bluuebunny/crossref_metadata_2025 huggingface dataset:
Inflow effects on hemodynamic responses characterized by event‐related using gradient‐echo EPI sequences
Authors: Liu Ho‐Ling , Wei Pei‐Shan , Wai Yau‐Yau , Kuan Wan‐Chun , Huang Chih‐Mao , Wu Changwei W. , Buckle Christopher , Wan Yung‐Liang , Gao Jia‐Hong
Published: October 2008

The purpose of this study is to determine whether blood inflow impacts the temporal behavior of BOLD‐contrast signal changes in a typical event‐related paradigm. The inflow contributions in the hemodynamic response to repeated single trials of short visual stimulation were assessed with a gradient‐echo EPI sequence by altering the flip angle (FA) from 30° to 90° at a repetition time of . For each FA condition (30°, 60°, and 90°), 30 trials were performed on 15 healthy volunteers on a 3T MRI scanner. Comparing the percent BOLD contrast, prominent inflow effects were found with statistical significance between the 90°‐ and 30°‐FA conditions ( versus , ). BOLD responses with exhibited latencies significantly slower than those with ( versus , ). The falling time of the 30°‐FA responses was earlier but not statistically different from that of the 90°‐FA ( versus , . Using a voxelwise analysis, the latency variations of the activated visual areas were determined at several contrast‐to‐noise ratio (CNR) levels (controlled by averaging different numbers of randomly selected trials). The latency variations from the 90°‐FA responses were greater at lower CNR but similar at higher CNR levels when comparing to the 30°‐FA ones. This study suggests that inflow effects contribute to the BOLD signal, resulting in hemodynamic response with shorter latency.
Statistical process control for IMRT dosimetric verification
Authors: Breen Stephen L. , Moseley Douglas J. , Zhang Beibei , Sharpe Michael B.
Published: October 2008

Patient‐specific measurements are typically used to validate the dosimetry of intensity‐modulated radiotherapy (IMRT). To evaluate the dosimetric performance over time of our IMRT process, we have used statistical process control (SPC) concepts to analyze the measurements from 330 head and neck (H&N) treatment plans. The objectives of the present work are to: (i) Review the dosimetric measurements of a large series of consecutive head and neck treatment plans to better understand appropriate dosimetric tolerances; (ii) analyze the results with SPC to develop action levels for measured discrepancies; (iii) develop estimates for the number of measurements that are required to describe IMRT dosimetry in the clinical setting; and (iv) evaluate with SPC a new beam model in our planning system. H&N IMRT cases were planned with the PINNACLE3 treatment planning system versions 6.2b or 7.6c (Philips Medical Systems, Madison, WI) and treated on Varian (Palo Alto, CA) or Elekta (Crawley, UK) linacs. As part of regular quality assurance, plans were recalculated on a ‐diam cylindrical phantom, and ion chamber measurements were made in high‐dose volumes (the PTV with highest dose) and in low‐dose volumes (spinal cord organ‐at‐risk, OR). Differences between the planned and measured doses were recorded as a percentage of the planned dose. Differences were stable over time. Measurements with PINNACLE3 6.2b and Varian linacs showed a mean difference of 0.6% for PTVs (, range, to 6.6%), while OR measurements showed a larger systematic discrepancy (mean , range to 16.3%) that was due to well‐known limitations of the MLC model in the earlier version of the planning system. Measurements with PINNACLE3 7.6c and Varian linacs demonstrated a mean difference of 0.2% for PTVs (, range, , to 5.0%) and for ORs (range to 4.4%). The capability index (ratio of specification range to range of the data) was 1.3 for the PTV data, indicating that almost all measurements were within . We have used SPC tools to evaluate a new beam model in our planning system to produce a systematic difference of for PTVs and 0.4% for ORs, although the number of measurements is smaller . Analysis of this large series of H&N IMRT measurements demonstrated that our IMRT dosimetry was stable over time and within accepted tolerances. These data provide useful information for assessing alterations to beam models in the planning system. IMRT is enhanced by the addition of statistical process control to traditional quality control procedures.
Isolated kidney phantom for development of biothermal vascular models with application to high intensity focused ultrasound therapy
Authors: Payne Allison H. , Goodrich K. Craig , Kholmovski Eugene G. , Roemer Robert B. , Parker Dennis L.
Published: October 2008

A methodology using magnetic resonance angiography (MRA) is presented for identifying thermally significant blood vessels in isolated kidneys, specifically for use in biothermal model development with application to high intensity focused ultrasound (HIFU). A combination of a proven preservation technique, newly developed MR‐compatible experimental procedures and the refinement of MR pulse sequence parameters was used to determine vascular characteristics using high‐resolution three‐dimensional time‐of‐flight MRA image of flow through isolated kidneys. Results presented are twofold. First, improved vessel visibility was attained through decreasing the magnetic resonance imaging bandwidth from while simultaneously increasing the echo time, repetition time, and flip angle; vascular center line extraction showed an 18% improvement in the number of vessel segments detected and a 23% increase in length of the terminal segments over a base line technique without improvements. Second, the overall system was shown to be practical to determine vascular flow effects during HIFU heating; testing results from heating the kidney with HIFU are presented, showing a decrease of average kidney temperature with an increase of flow rate through the kidney with localized cooling demonstrated surrounding known vessel locations.
A theoretical framework for prescribing radiotherapy dose distributions using patient‐specific biological information
Authors: South C. P. , Partridge M. , Evans P. M.
Published: October 2008

We present a formalism for using functional imaging both to derive patient‐specific radiobiological properties and consequently to prescribe optimal nonuniform radiotherapy dose distributions. The ability to quantitatively assess the response to an initial course of radiotherapy would allow the derivation of radiobiological parameters for individual patients. Both an iterative optimization and an analytical approach to this problem were investigated and illustrated by application to the linear‐quadratic model of cell killing using simulated parametric data for a modeled tumor. Potential gains in local control were assessed by comparing uniform dose distributions with optimized dose distributions of equal integral dose. The effect on local prescribed dose of variations in effective radiosensitivity, tumor burden, and proliferation rate was investigated, with results suggesting that dose variations would be significant but clinically achievable. The sensitivity of derived parameters to image noise and the effect of varying the initial fractionation and imaging schedule were assessed. The analytical approach proved remarkably robust, with 10% image noise resulting in dose errors of approximately 1% for a clinically relevant set of parameters. Potential benefits were demonstrated by using this formalism to prescribe nonuniform dose distributions for model tumors using a range of literature‐derived parameters. The redistribution of dose improved tumor control probability by factors between 1.03 and 4.27 for a range of model tumors.
Temperature and hydration effects on absorbance spectra and radiation sensitivity of a radiochromic medium
Authors: Rink Alexandra , Lewis David F. , Varma Sangya , Vitkin I. Alex , Jaffray David A.
Published: October 2008

The effects of temperature on real time changes in optical density of GAFCHROMIC® EBT film were investigated. The spectral peak of maximum change in absorbance was shown to downshift linearly when the temperature of the film was increased from . The values were also shown to decrease linearly with temperature, and this decrease could not be attributed to the shift in . A compensation scheme using and a temperature‐dependent correction factor was investigated, but provided limited improvement. Part of the reason may be the fluctuations in hydration of the active component, which were found to affect both position of absorbance peaks and the sensitivity of the film. To test the effect of hydration, laminated and unlaminated films were desiccated. This shifted both the major and minor absorbance peaks in the opposite direction to the change observed with temperature. The desiccated film also exhibited reduced sensitivity to ionizing radiation. Rehydration of the desiccated films did not reverse the effects, but rather gave rise to another form of the polymer with absorbance maxima upshifted further . Hence, the spectral characteristics and sensitivity of the film can be dependent on its history, potentially complicating both real‐time and conventional radiation dosimetry.
Optimization of couch translational corrections to compensate for rotational and deformable target deviations in image guided radiotherapy
Authors: Yue Ning J. , Kim Sung , Lewis Brett E. , Jabbour Salma , Narra Venkat , Goyal Sharad , Haffty Bruce G.
Published: October 2008

The utilization of image‐guided radiotherapy (IGRT) technologies helps correct temporal and spatial deviations of the target volume relative to planned radiation beams. With the aid of these IGRT technologies, it becomes possible to better identify the target volume before and even during radiation treatment. However, since components of the detected deviations may be translational, rotational, and deformable, the question remains whether simple treatment‐couch translational movement can be optimized to compensate for these complicated deviations. Deviation of the target volume and changes in patient body shape from that acquired for treatment planning may further add to the variations from planned dose distribution. In this study, an optimization strategy is developed to investigate these issues. The optimization process involved the use of the hill climbing algorithm, the detected target volume and patient body shape, and the dose distribution based on acquired images at treatment. During the process, the planned dose distribution was iteratively adjusted to reflect the changes of depth and distance as the translational treatment couch movement was being optimized. The optimal treatment couch movement was considered achieved when the highest fraction of the detected target volume was covered by prescription dose. This optimization strategy was evaluated on clinical prostate cancer cases. For each of the cases, cone beam computed tomography (CBCT) images were acquired right after fiducial marker‐based kilovolt orthogonal imaging verification and setup adjustment. Based on the CBCT images, the clinical target volume at the treatment was delineated and the translational treatment‐couch movements were optimized with the developed strategy. The resultant dose coverage was compared to that without the optimization. The results showed that with the present strategy, rotational and deformable target deviations can be further compensated with translational couch correction.
Peripheral dose measurements for 6 and photon beams on a linear accelerator with multileaf collimator
Authors: Mazonakis Michalis , Zacharopoulou Fotini , Varveris Haralambos , Damilakis John
Published: October 2008

Peripheral dose (PD) to critical structures outside treatment volume is of clinical importance. The aim of the current study was to estimate PD on a linear accelerator equipped with multileaf collimator (MLC). Dose measurements were carried out using an ionization chamber embedded in a water phantom for 6 and photon beams. PD values were acquired for field sizes from in increments of at distances up to from the field edge. Dose data were obtained at two collimator orientations where the measurement points are shielded by MLC and jaws. The variation of PD with the source to skin distance (SSD), depth, and lateral displacement of the measurement point was evaluated. To examine the dependence of PD upon the tissue thickness at the entrance point of the beam, scattered dose was measured using thermoluminescent dosemeters placed on three anthropomorphic phantoms simulating 5‐ and ‐old children and an average adult patient. PD from photons varied from 0.13% to 6.75% of the central‐axis maximum dose depending upon the collimator orientation, extent of irradiated area, and distance from the treatment field. The corresponding dose range from x rays was 0.09% to 5.61%. The variation of PD with depth and with lateral displacements up to 80% of the field dimension was very small. The scattered dose from both photon beams increased with the increase of SSD or tissue thickness along beam axis. The presented dosimetric data set allows the estimation of scattered dose outside the primary beam.
Noninvasive photoacoustic imaging of the thoracic cavity and the kidney in small and large animals
Authors: Song Kwang Hyun , Wang Lihong V.
Published: October 2008

The internal organs of rats and rabbits were clearly imaged noninvasively using a deeply penetrating reflection‐mode photoacoustic imaging system. This imaging system had previously been found to provide an imaging depth limit of . In the thoracic cavity, major blood vessels connecting to the heart were imaged, and the right atrium was imaged as deeply as . In the abdominal cavities, the kidney and vena cava inferior were also imaged in situ. The vena cava inferior deep was imaged. The kidney of a New Zealand white rabbit was also imaged. This study shows the deep internal organ imaging capability of the system in animals. This technology can potentially be used to study tumors in internal organs, and be adapted to clinical diagnosis.
Prospective displacement and velocity‐based cine 4D CT
Authors: Langner U. W. , Keall P. J.
Published: October 2008

Four dimensional (4D) computed tomography (CT) image sorting is currently a retrospective procedure. Mismatches in displacement and/or phase of a patient's respiratory signal, corresponding with two dimensional images taken at subsequent couch positions, become visible as artifacts in reconstructed 4D CT images. These artifacts appear as undefined or irregular boundaries in the 4D CT images and cause systematic errors in patient contouring and dose calculations. In addition, the substantially higher dose required for 4D CT, compared with 3D CT, is of concern. To minimize these problems, we developed a prospective respiratory displacement and velocity based cine 4D CT (PDV CT) method to trigger image acquisition if the displacement and velocity of the respiratory signal occurred within predetermined tolerances simultaneously. The use of velocity avoids real‐time phase estimation. Real‐time image acquisition ensures data sufficiency, while avoiding the need for redundant data. This may potentially result in a lower dose to the patient. PDV CT was compared with retrospective 4D CT acquisition methods, using respiratory signals of 24 lung cancer patients (103 sessions) under free breathing conditions. Image acquisition was simulated for each of these sessions from the respiratory signal. The root mean square (RMS) of differences between displacements and velocities of the respiratory signal corresponding to subsequent images was calculated in order to evaluate the image‐sorting accuracy of each method. Patient dose reductions of 22 to 50% were achieved during image acquisition depending on the model parameters chosen. The mean RMS differences over all sessions and image bins show that PDV CT produces similar results to retrospective displacement sorting overall, although improvements of the RMS difference up to 20% were achieved depending on the model parameters chosen. Velocity RMS differences improved between 30 and 45% when compared with retrospective phase sorting. The efficiency in acquisition compared with retrospective phase sorting varied from for displacement and velocity tolerances of and , respectively, to 80 to 93% for and . The lower variation in the displacement and velocity of the respiratory signal in each image bin indicates that PDV CT could be a valuable tool for reducing artifacts in 4D CT images and lowering patient dose, although the cost may be increased acquisition time.
Quantitative comparison of imaging performance of x‐ray interferometric imaging and diffraction enhanced imaging
Authors: Akio Yoneyama , Jin Wu , Kazuyuki Hyodo , Tohoru Takeda
Published: October 2008

For detailed biomedical observations using the optimum phase‐contrast x‐ray imaging, quantitative comparisons of imaging performances of two major imaging methods—x‐ray interferometric imaging (XII) and diffraction enhanced imaging (DEI)—were performed. Density sensitivity and spatial resolution of each imaging method were evaluated using phantom tomograms obtained by each method with the same x‐ray dosage. For practical comparison of the methods, biological samples were also observed under the same conditions. The results show that XII has a higher sensitivity than that of DEI and is thus suitable for observation of soft biological tissues. On the other hand, DEI has a wider dynamic range of density and is thus suitable for observation of samples with large differences in density of different regions.
X‐ray scattering for classifying tissue types associated with breast disease
Authors: Sidhu Sabeena , Siu Karen K. W. , Falzon Gregory , Nazaretian Simon , Hart Stewart A. , Fox Jane G. , Susil Beatrice J. , Lewis Robert A.
Published: October 2008

Collagen types I and III can be characterized at the molecular level (at the tens to hundreds of nanometers scale) using small angle x‐ray scattering (SAXS). Although collagen fibril structural parameters at this length scale have shown differences between diseased and nondiseased breast tissues, a comprehensive analysis involving a multitude of features with a large patient cohort has not previously been investigated. Breast tissue samples were excised from 80 patients presenting with either a breast lump or reduction mammoplasty. From these, invasive carcinoma, benign tissue, and normal parenchyma were analyzed. Parameters related to collagen structure, including longitudinal (axial) and lateral (equatorial) features, polar angle features, total scattering intensity, and tissue heterogeneity effects, were extracted from the SAXS patterns and examined. The amplitude of the third‐order axial peak and the total scattering intensity (amorphous scatter) showed the most separation between tissue groups and a classification model using these two parameters demonstrated an accuracy of over 95% between invasive carcinoma and mammoplasty patients. Normal tissue taken from disease‐free patients (mammoplasty) and normal tissue taken from patients with presence of disease showed significant differences, suggesting that SAXS may provide different diagnostic information from that of conventional histopathology.
Dosimetric characteristics of Novalis Tx system with high definition multileaf collimator
Authors: Chang Zheng , Wang Zhiheng , Wu Q. Jackie , Yan Hui , Bowsher Jim , Zhang Junan , Yin Fang‐Fang
Published: October 2008

A new Novalis Tx system equipped with a high definition multileaf collimator (HDMLC) recently became available to perform both image‐guided radiosurgery and conventional radiotherapy. It is capable of delivering a highly conformal radiation dose with three energy modes: photon energy, photon energy, and photon energy in a stereotactic radiosurgery mode with dose rate. Dosimetric characteristics of the new Novalis Tx treatment unit with the HDMLC are systematically measured for commissioning. A high resolution diode detector and miniion‐chamber detector are used to measure dosimetric data for a range of field sizes from . The commissioned Novalis Tx system has passed the RPC stereotactic radiosurgery head phantom irradiation test. The Novalis Tx system not only expands its capabilities with three energy modes, but also achieves better beam conformity and sharer beam penumbra with HDMLC. Since there is little beam data information available for the new Novalis Tx system, we present in this work the dosimetric data of the new modality for reference and comparison.
Binary and multi‐category ratings in a laboratory observer performance study: A comparison
Authors: Gur David , Bandos Andriy I. , King Jill L. , Klym Amy H. , Cohen Cathy S. , Hakim Christiane M. , Hardesty Lara A. , Ganott Marie A. , Perrin Ronald L. , Poller William R. , Shah Ratan , Sumkin Jules H. , Wallace Luisa P. , Rockette Howard E.
Published: October 2008

The authors investigated radiologists, performances during retrospective interpretation of screening mammograms when using a binary decision whether to recall a woman for additional procedures or not and compared it with their receiver operating characteristic (ROC) type performance curves using a semi‐continuous rating scale. Under an Institutional Review Board approved protocol nine experienced radiologists independently rated an enriched set of 155 examinations that they had not personally read in the clinic, mixed with other enriched sets of examinations that they had individually read in the clinic, using both a screening BI‐RADS rating scale (recall/not recall) and a semi‐continuous ROC type rating scale (0 to 100). The vertical distance, namely the difference in sensitivity levels at the same specificity levels, between the empirical ROC curve and the binary operating point were computed for each reader. The vertical distance averaged over all readers was used to assess the proximity of the performance levels under the binary and ROC‐type rating scale. There does not appear to be any systematic tendency of the readers towards a better performance when using either of the two rating approaches, namely four readers performed better using the semi‐continuous rating scale, four readers performed better with the binary scale, and one reader had the point exactly on the empirical ROC curve. Only one of the nine readers had a binary “operating point” that was statistically distant from the same reader's empirical ROC curve. Reader‐specific differences ranged from to 0.128 with an average width of the corresponding 95% confidence intervals of 0.2 and ‐values ranging for individual readers from 0.050 to 0.966. On average, radiologists performed similarly when using the two rating scales in that the average distance between the run in individual reader's binary operating point and their ROC curve was close to zero. The 95% confidence interval for the fixed‐reader average (0.016) was (, 0.0631) (two‐sided ‐value 0.35). In conclusion the authors found that in retrospective observer performance studies the use of a binary response or a semi‐continuous rating scale led to consistent results in terms of performance as measured by sensitivity‐specificity operating points.
4D‐CT motion estimation using deformable image registration and 5D respiratory motion modeling
Authors: Yang Deshan , Lu Wei , Low Daniel A. , Deasy Joseph O. , Hope Andrew J. , El Naqa Issam
Published: October 2008

Four‐dimensional computed tomography (4D‐CT) imaging technology has been developed for radiation therapy to provide tumor and organ images at the different breathing phases. In this work, a procedure is proposed for estimating and modeling the respiratory motion field from acquired 4D‐CT imaging data and predicting tissue motion at the different breathing phases. The 4D‐CT image data consist of series of multislice CT volume segments acquired in ciné mode. A modified optical flow deformable image registration algorithm is used to compute the image motion from the CT segments to a common full volume 3D‐CT reference. This reference volume is reconstructed using the acquired 4D‐CT data at the end‐of‐exhalation phase. The segments are optimally aligned to the reference volume according to a proposed a priori alignment procedure. The registration is applied using a multigrid approach and a feature‐preserving image downsampling maxfilter to achieve better computational speed and higher registration accuracy. The registration accuracy is about for the lung region according to our verification using manually selected landmarks and artificially deformed CT volumes. The estimated motion fields are fitted to two 5D (spatial rate) motion models: forward model and inverse model. The forward model predicts tissue movements and the inverse model predicts CT density changes as a function of tidal volume and airflow rate. A leave‐one‐out procedure is used to validate these motion models. The estimated modeling prediction errors are about for the forward model and for the inverse model.
In Vitro Activity of TR-700, the Antibacterial Moiety of the Prodrug TR-701, against Linezolid-Resistant Strains
Authors: Shaw K. J. , Poppe S. , Schaadt R. , Brown-Driver V. , Finn J. , Pillar C. M. , Shinabarger D. , Zurenko G.
Published: October 2008

TR-701 is the orally active prodrug of TR-700, a novel oxazolidinone that demonstrates four- to eightfold-greater activity than linezolid (LZD) against
Staphylococcus
and
Enterococcus
spp. In this study evaluating the in vitro sensitivity of LZD-resistant isolates, TR-700 demonstrated 8- to 16-fold-greater potency than LZD against all strains tested, including methicillin-resistant
Staphylococcus aureus
(MRSA), strains of MRSA carrying the mobile
cfr
methyltransferase gene, and vancomycin-resistant enterococci. The MIC
90
for TR-700 against LZD-resistant
S. aureus
was 2 μg/ml, demonstrating the utility of TR-700 against LZD-resistant strains. A model of TR-700 binding to 23S rRNA suggests that the increased potency of TR-700 is due to additional target site interactions and that TR-700 binding is less reliant on target residues associated with resistance to LZD.
Proteomic and Transcriptomic Analysis of
Aspergillus fumigatus
on Exposure to Amphotericin B
Authors: Gautam Poonam , Shankar Jata , Madan Taruna , Sirdeshmukh Ravi , Sundaram Curam Sreenivasacharlu , Gade Wasudev Namdeo , Basir Seemi Farhat , Sarma Puranam Usha
Published: October 2008

Amphotericin B (AMB) is the most widely used polyene antifungal drug for the treatment of systemic fungal infections, including invasive aspergillosis. It has been our aim to understand the molecular targets of AMB in
Aspergillus fumigatus
by genomic and proteomic approaches. In transcriptomic analysis, a total of 295 genes were found to be differentially expressed (165 upregulated and 130 downregulated), including many involving the ergosterol pathway, cell stress proteins, cell wall proteins, transport proteins, and hypothetical proteins. Proteomic profiles of
A. fumigatus
alone or
A. fumigatus
treated with AMB showed differential expression levels for 85 proteins (76 upregulated and 9 downregulated). Forty-eight of them were identified with high confidence and belonged to the above-mentioned categories. Differential expression levels for Rho-GDP dissociation inhibitor (Rho-GDI), secretory-pathway GDI, clathrin, Sec 31 (a subunit of the exocyst complex), and RAB GTPase Ypt51 in response to an antifungal drug are reported here for the first time and may represent a specific response of
A. fumigatus
to AMB. The expression of some of these genes was validated by real-time reverse transcription-PCR. The AMB responsive genes/proteins observed to be differentially expressed in
A. fumigatus
may be further explored for novel drug development.
Analysis of the Specificity of Panton-Valentine Leucocidin and Gamma-Hemolysin F Component Binding
Authors: Meyer Florent , Girardot Raymonde , Piémont Yves , Prévost Gilles , Colin Didier A.
Published: October 2008

In this study, the binding of F components of the staphylococcal bicomponent leukotoxins Panton-Valentine leucocidin (LukF-PV) and gamma-hemolysin (HlgB) on polymorphonuclear neutrophils (PMNs), monocytes, and lymphocytes was determined using labeled mutants and flow cytometry. Leukotoxin activity was evaluated by measuring Ca
2+
entry or pore formation using spectrofluorometry or flow cytometry. Although HlgB had no affinity for cells in the absence of an S component, LukF-PV had high affinity for PMNs (dissociation constant [
K

d

], 6.2 ± 1.9 nM;
n
= 8), monocytes (
K

d

, 2.8 ± 0.8 nM;
n
= 7), and lymphocytes (
K

d

, 1.2 ± 0.2 nM;
n
= 7). Specific binding of HlgB was observed only after addition of LukS-PV on PMNs (
K

d

, 1.1 ± 0.2 nM;
n
= 4) and monocytes (
K

d

, 0.84 ± 0.31 nM;
n
= 4) or after addition of HlgC on PMNs, monocytes, and lymphocytes. Addition of LukS-PV or HlgC induced a second specific binding of LukF-PV on PMNs. HlgB and LukD competed only with LukF-PV molecules bound after addition of LukS-PV. LukF-PV and LukD competed with HlgB in the presence of LukS-PV on PMNs and monocytes. Use of antibodies and comparisons between binding and activity time courses showed that the LukF-PV molecules that bound to target cells before addition of LukS-PV were the only LukF-PV molecules responsible for Ca
2+
entry and pore formation. In contrast, the active HlgB molecules were the HlgB molecules bound after addition of LukS-PV. In conclusion, LukF-PV must be linked to LukS-PV and to a binding site of the membrane to have toxin activity.
Probing the Active Conformers of Paraoxon Through Theoretical Conformational Studies
Authors: Ford-Green Jason , Majumdar Devashis , Leszczynski Jerzy
Published: October 2008

Theoretical conformational studies have been carried out at the density functional (DFT) level of theory on paraoxon (O,O-diethyl-O-p-nitrophenylphosphonate) to correlate its conformational and enzyme inhibition properties. The aqueous solvation of the various conformers has been studied at the DFT level using polarized continuum model with conductor-like solvation approach. The results show that paraoxon has high conformational flexibility in aqueous medium, although in gas phase the molecule is less flexible. The barriers to transition to different low-energy conformers in aqueous medium are thermally accessible. The molecular electrostatic potential surfaces of the various low-energy conformers of this molecule have been compared with the related enzyme-bound organophosphorus structures to investigate the role of the calculated conformers on the biological activity of this molecule.
Rotator cuff tendinopathy/subacromial impingement syndrome: is it time for a new method of assessment?
Authors: Lewis J S
Published: October 2008

Disorders of the shoulder are extremely common, with reports of prevalence ranging from 30% of people experiencing shoulder pain at some stage of their lives up to 50% of the population experiencing at least one episode of shoulder pain annually. In addition to the high incidence, shoulder dysfunction is often persistent and recurrent, with 54% of sufferers reporting ongoing symptoms after 3 years. To a large extent the substantial morbidity reflects (i) a current lack of understanding of the pathoaetiology, (ii) a lack of diagnostic accuracy in the assessment process, and (iii) inadequacies in current intervention techniques. Pathology of the rotator cuff and subacromial bursa is considered to be the principal cause of pain and symptoms arising from the shoulder. Generally these diagnostic labels relate more to a clinical hypothesis as to the underlying cause of the symptoms than to definitive evidence of the histological basis for the diagnosis or the correlation between structural failure and symptoms.

Diagnosing rotator cuff tendinopathy or subacromial impingement syndrome currently involves performing a structured assessment that includes taking the patient’s history in conjunction with performing clinical assessment procedures that generally involve tests used to implicate an isolated structure. Based on the response to the clinical tests, a diagnosis of rotator cuff tendinopathy or subacromial impingement syndrome is achieved. The clinical diagnosis is strengthened with the findings from supporting investigations such as blood tests, radiographs, ultrasound, magnetic resonance imaging (MRI), computed axial tomography (CT), radionucleotide isotope scan, single photon emission computed tomography, electromyography, nerve conduction and diagnostic analgesic injection. This process eventually results in the formation of a clinical hypothesis, and then, in conjunction with the patient, a management plan is decided upon and implemented.

This paper focuses on the dilemmas associated with the current process, and an alternative method for the clinical examination of the shoulder for this group of patients is proposed.
Functions of the ERF transcription factor family in plants
Authors: Xu Zhao-Shi , Chen Ming , Li Lian-Cheng , Ma You-Zhi
Published: October 2008

Ethylene responsive factors (ERFs) play vital regulatory roles in a variety of developmental processes and stress responses in plants. In this study, ERF family genes in a wide range of plant species were classified into 8 clusters and 14 subclusters on the basis of phylogenetic relationships, gene structures, conserved motifs, and biological functions. ERF genes, especially those in Clusters II and VII, can be used as candidates to improve crop-plant resistance because their over-expression enhances multiple disease resistances and improves tolerances to drought, salt, and freezing in transgenic plants. The comprehensive analysis of phylogenetic relationships, conserved motifs, and physiological functions is useful in elucidating the biological roles of ERF family genes in signal transduction, gene regulation, and defense response under stress environments.
Biosynthesis and potential functions of the ecdysteroid 20-hydroxyecdysone — a review
Authors: Festucci-Buselli Reginaldo A. , Contim Luis A. S. , Barbosa Luiz Cláudio A. , Stuart Jeff , Otoni Wagner C.
Published: October 2008

The ecdysteroid 20-hydroxyecdysone (20E) is a steroid hormone found in arthropods and plants. It is suspected to have agrochemical, biotechnological, medicinal, and pharmaceutical applicability. In insects, 20E controls or elicits molting and other developmental processes, and several characterized P450 enzymes are involved in its biosynthesis. In plants, it may act as a defensive substance against insects and nematodes. It is suspected that 20E, being a physiologically active compound, may affect morphological and physiological processes in plants and that C27phytosterols may be its precursors. However, neither its precise function nor its mechanism of biosynthesis in plants is fully understood. Here, the importance of 20E and current understanding of its structure, potential functions, and biosynthesis in both plants and insects are reviewed.
Spatial structure and inbreeding depression in slickspot peppergrass, Lepidium papilliferum (Brassicaceae)
Authors: Billinge Stephanie A. , Robertson Ian C.
Published: October 2008

In plants with limited pollen and seed dispersal, populations are often spatially structured such that neighboring individuals are more closely related to one another than to distant individuals. Mating among close relatives, including selfing, may lead to a reduction in reproductive performance through the effects of prezygotic mating barriers and inbreeding depression. Studying 11 populations of slickspot peppergrass, Lepidium papilliferum (L.F. Hend.) A. Nels. and J.F. Macbr (Brassicaceae), a rare mustard endemic to southwestern Idaho, we investigated whether small populations (16–746 flowering individuals) exhibit spatial structure as previously reported for large populations (>3000 flowering individuals). Through hand-pollination experiments we found that percent fruit set increased with increasing distance between parents up to a distance of 3 m, and declined slightly but nonsignificantly at greater outcrossing distances. Self-pollinated plants produced little or no fruit. Germination of seeds from the hand-pollination experiment revealed signs of inbreeding depression in the offspring. Specifically, leaf length of developing seedlings increased significantly as a function of outcrossing distance. Total leaf number showed a similar, yet statistically nonsignificant, response to outcrossing distance. Overall, our experiments reveal spatial structuring and suggest the occurrence of inbreeding depression in small populations of L. papilliferum.
Nectary structure and nectar presentation in the Mediterranean geophyte,Urginea maritima(Hyacinthaceae)
Authors: Al-Tardeh Sharaf , Sawidis Thomas , Diannelidis Barbara-Evelin , Delivopoulos Stylianos
Published: October 2008

The morphology, anatomy, and ultrastructure of the floral nectary of Urginea maritima (L.) Baker were investigated at three stages of nectary development. The plant possesses a typical gynopleural (septal) nectary with secondary presentation. The nectary consists of one layer of epithelium secretory cells and one to four layers of subsidiary cells subtended by two to six layers of parenchyma (subnectary) cells. The nectary releases the nectar at a point two-thirds towards the summit of the ovary by means of carpellary sutures. Nectar secretion appears to depend largely on the hydrolysis of starch grains stored in amyloplasts at the intermediate stage. The hydrolysis process most likely commences in the epithelium layer followed by the subsidiary tissue and then the parenchyma cells of the ovary wall. A symplastic transfer of the secreted nectar occurs by plasmodesmata connecting the subsidiary cells to the parenchyma and the epithelial secretory cells. However, microchannels in the cell wall of the epithelial cells may facilitate the apoplastic transfer of the nectar into the nectary cavity. The old stage of nectary development is characterized by a crystallized form of nectar, collapse of the parenchyma cells, complete starch hydrolysis, and disappearance of the amyloplasts and endoplasmic reticulum.
Subindividual variation and genetic versus environmental effects on seed traits in a EuropeanAquilegia
Authors: Castellanos M. C. , Medrano M. , Herrera C. M.
Published: October 2008

Repetitive plant parts such as seeds can be characterized at the within-individual level not only by average values but also by higher moments of their distributions, such as the standard deviation, skewness, and kurtosis. These parameters can potentially be adaptive and shaped by selection like any other individual trait, but tend to be understudied. We present an example of how within-individual variation might be studied. We used a diallel crossing design to investigate the sources of phenotypic variance of among- and within-individual variation in seed and germination traits of the endemic columbine Aquilegia pyrenaica subsp. cazorlensis (Heywood) Galiano & Rivas Martínez. Individual plants and even fruits have their characteristic mean, standard deviation, skewness, and kurtosis and therefore these parameters could potentially respond to selection. However, we only found evidence of genetic variance in mean within-fruit seed mass, mean time to seedling emergence, and number of seeds: these effects were attributable to maternal effects. Variance in higher moments of the within-fruit distributions in this species could instead reflect developmental instability or plastic responses to localized environmental conditions as fruits develop. Large sample sizes are required to make final conclusions in this case, but this study illustrates how the novel approach of considering high moments of intra-individual variation will enhance our view of plant trait evolution.
Sources of placer platinum in Yukon: provenance study from detrital minerals
Authors: Fedortchouk Yana , LeBarge William
Published: October 2008

Source rocks for the platinum group minerals (PGM), historically reported in a number of Yukon placers, remain either unknown or poorly understood. A study of heavy-mineral samples from five creeks draining bedrock in west and central Yukon was undertaken to confirm the presence of placer platinum, to determine which mafic–ultramafic rock is the source of PGM in Kluane area, southern Yukon, and to explain platinum occurrences in Canadian and Florence creeks, central Yukon, where no known mafic–ultramafic rocks are present. Diverse composition of chromian spinel and clinopyroxenes from three creeks in the Kluane area indicate several sources of ultramafic rocks, including fragments of Alpine-type peridotites formed in back-arc basin and mid-ocean-ridge settings, and a source rock for zoned zinc-rich chromites of unknown origin. The Kluane ultramafic sills are the most likely source of PGM in this area. The heavy-mineral sample from Canadian Creek returned one PGM grain, no chromite, and abundant ilmenite and titanomagnetite. A group of chromium-rich magnesian ilmenites (∼4 wt.% MgO) closely match the composition of ilmenites from continental mafic intrusions produced during continental rift magmatism. This supports the continental rifting event recently proposed for this part of Yukon and indicates the economic potential of the Canadian Creek platinum occurrence. Composition of spinel from Florence Creek sample indicates an Alaskan-type intrusion as the source of PGM.
Mineralogy, geochemistry, and Sr–Nd isotopes of the Cretaceous leucogranite from Karamadazı (Kayseri), central Turkey: implications for their sources and geological setting
Authors: Kocak Kerim
Published: October 2008

The leucogranite is the major constituent of the bimodal Late Cretaceous Karamadazı granitoid, developed in relation with evolution of the Inner Tauride Ocean along the northern margin of the Taurides in central Turkey. New analyses of minerals major and trace elements (including rare-earth elements (REE)), and of Sr and Nd isotopes are performed to determine the origin and geochemical characteristics of the leucogranites. Medium-coarse-grained leucogranite contains normally zoned plagioclase (An12–20), mildly alkaline biotite, and xenocrystic magneziohornblende, actinolite, and ferrohornblende. It is characterized by concave-up REE patterns with respect to middle–heavy REE. Field relations, mineral chemistry, geochemical data, and isotopic data suggest that the leucogranite could have originated from an amphibole-bearing igneous source in lower to middle crust by low-rate partial melting (<40%) under low pressure and low H2O activity conditions, possibly coupled by mixing–mingling with mafic magma and high-level feldspar and minor biotite fractionation. In contrast, the quartz diorite and mafic microgranular enclave (MME) are probably developed from an enriched mantle, with possible mingling–mixing. MME, quartz diorite, and leucogranite may represent a magmatic suite, which formed in an extensional tectonic regime by bimodal magmatic activity probably because of lithospheric delamination or slab break off or after the Alpine thicken within the Gondwanan Tauride–Anatolide platform. Initial Sr data exhibit an age of 65 ± 13 Ma for the leucogranite, but it does not indicate a true intrusion age of the magma due to isotopic modification of the magma.
Proterozoic anorthosite–granite Nain batholith: structure and intrusion processes in an active lithosphere-scale fault zone, northern Labrador
Authors: Myers John S. , Voordouw Ronald J. , Tettelaar Tanya A.
Published: October 2008

We present field evidence of the structure and evolution of a typical Proterozoic massif-type anorthosite. The anorthosite forms a batholith composed of numerous plutons and ring complexes intruded episodically in two main sequences, each producing anorthositic rocks and monzonite–ferrodiorite followed by granite. The batholith is located where a lithosphere-scale fault zone, ∼50 km wide and extending over 1000 km from Greenland to Labrador, intersected an older continental suture. Intermittent episodes of mainly sinistral transtension along this Gardar – Voisey’s Bay fault zone were associated with the generation of a number of pulses of magmatism and controlled the rise of magmas to middle and upper crustal levels between ∼1363 and 1289 Ma. Both the large- and small-scale structures and magma intrusion processes are similar to those of many cordilleran batholiths, with tabular plutons associated with ring dykes emplaced by cauldron subsidence, and basin-shaped plutons associated with cone sheets. These structures are well known in subvolcanic situations but little known at the mid-crustal depth of the Nain batholith. The location of these structures within the batholith was controlled by intersecting, externally generated faults and shear zones. We conclude that this typical massif-type anorthosite is an intracratonic structural equivalent of cordilleran batholiths of continental margins.
Survival, Distribution, and Ion Composition in Two Strains of Brook Trout (Salvelinus fontinalis) Fry after Exposure to Episodic pH Depressions in an Adirondack Lake
Authors: Offelen Henry K. Van , Krueger Charles C. , Schofield Carl L. , Keleher Chris
Published: October 2008

Brook trout (Salvelinus fontinalis) fry are susceptible to high mortality in acidified waters because of their low tolerance to acidic conditions and the potential occurrence of this life stage with episodic acidification associated with snowmelt. Prior to snowmelt, equal numbers of Assinica and Temiscamie strain fry were placed into enclosures. Twelve days after stocking, no consistent differences between strains were observed in survival, distribution, or ion composition. No fry of either strain survived in enclosures placed in shallow water (pH 4.8; 0.7 m depth). Fifty to 100% of fry of both strains survived in enclosures placed in deep water (pH 6.3; > 2.0 m depth). Fry survival in long enclosures that extended from shallow to deep water was 80–99%. Within long enclosures, both strains were recovered in higher densities from middle and deep sections of the enclosures than from shallow sections. High fry survival and non-random distributions in the long enclosures indicated that both strains were able to avoid lethal, nearshore waters during spring snowmelt by moving to deeper water.
Muscle Tissue Growth and Muscle Fibre Dynamics in the Tropical Loliginid SquidPhotololigosp. (Cephalopoda: Loliginidae)
Authors: Moltschaniwskyj N. A.
Published: October 2008

Growth of somatic tissue in Photololigo sp. was examined in terms of muscle fibre recruitment and growth. Muscle blocks and muscle fibres were measured and size frequency distributions compared between different size-classes of squid. Muscle blocks increased in size as individuals grew. The size frequency distribution of the muscle blocks suggested that this increase was due to both the generation of new muscle fibres and an increase in the size of existing muscle fibres. The size frequency distribution of muscle fibres was very similar in all size-classes of squid examined, and the presence of small muscle fibres in all individuals suggested that fibre recruitment may be continuous. Growth of muscle tissue, by muscle fibre growth and recruitment, provides a mechanism to explain constant growth throughout the life cycle described for tropical squid. Two structural types of muscle fibres, mitochondria-poor and mitochondria-rich, are present in juvenile and adult squid. A weak relationship between the ratio of the two muscle fibre types and dorsal mantle length suggests that generation of mitochondria-rich fibres may not be influenced by growth.