bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA barcoding in Tardigrada: the first case study onMacrobiotus macrocalix Bertolani & Rebecchi 1993 (Eutardigrada, Macrobiotidae)
Authors: CESARI MICHELE , BERTOLANI ROBERTO , REBECCHI LORENA , GUIDETTI ROBERTO 
Published: February 2009

AbstractMorphological and molecular studies on a tardigrade species have been carried out to verify the possibility of using a DNA barcoding approach for species identification in this phylum.Macrobiotus macrocalixBertolani & Rebecchi,1993 was chosen as the test species since it belongs to a group of species in which the taxonomy is quite problematic. Animals and eggs belonging to three Italian and one Swedish populations have been investigated. Both morphological and molecular analyses show that all the populations belong to the same species. The low genetic distances recorded among the studied populations (0.3–1.0%) and the high genetic distance (15.9–16.3%) between these populations and a closely related species confirm the possibility of identifying a specimen of this species by its cytochrome oxidase subunit I sequence. Data from other authors support our results indicating that DNA barcoding can be applied to tardigrades. With our protocols, we have obtained voucher specimens that enable us to show a correspondence between morphology and molecular data.
Isolation and characterization of 17 microsatellite loci for the Chinese longsnout catfish (Leiocassis longirostris)
Authors: XIAO MINGSONG , YANG GUANG 
Published: February 2009

AbstractWe describe the isolation and development of 17 polymorphic dinucleotide microsatellite loci for the Chinese longsnout catfish (Leiocassis longirostris). All loci were polymorphic in the 30 individuals tested. The number of alleles per variable locus ranged from 6 to 18, with a mean of 11.71. Observed and expected heterozygosities ranged from 0.467 to 1.000 and from 0.540 to 0.929, respectively. Eight loci were found to have deviated from HWE in the sampled population after Bonferroni correction. Linkage disequilibrium tests revealed significant linkage between two loci (LLW5 and LL27). These microsatellite loci will be useful for revealing population structure, genetic diversity, and phylogeography of the Chinese longsnout catfish.
DNA barcoding of stylommatophoran land snails: a test of existing sequences
Authors: DAVISON ANGUS , BLACKIE ROSE L. E. , SCOTHERN GARY P. 
Published: February 2009

AbstractDNA barcoding has attracted attention because it is a potentially simple and universal method for taxonomic assignment. One anticipated problem in applying the method to stylommatophoran land snails is that they frequently exhibit extreme divergence of mitochondrial DNA sequences, sometimes reaching 30% within species. We therefore trialled the utility of barcodes in identifying land snails, by analysing the stylommatophoran cytochrome oxidase subunit I sequences from GenBank. Two alignments of 381 and 228 base pairs were used to determine potential error rates among a test data set of 97 or 127 species, respectively. Identification success rates using neighbour‐joining phylogenies were 92% for the longer sequence and 82% for the shorter sequence, indicating that a high degree of mitochondrial variation may actually be an advantage when using phylogeny‐based methods for barcoding. There was, however, a large overlap between intra‐ and interspecific variation, with assignment failure (per cent of samples not placed with correct species) particularly associated with a low degree of mitochondrial variation (Kimura 2‐parameter distance < 0.05) and a small GenBank sample size (< 25 per species). Thus, while the optimum intra/interspecific threshold value was 4%, this was associated with an overall error of 32% for the longer sequences and 44% for the shorter sequences. The high error rate necessitates that barcoding of land snails is a potentially useful method to discriminate species of land snail, but only when a baseline has first been established using conventional taxonomy and sample DNA sequences. There is no evidence for a barcoding gap, ruling out species discovery based on a threshold value alone.
A new test for genotype–fitness associations reveals a single microsatellite allele that strongly predicts the nature of tuberculosis infections in wild boar
Authors: AMOS WILLIAM , ACEVEDO‐WHITEHOUSE KARINA 
Published: February 2009

AbstractThere is increasing interest in the basis of commonly observed heterozygosity–fitness correlations (HFCs). Two models appear possible, a genome‐wide effect due to inbreeding depression, and a single‐locus effect due to chance linkage to a gene(s) experiencing balancing selection. Recent studies suggest that the latter tends to be more important in the majority of studies, but tests for the presence of single‐locus effects tend to be rather weak. One of the problems is that the linkage disequilibrium between a microsatellite and a nearby gene experiencing balancing selection is never likely to be 100%. With this in mind, we conduct stochastic simulations aimed at determining the conditions under which single‐locus HFCs may develop. We also suggest a new approach that could offer improved detection of HFCs but which also offers a more general method for detecting genotype–fitness correlations. Our method is based on looking for the maximum possible strength of association between genotype and fitness, and then asking whether randomized data sets are able to generate similarly strong associations. This method is tested on both simulated and real data. In both cases, our method generates greater levels of significance than current tests. Applied to previously published data from wild boar affected by tuberculosis, the method uncovers a strong single‐allele association that is strongly predictive of whether the disease is localized or spreads throughout the body. We further suggest a simple method for dealing with the problem of population structure, and believe this approach will help to identify genomic regions associated with fitness.
Independent calculation of dose from a helical TomoTherapy unit
Authors: Gibbons John P. , Smith Koren , Cheek Dennis , Rosen Isaac 
Published: February 2009

A new calculation algorithm has been developed for independently verifying doses calculated by the TomoTherapy® Hi·Art® treatment planning system (TPS). The algorithm is designed to confi rm the dose to a point in a high dose, low dose‐gradient region. Patient data used by the algorithm include the radiological depth to the point for each projection angle and the treatment sinogram file controlling the leaf opening time for each projection. The algorithm uses common dosimetric functions [tissue phantom ratio (TPR) and output factor ()] for the central axis combined with lateral and longitudinal beam profile data to quantify the off‐axis dose dependence. Machine data for the dosimetric functions were measured on the Hi·Art machine and simulated using the TPS. Point dose calculations were made for several test phantoms and for 97 patient treatment plans using the simulated machine data. Comparisons with TPS‐predicted point doses for the phantom treatment plans demonstrated agreement within 2% for both on‐axis and off‐axis planning target volumes (PTVs). Comparisons with TPS‐predicted point doses for the patient treatment plans also showed good agreement. For calculations at sites other than lung and superficial PTVs, agreement between the calculations was within 2% for 94% of the patient calculations (64 of 68). Calculations within lung and superficial PTVs overestimated the dose by an average of 3.1% () and 3.2% (), respectively. Systematic errors within lung are probably due to the weakness of the algorithm in correcting for missing tissue and/or tissue density heterogeneities. Errors encountered within superficial PTVs probably result from the algorithm overestimating the scatter dose within the patient. Our results demonstrate that for the majority of cases, the algorithm could be used without further refinement to independently verify patient treatment plans.PACS number(s): 87.53.Bn, 87.53.Dq, 87.53.Xd
Comparison of IPSM 1990 photon dosimetry code of practice with IAEA TRS‐398 and AAPM TG‐51.
Authors: Castrillón Silvia Vargas , Henríquez Francisco Cutanda 
Published: February 2009

Several codes of practice for photon dosimetry are currently used around the world, supported by different organizations. A comparison of IPSM 1990 with both IAEA TRS‐398 and AAPM TG‐51 has been performed. All three protocols are based on the calibration of ionization chambers in terms of standards of absorbed dose to water, as it is the case with other modern codes of practice. This comparison has been carried out for photon beams of nominal energies: 4 MV, 6 MV, 8 MV, 10 MV and 18 MV.An NE 2571 graphite ionization chamber was used in this study, cross‐calibrated against an NE 2611A Secondary Standard, calibrated in the National Physical Laboratory (NPL). Absolute dose in reference conditions was obtained using each of these three protocols including: beam quality indices, beam quality conversion factors both theoretical and NPL experimental ones, correction factors for influence quantities and absolute dose measurements. Each protocol recommendations have been strictly followed. Uncertainties have been obtained according to the ISO Guide to the Expression of Uncertainty in Measurement. Absorbed dose obtained according to all three protocols agree within experimental uncertainty. The largest difference between absolute dose results for two protocols is obtained for the highest energy: 0.7% between IPSM 1990 and IAEA TRS‐398 using theoretical beam quality conversion factors.PACS number: 87.55.tm
Cardiac dose evaluation for 3Dimensional conformal partial breast irradiation compared with whole breast irradiation
Authors: Gale Ashley A. , Jain Anudh K. , Vallow Laura A. , Serago Christopher F. , Buskirk Steven J. , Heckman Michael G. 
Published: February 2009

To compare the radiation dose to normal cardiac tissue for 3Dimensional (3D) conformal external beam partial breast irradiation (PBI) and standard whole breast irradiation (WBI), and examine the effect of tumor bed location.For 14 patients with left breast tumors randomized on the National Surgical Adjuvant Breast and Bowel Project B‐39 protocol, computer‐generated radiotherapy treatment plans were devised for WBI and PBI. Tumor bed location was designated according to whether more than 50% of the excision cavity was medial or lateral to the nipple line. The volume of heart receiving doses of 2.5, 5, 10, and 20 Gy was calculated for all PBI and WBI plans. Dose to 5% of the heart volume (D5) and mean heart dose were also calculated. The biologically‐equivalent dose (BED) was calculated to account for the different fractionation used in PBI and WBI.Of the 14 patients, 8 had lateral tumor beds, and 6 had medial tumor beds. The volumes of heart receiving 2.5, 5, 10, and 20 Gy were significantly lower for lateral PBI compared with WBI. For medial PBI, significant cardiac sparing was only seen at a dose of 20 Gy. The difference of D5 values was significant for lateral PBI compared with WBI , but not for medial PBI compared with WBI . The mean dose was also significantly lower for lateral PBI compared with WBI , but not for medial PBI . The results from BED calculations did not change this outcome.Both 3D conformal PBI and standard WBI can deliver relatively low doses to the heart. For patients with lateralized tumor beds, PBI offers significant cardiac sparing compared with WBI. Patients with medial lesions have relatively similar heart dosimetry with PBI and WBI. 3D conformal PBI is an emerging treatment modality and continued participation on clinical trials is encouraged. Patients with left‐sided lesions and lateralized tumor beds warrant special consideration for PBI, given the significant cardiac dose sparing.PACS numbers: 87.53.Tf
Dose perturbations from implanted helical gold markers in proton therapy of prostate cancer
Authors: Giebeler Annelise , Fontenot Jonas , Balter Peter , Ciangaru George , Zhu Ronald , Newhauser Wayne 
Published: February 2009

Implanted gold fiducial markers are widely used in radiation therapy to improve targeting accuracy. Recent investigations have revealed that metallic fiducial markers can cause severe perturbations in dose distributions for proton therapy, suggesting smaller markers should be considered. The objective of this study was to estimate the dosimetric impact of small gold markers in patients receiving proton therapy for prostate cancer. Small, medium, and large helical wire markers with lengths of 10 mm and helix diameters of 0.35 mm, 0.75 mm, and 1.15 mm, respectively, were implanted in an anthropomorphic phantom. Radiographic visibility was confirmed using a kilovoltage x‐ray imaging system, and dose perturbations were predicted from Monte Carlo simulations and confirmed by measurements. Monte Carlo simulations indicated that size of dose perturbation depended on marker size, orientation, and distance from the beam's end of range. Specifically, the perturbation of proton dose for the lateral‐opposed‐pair treatment technique was 31% for large markers and 23% for medium markers in a typical oblique orientation. Results for perpendicular and parallel orientations were respectively lower and higher. Consequently, these markers are not well suited for use in patients receiving proton therapy for prostate cancer. Dose perturbation was not observed for the small markers, but these markers were deemed too fragile for transrectal implantation in the prostate.PACS number: 87.53.Pb
Stereotactic radiotherapy for lung cancer using a flattening filter free Clinac
Authors: Vassiliev Oleg N. , Kry Stephen F. , Chang Joe Y. , Balter Peter A. , Titt Uwe , Mohan Radhe 
Published: February 2009

The objective of this study was to assess the feasibility of stereotactic radiotherapy for early stage lung cancer using photon beams from a Varian Clinac accelerator operated without a flattening filter. Treatment plans were generated for 10 lung cancer patients with isolated lesions less than 3 cm in diameter. For each patient, two plans were generated, one with and one without the flattening filter. Plans were generated with Eclipse 8.0 (Varian Medical Systems) commissioned with beam data measured on a Clinac 21EX (Varian Medical Systems) operated with and without the flattening filter. Removal of the flattening filter increased the dose rate. The median beam‐on time per field was reduced from 25 sec (with the filter) to 11 sec (without the filter), increasing the feasibility of breath‐hold treatments and the efficiency of gated treatments. Differences in a dose heterogeneity index for the planning target volume between plans with flattened and unflattened beams were statistically insignificant. Differences in mean doses to organs at risk were small, typically about 10 cGy over the entire treatment. The study concludes that radiotherapy with unflattened beams is feasible and requires substantially less beam‐on time, facilitating breath‐hold and gating techniques.PACS numbers: 87.56.bd, 87.53.Ly
Application of a Monte Carlo‐based method for total scatter factors of small beams to new solid state micro‐detectors
Authors: Francescon Paolo , Cora Stefania , Cavedon Carlo , Scalchi Paolo 
Published: February 2009

The scope of this work was to apply a method for estimation of total scatter factors of the smallest beams of the Cyberknife radiosurgery system to newly available solid‐state detectors: the PTW 60008 diode, the SunNuclear EdgeDetector™ diode, and the Thomson and Nielsen TN502RDM micromosfet. The method is based on a consistency check between Monte Carlo simulation of the detectors and experimental results, and was described in a recent publication. Corrected total scatter factors were in excellent agreement with the findings of the former study. The results showed that the diodes tend to overestimate the total scatter factor of small beams, probably due to excessive scatter from the material surrounding the active layer. The correction factor for diodes and for the micromosfet, however, was found to be independent of the electron beam width. This is a desirable characteristic because it allows standard correction factors to be used for treatment units of the same type, without the need of case‐by‐case Monte Carlo simulation.PACS numbers: 87.55.kh; 87.55.ne; 87.56.Fc.
Is farm-related job title an adequate surrogate for pesticide exposure in occupational cancer epidemiology?
Authors: MacFarlane E , Glass D , Fritschi L 
Published: February 2009

Objectives:Accurate assessment of exposure is a key factor in occupational epidemiology but can be problematic, particularly where exposures of interest may be many decades removed from relevant health outcomes. Studies have traditionally relied on crude surrogates of exposure based on job title only, for instance farm-related job title as a surrogate for pesticide exposure.Methods:This analysis was based on data collected in Western Australia in 2000–2001. Using a multivariate regression model, we compared expert-assessed likelihood of pesticide exposure based on detailed, individual-specific questionnaire and job specific module interview information with reported farm-related job titles as a surrogate for pesticide exposure.Results:Most (68.8%) jobs with likely pesticide exposure were farm jobs, but 78.3% of farm jobs were assessed as having no likelihood of pesticide exposure. Likely pesticide exposure was more frequent among jobs on crop farms than on livestock farms. Likely pesticide exposure was also more frequent among jobs commenced in more recent decades and jobs of longer duration. Our results suggest that very little misclassification would have resulted from the inverse assumption that all non-farming jobs are not pesticide exposed since only a very small fraction of non-agricultural jobs were likely to have had pesticide exposure.Conclusions:Classification of all farm jobs as pesticide exposed is likely to substantially over-estimate the number of individuals exposed. Our results also suggest that researchers should pay special attention to farm type, length of service and historical period of employment when assessing the likelihood of pesticide exposure in farming jobs.
Improving the prediction of the dynamic modulus of fine-graded asphalt concrete mixtures at high temperatures
Authors: Harran Ghareib , Shalaby Ahmed 
Published: February 2009

Predictive techniques for estimating the asphalt concrete dynamic modulus, |E*|, from mixture volumetric properties are widely used in pavement design and evaluation. The reliability of these techniques is lowest at high service temperatures above 35 °C. Rutting is one of the major distresses in asphalt pavements and is considered highly sensitive to |E*| at high temperatures. The objective of this paper is to improve the reliability in the prediction of |E*| at high temperatures using parameters that reflect the gradation of aggregates. A linear model is proposed to adjust the predicted |E*| for fine-graded mixtures using a new gradation parameter. The analysis was performed on 24 mixtures prepared from various aggregate gradations and types, and several binder grades. Reasonable results were predicted for the calibration data and a validation dataset from the literature. The correlation between |E*| at high temperatures and the gradation parameter improved when it was carried out independently on fine- and coarse-graded mixtures.
Hydrometeorological validation of a Canadian Regional Climate Model simulation within the Chaudière and Châteauguay watersheds (Québec, Canada)
Authors: Gagnon P. , Konan B. , Rousseau A.N. , Slivitzky M. 
Published: February 2009

This study involved regional validation of a recently developed Canadian Regional Climate Model (CRCM) simulation (version 4.1.1). Four hydrometeorological variables, minimum and maximum daily temperatures, total precipitation, and total runoff, were examined within the Châteauguay and Chaudière watersheds, Québec, Canada. These watersheds, located in southern Québec, are smaller in area (2530 and 6682 km2, respectively) than the size of watersheds usually used to validate this type of model (104–106 km2). The objective of the study was to evaluate if the model could reproduce data similar to field observations within these watersheds. A successful model could be used to produce reliable predictions regarding future climate change effects on watershed hydrology within any given watershed demonstrating similar climatological variables. Results show that even though the CRCM can produce reliable results, there remains a significant bias for each variable at least during one season. Analyses show that the bias for maximum temperature is not very strong (<1 °C) within either of the studied watersheds. However, minimum temperature is clearly underestimated (≈2 °C) in winter and in spring within both watersheds. Total precipitation is significantly overestimated in winter, spring and summer within the Châteauguay watershed (11%, 35%, and 30%, respectively), but for the Chaudière watershed overestimation is less than 5%. Total runoff is strongly overestimated in both watersheds for most of the annual cycle (>30%) and is highly variable in winter and spring. Ideally, the results of this study will be used to guide future studies on the causes of CRCM bias and ultimately lead to model improvement.
THE PERIODIC MAINTENANCE POLICY FOR A WEIBULL LIFE-TIME SYSTEM WITH DEGRADATION RATE REDUCTION UNDER RELIABILITY LIMIT
Authors: CHENG CHUN-YUAN , CHEN MINGCHIH 
Published: February 2009

From the literature, it is known that preventive maintenance (PM) can reduce the deterioration of system or equipment to a younger level. Researchers usually develop optimal PM policies based on the assumption that the PM can reduce system's age or failure rate. However, the PM actions, such as cleaning, adjustment, alignment, and lubrication work, may not always reduce system's age or failure rate. Instead, it may only reduce the degradation rate of the system to a certain level. In addition, most of the existing optimal PM policies are developed by minimizing the expected cost rate only. Yet, as demonstrated in this paper, the system will have very low reliability at the time of preventive replacement if the reliability limit is not considered. Hence, this paper is to develop an optimal periodic PM model by minimizing the expected cost rate per unit time with the consideration of reliability limit for repairable systems with degradation rate reduction after each PM. The improvement factor method is used to measure the reduction effect of the degradation rate. The algorithm for searching the optimal solutions for this PM model is developed. Examples are also presented with discussions of parameter sensitivity and special cases.