bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early cortical lens opacities: a short overview
Authors: Vrensen Gijs F.J.M. 
Published: August 2009

Abstract.Cataract is still the dominant cause of blindness worldwide. Cortical cataract is the most prevalent of the age‐related changes in the human lenses that require surgical intervention to restore vision. The absence of adequate cataract surgery in most developing countries is the main cause of the high prevalence of cataract blindness worldwide. Lens ageing is accompanied by dramatic increases in stiffness, light scattering and coloration of the lens nucleus. These changes start to become manifest as early as the fourth or fifth decade of life and lead to nuclear cataract in old age. In the same period the equatorial deep lens cortex starts to show small opaque shades, which eventually grow out to segmental and annular opacities. These opaque shades are filled with small vesicles and contain abnormal amounts of cross‐linked proteins, cholesterol and phospholipids. They are bordered by membranes that are rich in square arrays, have ‘degenerate’ gap junctions and have few intramembranous particles. It has been shown that the opaque shades represent cohorts of locally affected fibres segregated from unaffected neighbouring fibres by ‘non‐leaky’ membranes. This segregation is an effective mechanism delaying the outgrowth of these opacities to cuneiform cataracts entering the pupillary space and thus leading to blinding cortical cataracts. Although cataract formation is mostly considered to be a multi‐factorial disease, oxidative stress might be one of the leading causes for both nuclear and cortical cataract. In cortical cataracts shear stress between cortex and nucleus during accommodation may also play a significant role.
Considering marker visibility during leaf sequencing for segmental intensity‐modulated radiation therapy
Authors: Zhao Bo , Dai Jianrong , Ling C. Clifton 
Published: August 2009

Purpose:Segmental intensity‐modulated radiation therapy (IMRT) delivers a sequence of segments to obtain a desired intensity distribution. Many leaf sequencing algorithms for segmental IMRT have been developed with the aim of reducing delivered monitor units (MUs) and (or) number of segments and, consequently, to reduce the total treatment delivery time. With the development of real‐time detection technology, it is useful to develop leaf sequencing algorithms that consider the detecting probability of markers implanted into or near the target volume.Methods:In this study, the authors defined the concept of marker visibility to denote the marker's detecting probability and proposed a new leaf sequencing algorithm based on the Kamath algorithm. The new algorithm first uses the Kamath algorithm to generate an initial leaf sequence and then performs a series of column transformations to obtain a new leaf sequence that is optimal in terms of MU efficiency and marker visibility. The authors evaluated the performance of the new algorithm with six artificial fields that had randomly generated intensity matrices and 15 clinical fields that had intensity matrices from the IMRT plans for three prostate cancer patients.Results:Compared to the Kamath algorithm, the new algorithm does not increase the total delivered intensity but increases the marker visibility. For the artificial fields, the marker visibility increased from 66.67% to 91.67% for small radiation fields, from 39.29% to 42.86% for medium size fields, and from 31.48% to 37.04% for large fields. For the clinical fields, the marker visibility increased 9%–20% for four fields, 20%–30% for three fields, 30%–40% for two fields, and more than 40% for one field. However, the marker visibility did not change for 4 out of 15 fields.Conclusions:The authors developed a new leaf sequencing algorithm for optimal MU efficiency and marker visibility and also rigorously proved its optimality.
Gamma Knife output factor measurements using VIP polymer gel dosimetry
Authors: Moutsatsos A. , Petrokokkinos L. , Karaiskos P. , Papagiannis P. , Georgiou E. , Dardoufas K. , Sandilos P. , Torrens M. , Pantelis E. , Kantemiris I. , Sakelliou L. , Seimenis I. 
Published: August 2009

Purpose:Water equivalent polymer gel dosimeters and magnetic resonance imaging were employed to measure the output factors of the two smallest treatment fields available in a Gamma Knife model C radiosurgery unit, those formed employing the 4 and 8 mm final collimator helmets.Methods:Three samples of the VIP normoxic gel formulation were prepared and irradiated so that a single shot of the field whose output factor is to be measured and a single shot of the reference 18 mm field were delivered in each one. Emphasis is given to the development and benchmarking of a refined data processing methodology of reduced uncertainty that fully exploits the 3D dose distributions registered in the dosimeters.Results:Polymer gel results for the output factor of the 8 mm collimator helmet are found to be in close agreement with the corresponding value recommended by the vendor ( versus 0.956, respectively). For the 4 mm collimator helmet, however, polymer gel results suggest an output factor 3% lower than the value recommended by the vendor ( versus 0.870, respectively).Conclusions:A comparison with corresponding measurements published in the literature indicates that output factor results of this work are in agreement with those obtained using dosimetric systems which, besides fine spatial resolution and lack of angular and dose rate dependence of the dosimeter's response, share with polymer gels the favorable characteristic of minimal radiation field perturbation.
Uncertainties in effective dose estimates of adult CT head scans: The effect of head size
Authors: Gregory Kent J. , Bibbo Giovanni , Pattison John E. 
Published: August 2009

Purpose: This study is an extension of a previous study where the uncertainties in effective dose estimates from adult CT head scans were calculated using four CT effective dose estimation methods, three of which were computer programs (CT‐EXPO, CTDOSIMETRY, and IMPACTDOSE) and one that involved the dose length product (DLP). However, that study did not include the uncertainty contribution due to variations in head sizes.Methods: The uncertainties due to head size variations were estimated by first using the computer program data to calculate doses to small and large heads. These doses were then compared with doses calculated for the phantom heads used by the computer programs. An uncertainty was then assigned based on the difference between the small and large head doses and the doses of the phantom heads.Results: The uncertainties due to head size variations alone were found to be between 4% and 26% depending on the method used and the patient gender. When these uncertainties were included with the results of the previous study, the overall uncertainties in effective dose estimates (stated at the 95% confidence interval) were 20%–31% (CT‐EXPO), 15%–30% (CTDOSIMETRY), 20%–36% (IMPACTDOSE), and 31%–40% (DLP).Conclusions: For the computer programs, the lower overall uncertainties were still achieved when measured values of CT dose index were used rather than tabulated values. For DLP dose estimates, head size variations made the largest (for males) and second largest (for females) contributions to effective dose uncertainty. An improvement in the uncertainty of the DLP method dose estimates will be achieved if head size variation can be taken into account.
Evaluation of nonrigid registration models for interfraction dose accumulation in radiotherapy
Authors: Janssens Guillaume , Orban de Xivry Jonathan , Fekkes Stein , Dekker André , Macq Benoit , Lambin Philippe , van Elmpt Wouter 
Published: August 2009

Purpose:Interfraction dose accumulation is necessary to evaluate the dose distribution of an entire course of treatment by adding up multiple dose distributions of different treatment fractions. This accumulation of dose distributions is not straightforward as changes in the patient anatomy may occur during treatment. For this purpose, the accuracy of nonrigid registration methods is assessed for dose accumulation based on the calculated deformations fields.Methods:A phantom study using a deformable cubic silicon phantom with implanted markers and a cylindrical silicon phantom with MOSFET detectors has been performed. The phantoms were deformed and images were acquired using a cone‐beam CT imager. Dose calculations were performed on these CT scans using the treatment planning system. Nonrigid CT‐based registration was performed using two different methods, the Morphons and Demons. The resulting deformation field was applied on the dose distribution. For both phantoms, accuracy of the registered dose distribution was assessed. For the cylindrical phantom, also measured dose values in the deformed conditions were compared with the dose values of the registered dose distributions. Finally, interfraction dose accumulation for two treatment fractions of a patient with primary rectal cancer has been performed and evaluated using isodose lines and the dose volume histograms of the target volume and normal tissue.Results:A significant decrease in the difference in marker or MOSFET position was observed after nonrigid registration methods for both phantoms and with both methods, as well as a significant decrease in the dose estimation error ( for the cubic phantom and for the cylindrical) with both methods. Considering the whole data set at once, the difference between estimated and measured doses was also significantly decreased using registration ( for both methods). The patient case showed a slightly underdosed planning target volume and an overdosed bladder volume due to anatomical deformations.Conclusions:Dose accumulation using nonrigid registration methods is possible using repeated CT imaging. This opens possibilities for interfraction dose accumulation and adaptive radiotherapy to incorporate possible differences in dose delivered to the target volume and organs at risk due to anatomical deformations.
Mycotic Keratitis Due to
Aspergillus nomius
Authors: Manikandan Palanisamy , Varga János , Kocsubé Sándor , Samson Robert A. , Anita Raghavan , Revathi Rajaraman , Dóczi Ilona , Németh Tibor Mihály , Narendran Venkatapathy , Vágvölgyi Csaba , Manoharan Chockaiya , Kredics László 
Published: August 2009

ABSTRACT

We report the first known case of fungal keratitis caused by
Aspergillus nomius.
Ocular injury was known as a predisposing factor. The patient was treated with natamycin and econazole eye drops, itraconazole eye ointment, and oral ketoconazole. A therapeutic penetrating keratoplasty was performed 16 days after presentation. A sequence-based approach was used to assign the isolate to a species.
Broth Microdilution Method To Detect Extended-Spectrum β-Lactamases and AmpC β-Lactamases in
Enterobacteriaceae
Isolates by Use of Clavulanic Acid and Boronic Acid as Inhibitors
Authors: Jeong Seok Hoon , Song Wonkeun , Kim Jae-Seok , Kim Han-Sung , Lee Kyu Man 
Published: August 2009

ABSTRACT

This study was designed to evaluate the performance of the broth microdilution (BMD) method to detect production of extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases in
Enterobacteriaceae
by using clavulanic acid (CA) and boronic acid (BA) as ESBL and AmpC β-lactamase inhibitors, respectively. A total of 100 clinical isolates of
Enterobacteriaceae
were analyzed. Mueller-Hinton broth containing serial twofold dilutions of cefotaxime (CTX), ceftazidime (CAZ), aztreonam (ATM), or cefepime (FEP) with or without either or both CA and BA was prepared. An eightfold or greater decrease in the MIC of CTX, CAZ, ATM, or FEP in the presence of CA and BA was considered a positive result for ESBL and plasmid-mediated AmpC β-lactamase (PABL), respectively. In tests with CA, expanded-spectrum β-lactams containing BA (CTX-BA, CAZ-BA, ATM-BA, and FEP-BA) showed higher positive rates in detecting ESBL producers than those without BA. The combination of CTX- and CAZ-based BMD tests with CA and BA showed sensitivity and specificity of 100% for the detection of ESBLs and PABLs. The BMD testing could be applicable for routine use in commercially available semiautomated systems for the detection of ESBLs and PABLs in
Enterobacteriaceae
.
Blocking Hepatitis C Virus Infection with Recombinant Form of Envelope Protein 2 Ectodomain
Authors: Whidby Jillian , Mateu Guaniri , Scarborough Hannah , Demeler Borries , Grakoui Arash , Marcotrigiano Joseph 
Published: August 2009

ABSTRACT
More than 120 million people worldwide are chronically infected with hepatitis C virus (HCV), making HCV infection the leading cause of liver transplantation in developed countries. Treatment is limited, and efficacy depends upon the infecting strain and the initial viral load. The HCV envelope glycoproteins (E1 and E2) are involved in receptor binding, virus-cell fusion, and entry into the host cell. HCV infection proceeds by endosomal acidification, suggesting that fusion of the viral envelope with cellular membranes is a pH-triggered event. E2 consists of an amino-terminal ectodomain, an amphipathic helix that forms a stem region, and a carboxy-terminal membrane-associating segment. We have devised a novel expression system for the production of a secreted form of E2 ectodomain (eE2) from mammalian cells and performed a comprehensive biochemical and biophysical characterization. eE2 is properly folded, as determined by binding to human CD81, blocking of infection of cell culture-derived HCV, and recognition by antibodies from patients chronically infected with different genotypes of HCV. The glycosylation pattern, number of disulfide bonds, oligomerization state, and secondary structure of eE2 have been characterized using mass spectrometry, size exclusion chromatography, circular dichroism, and analytical ultracentrifugation. These results advance the understanding of E2 and may assist in the design of an HCV vaccine and entry inhibitor.
Human Immunodeficiency Virus Type 1 Envelope gp120-Induced Partial T-Cell Receptor Signaling Creates an F-Actin-Depleted Zone in the Virological Synapse
Authors: Vasiliver-Shamis Gaia , Cho Michael W. , Hioe Catarina E. , Dustin Michael L. 
Published: August 2009

ABSTRACTCell-to-cell transmission of human immunodeficiency virus type 1 (HIV-1) occurs via a virological synapse (VS), a tight cell-cell junction formed between HIV-infected cells and target cells in which the HIV-1-infected cell polarizes and releases virions toward the noninfected target cell in a gp120- and intercellular adhesion molecule 1 (ICAM-1)-dependent process. The response of the target cell has been less studied. We utilized supported planar bilayers presenting gp120 and ICAM-1 as a reductionist model for the infected-cell membrane and investigated its effect on the target CD4 T cell. This study shows that HIV-1 gp120 interaction with its receptors is initially organized into microclusters that undergo F-actin-dependent consolidation into a central supramolecular activation complex (cSMAC). Src kinases are active in both gp120 microclusters and in the VS cSMAC. The early T-cell receptor (TCR) signaling machinery is partially activated at the VS, and signaling does not propagate to trigger Ca2+elevation or increase CD69 expression. However, these partial TCR signals act locally to create an F-actin-depleted zone. We propose a model in which the F-actin-depleted zone formed within the target CD4 T cell enhances the reception of virions by releasing the physical barrier for HIV-1 entry and facilitating postentry events.
Performance-based readability testing of participant materials for a phase I trial: TGN1412: Table 1
Authors: Knapp P , Raynor D K , Silcock J , Parkinson B 
Published: August 2009

Background:Concern has been expressed about the process of consent to clinical trials, particularly in phase I “first-in-man” trials. Trial participant information sheets are often lengthy and technical. Content-based readability testing of sheets, which is often required to obtain research ethics approval for trials in the USA, is limited and cannot indicate how information will perform.Methods:An independent-groups design was used to study the user-testing performance of the participant information sheet from the phase I TGN1412 trial. Members of the public were asked to read it, then find and demonstrate understanding of 21 key aspects of the trial. The participant information sheet was then rewritten, redesigned and tested on 20 members of the public, using the same 21-item questionnaire.Results:On the original TGN1412 participant information sheet, participants could not find answers and some of the found information was not understood. Six of 21 questions, including those relating to placebo, follow-up visits and the emergency phone number, were found by eight or fewer of 10 participants. The revised information sheet performed better, with the answers to 17 of 21 questions found and understood by all 20 participants.Conclusions:Tests showed that the TGN1412 participant information sheet may not inform participants adequately for consent. Revising its content and design led to significant improvements. Writers of materials for trial participants should take account of good practice in information design. Performance-based user testing may be a useful method to indicate strengths and weaknesses in trial materials.
Top-down and bottom-up forces in mammalian herbivore – vegetation systems: an essay review
Authors: Turkington Roy 
Published: August 2009

For almost 50 years ecologists have debated why herbivores generally don’t increase in numbers to such levels as to deplete or devastate vegetation. One hypothesis is that herbivore populations are regulated at low densities by predators, and a second hypotheses is that plants are fundamentally poor food for herbivores. This has lead to two main hypotheses about the role of herbivores in structuring vegetation: the “bottom-up” and “top-down” hypotheses. Here I survey the literature, with a focus on field experiments designed to investigate the soil resource – vegetation – mammalian herbivore system, specifically asking five questions about how each trophic level responds to (i) resource addition, (ii) vegetation removal, (iii) herbivore removal or reduction, (iv) herbivore addition, and (v) the interaction of resource levels and herbivory? I use these to develop 12 testable predictions. I document the major areas of research as they relate to these 12 predictions, and use these to evaluate weaknesses and limitations in field methods. There are surprisingly few terrestrial studies that conduct factorial manipulations of multiple nutrients or herbivores, even though it is clear that these are essential. Specifically, I argue that a manipulative experimental approach is the most valuable way to advance our theory and understanding, and I advocate the continued use of long-term factorial field experiments that simultaneously manipulate soil resources levels and herbivory (preferably at multiple levels), repeated in a range of environments in which individual species or functional groups are monitored.
Iodine-catalyzed efficient synthesis of chalcones by grinding under solvent-free conditions
Authors: Wang Hongshe , Zeng June 
Published: August 2009

Chalcones are useful intermediates in organic synthesis and exhibit a large number of different biological activities. Chalcones have been synthesized in high yields by Claisen–Schmidt condensation of substituted acetophenones with various aromatic aldehydes in the presence of 10 mol% of iodine at room temperature by grinding under solvent-free conditions.
MONSTERS, BLACK HOLES AND THE STATISTICAL MECHANICS OF GRAVITY
Authors: HSU STEPHEN D. H. , REEB DAVID 
Published: August 2009

We review the construction of monsters in classical general relativity. Monsters have finite ADM mass and surface area, but potentially unbounded entropy. From the curved space perspective, they are objects with large proper volume that can be glued on to an asymptotically flat space. At no point is the curvature or energy density required to be large in Planck units, and quantum gravitational effects are, in the conventional effective field theory framework, small everywhere. Since they can have more entropy than a black hole of equal mass, monsters are problematic for certain interpretations of black hole entropy and the AdS/CFT duality. In the second part of the paper we review recent developments in the foundations of statistical mechanics which make use of properties of high-dimensional (Hilbert) spaces. These results primarily depend on kinematics — essentially, the geometry of Hilbert space — and are relatively insensitive to dynamics. We discuss how this approach might be adopted as a basis for the statistical mechanics of gravity. Interestingly, monsters and other highly entropic configurations play an important role.
FLOATING-POINT ARITHMETIC FOR COMPUTATIONAL GEOMETRY PROBLEMS WITH UNCERTAIN DATA
Authors: JIANG D. , STEWART N. F. 
Published: August 2009

It has been suggested in the literature that ordinary finite-precision floating-point arithmetic is inadequate for geometric computation, and that researchers in numerical analysis may believe that the difficulties of error in geometric computation can be overcome by simple approaches. It is the purpose of this paper to show that these suggestions, based on an example showing failure of a certain algorithm for computing planar convex hulls, are misleading, and why this is so.It is first shown how the now-classical backward error analysis can be applied in the area of computational geometry. This analysis is relevant in the context of uncertain data, which may well be the practical context for computational-geometry algorithms such as, say, those for computing convex hulls. The exposition will illustrate the fact that the backward error analysis does not pretend to overcome the problem of finite precision: it merely provides a way to distinguish those algorithms that overcome the problem to whatever extent it is possible to do so.It is then shown that often the situation in computational geometry is exactly parallel to other areas, such as the numerical solution of linear equations, or the algebraic eigenvalue problem. Indeed, the example mentioned can be viewed simply as an example of the use of an unstable algorithm, for a problem for which computational geometry has already discovered provably stable algorithms.Finally, the paper discusses the implications of these analyses for applications in three-dimensional solid modeling. This is done by considering a problem defined in terms of a simple extension of the planar convex-hull algorithm, namely, the verification of the well-formedness of extruded objects. A brief discussion concerning more difficult problems in solid modeling is also included.