass correlation coefficient (ICC) 0.96–0.97, interobserver ICC 0.88; modified ABC/2 intraobserver ICC 0.95–0.97, interobserver ICC 0.91; SAS intraobserver ICC 0.95–0.99, interobserver ICC 0.93; largest diameter: (visual) interadjudicator ICC 0.82, (visual vs measured) adjudicator vs observer ICC 0.71; shape intraobserver ICC 0.88 interobserver ICC 0.75; density intraobserver ICC 0.86, interobserver ICC 0.73. Graeb score (mean 3.53) and modified Graeb (5.22) scores were highly correlated. Using modified ABC/2, ICH volume was underestimated in regular (by 2.2-2.5 cm3, p<0.0001) and irregular-shaped haemorrhages (by 4.8-4.9 cm3, p<0.0001). Fully automated measurement of haemorrhage volume was possible in only 5% of cases.

Conclusions

Formal measurement of haemorrhage characteristics and visual estimates are reproducible. The standard ABC/2 method is superior to the modified ABC/2 method for quantifying ICH volume.

Clinical trial registration

ISRCTN9941422.
American beech and sugar maple sapling relative abundance and growth are not modified by light availability following partial and total canopy disturbances
Authors: Bannon Kim , Delagrange Sylvain , Bélanger Nicolas , Messier Christian
Published: January 2015

Studies have reported divergent results on the effect of soil fertility and canopy opening on understory density and growth of sugar maple (AS; Acer saccharum Marsh.) and American beech (FG; Fagus grandifolia Ehrh.). The main objective of this study was to evaluate the effect of a gradient of canopy opening and soil fertility on the density and growth of AS and FG saplings in southwestern Quebec, Canada. We investigated 56 stands containing both AS and FG that were subjected to different disturbance history types (DHTs) (UF, unmanaged forest; PC, partial cut; and CC, clearcut) on various soil types. AS and FG absolute and relative sapling density varied greatly among the 56 stands; however, no significant effects of DHT, soil nutrient availability, or their interaction were found. Both species responded positively in terms of radial growth to canopy openings, with FG growth being slightly better than AS growth in PC stands compared with other canopy treatments. Contrary to our hypothesis, AS did not show significantly higher growth than FG following clear-cutting. These results do not support the idea that AS abundance and growth could be promoted by increasing the intensity of the canopy opening during harvest, at least on the generally acidic and base-poor soils that were investigated.
Implications of exotic Pinus radiata plantations for macrofungal diversity in the Urdaibai Biosphere Reserve (northern Spain)
Authors: Sarrionandia E. , Olariaga I. , Picón R. , Duñabeitia M. , Robredo A. , Rodríguez N. , Salcedo I.
Published: January 2015

To analyze the implications of exotic radiata pine (Pinus radiata D. Don) plantations for macrofungal diversity, a comparative mycocoenological survey was conducted over three consecutive years in pine plantations and native oak forests (Quercus robur L.) in the Urdaibai Biosphere Reserve. Macrofungal diversity was analyzed at species and community levels, and multivariate techniques were used to obtain insight into the fungal community in all functional groups. A total of 513 species was recorded, with ectomycorrhizal fungi being the most abundant, followed by the lignicolous saprotrophs. Measurements at both the overall level and the plot level showed that oak forests were richer in macrofungal species than pine plantations. The two ecosystems shared 107 species, but they possessed distinct species assemblages in all functional groups, as confirmed by PERMANOVA analysis. Although more abundant in oak stands, host-specific fungi were recorded in both ecosystems, revealing that exotic pine plantations can easily access fungal inocula from natural pine forests in the vicinity. However, even though the macrofungal richness in plantations is comparable with that in other native conifer forests in Europe, the community was made up of generalists, i.e., species that were not habitat specialists. In contrast, rarely reported, uncommon fungi were recorded in oak plots, revealing the importance of residual, native forest patches for fungal conservation.
The evolution of genomic GC content undergoes a rapid reversal within the genusPlasmodium
Authors: Nikbakht Hamid , Xia Xuhua , Hickey Donal A.
Published: January 2015

The genome of the malarial parasite Plasmodium falciparum is extremely AT rich. This bias toward a low GC content is a characteristic of several, but not all, species within the genus Plasmodium. We compared 4283 orthologous pairs of protein-coding sequences between Plasmodium falciparum and the less AT-biased Plasmodium vivax. Our results indicate that the common ancestor of these two species was also extremely AT rich. This means that, although there was a strong bias toward A+T during the early evolution of the ancestral Plasmodium lineage, there was a subsequent reversal of this trend during the more recent evolution of some species, such as P. vivax. Moreover, we show that not only is the P. vivax genome losing its AT richness, it is actually gaining a very significant degree of GC richness. This example illustrates the potential volatility of nucleotide content during the course of molecular evolution. Such reversible fluxes in nucleotide content within lineages could have important implications for phylogenetic reconstruction based on molecular sequence data.
Multi-Level Residue Harmonic Balance Method for the Transmission Loss of a Nonlinearly Vibrating Perforated Panel
Authors: Lee Y. Y.
Published: January 2015

This paper investigates the transmission loss of a nonlinearly vibrating perforated panel using the multi-level residue harmonic balance method. The coupled governing differential equations which represent the air mass movement at each hole and the nonlinear panel vibration are developed. The proposed analytical solution method, which is revised from a previous harmonic balance method for single mode problems, is newly applied for solving the coupled differential equations. The main advantage of this solution method is that only one set of nonlinear algebraic equations is generated in the zero level solution procedure while the higher level solutions to any desired accuracy can be obtained by solving a set of linear algebraic equations. The results obtained from the multi-level residue harmonic balance method agree reasonably with those obtained from a numerical integration method. In the parametric study, the velocity amplitude convergences have been checked. The effects of excitation level, perforation ratio, diameter of hole, and panel thickness are examined.
Large-Area, Multilayered, and High-Resolution Visual Monitoring Using a Dual-Camera System
Authors: Lin Chih-Wei , Chen Kuan-Wen , Chen Shen-Chi , Chen Cheng-Wu , Hung Yi-Ping
Published: January 2015

Large-area, high-resolution visual monitoring systems are indispensable in surveillance applications. To construct such systems, high-quality image capture and display devices are required. Whereas high-quality displays have rapidly developed, as exemplified by the announcement of the 85-inch 4K ultrahigh-definition TV by Samsung at the 2013 Consumer Electronics Show (CES), high-resolution surveillance cameras have progressed slowly and remain not widely used compared with displays. In this study, we designed an innovative framework, using a dual-camera system comprising a wide-angle fixed camera and a high-resolution pan-tilt-zoom (PTZ) camera to construct a large-area, multilayered, and high-resolution visual monitoring system that features multiresolution monitoring of moving objects. First, we developed a novel calibration approach to estimate the relationship between the two cameras and calibrate the PTZ camera. The PTZ camera was calibrated based on the consistent property of distinct pan-tilt angle at various zooming factors, accelerating the calibration process without affecting accuracy; this calibration process has not been reported previously. After calibrating the dual-camera system, we used the PTZ camera and synthesized a large-area and high-resolution background image. When foreground targets were detected in the images captured by the wide-angle camera, the PTZ camera was controlled to continuously track the user-selected target. Last, we integrated preconstructed high-resolution background and low-resolution foreground images captured using the wide-angle camera and the high-resolution foreground image captured using the PTZ camera to generate a large-area, multilayered, and high-resolution view of the scene.