bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hierarchical analysis of spatially autocorrelated ecological data using integrated nested Laplace approximation
Authors: Beguin Julien , Martino Sara , Rue Håvard , Cumming Steven G. 
Published: May 2012

Summary1. Spatial analysis of ecological data is central to many interesting questions in ecology. Bayesian implementation of spatially explicit models has received increasing attention from ecologists as Monte Carlo Markov Chain (MCMC) methods have become freely accessible. MCMC simulations offer a flexible framework for modelling extensive ecological data, but they also come with a wide range of problems regarding convergence, processing time and implementation.2. We introduce to ecologists an alternative procedure for fitting Bayesian hierarchical spatial models (BHSM) with quite general spatial covariance structures. This procedure uses integrated nested Laplace approximations (INLA) as an alternative to MCMC.3. We show, using a case study of species distribution model with binary areal data, that implementing BHSM with INLA does not require advanced programming skills, yields accurate results compared with MCMC and is rapid (e.g. a few seconds with small to moderate data sets). BHSMs efficiently removed spatial autocorrelation in the residuals and fairly evaluated uncertainty in parameter estimates and predictions.4. The rapidity of INLA significantly decreased the processing time and allowed both sensitivity analyses on priors and cross‐validation tests to be performed within a reasonable amount of time, which ultimately increased model transparency.
Hesperidin-mediated expression of Nrf2 and upregulation of antioxidant status in senescent rat heart
Authors: Elavarasan Jayasudha , Velusamy Prema , Ganesan Thellamudhu , Ramakrishnan Suresh Krishna , Rajasekaran Devaraja , Periandavan Kalaiselvi 
Published: May 2012

Abstract

Objectives
Oxidative stress is recognized as a key element responsible for the development of age-related pathologies. A declining endogenous defence system during senescence dictates the need for supplementation with exogenous antioxidants through diet. Hesperidin is a naturally occurring flavonone present in citrus fruits and has been shown to have many biological properties, including antioxidant activity. We investigated whether hesperidin supplementation could be valuable in protecting cardiac tissue of aged rats against age-related increase in oxidative stress, as well as the mechanism by which it can boost the antioxidant status of the cell.

Methods
The activity of antioxidant enzymes, mRNA expression of Nrf2, protein levels of superoxide dismutase and catalase were measured using standard protocols.

Key findings
Hesperidin treatment effectively protected aged rat heart by increasing the activity of enzymic antioxidants. Hesperidin upregulated the protein levels of nuclear factor erythroid 2-related factor 2, which is responsible for maintaining the antioxidant status of the cell.

Conclusions
Hesperidin could be useful in protecting cardiomyocytes against age-related increase in oxidative stress mediated by Nrf2 upregulation.
Berberine suppresses amyloid-beta-induced inflammatory response in microglia by inhibiting nuclear factor-kappaB and mitogen-activated protein kinase signalling pathways
Authors: Jia Liyun , Liu Jing , Song Zhen , Pan Xiaohua , Chen Liang , Cui Xing , Wang Molin 
Published: May 2012

Abstract

Objectives
The neuroinflammation induced by amyloid-beta peptide (Aβ) is one of the key events in Alzheimer's disease (AD) progress in which microglia are the main cells involved. Berberine, one of the major constituents of Chinese herb Rhizoma coptidis, is known for its anti-inflammatory, anti-oxidative and anti-microbial activity. In this study, we examined the effects and possible underlying mechanisms of berberine in Aβ-induced neuroinflammation using murine primary microglia cells and cultured BV2 microglia cells.

Methods
The effects of berberine on Aβ-stimulated inflammatory factor expression and secretion were examined using RT-PCR and ELISA analysis. The signal pathways involved in berberine's effects were also investigated using Western blot and immunofluorescence analysis.

Results
In primary microglial and BV2 cells, berberine treatment significantly inhibited Aβ-stimulated production of interleukin-6 and monocyte chemotactic protein-1. Berberine treatment down-regulated the expression of cyclo-oxygenase-2 and induced nitric oxide synthase in these cells. Moreover, berberine strongly inhibited the nuclear factor-kappaB (NF-κB) activation, presumably through blocking the phosphoinositide 3-kinase/protein kinase B and mitogen-activated protein kinase signalling pathways.

Conclusions
Our data indicated berberine is a potent suppressor of neuroflammation, presumably through inhibition of NF-κB activation, and suggested berberine has therapeutic potential for the treatment of neuroinflammation that is involved in neurological diseases such as AD.
Comparative study of liposomes, transfersomes, ethosomes and cubosomes for transcutaneous immunisation: characterisation and in vitro skin penetration
Authors: Rattanapak Teerawan , Young Katie , Rades Thomas , Hook Sarah 
Published: May 2012

Abstract

Objectives
Lipid colloidal vaccines, including liposomes, transfersomes, ethosomes and cubosomes, were formulated, characterised and investigated for their ability to enhance penetration of a peptide vaccine through stillborn piglet skin in vitro.

Methods
Liposomes and transfersomes were formulated using a film-hydration method, ethosomes using a modified reverse phase method and cubosomes using a lipid precursor method. The size, zeta potential, peptide loading and interfacial behaviour of the formulations were characterised. Skin penetration studies were performed using Franz diffusion cells with piglet skin as the membrane. The localization of peptide in the skin was examined using confocal laser scanning microscopy.

Key finding
The various formulations contained negatively charged particles of similar size (range: 134–200 nm). Addition of the saponin adjuvant Quil A to the formulations destabilised the monolayers and reduced peptide loading. Cubosomes and ethosomes showed superior skin retention compared with the other systems. Confocal laser scanning microscopy showed greater peptide penetration and accumulation in the skin treated with cubosomes and ethosomes. With the other systems peptide was only located in the vicinity of the hair follicles and within the hair shaft.

Conclusions
We conclude from the in-vitro studies that cubosomes and ethosomes are promising lipid carriers for transcutaneous immunisation.
Relationship of insulin, glucose, leptin, IL‐6 and TNF‐α in human breast milk with infant growth and body composition
Authors: Fields D. A. , Demerath E. W. 
Published: May 2012

SummaryBackgroundNumerous appetite, growth, obesity‐related hormones and inflammatory factors are found in human breast‐milk, but there is little evidence on their relationship with infant body composition.ObjectvieThe purpose of the present cross‐sectional pilot study was to assess the cross‐sectional associations of appetite‐regulating hormones and growth factors (leptin, insulin and glucose) and inflammatory factors (interleukin 6 (IL‐6) and tumor necrosis factor alpha (TNF‐α)) in human breast‐milk with infant size, adiposity, and lean tissue at 1‐month of age in healthy term infants.MethodsHuman breast‐milk was collected from nineteen exclusively breast‐feeding mothers using one full breast expression between 8:00 and 10:00 a.m. The milk was then mixed, aliquoted, stored at −80°C and then centrifuged to remove the milk fat, prior to analyses using commercially available immunoassay kits; milk analytes were natural log transformed prior to analysis. Infant body composition was assessed using a Lunar iDXA v11‐30.062 scanner (Infant whole body analysis enCore 2007 software, GE, Fairfield, CT).ResultsMaternal pre‐pregnancy BMI was positively associated with milk leptin concentration (P = 0.0027), and so maternal‐BMI‐adjusted Spearman correlations were examined between breast‐milk analytes and infant growth and body composition variables. As previously reported, greater milk leptin was associated with lower BMIZ (BMI‐for‐age z‐score based on WHO 2006 growth charts; r = −0.54, P = 0.03). Glucose was positively associated with relative weight (r = 0.6, P = 0.01), and both fat and lean mass (0.43–0.44, P < 0.10). Higher concentrations of milk insulin were associated with lower infant weight, relative weight, and lean mass (r = −0.49–0.58, P < 0.06). Higher milk IL‐6 was associated with lower relative weight, weight gain, percent fat, and fat mass (r = −0.55–0.70, P< 0.03 for all), while higher TNF‐α was associated with lower lean mass (r = −0.58, P = 0.05), but not measures of adiposity.ConclusionsThese preliminary data suggest for the first time that in the first months of life, breast‐milk concentrations of insulin, glucose, IL‐6 and TNF‐α, in addition to leptin, may be bioactive and differentially influence the accrual of fat and lean body mass.
Groups acting simply transitively on vertex sets of hyperbolic triangular buildings
Authors: Carbone Lisa , Kangaslampi Riikka , Vdovina Alina 
Published: May 2012

AbstractWe construct and classify all groups given by triangular presentations associated to the smallest thick generalized quadrangle that act simply transitively on the vertices of hyperbolic triangular buildings of the smallest non-trivial thickness. Our classification yields 23 non-isomorphic torsion-free groups (which were obtained in an earlier work) and 168 non-isomorphic torsion groups acting on one of two possible buildings with the smallest thick generalized quadrangle as the link of each vertex. In analogy with the $\widetilde {A}_2$ case, we find both torsion and torsion-free groups acting on the same building.
Potential increase in biological effectiveness from field timing optimization for stereotactic body radiation therapy
Authors: Schmitt Jonathan D. , Warren Graham W. , Wang Iris Z. 
Published: May 2012

Purpose:Stereotactic body radiation therapy (SBRT) is a radiotherapy technique which uses high dose fractions with multiple coplanar and noncoplanar beams. Due to the large fractional doses, treatments are typically protracted and there are more fields than in conventional radiation treatment schemes. The effect of temporal optimization on the biological effectiveness of SBRT is not well established.Methods:In a cohort of actual SBRT patient treatments, the Lea–Catcheside protraction factor (G‐value) was used to determine the optimal () and the least favorable (V) field. An actual field timing delivered in the clinic was included (C) for comparison. The lethal potential lethal (LPL) model was used to quantify the difference in survival fractions. Published data from three cell lines for non‐small cell lung cancers: H460, H660, and H157 were used to acquire the parameters needed by the LPL model. The results are expressed as the ratios and , where N is the number fractions in the SBRT protocols and , V, and C are the survival fractions calculated from the corresponding temporal patterns.Results:The results indicate that variability in the dose rate between fields does impact the optimization results. This dependence on dose rate, however, is small compared to the impact from the variability in doses between fields. The optimized field arrangements resembled previous studies, that maximization of cell kill is achieved by orienting the fields in a shape sequence, where the fields with greatest dose are positioned in the center. Minimization of cell kill was achieved with a V‐shaped orientation. Smallest dose fields were positioned centrally, and higher dose fields were placed in the beginning and end of the fraction. The survival fraction ratios calculated using the LPL demonstrated that regardless of the cell type the shape had lower cell survival fractions compared to both the clinical example (C) and the V arrangement. For H460, with  = 0.25 h, an average ratio of , suggesting the pattern is approximately 14 times more effective than the clinical plan, after 5 fractions.Conclusions:Rearranging field timing for a SBRT treatment so that maximal dose is deposited in the central fields of treatment may optimize cell kill and potentially affect overall treatment outcome.
A hybrid electron and photon IMRT planning technique that lowers normal tissue integral patient dose using standard hardware
Authors: Rosca Florin 
Published: May 2012

Purpose:To present a mixed electron and photon IMRT planning technique using electron beams with an energy range of 6–22 MeV and standard hardware that minimizes integral dose to patients for targets as deep as 7.5 cm.Methods:Ten brain cases, two lung, a thyroid, an abdominal, and a parotid case were planned using two planning techniques: a photon‐only IMRT (IMRT) versus a mixed modality treatment (E + IMRT) that includes anenface electron beam and a photon IMRT portion that ensures a uniform target coverage. The electron beam is delivered using a regular cutout placed in an electron cone. The electron energy was chosen to provide a good trade‐off between minimizing integral dose and generating a uniform, deliverable plan. The authors choose electron energies that cover the deepest part of PTV with the 65%–70% isodose line. The normal tissue integral dose, the dose for ring structures around the PTV, and the volumes of the 75%, 50%, and 25% isosurfaces were used to compare the dose distributions generated by the two planning techniques.Results:The normal tissue integral dose was lowered by about 20% by the E + IMRT plans compared to the photon‐only IMRT ones for most studied cases. With the exception of lungs, the dose reduction associated to the E + IMRT plans was more pronounced further away from the target. The average dose ratio delivered to the 0–2 cm and the 2–4 cm ring structures for brain patients for the two planning techniques were 89.6% and 70.8%, respectively. The enhanced dose sparing away from the target for the brain patients can also be observed in the ratio of the 75%, 50%, and 25% isodose line volumes for the two techniques, which decreases from 85.5% to 72.6% and further to 65.1%, respectively. For lungs, the lateral electron beams used in the E + IMRT plans were perpendicular to the mostly anterior/posterior photon beams, generating much more conformal plans.Conclusions:The authors proved that even using the existing electron delivery hardware, a mixed electron/photon planning technique (E + IMRT) can decrease the normal tissue integral dose compared to a photon‐only IMRT plan. Different planning approaches can be enabled by the use of an electron beam directed toward organs at risk distal to the target, which are still spared due the rapid dose fall‐off of the electron beam. Examples of such cases are the lateral electron beams in the thoracic region that do not irradiate the heart and contralateral lung, electron beams pointed toward kidneys in the abdominal region, or beams treating brain lesions pointed toward the brainstem or optical apparatus. For brain, electron vertex beams can also be used without irradiating the whole body. Since radiation retreatments become more and more common, minimizing the normal tissue integral dose and the dose delivered to tissues surrounding the target, as enabled by E + IMRT type techniques, should receive more attention.
On proton CT reconstruction using MVCT‐converted virtual proton projections
Authors: Wang Dongxu , Mackie T. Rockwell , Tomé Wolfgang A. 
Published: May 2012

Purpose:To describe a novel methodology of converting megavoltage x‐ray projections into virtual proton projections that are otherwise missing due to the proton range limit. These converted virtual proton projections can be used in the reconstruction of proton computed tomography (pCT).Methods:Relations exist between proton projections and multispectral megavoltage x‐ray projections for human tissue. Based on these relations, these tissues can be categorized into: (a) adipose tissue; (b) nonadipose soft tissues; and (c) bone. These three tissue categories can be visibly identified on a regular megavoltage x‐ray computed tomography (MVCT) image. With an MVCT image and its projection data available, the x‐ray projections through heterogeneous anatomy can be converted to the corresponding proton projections using predetermined calibration curves for individual materials, aided by a coarse segmentation on the x‐ray CT image. To show the feasibility of this approach, mathematical simulations were carried out. The converted proton projections, plotted on a proton sinogram, were compared to the simulated ground truth. Proton stopping power images were reconstructed using either the virtual proton projections only or a blend of physically available proton projections and virtual proton projections that make up for those missing due to the range limit. These images were compared to a reference image reconstructed from theoretically calculated proton projections.Results:The converted virtual projections had an uncertainty of ±0.8% compared to the calculated ground truth. Proton stopping power images reconstructed using a blend of converted virtual projections (48%) and physically available projections (52%) had an uncertainty of ±0.86% compared with that reconstructed from theoretically calculated projections. Reconstruction solely from converted virtual proton projections had an uncertainty of ±1.1% compared with that reconstructed from theoretical projections. If these images are used for treatment planning, the average proton range uncertainty is estimated to be less than 1.5% for an imaging dose in the milligray range.Conclusions:The proposed method can be used to convert x‐ray projections into virtual proton projections. The converted proton projections can be blended with existing proton projections or can be used solely for pCT reconstruction, addressing the range limit problem of pCT using current therapeutic proton machines.
Investigations of cabin design in UV phototherapy
Authors: Grimes David Robert , Martin Colin J , Phanco Graeme 
Published: May 2012

Purpose:UVR phototherapy cabins exist in a huge variety of configurations and geometries. An accurate dose model has been developed which can be used to examine the question of cabin design to investigate factors influencing dose on a patient.Methods:This work extends the existing dose model to entire cabins and investigates how cabin and reflector geometry influence resultant dose.Results:The model predictions are in line with what is measured. It is found that the length and angle of the reflectors have a large influence on received dose.Conclusions:The influence of cabin geometry is important in estimating patient dose, and the findings of this work are applicable to future cabin designs.
Establishing a standard calibration methodology for MOSFET detectors in computed tomography dosimetry
Authors: Brady S. L. , Kaufman R. A. 
Published: May 2012

Purpose:The use of metal‐oxide‐semiconductor field‐effect transistor (MOSFET) detectors for patient dosimetry has increased by ∼25% since 2005. Despite this increase, no standard calibration methodology has been identified nor calibration uncertainty quantified for the use of MOSFET dosimetry in CT. This work compares three MOSFET calibration methodologies proposed in the literature, and additionally investigates questions relating to optimal time for signal equilibration and exposure levels for maximum calibration precision.Methods:The calibration methodologies tested were (1) free in‐air (FIA) with radiographic x‐ray tube, (2) FIA with stationary CT x‐ray tube, and (3) within scatter phantom with rotational CT x‐ray tube. Each calibration was performed at absorbed dose levels of 10, 23, and 35 mGy. Times of 0 min or 5 min were investigated for signal equilibration before or after signal read out.Results:Calibration precision was measured to be better than 5%–7%, 3%–5%, and 2%–4% for the 10, 23, and 35 mGy respective dose levels, and independent of calibration methodology. No correlation was demonstrated for precision and signal equilibration time when allowing 5 min before or after signal read out. Differences in average calibration coefficients were demonstrated between the FIA with CT calibration methodology 26.7 ± 1.1 mV cGy−1 versus the CT scatter phantom 29.2 ± 1.0 mV cGy−1 and FIA with x‐ray 29.9 ± 1.1 mV cGy−1 methodologies. A decrease in MOSFET sensitivity was seen at an average change in read out voltage of ∼3000 mV.Conclusions:The best measured calibration precision was obtained by exposing the MOSFET detectors to 23 mGy. No signal equilibration time is necessary to improve calibration precision. A significant difference between calibration outcomes was demonstrated for FIA with CT compared to the other two methodologies. If the FIA with a CT calibration methodology was used to create calibration coefficients for the eventual use for phantom dosimetry, a measurement error ∼12% will be reflected in the dosimetry results. The calibration process must emulate the eventual CT dosimetry process by matching or excluding scatter when calibrating the MOSFETs. Finally, the authors recommend that the MOSFETs are energy calibrated approximately every 2500–3000 mV.
Molecular Detection of Plasmodium knowlesi in a Dutch Traveler by Real-Time PCR
Authors: Link Lonneke , Bart Aldert , Verhaar Nienke , van Gool Tom , Pronk Marjolijn , Scharnhorst Volkher 
Published: May 2012

ABSTRACT

Plasmodium knowlesi
infection with low parasitemia presents a diagnostic challenge, as rapid diagnostic tests are often negative and identification to the species level by microscopy is difficult.
P. knowlesi
malaria in a traveler is described, and real-time PCR is demonstrated to support fast and reliable diagnosis and identification to the species level.
Crystal Structure of the Superfamily 1 Helicase from Tomato Mosaic Virus
Authors: Nishikiori Masaki , Sugiyama Shigeru , Xiang Hongyu , Niiyama Mayumi , Ishibashi Kazuhiro , Inoue Tsuyoshi , Ishikawa Masayuki , Matsumura Hiroyoshi , Katoh Etsuko 
Published: May 2012

ABSTRACT

The genomes of the
Tomato mosaic virus
and many other plant and animal positive-strand RNA viruses of agronomic and medical importance encode superfamily 1 helicases. Although helicases play important roles in viral replication, the crystal structures of viral superfamily 1 helicases have not been determined. Here, we report the crystal structure of a fragment (S666 to Q1116) of the replication protein from
Tomato mosaic virus
. The structure reveals a novel N-terminal domain tightly associated with a helicase core. The helicase core contains two RecA-like α/β domains without any of the accessory domain insertions that are found in other superfamily 1 helicases. The N-terminal domain contains a flexible loop, a long α-helix, and an antiparallel six-stranded β-sheet. On the basis of the structure, we constructed deletion mutants of the S666-to-Q1116 fragment and performed split-ubiquitin-based interaction assays in
Saccharomyces cerevisiae
with TOM1 and ARL8, host proteins that are essential for tomato mosaic virus RNA replication. The results suggested that both TOM1 and ARL8 interact with the long α-helix in the N-terminal domain and that TOM1 also interacts with the helicase core. Prediction of secondary structures in other viral superfamily 1 helicases and comparison of those structures with the S666-to-Q1116 structure suggested that these helicases have a similar fold. Our results provide a structural basis of viral superfamily 1 helicases.