bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radiosurgery in the Treatment of Malignant Gliomas: The University of Florida Experience
Authors: Ulm Arthur J. , Friedman William A. , Bradshaw Patrick , Foote Kelly D. , Bova Frank J. 
Published: September 2005

ABSTRACT

OBJECTIVE:
To review a single-institution's 12-year experience of treating malignant gliomas with linear accelerator-based radiosurgery.

METHODS:
One hundred patients were treated for malignant gliomas at the University of Florida between May 1, 1989, and June 12, 2002. Patient variables were entered into a radiosurgery database in a prospective manner. The endpoint of the study was length of survival from the time of diagnosis. The minimum length of follow-up was 18 months or until death. In an attempt to control for selection bias, we used the Radiation Oncology Therapy Group's (RTOG) recursive partitioning categories to compare survival in our group of radiosurgically boosted patients with the RTOG historical database.

RESULTS:
Recursive partitioning analysis classification was significantly associated with survival. Compared with historical controls, this cohort of patients demonstrated a decreased survival for recursive partitioning analysis Class I and II patients, similar survival for Class III and IV patients, and increased median survival for Class V patients. Other variables demonstrating a statistically significant impact on survival were eloquent location and recurrent disease.

CONCLUSION:
The results of this study and those of RTOG 93-05 suggest that the reported benefit of upfront radiosurgical boost for malignant gliomas is the result of selection bias. The possibility remains that radiosurgical boost is of benefit in recurrent tumors, especially those in RTOG Class V.
A Prospective Study of Quality of Life in Adults with Newly Diagnosed High-grade Gliomas: The Impact of the Extent of Resection on Quality of Life and Survival
Authors: Brown Paul D. , Maurer Matthew J. , Rummans Teresa A. , Pollock Bruce E. , Ballman Karla V. , Sloan Jeff A. , Boeve Bradley F. , Arusell Robert M. , Clark Matthew M. , Buckner Jan C. 
Published: September 2005

ABSTRACTOBJECTIVE:To describe the quality of life (QOL) over time for adults with newly diagnosed high-grade gliomas and to examine the relationship between QOL and outcome data collected in three prospective cooperative group clinical trials.METHODS:The QOL study was a companion protocol for three Phase II high-grade glioma protocols. Five self-administered forms were completed by patients to assess QOL at study entry, 2 months, and 4 months after enrollment.RESULTS:QOL data were available for baseline, first, and second subsequent follow-up evaluations for 89%, 71%, and 69% of patients, respectively. A significant proportion of patients (47.1%) experienced impaired QOL (QOL ≤ 50) in at least one measure at subsequent evaluations, whereas most patients (88%) with impaired QOL at baseline continued to have impaired QOL at subsequent evaluations. On multivariable analyses, baseline QOL measures were predictive of QOL at the time of follow-up. In addition, patients who underwent a gross total resection were much less likely to have impaired QOL (P = 0.006), were less likely to experience worsening depression (P = 0.0008), and were more likely to have improved QOL (P = 0.003) at their first follow-up evaluation. Changes in QOL measures over time were not found to be associated with survival in multivariable analyses that adjusted for known prognostic variables; variables that were independently associated with improved survival were better performance status (P &lt; 0.001), younger age (P &lt; 0.001), and greater extent of resection (P &lt; 0.001).CONCLUSION:Baseline QOL was predictive of QOL over time. Gross total resection was associated with longer survival and improved QOL over time for patients with high-grade gliomas.
Diagnosis and Treatment of Atypical and Anaplastic Meningiomas: A Review
Authors: Modha Ashok , Gutin Philip H. 
Published: September 2005

ABSTRACTATYPICAL AND ANAPLASTIC meningiomas are uncommon tumors with a poorer prognosis than benign meningiomas. We reviewed the current literature and attempted to integrate and summarize available information to determine a logical approach to these tumors. Both tumors are rare and are often integrated with benign meningiomas when treatments are evaluated. In addition, because there has not been one histopathological classification scheme for atypical and anaplastic meningiomas in the past, there are numerous inconsistencies in the literature. Malignant progression with accumulation of mutations in a benign meningioma can result in an atypical and/or anaplastic meningioma. Both tumors are difficult to manage and have high recurrence and poor survival rates. The extent of tumor resection and histological grade are the key determinants for recurrence. In addition, metastases are unusual, but they do occur. We also review the evidence available that has resulted in the current World Health Organization classification. Radiation therapy can be used as an adjunctive treatment after both total and subtotal resection. In addition, the role of stereotactic radiosurgery is increasing, along with a possible role for brachytherapy. There are no effective chemotherapeutic agents available. A treatment algorithm is suggested.
Genetic Variation and Selection Response in Model Breeding Populations of Brassica rapa Following a Diversity Bottleneck
Authors: Briggs William H , Goldman Irwin L 
Published: September 2005

Abstract
Domestication and breeding share a common feature of population bottlenecks followed by significant genetic gain. To date, no crop models for investigating the evolution of genetic variance, selection response, and population diversity following bottlenecks have been developed. We developed a model artificial selection system in the laboratory using rapid-cycling Brassica rapa. Responses to 10 cycles of recurrent selection for cotyledon size were compared across a broad population founded with 200 individuals, three bottleneck populations initiated with two individuals each, and unselected controls. Additive genetic variance and heritability were significantly larger in the bottleneck populations prior to selection and this corresponded to a heightened response of bottleneck populations during the first three cycles. However, the overall response was ultimately greater and more sustained in the broad population. AFLP marker analyses revealed the pattern and extent of population subdivision were unaffected by a bottleneck even though the diversity retained in a selection population was significantly limited. Rapid gain in genetically more uniform bottlenecked populations, particularly in the short term, may offer an explanation for why domesticators and breeders have realized significant selection progress over relatively short time periods.
Human Endogenous Retroviral Elements as Indicators of Ectopic Recombination Events in the Primate Genome
Authors: Hughes Jennifer F , Coffin John M 
Published: September 2005

Abstract
HERV elements make up a significant fraction of the human genome and, as interspersed repetitive elements, have the capacity to provide substrates for ectopic recombination and gene conversion events. To understand the extent to which these events occur and gain further insight into the complex evolutionary history of these elements in our genome, we undertook a phylogenetic study of the long terminal repeat sequences of 15 HERV-K(HML-2) elements in various primate species. This family of human endogenous retroviruses first entered the primate genome between 35 and 45 million years ago. Throughout primate evolution, these elements have undergone bursts of amplification. From this analysis, which is the largest-scale study of HERV sequence dynamics during primate evolution to date, we were able to detect intraelement gene conversion and recombination at five HERV-K loci. We also found evidence for replacement of an ancient element by another HERV-K provirus, apparently reflecting an occurrence of retroviral integration by homologous recombination. The high frequency of these events casts doubt on the accuracy of integration time estimates based only on divergence between retroelement LTRs.
A Hyperspace Model to Decipher the Genetic Architecture of Developmental Processes: Allometry Meets Ontogeny
Authors: Wu Rongling , Hou Wei 
Published: September 2005

AbstractTo better utilize limited resources for their survival and reproduction, all organisms undergo developmental changes in both body size and shape during ontogeny. The genetic analysis of size change with increasing age, i.e., growth, has received considerable attention in quantitative developmental genetic studies, but the genetic architecture of ontogenetic changes in body shape and its associated allometry have been poorly understood partly due to the lack of analytical tools. In this article, we attempt to construct a multivariate statistical framework for studying the genetic regulation of ontogenetic growth and shape. We have integrated biologically meaningful mathematical functions of growth curves and developmental allometry into the estimation process of genetic mapping aimed at identifying individual quantitative trait loci (QTL) for phenotypic variation. This model defined with high dimensions can characterize the ontogenetic patterns of genetic effects of QTL over the lifetime of an organism and assess the interplay between genetic actions/interactions and phenotypic integration. The closed forms for the residual covariance matrix and its determinant and inverse were derived to overcome the computational complexity typical of our high-dimensional model. We used a worked example to validate the utility of this model. The implications of this model for genetic research of evo–devo are discussed.
The Evolution of Antifungal Peptides in Drosophila
Authors: Jiggins Francis M , Kim Kang-Wook 
Published: September 2005

Abstract
An essential component of the immune system of animals is the production of antimicrobial peptides (AMPs). In vertebrates and termites the protein sequence of some AMPs evolves rapidly under positive selection, suggesting that they may be coevolving with pathogens. However, antibacterial peptides in Drosophila tend to be highly conserved. We have inferred the selection pressures acting on Drosophila antifungal peptides (drosomycins) from both the divergence of drosomycin genes within and between five species of Drosophila and polymorphism data from Drosophila simulans and D. melanogaster. In common with Drosophila antibacterial peptides, there is no evidence of adaptive protein evolution in any of the drosomycin genes, suggesting that they do not coevolve with pathogens. It is possible that this reflects a lack of specific fungal and bacterial parasites in Drosophila populations. The polymorphism data from both species differed from neutrality at one locus, but this was not associated with changes in the protein sequence. The synonymous site diversity was greater in D. simulans than in D. melanogaster, but the diversity both upstream of the genes and at nonsynonymous sites was similar. This can be explained if both upstream and nonsynonymous mutations are slightly deleterious and are removed more effectively from D. simulans due to its larger effective population size.
Eliminating Gene Conversion Improves High-Throughput Genetics in Saccharomyces cerevisiae
Authors: Daniel Jewel A , Yoo Jiyoun , Bettinger Blaine T , Amberg David C , Burke Daniel J 
Published: September 2005

Abstract
Synthetic genetic analysis was improved by eliminating leaky expression of the HIS3 reporter and gene conversion between the HIS3 reporter and his3Δ1. Leaky expression was eliminated using 3-aminotriazole and gene conversion was eliminated by using the Schizosaccharomyces pombe his5+ gene, resulting in a 5- to 10-fold improvement in the efficiency of SGA.
Pkc1 Acts Through Zds1 and Gic1 to Suppress Growth and Cell Polarity Defects of a Yeast eIF5A Mutant
Authors: Zanelli Cleslei F , Valentini Sandro R 
Published: September 2005

Abstract
eIF5A is a highly conserved putative eukaryotic translation initiation factor that has been implicated in translation initiation, nucleocytoplasmic transport, mRNA decay, and cell proliferation, but with no precise function assigned so far. We have previously shown that high-copy PKC1 suppresses the phenotype of tif51A-1, a temperature-sensitive mutant of eIF5A in S. cerevisiae. Here, in an attempt to further understand how Pkc1 functionally interacts with eIF-5A, it was determined that PKC1 suppression of tif51A-1 is independent of the cell integrity MAP kinase cascade. Furthermore, two new suppressor genes, ZDS1 and GIC1, were identified. We demonstrated that ZDS1 and ZDS2 are necessary for PKC1, but not for GIC1 suppression. Moreover, high-copy GIC1 also suppresses the growth defect of a PKC1 mutant (stt1), suggesting the existence of a Pkc1-Zds1-Gic1 pathway. Consistent with the function of Gic1 in actin organization, the tif51A-1 strain shows an actin polarity defect that is partially recovered by overexpression of Pkc1 and Zds1 as well as Gic1. Additionally, PCL1 and BNI1, important regulators of yeast cell polarity, also suppress tif51A-1 temperature sensitivity. Taken together, these data strongly support the correlated involvement of Pkc1 and eIF5A in establishing actin polarity, which is essential for bud formation and G1/S transition in S. cerevisiae.
Sister Chromatids Are Often Incompletely Aligned in Meristematic and Endopolyploid Interphase Nuclei of Arabidopsis thaliana
Authors: Schubert Veit , Klatte Marco , Pecinka Ales , Meister Armin , Jasencakova Zuzana , Schubert Ingo 
Published: September 2005

Abstract
We analyzed whether sister chromatids are continuously aligned in meristematic and endopolyploid Arabidopsis interphase nuclei by studying sister-chromatid alignment at various chromosomal positions. FISH with individual BACs to flow-sorted 4C root and leaf nuclei frequently yielded more than two hybridization signals, indicating incomplete or absent sister-chromatid alignment. Up to 100% of 8C, 16C, and 32C nuclei showed no sister-chromatid alignment at defined positions. Simultaneous FISH with BACs from different chromosomal positions revealed more frequent sister-chromatid alignment in terminal than in midarm positions. Centromeric positions were mainly aligned up to a ploidy level of 16C but became separated or dispersed in 32C nuclei. DNA hypomethylation (of the whole genome) and transcriptional activity (at FWA gene position) did not impair sister-chromatid alignment. Only 6.1% of 4C leaf nuclei showed sister-chromatid separation of the entire chromosome 1 top arm territories. Homozygous transgenic tandem repeat (lac operator) arrays showing somatic homologous pairing more often than average euchromatic loci did not promote an increased frequency of sister-chromatid alignment. The high frequency of separated sister-chromatid arm positions in ≥4C nuclei suggests that sister-chromatid cohesion is variable, dynamic, and not obligatory along the entire chromosome arm in meristematic and differentiated Arabidopsis nuclei.
Temporal and Spatial Genetic Structure among Some Pacific Herring Populations in Puget Sound and the Southern Strait of Georgia
Authors: Small Maureen P. , Loxterman Janet L. , Frye Alice E. , Von Bargen Jennifer F. , Bowman Cherril , Young Sewall F. 
Published: September 2005

AbstractWe investigated temporal and spatial genetic variation in Pacific herring Clupea pallasii collections from six sites in Puget Sound (PS) and the southern Strait of Georgia (SOG), using 12 microsatellite loci. Loci were highly variable with up to 70 alleles per locus (mean = 30.67 alleles), and observed heterozygosity was high (mean = 0.823). Analysis of molecular variance (AMOVA) indicated significant structure, with over twice as much variance among sites as among collection years, although among‐site variance was mainly due to Cherry Point and Squaxin Pass collections. In an AMOVA excluding Cherry Point and Squaxin Pass, only temporal variance was significant. With the exception of the Cherry Point and Squaxin Pass collections, pairwise genotypic and FST tests show some differences among collection years within a site and some genetic overlap among most PS and SOG collections. The Cherry Point and Squaxin Pass collections had no differences in genotypic distributions among collection years, and in cluster analyses the Cherry Point and Squaxin Pass collections each formed groups separate from other PS and SOG collections. Cherry Point herring have a later spawning time than other PS and SOG herring, and Squaxin Pass is physically isolated in southern Puget Sound. We hypothesize that spawn timing differences and spatial isolation generated genetic structure among some Pacific herring in PS and SOG. We suspect that, as in the case of Atlantic herring C. harengus, population genetic structure in Pacific herring in PS and southern SOG is a combination of a larval retention model and a metapopulation model. Because Cherry Point and Squaxin Pass herring are genetically and behaviorally differentiated from other PS and SOG herring populations, this unique variation should be preserved through careful management.
Passivity based control of transport reaction systems
Authors: Ruszkowski Martin , Garcia‐Osorio Vianey , Ydstie B. Erik 
Published: September 2005

AbstractInventory control is based on the idea manipulating process flows so that the inventories follow their set points. The operator mapping flows to inventories in a coarse grained (macroscopic) system is passive and any input strictly passive (ISP) feedback controller can, therefore, be used to achieve input‐output stability. Examples of ISP controllers include the PID controller, parameter adaptive feedforward control, optimal controllers and many nonlinear and gain scheduling controllers. Input‐output stability and convergence of inventories, such as total mass and energy can be used to show that other internal state variables are bounded and belong to an invariant set. However, this does not necessarily imply convergence of all state variables to stationary valves because a stabilizability condition, known as strict state passivity, must be satisfied. The 2ndlaw of thermodynamics is used to develop sufficient conditions for strict state passivity in the space of intensive variables. The theory relies on following two assumptions concerning nonequilibrium systems: (1) The hypothesis of local equilibrium, and (2) That a local entropy is defined using semiclassical statistical mechanics. These assumptions allow us to define a local entropy function for the coarse grained system which is homogeneous degree one, concave, and has positive temperature. Subject to these conditions stability theory is developed for conjugate variables, such as temperature, pressure and chemical potential in infinite dimensional reaction‐diffusion‐convection systems. In classical irreversible thermodynamics this type of analysis assumes linearity and symmetry of transport relations. The use of Gibbs tangent plane condition allows us to define a Lyapunov like storage function for passivity design, which gives stability criteria for nonlinear problems. The resulting sufficient condition for stability can be expressed in terms of dimensionless groups, similar to the (second) Damkohler number. Simple simulation examples illustrate the application of the theory. © 2005 American Institute of Chemical Engineers AIChE J, 2005
Liquid drop growth on a fiber
Authors: Yarin A. L. , Chase G. G. , Liu W. , Doiphode S. V. , Reneker D. H. 
Published: September 2005

AbstractA quantitative model is described and verified to predict the growth of oil droplets by coalescence on a single nanofiber. The model considers a stream of fluid carrying many tiny droplets of a different fluid. The mechanisms by which the tiny droplets are captured by a drop growing on a fiber are considered. Different capture mechanisms are examined, including interception, Brownian motion of droplets, and vapor deposition by diffusion. It is shown that droplet interception and Brownian diffusion contribute to drop growth on nanofibers for airborne oil droplets in the size range from 100 to 1000 nm. Merging of growing drops on the fiber is also modeled and experimentally observed. © 2005 American Institute of Chemical Engineers AIChE J, 2006
Detection of low level sex chromosome mosaicism in Ullrich–Turner syndrome patients
Authors: Wiktor Anne E. , Van Dyke Daniel L. 
Published: September 2005

AbstractUllrich–Turner syndrome (UTS) is most commonly due to a 45,X chromosome defect, but is also seen in patients with a variety of X‐chromosome abnormalities or 45,X/46,XY mosaicism. The phenotype of UTS patients is highly variable, and depends largely on the karyotype. Patients are at an increased risk of gonadoblastoma when a Y‐derived chromosome or chromosome fragment is present. Since constitutional mosaicism is present in approximately 50% of UTS patients, the identification of minor cell populations is clinically important and a challenge to laboratories. We identified 50 females with a 45,X karyotype as the sole abnormality or as part of a more complex karyotype. Twenty two (44%) had a 45,X karyotype; mosaicism for a second normal or structurally abnormal X was observed in 24 (48%) samples, and mosaicism for Y chromosomal material in 4 (8%) cases. To further investigate the possibility of mosaicism in the 22 patients with an apparently non‐mosaic 45,X karyotype, we performed FISH using centromere probes for the X and Y chromosomes. A minor XX cell line was identified in 3 patients, and the 45,X result was confirmed in 19 samples. No samples with XY mosaicism were identified. We describe our validation process for a FISH assay to be used in clinical practice to identify XX or XY mosaicism. FISH as an adjunct to karyotype analysis provides a sensitive and cost‐effective technique to identify sex chromosome mosaicism in UTS patients. © 2005 Wiley‐Liss, Inc.
Intrachromosomal insertion mimicking a pericentric inversion: Molecular cytogenetic characterization of a three break rearrangement of chromosome 20
Authors: Ardalan Azarnouche , Prieur Marguerite , Choiset Agnès , Turleau Catherine , Goutieres Françoise , Girard‐Orgeolet Sylvie 
Published: September 2005

AbstractIntrachromosomal insertions are uncommon rearrangements, in which a chromosomal segment is intercalated into another part of the same chromosome. The insertion may occur in the same arm (paracentric) or in the other arm (pericentric). The cytogenetic recognition of these structurally rearranged chromosomes can be difficult, and intrachromosomal insertions can be easily mistaken for inversions. We describe a case of a familial pericentric insertion of chromosome 20, initially misdiagnosed as a pericentric inversion in the healthy carrier and then reinterpreted as insertion in an abnormal child with a recombinant chromosome. Fluorescence in situ hybridization (FISH) allowed us to confirm the mechanism of recombinant formation and to locate the three breakpoints precisely. Our cytogenetically unbalanced epileptic patient carried a 20q deletion and 20p duplication, and the genes, CHRNA4 and KCNQ2 that have been implicated in autosomal dominant epilepsy, were deleted. The haplo‐insufficiency of these two genes may contribute to the cause of epilepsy in patients with ring chromosome 20. © 2005 Wiley‐Liss, Inc.