bluuebunny/crossref_metadata_2025_split huggingface dataset:
West Nile virus in 2006 and 2007: the Canadian Blood Services' experience
Authors: O'Brien Sheila F. , Scalia Vito , Zuber Edna , Hawes Gordon , Alport Edward C. , Goldman Mindy , Fearon Margaret A. 
Published: December 2009

BACKGROUND: The Canadian blood supply has been screened for West Nile virus (WNV) since 2003. A strategy for targeted individual‐donation nucleic acid testing (ID‐NAT) was implemented in 2004 to identify potentially infectious donations that may be missed by minipool (MP) testing. In 2007, Canada experienced a larger epidemic than in previous years providing an opportunity to evaluate the ID‐NAT triggering algorithm in higher‐risk areas.STUDY DESIGN AND METHODS: A specially created database and internal‐external communication identified regions for targeted ID‐NAT using MP and community triggers. WNV‐positive donations identified by ID‐NAT were reexamined in MP to assess the efficacy of targeted ID‐NAT in identifying potentially infectious donations that may have been missed by MP testing. WNV‐positive donation data from 2006 and 2007 were analyzed to examine temporal and geographic trends. A telephone survey about symptoms was carried out after the 2007 season.RESULTS: In total 78 WNV‐positive donations were identified (66 true‐positives and four false‐positives being in 2007). Most positive donations were in the late summer, concentrated in the same western provinces as community cases. Fifty‐two donations were identified by ID‐NAT and 46% were consistently positive in MP. Of the other 54%, 74% were immunoglobulin (Ig)M‐ and/or IgG‐positive. Fifty‐six percent of donors experienced mostly mild symptoms before or after donation (but all said they were well at the time of donation).CONCLUSION: WNV‐positive donations correspond geographically with the epidemic. MP testing identifies most potentially infectious donations with a smaller potential benefit from targeted ID‐NAT. Mild symptoms are common but may not deter donation.
Rigid confocal endoscopy for in vivo imaging of experimental oral squamous intra‐epithelial lesions
Authors: Farahati Behnaz , Stachs Oliver , Prall Friedrich , Stave Joachim , Guthoff Rudolf , Pau Hans Wilhelm , Just Tino 
Published: December 2009

J Oral Pathol Med (2010) 39: 318–327Background:  A rigid confocal endoscope has been developed to assess the oral squamous epithelium of mice and to determine sensitivity, specificity, and accuracy of this new technology.Methods:  This endoscope is connected to the commercially available Heidelberg Retina Tomograph (HRT). HRT is a device with a 670‐nm diode laser designed to acquire topographical measurements of the optic nerve head. Real‐time rigid confocal endoscopy is demonstrated by imaging the epithelial lesions of a mice model. Six‐week‐old male C57Bl/6 mice were randomly divided into a non‐treated group (n = 10) and into a 4‐nitroquinoline 1‐oxide (4‐NQO)‐treated group (n = 50). In the 4‐NQO‐treated group, the mice obtained 4‐nitroquinoline 1‐oxide in the drinking water (100 μg/ml) to induce tumourigenesis in the mouse tongue. The 4‐NQO‐solution was diluted in the drinking water for mice. After an 8–16‐week carcinogen treatment with 4‐NQO (ad libitum), mouse tongues were dissected within 3 h after CO2 overdose. After confocal microscopy of all lesions of the tongue, conventional histopathological investigation was performed.Results:  The inter‐rater reliability for the two observers of the confocal microscopic findings was found to be Kappa = 0.59 (P < 0.001). The penetration depth varied in the healthy tissue of the underside of the tongue throughout this study and was measured between 104 and 240 μm. In keratotic lesions, the penetration depths were diminished and varied between 80 and 140 μm. Strong keratinization inhibits the evaluation of the epithelium. For differentiation between low‐grade and high‐grade squamous intra‐epithelial lesions, a sensitivity and specificity of 73% and 88% was reached.Conclusions:  The animal experiment with this non‐invasive new technology indicates that this imaging technology facilitates the detection of pre‐cancerous lesions of the underside of the oropharynx. Human studies on oropharyngeal and laryngeal lesions are needed to prove the applicability of this method in the field of otorhinolaryngology.
Evaluation of survivin as a prognostic marker in oral squamous cell carcinoma
Authors: Kim Yong‐Hun , Kim Soung‐Min , Kim Yu‐Kyoung , Hong Sam‐Pyo , Kim Myung‐Jin , Myoung Hoon 
Published: December 2009

J Oral Pathol Med (2010) 39: 368–375Background:  Poor prognosis of oral squamous cell carcinoma (OSCC) is partly attributed to the lack of significant tumor marker for accurate staging and prognostication. We have evaluated survivin, which is a member of the inhibitor of apoptosis family as a cancer marker associated with proliferation, angiogenesis, oral carcinogenesis, and OSCC patient survival, as we reported a prognostic significance of survivin expression in lymph node previously.Methods:  To evaluate survivin expression in six OSCC cell lines, Western blotting was performed. Hamster oral carcinogenesis model was used to observe changes of survivin expression in oral carcinogenesis. Finally, we assessed the diagnostic and prognostic significance of survivin in a series of 38 primary OSCC through immunohistochemistry (CD31, PCNA) and Kaplan–Meier’s test.Results:  Survivin expression was detected in all OSCC cell lines at a varying level but not observed in normal gingival keratinocyte cells. In hamster model, survivin expression was observed from 8 weeks through 16 weeks and the intensity of expression became strong until 16 weeks. Clinicopathological analysis revealed a significant correlation between survivin expression and lymph node metastasis (P = 0.006) and proliferation (P < 0.001). However, there was no significant relationship with differentiation, micro vessel density, and cancer stage based on TNM. Survivin overexpression had a significant negative effect on survival of patients.Conclusions:  These results demonstrate the significant relationship between survivin expression and oral carcinogenesis and aggressiveness of OSCC including survival rate of patient. Survivin therefore may be used as a significant cancer marker to gain prognostic information of OSCC.
Crystal structure of salt‐tolerant glutaminase from Micrococcus luteus K‐3 in the presence and absence of its product l‐glutamate and its activator Tris
Authors: Yoshimune Kazuaki , Shirakihara Yasuo , Wakayama Mamoru , Yumoto Isao 
Published: December 2009

Glutaminase from Micrococcus luteus K‐3 [Micrococcus glutaminase (Mglu); 456 amino acid residues (aa); 48 kDa] is a salt‐tolerant enzyme. Our previous study determined the structure of its major 42‐kDa fragment. Here, using new crystallization conditions, we determined the structures of the intact enzyme in the presence and absence of its product l‐glutamate and its activator Tris, which activates the enzyme by sixfold. With the exception of a ‘lid’ part (26‐29 aa) and a few other short stretches, the structures were all very similar over the entire polypeptide chain. However, the presence of the ligands significantly reduced the length of the disordered regions: 41 aa in the unliganded structure (N), 21 aa for l‐glutamate (G), 8 aa for Tris (T) and 6 aa for both l‐glutamate and Tris (TG). l‐Glutamate was identified in both the G and TG structures, whereas Tris was only identified in the TG structure. Comparison of the glutamate‐binding site between Mglu and salt‐labile glutaminase (YbgJ) from Bacillus subtilis showed significantly smaller structural changes of the protein part in Mglu. A comparison of the substrate‐binding pocket of Mglu, which is highly specific for l‐glutamine, with that of Erwinia carotovora asparaginase, which has substrates other than l‐glutamine, shows that Mglu has a larger substrate‐binding pocket that prevents the binding of l‐asparagine with proper interactions.Structured digital abstract
MINT‐7305730: Mglu (uniprotkb:Q4U1A6) and Mglu (uniprotkb:Q4U1A6) bind (MI:0407) by x‐ray crystallography (MI:0114)
Bacterial genotoxicity bioreporters
Authors: Biran Alva , Yagur‐Kroll Sharon , Pedahzur Rami , Buchinger Sebastian , Reifferscheid Georg , Ben‐Yoav Hadar , Shacham‐Diamand Yosi , Belkin Shimshon 
Published: December 2009

SummaryEver since the introduction of theSalmonella typhimuriummammalian microsome mutagenicity assay (the ‘Ames test’) over three decades ago, there has been a constant development of additional genotoxicity assays based upon the use of genetically engineered microorganisms. Such assays rely either on reversion principles similar to those of the Ames test, or on promoter–reporter fusions that generate a quantifiable dose‐dependent signal in the presence of potential DNA damaging compounds and the induction of repair mechanisms; the latter group is the subject of the present review. Some of these assays were only briefly described in the scientific literature, whereas others have been developed all the way to commercial products. Out of these, only one, theumu‐test, has been fully validated and ISO‐ and OECD standardized. Here we review the main directions undertaken in the construction and testing of bacterial‐based genotoxicity bioassays, including the attempts to incorporate at least a partial metabolic activation capacity into the molecular design. We list the genetic modifications introduced into the tester strains, compare the performance of the different assays, and briefly describe the first attempts to incorporate such bacterial reporters into actual genotoxicity testing devices.
Compositional breast imaging using a dual‐energy mammography protocol
Authors: Laidevant Aurelie D. , Malkov Serghei , Flowers Chris I. , Kerlikowske Karla , Shepherd John A. 
Published: December 2009

PurposeMammography has a low sensitivity in dense breasts due to low contrast between malignant and normal tissue confounded by the predominant water density of the breast. Water is found in both adipose and fibroglandular tissue and constitutes most of the mass of a breast. However, significant protein mass is mainly found in the fibroglandular tissue where most cancers originate. If the protein compartment in a mammogram could be imaged without the influence of water, the sensitivity and specificity of the mammogram may be improved. This article describes a novel approach to dual‐energy mammography, full‐field digital compositional mammography (FFDCM), which can independently image the three compositional components of breast tissue: water, lipid, and protein.MethodsDual‐energy attenuation and breast shape measures are used together to solve for the three compositional thicknesses. Dual‐energy measurements were performed on breast‐mimicking phantoms using a full‐field digital mammography unit. The phantoms were made of materials shown to have similar x‐ray attenuation properties of the compositional compartments. They were made of two main stacks of thicknesses around 2 and 4 cm. Twenty‐six thickness and composition combinations were used to derive the compositional calibration using a least‐squares fitting approach.ResultsVery high accuracy was achieved with a simple cubic fitting function with root mean square errors of 0.023, 0.011, and 0.012 cm for the water, lipid, and protein thicknesses, respectively. The repeatability (percent coefficient of variation) of these measures was tested using sequential images and was found to be 0.5%, 0.5%, and 3.3% for water, lipid, and protein, respectively. However, swapping the location of the two stacks of the phantom on the imaging plate introduced further errors showing the need for more complete system uniformity corrections. Finally, a preliminary breast image is presented of each of the compositional compartments separately.ConclusionsFFDCM has been derived and exhibited good compositional thickness accuracy on phantoms. Preliminary breast images demonstrated the feasibility of creating individual compositional diagnostic images in a clinical environment.
Commissioning of the discrete spot scanning proton beam delivery system at the University of Texas M.D. Anderson Cancer Center, Proton Therapy Center, Houston
Authors: Gillin Michael T. , Sahoo Narayan , Bues Martin , Ciangaru George , Sawakuchi Gabriel , Poenisch Falk , Arjomandy Bijan , Martin Craig , Titt Uwe , Suzuki Kazumichi , Smith Alfred R. , Zhu X. Ronald 
Published: December 2009

PurposeTo describe a summary of the clinical commissioning of the discrete spot scanning proton beam at the Proton Therapy Center, Houston (PTC‐H).MethodsDiscrete spot scanning system is composed of a delivery system (Hitachi ProBeat), an electronic medical record (Mosaiq V 1.5), and a treatment planning system (TPS) (Eclipse V 8.1). Discrete proton pencil beams (spots) are used to deposit dose spot by spot and layer by layer for the proton distal ranges spanning from and over a maximum scan area at the isocenter of . An arbitrarily chosen reference calibration condition has been selected to define the monitor units (MUs). Using radiochromic film and ion chambers, the authors have measured spot positions, the spot sizes in air, depth dose curves, and profiles for proton beams with various energies in water, and studied the linearity of the dose monitors. In addition to dosimetric measurements and TPS modeling, significant efforts were spent in testing information flow and recovery of the delivery system from treatment interruptions.ResultsThe main dose monitors have been adjusted such that a specific amount of charge is collected in the monitor chamber corresponding to a single MU, following the IAEA TRS 398 protocol under a specific reference condition. The dose monitor calibration method is based on the absolute dose per MU, which is equivalent to the absolute dose per particle, the approach used by other scanning beam institutions. The full width at half maximum for the spot size in air varies from approximately for for . The measured versus requested 90% depth dose in water agrees to within over ranges of . The beam delivery interlocks perform as expected, guarantying the safe and accurate delivery of the planned dose.ConclusionsThe dosimetric parameters of the discrete spot scanning proton beam have been measured as part of the clinical commissioning program, and the machine is found to function in a safe manner, making it suitable for patient treatment.
Detection of longitudinal lung structural and functional changes after diagnosis of radiation‐induced lung injury using hyperpolarized magnetic resonance imaging
Authors: Mathew Lindsay , Gaede Stewart , Wheatley Andrew , Etemad‐Rezai Roya , Rodrigues George B. , Parraga Grace 
Published: December 2009

PurposeTherapeutic radiation doses for thoracic tumors are significantly restricted to decrease the risk of nontumor tissue damage, yet radiation‐induced lung injury (RILI) still occurs in over of thoracic radiation treatment cases. Although RILI can be clinically monitored using pulmonary function measurements, the regional functional effects of the injury are not well understood. Hyperpolarized magnetic resonance imaging provides measurements of regional lung function and structure with high spatial and temporal resolution; the authors use this tool longitudinally for the first time in seven subjects after clinical diagnosis of RILI in order to better understand regional changes in lung function and structure post‐RILI.MethodsAll subjects underwent spirometry, plethysmography, and MRI at after radiation therapy commenced. Thoracic , static ventilation, and diffusion‐weighted images were acquired to generate the apparent diffusion coefficient (ADC) and percent ventilated volume (PVV). Four subjects returned after baseline imaging for follow‐up spirometry and MRI measurements of ADC and PVV.ResultsAt baseline, PVV was significantly different and lower in the ipsilateral diseased lung compared to the contralateral nondiseased lung . Longitudinally, significant increases were observed for MRI PVV (, ) and MRI ADC (, ) in the contralateral lung only, in the four subjects who returned for follow‐up, while no changes in the ipsilateral lung were reported.ConclusionsHyperpolarized MRI was well tolerated in all subjects with moderate to severe RILI. Functional improvements and microstructural changes were observed in the contralateral lung, while the ipsilateral lung remained stable, suggesting that functional compensatory changes may have occurred in the contralateral lung due to ipsilateral lung radiation‐induced injury.
A BPF‐FBP tandem algorithm for image reconstruction in reverse helical cone‐beam CT
Authors: Cho Seungryong , Xia Dan , Pellizzari Charles A. , Pan Xiaochuan 
Published: December 2009

PurposeReverse helical cone‐beam computed tomography (CBCT) is a scanning configuration for potential applications in image‐guided radiation therapy in which an accurate anatomic image of the patient is needed for image‐guidance procedures. The authors previously developed an algorithm for image reconstruction from nontruncated data of an object that is completely within the reverse helix. The purpose of this work is to develop an image reconstruction approach for reverse helical CBCT of a long object that extends out of the reverse helix and therefore constitutes data truncation.MethodsThe proposed approach comprises of two reconstruction steps. In the first step, a chord‐based backprojection‐filtration (BPF) algorithm reconstructs a volumetric image of an object from the original cone‐beam data. Because there exists a chordless region in the middle of the reverse helix, the image obtained in the first step contains an unreconstructed central‐gap region. In the second step, the gap region is reconstructed by use of a Pack–Noo‐formula‐based filteredbackprojection (FBP) algorithm from the modified cone‐beam data obtained by subtracting from the original cone‐beam data the reprojection of the image reconstructed in the first step.ResultsThe authors have performed numerical studies to validate the proposed approach in image reconstruction from reverse helical cone‐beam data. The results confirm that the proposed approach can reconstruct accurate images of a long object without suffering from data‐truncation artifacts or cone‐angle artifacts.ConclusionsThey developed and validated a BPF‐FBP tandem algorithm to reconstruct images of a long object from reverse helical cone‐beam data. The chord‐based BPF algorithm was utilized for converting the long‐object problem into a short‐object problem. The proposed approach is applicable to other scanning configurations such as reduced circular sinusoidal trajectories.
On the scattering power of radiotherapy protons
Authors: Gottschalk Bernard 
Published: December 2009

PurposeFirst, to show that accurate formulas for scattering power must take into account the competition between the Gaussian core and the single scattering tail of the angular distribution, which affects the rate of change in the Gaussian width and leads to the single scattering correction (SSC). Second, to show that the SSC requires that be nonlocal: Besides material properties and energy at the point of interest, it must depend in some fashion on how much multiple scattering has already taken place. Third, after reviewing five previous formulas (three local and two nonlocal), to derive an improved “differential Molière” formula . Last, to investigate, by studying some practical cases, when an accurate formula for is actually needed.MethodsWe first take the numerical derivative of the Molière/Fano/Hanson in order to find the true SSC. We simplify the formula for (ICRU Report 35) for protons, introducing a new material dependent property, the “scattering length” , analogous to radiation length . We then use as a basis for by including a nonlocal correction factor which, by virtue of the Øverås approximation, parametrizes the single scattering correction.ResultsThe improved scattering power is where , (MeV) is the initial product of proton momentum and speed, is the same at the point of interest, and . is easily computed and generalizes readily to mixed slabs because is not material dependent.ConclusionsWhether an accurate formula for is required depends very much on the problem at hand. For beam spreading in water, five of the six formulas for give almost identical results, suggesting that patient dose calculations are insensitive to . That is not true, however, of beam spreading in Pb. At the opposite extreme, the projected rms beam width at the end of a Pb/Lexan/air stack, analogous to the upstream modulator in a passive beam spreading system, is sensitive to . In this case a simple experiment would discriminate between all but two of the six formulas discussed. Scattering power applies as much to Monte Carlo as to deterministic transport calculations. Using in any of its forms will avoid step size dependence. Using the best available could be important in general purpose Monte Carlo codes, which are expected to give the correct answer to many different problems.
Local bone enhancement fuzzy clustering for segmentation of MR trabecular bone images
Authors: Folkesson Jenny , Carballido‐Gamio Julio , Eckstein Felix , Link Thomas M. , Majumdar Sharmila 
Published: December 2009

PurposeSegmentation of trabecular bone from magnetic resonance (MR) images is a challenging task due to spatial resolution limitations, signal‐to‐noise ratio constraints, and signal intensity inhomogeneities. This article examines an alternative approach to trabecular bone segmentation using partial membership segmentation termed fuzzy ‐means clustering incorporating local second order features for bone enhancement (BE‐FCM) at multiple scales. This approach is meant to allow for a soft segmentation that accounts for partial volume effects while suppressing the influence of noise.MethodsA soft segmentation method was developed and evaluated on three different sets of data; interscan reproducibility was evaluated on six test‐retestin vivo MR scans of the proximal femur, correlation between MR and HR‐pQCT measurements was evaluated on 49 in vivo scans from the distal tibia, and the potential for fracture discrimination was evaluated using MR scans of calcaneus specimens from 15 participants with and 15 participants without vertebral fracture. The algorithm was compared to fuzzy clustering using the intensity as the only feature (I‐FCM) and a dual thresholding algorithm. The metric evaluated was bone volume over total volume (BV/TV) within user‐defined regions of interest.ResultsBE‐FCM had a higher interscan reproducibility (rms CV: 2.0%) compared to I‐FCM (5.6%) and thresholding (4.2%), and expressed higher correlation to HR‐pQCT data compared to I‐FCM and thresholding . BE‐FCM was also the method that was best able to differentiate between a control and a vertebral fracture group at a 95% significance level.ConclusionsThe results suggest that trabecular bone segmentation by BE‐FCM can provide a precise BV/TV measurement that is sensitive to pathology. The segmentation method may become useful in MR imaging‐based quantification of bone microarchitecture.