bluuebunny/crossref_metadata_2025_split huggingface dataset:
A prospective study of XRCC1(X-ray cross-complementing group 1) polymorphisms and breast cancer risk
Authors: Patel Alpa V , Calle Eugenia E , Pavluck Alexandre L , Feigelson Heather Spencer , Thun Michael J , Rodriguez Carmen 
Published: November 2005

Abstract
Introduction
The gene XRCC1 (X-ray repair cross-complementing group 1) encodes a protein involved in DNA base excision repair. Two non-synonymous polymorphisms in XRCC1 (Arg194Trp and Arg399Gln) have been shown to alter DNA repair capacity in some studies in vitro. However, results of previous association studies of these two XRCC1 variants and breast cancer have been inconsistent. We examined the association between polymorphisms in XRCC1 and breast cancer in the American Cancer Society Cancer Prevention Study II (CPS-II) Nutrition Cohort, a large prospective study of cancer incidence in the USA.

Methods
Among the 21,965 women who were cancer-free in 1992 and gave blood between 1998 and 2001, 502 postmenopausal breast cancer cases were diagnosed between 1992 and 2001; 502 controls were matched to cases on age, race/ethnicity, and date of blood collection. Genotyping on DNA extracted from buffy coat was performed with Taqman. Conditional logistic regression was used to examine the association between each polymorphism and breast cancer risk controlling for breast cancer risk factors. We also examined whether factors associated with DNA damage, such as smoking and antioxidant intake, modified the association between XRCC1 polymorphisms and breast cancer.

Results
We observed a significant inverse association between Trp194 carriers (Trp/Trp and Trp/Arg) compared with Trp194 non-carriers in relation to breast cancer (Arg/Arg) (odds ratio (OR) 0.62, 95% confidence interval (CI) 0.40 to 0.95). The inverse association between breast cancer and Trp194 carriers compared with non-carriers was slightly stronger among smokers (OR 0.47, 95% CI 0.24 to 0.94) than never smokers (OR 0.78, 95% CI 0.43 to 1.40). An increased risk associated with the Arg399Gln polymorphism (Gln/Gln versus Arg/Arg) was observed only among women who reported ever smoking cigarettes (OR 2.76, 95% CI 1.36 to 5.63), and not in women who were lifelong non-smokers (OR 0.64, 95% CI 0.33 to 1.26). No other factor examined modified the association between XRCC1 polymorphisms and breast cancer risk.

Conclusion
Our results support the hypothesis that genetic variation in XRCC1, particularly in Arg194Trp, may influence postmenopausal breast cancer risk. In our study, genetic variation in XRCC1 Arg399Gln was associated with breast cancer risk only among women with a history of smoking cigarettes.
The genomic response to 20-hydroxyecdysone at the onset of Drosophila metamorphosis
Authors: Beckstead Robert B , Lam Geanette , Thummel Carl S 
Published: November 2005

Abstract
Background
The steroid hormone 20-hydroxyecdysone (20E) triggers the major developmental transitions in Drosophila, including molting and metamorphosis, and provides a model system for defining the developmental and molecular mechanisms of steroid signaling. 20E acts via a heterodimer of two nuclear receptors, the ecdysone receptor (EcR) and Ultraspiracle, to directly regulate target gene transcription.

Results
Here we identify the genomic transcriptional response to 20E as well as those genes that are dependent on EcR for their proper regulation. We show that genes regulated by 20E, and dependent on EcR, account for many transcripts that are significantly up- or downregulated at puparium formation. We provide evidence that 20E and EcR participate in the regulation of genes involved in metabolism, stress, and immunity at the onset of metamorphosis. We also present an initial characterization of a 20E primary-response regulatory gene identified in this study, brain tumor (brat), showing that brat mutations lead to defects during metamorphosis and changes in the expression of key 20E-regulated genes.

Conclusion
This study provides a genome-wide basis for understanding how 20E and its receptor control metamorphosis, as well as a foundation for functional genomic analysis of key regulatory genes in the 20E signaling pathway during insect development.
Complement regulatory protein Crry/p65-mediated signaling in T lymphocytes: role of its cytoplasmic domain and partitioning into lipid rafts
Authors: Jiménez-Periañez Arturo , Ojeda Gloria , Criado Gabriel , Sánchez Alejandra , Pini Eliana , Madrenas Joaquín , Rojo Jose Maria , Portolés Pilar 
Published: November 2005

AbstractCrry/p65 is a type I glycoprotein, which protects mouse T cells from complement attack. We have previously shown that complement receptor I-related protein Crry/p65 (Crry) ligation has a costimulatory effect on mouse CD4+ T cell activation. Here, we have examined the mechanisms responsible for Crry costimulation, addressing the question of whether Crry potentiates signal transduction starting at the T cell receptor (TCR)/CD3 complex or promotes distinct costimulatory signals. We show that Crry increases early TCR-dependent activation signals, including p56lck-, ζ-associated protein-70 (ZAP-70), Vav-1, Akt, and extracellular signal-regulated kinase (ERK) phosphorylation but also costimulation-dependent mitogen-activated protein kinases (MAPK), such as the stress-activated c-Jun N-terminal kinase (JNK). It is intriguing that Crry costimulus enhanced p38 MAPK activation in T helper cell type 1 (Th1) but not in Th2 cells. A fraction of Crry is found consistently in the detergent-insoluble membrane fraction of Th1 or Th2 cells or CD4+ lymphoblasts. Crry costimulation induced clustering of lipid rafts, increasing their content in Crry, CD3ɛ, and p59-60 forms of p56lck, and caused actin polymerization close to the site of activation in Th2 cells. Such events were inhibited by wortmannin, suggesting a role for phosphatidylinositol-3 kinase in these effects. The Crry cytoplasmic domain was required for JNK activation and interleukin-4 secretion but not for the presence of Crry in rafts or activation of p56lck, ZAP-70, Akt, Vav-1, or ERK. This suggests that Crry costimulation involves two different but not mutually exclusive signal transduction modules. The dual function of Crry as a complement regulatory protein and as a T cell costimulator illustrates the importance of complement regulatory proteins as links between innate and adaptive immunity.
First-order ray tracing for qP waves in inhomogeneous, weakly anisotropic media
Authors: Pšenčík Ivan , Farra Véronique 
Published: November 2005

We propose approximate ray-tracing equations for qP-waves propagating in smooth, inhomogeneous, weakly anisotropic media. For their derivation, we use perturbation theory, in which deviations of anisotropy from isotropy are considered to be the first-order quantities. The proposed ray-tracing equations and corresponding traveltimes are of the first order. Accuracy of the traveltimes can be increased by calculating a secondorder correction along first-order rays.The first-order ray-tracing equations for qP-waves propagating in a general weakly anisotropic medium depend on only 15 weak-anisotropy parameters (generalization of Thomsen’s parameters). The equations are thus considerably simpler than the exact ray-tracing equations. For higher-symmetry anisotropic media the equations differ only slightly from equations for isotropic media. They can thus substitute for the traditional isotropic ray tracers used in seismic processing. For vanishing anisotropy, the first-order ray-tracing equations reduce to standard, exact ray-tracing equations for isotropic media. Numerical tests for configuration and models used in seismic prospecting indicate negligible dependence of accuracy of calculated traveltimes on inhomogeneity of the medium. For anisotropy of about 8%, considered in the examples presented, the relative errors of the traveltimes, including the second-order correction, are well under 0.05%; for anisotropy of about 20%, they do not exceed 0.3%.
Wide-angle seismic imaging of the Elberton granite, Georgia: A pilot study using instantaneous blasts at dimension-stone quarries
Authors: Khalifa Mohamed O. , Hawman Robert B. 
Published: November 2005

Wide-angle recordings of small, multiple-hole blasts at dimension-stone quarries in the Elberton granite show coherent reflections at offsets between 7 and 15 km. In contrast with much larger blasts at crushed-stone quarries, this type of blast is fired without delays between holes. The data were recorded with an array of twenty portable seismographs using three-component, 4.5-Hz geophones. Migration of source gathers for two of the blasts shows a number of subhorizontal interfaces at depths between 2 and 4 km that may represent a layered complex near the base of the granite. Other reflectors include southeast-dipping interfaces at depths between 6 and 9.3 km and a more gently southeast-dipping complex at 9.5–11 km that may represent the master decollement. The results of the pilot study show that this type of quarry blast can be useful for imaging structure within the upper crust. Although preliminary, the wide-angle results support the interpretation that the Elberton granite is a tabular body less than 4 km thick.
Insurance Status and the Use of Guideline Therapy in the Treatment of Selected Cancers
Authors: Harlan Linda C. , Greene Amanda L. , Clegg Limin X. , Mooney Margaret , Stevens Jennifer L. , Brown Martin L. 
Published: November 2005

Purpose This study estimates the impact of type of insurance coverage on the receipt of guideline therapy in a population-based sample of cancer patients treated in the community. Patients and Methods Patients (n = 7,134) from the National Cancer Institute's Patterns of Care studies who were newly diagnosed with 11 different types of cancer were analyzed. The definition of guideline therapy was based on the National Comprehensive Cancer Network treatment recommendations. Insurance status was categorized as a mutually exclusive hierarchical variable (no insurance, any private insurance, any Medicaid, Medicare only, and all other). Multivariate analyses were used to examine the association between insurance and receipt of guideline therapy. Results Adjusting for clinical and nonclinical variables, insurance status was a modest, although statistically significant, determinant of receipt of guideline therapy, with 65% of the privately insured patients receiving recommended therapy compared with 60% of patients with Medicaid. Seventy percent of the uninsured patients received guideline therapy, which was nonsignificantly different compared with private insurance. When stratified by race, insurance was a statistically significant predictor of the receipt of guideline therapy only for non-Hispanic blacks. Conclusion Overall, levels of guideline treatment were lower than expected and particularly low for patients with Medicaid or Medicare only. The use of guideline therapy for ovarian and cervical cancer patients and for patients with rectal cancers was unrelated to type of insurance. Of particular concern is the significantly lower use of guideline therapy for non-Hispanic black patients with Medicaid. After adjusting for other factors, only half of these patients received guideline therapy.
Decision-Aiding Methodology for the School Bus Routing and Scheduling Problem
Authors: Spada M. , Bierlaire M. , Liebling Th. M. 
Published: November 2005

We consider the school bus routing and scheduling problem, where transportation demand is known and bus scheduling can be planned in advance. We present a comprehensive methodology designed to support the decision of practitioners. We first propose a modeling framework where the focus is on optimizing the level of service for a given number of buses, then we describe an automatic procedure generating a solution to the problem. The procedure first builds a feasible solution, which is subsequently improved using a heuristic. We analyze two important issues associated with this methodology. On the one hand, we analyze the performance of three types of heuristics both on real and synthetic data. We recommend the use of a simulated annealing technique exploring infeasible solutions, which performs slightly better than all others. More importantly, we find that the performance of all heuristics is not globally affected by the choice of the parameters. This is important from a practitioner viewpoint, because the fine-tuning of algorithm parameters is not critical for the algorithm’s performance. We have successfully applied our methods on real problems and on large-scale problems. On the other hand, we propose an interactive tool allowing the practitioner to visualize the proposed solution, to test its robustness, and to dynamically rebuild new solutions if the data of the original problem are modified.
ARMin – Roboter für die Bewegungstherapie der oberen Extremitäten (ARMin – Robot for Movement Therapy of the Upper Extremities)
Authors: Nef Tobias , Colombo Gery , Riener Robert 
Published: November 2005

Abstract
Aufgabenorientierte, repetitive Bewegungen können die motorische Erholung bei Patienten mit inkompletter Querschnittlähmung, Halbseitenlähmung oder orthopädischen Verletzungen verbessern. Dieser Artikel stellt die Technik des neuen Therapieroboters ARMin vor. ARMin unterstützt das Training von funktionellen Bewegungen und Aktivitäten des täglichen Lebens der oberen Extremitäten.
Belastungsregelung bei der Elektrostimulationsergometrie (Power Control of Electrical Stimulation Induced Cycle Ergometry)
Authors: Schauer Thomas , Salbert Robert C. , Negård Nils-Otto , Hunt Kenneth J. , Raisch Jörg 
Published: November 2005

Abstract
Für querschnittgelähmte Menschen stellt das Herz-Kreislauf-Training an Fahrradergometern mit Funktioneller Elektrischer Stimulation (FES) der gelähmten unteren Extremitäten eine sich zunehmend etablierende Rehabilitationsmaßnahme dar. Diese Arbeit stellt ein neues Ergometersystem mit Elektrostimulation vor, bei dem die Beine zusätzlich durch einen Hilfsmotor unterstützt werden. Durch den Motor kann ein isokinetisches Training realisiert werden. Der Patient arbeitet in diesem Fall mit den elektrisch stimulierten Muskeln gegen den Motor, der die Trittgeschwindigkeit konstant hält. Für die gezielte Anpassung der Belastung durch die Elektrostimulation wurde ein sich selbst einstellender Momentenregler entwickelt. Der Reglerentwurf erfolgt anhand der online identifizierten linearen Übertragungsfunktion zwischen Stimulationsintensität und gemitteltem muskulären Antriebsmoment. Erste experimentelle Ergebnisse mit einem neurologisch intakten Probanden werden vorgestellt.
Komponenten und Architektur eines navigierten Assistenzroboters für chirurgische Anwendungen (Components and Architecture of a Navigated Robot System for Surgical Applications)
Authors: Knappe Peter , Pieck Sebastian , Wahrburg Jürgen 
Published: November 2005

Abstract
Der Beitrag beschreibt ein universelles Chirurgieassistenzsystem, das durch die Kombination von Navigation und Robotik gekennzeichnet ist und eine neue, in hohem Maße interaktive Arbeitsweise der Roboter-Komponente realisiert. Damit wird es möglich, die spezifischen Vorteile beider Systemkomponenten auszunutzen: Das Navigationssystem dient zur genauen und schnellen Registrierung der Patientenanatomie mit Hilfe eines elektro-optischen 3D-Digitalisiersystems, während der Roboterarm als mechatronische Ergänzung der Navigation zur Führung und Positionierung der chirurgischen Instrumente eingesetzt wird und Probleme durch Abrutschen oder Zittern vermeidet. Außerdem ist es möglich, den Roboterarm bei kleinen Patientenbewegungen on-line nachzuführen, sodass die räumliche Zuordnung zwischen Patientenstruktur und chirurgischem Werkzeug stets erhalten bleibt. In diesem Beitrag wird vor allem die erzielbare statische Systemgenauigkeit diskutiert.
Immobilization of actinide ions in thin layers of polypyrrole/polyacrylamidoglycolic acid (PPy/PAGA) composite. Application to the preparation of alpha spectrometry sources
Authors: Leroy D. , Martinot L. , Mignonsin P. , Lambert B. , Jérôme C. , Jérôme R. 
Published: November 2005

SummaryWe propose a new fully aqueous electrochemical method for the preparation of high resolution alpha sources. Thin films of polypyrrole (PPy) are prepared by anodic electropolymerization, starting from aqueous solutions of the pyrrole monomer and an anionic polyelectrolyte which is able to complex actinide and play the role of PPy doping agent: polyacrylamidoglycolic acid (PAGA). These thin films can be prepared on various electrodes: stainless steel, platinum, glassy carbon and polyethylene doped by carbon-black. Peeling tests revealed their strong adhesion on stainless steel electrode. Alpha sources were prepared by simple immersion in actinide containing solutions. This easy process results in alpha sources with outstanding energy resolution (FWHM: around 9 keV for various isotopes).
Modeling the Oxygen Consumption Rates in Pacific Salmon and Steelhead: Model Development
Authors: Trudel Marc , Welch David W. 
Published: November 2005

AbstractWe derived a series of models for estimating the standard metabolic rates, swimming costs, and total metabolic rates for sockeye salmon Oncorhynchus nerka and steelhead O. mykiss. The performance of these models was compared statistically and used to predict optimal cruising speeds. These predictions were tested with independent estimates of swimming speed obtained under field conditions. Standard metabolic rates were correlated with body mass and temperature. Swimming costs were correlated with body mass and swimming speed, whereas total metabolic rates were correlated with body mass, water temperature, and swimming speed. Swimming costs were also correlated with temperature and salinity in steelhead but not in sockeye salmon. Regression models accounted for 94–99% of the variance in standard metabolic rates, swimming costs, and total metabolic rates. The oxygen consumption rate models we derived for sockeye salmon were inadequate for describing oxygen consumption in other species of Pacific salmon, Oncorhynchus spp., indicating that the practice of borrowing parameters from closely related species can induce serious biases in model predictions. The models derived in this study also produced realistic estimates of swimming speed in sockeye salmon but not in steelhead. The models derived in this study appear to be useful in estimating swimming speed and total metabolic rates of sockeye salmon in the field but are not appropriate predictors for other species of Pacific salmon.
Geostatistical Analysis of the Abundance and Winter Distribution Patterns of the Blue CrabCallinectes sapidusin Chesapeake Bay
Authors: Jensen Olaf P. , Miller Thomas J. 
Published: November 2005

AbstractSpatial heterogeneity is a striking life history feature of the blue crabCallinectes sapidusin the Chesapeake Bay. Spatial patterns of sex‐ and age‐specific habitat use have been well documented and affect the fisheries in the bay. However, a quantitative assessment of the spatial distribution of blue crabs during winter, when they are generally buried in the sediments, has been lacking. We applied geostatistical techniques (variogram modeling and kriging) to 13 years of winter dredge survey (WDS) data to map patterns of blue crab winter abundance. These maps were then quantified to derive a time series of baywide abundance and to examine changing patterns of habitat use and aggregation. Geostatistical abundance estimates were generally similar to those calculated from design‐based methods but were more highly correlated with fishery catch per unit of effort. Both abundance time series showed a large and significant decline from 1990 to 2002. Changes in spatial distribution were evaluated using trend maps and a density‐weighted centroid. Interannual variation in the latitude of the weighted centroid was positively correlated with baywide abundance, suggesting possible density‐dependent changes in distribution. The southward shift in winter distribution at low stock size may increase the vulnerability of blue crabs to exploitation in a winter dredge fishery that occurs only in the southern portion of the bay. Such quantitative and spatially explicit information provides a potentially useful base for constructing population models and evaluating alternative management options.
Physiological Effects of Swim Bladder Overexpansion and Catastrophic Decompression on Red Snapper
Authors: Rummer Jodie L. , Bennett Wayne A. 
Published: November 2005

AbstractThe commercial and recreational harvests of red snapper Lutjanus campechanus in the Gulf of Mexico have declined over the past five decades, prompting strict regulations. Release mortality associated with catastrophic decompression (CD) is a possible cause for the continuing decline, although to date no physiological data exist to support this assumption. Using a flow‐through high‐pressure chamber, subadult red snapper were acclimated to 101.2, 405.3, 608.0, and 1,215.9 kPa, simulating depths typical of their distribution (as deep as 200 m), and then decompressed at a rate of 10.1 kPa/s. Lateral and dorsal X‐ray imaging in combination with necropsy showed that swim bladders expanded in a predictable manner. Ventral expansion into the caudal body cavity space occurred at lower pressures, whereas expansion into the cranial portion of the body cavity occurred at the highest pressure. Expansion patterns resulted in over 70 different overexpansion injuries, the most severe being to vital organs. Our results suggest a specific suite of clearly identifiable injuries associated with CD that increase in number and severity as retrieval depth increases. A more thorough understanding of catastrophic decompression syndrome will provide insight into the declining fishery and aid in developing effective physiology‐based management strategies.
Upstream Migration of Minijack (Age‐2) Chinook Salmon in the Columbia River: Behavior, Abundance, Distribution, and Origin
Authors: Beckman Brian R. , Larsen Donald A. 
Published: November 2005

AbstractIt has recently been demonstrated that a large percentage of yearling Chinook salmon Oncorhynchus tshawytscha smolts released from a production‐scale hatchery on the Yakima River display an underappreciated life history strategy. Instead of migrating to the ocean for long‐term rearing and growth, males may instead undertake a short‐term migration downstream, turn around, and migrate back upstream where they reproductively mature at age 2. Following local hatchery traditions, these fish are referred to as “minijacks.” We used information produced from (1) large‐scale passive integrated transponder (PIT)‐tagging programs at hatcheries in the Columbia and Snake River basins and (2) the installation of PIT tag detectors in the fish passage ladders built into dams on these rivers to investigate the occurrence, behavior, distribution, and origin of minijacks. A minijack was operationally defined as a fish detected in a ladder after 1 June in the same year it was released. Minijacks were found in every hatchery release group of more than 7,500 PIT‐tagged Chinook salmon smolts reported (2002, 13 groups; 2003, 15 groups). Minijack population migration upstream past Bonneville Dam peaked in late June and July. This lagged migrations of age‐4 adults (from the same populations) by approximately 2 months. However, minijacks also displayed population‐specific variation in timing of upstream migrations past Bonneville Dam; minijacks from spring Chinook salmon populations appeared before fall Chinook salmon populations. Detection rates of minijacks at all dams ranged from 0.02% to 0.33% of the total smolts released for different hatchery groups. Expansion of this rate, based on the relation between minijack estimates at Cle Elum Hatchery (before release) and detections at Bonneville Dam (after release), suggests that minijack abundance in the Columbia and Snake River basins exceed hundreds of thousands of fish.