bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Gene expression Grade Index: a potential predictor of relapse for endocrine-treated breast cancer patients in the BIG 1–98 trial
Authors: Desmedt Christine , Giobbie-Hurder Anita , Neven Patrick , Paridaens Robert , Christiaens Marie-Rose , Smeets Ann , Lallemand Françoise , Haibe-Kains Benjamin , Viale Giuseppe , Gelber Richard D , Piccart Martine , Sotiriou Christos 
Published: July 2009

Abstract

Background
We have previously shown that the Gene expression Grade Index (GGI) was able to identify two subtypes of estrogen receptor (ER)-positive tumors that were associated with statistically distinct clinical outcomes in both untreated and tamoxifen-treated patients. Here, we aim to investigate the ability of the GGI to predict relapses in postmenopausal women who were treated with tamoxifen (T) or letrozole (L) within the BIG 1–98 trial.

Methods
We generated gene expression profiles (Affymetrix) and computed the GGI for a matched, case-control sample of patients enrolled in the BIG 1–98 trial from the two hospitals where frozen samples were available. All relapses (cases) were identified from patients randomized to receive monotherapy or from the switching treatment arms for whom relapse occurred before the switch. Each case was randomly matched with four controls based upon nodal status and treatment (T or L). The prognostic value of GGI was assessed as a continuous predictor and divided at the median. Predictive accuracy of GGI was estimated using time-dependent area under the curve (AUC) of the ROC curves.

Results
Frozen samples were analyzable for 48 patients (10 cases and 38 controls). Seven of the 10 cases had been assigned to receive L. Cases and controls were comparable with respect to menopausal and nodal status, local and chemotherapy, and HER2 positivity. Cases were slightly older than controls and had a larger proportion of large, poorly differentiated ER+/PgR- tumors. The GGI was significantly and linearly related to risk of relapse: each 10-unit increase in GGI resulted in an increase of approximately 11% in the hazard rate (p = 0.02). Within the subgroups of patients with node-positive disease or who were treated with L, the hazard of relapse was significantly greater for patients with GGI at or above the median. AUC reached a maximum of 78% at 27 months.

Conclusion
This analysis supports the GGI as a good predictor of relapse for ER-positive patients, even among patients who receive L. Validation of these results, in a larger series from BIG 1–98, is planned using the simplified GGI represented by a smaller set of genes and tested by qRT-PCR on paraffin-embedded tissues.
Apoptotic cell-mediated suppression of streptococcal cell wall-induced arthritis is associated with alteration of macrophage function and local regulatory T-cell increase: a potential cell-based therapy?
Authors: Perruche Sylvain , Saas Philippe , Chen Wanjun 
Published: July 2009

Abstract
Introduction
Experimental streptococcal cell wall (SCW)-induced arthritis is characterized by two successive phases of the disease. The acute phase occurs early and is associated with an inflammatory process and neutrophil infiltration into the synovium. The second chronic phase is related to effector T-cell activation and the dysregulation of macrophage function. Creation of an immunomodulatory environment has been attributed to apoptotic cells themselves, apoptotic cell uptake by phagocytes as well as a less sensibility of phagocytes capturing apoptotic bodies to activation. Therefore we evaluated the potential of apoptotic cell injection to influence the course of inflammation in SCW-induced arthritis in rats.

Methods
Rat apoptotic thymocytes were injected intraperitoneally (2 × 108) in addition to an arthritogenic dose of systemic SCW in LEW female rats. Control rats received SCW immunization and PBS. Rats were then followed for arthritis occurrence and circulating cytokine detection. At sacrifice, regulatory T cells (Tregs) and macrophages were analyzed.

Results
Apoptotic cell injection profoundly suppressed joint swelling and destruction typically observed during the acute and chronic phases of SCW-induced arthritis. Synovial inflammatory cell infiltration and bone destruction were also markedly suppressed. Ex vivo experiments revealed reduced levels of TNF in cultures of macrophages from rats challenged with SCW in the presence of apoptotic thymocytes as well as reduced macrophage response to lipopolysaccharide. Moreover, apoptotic cell injection induced higher Foxp3+ Tregs in the lymphoid organs, especially in the draining lymph nodes.

Conclusions
Our data indicate that apoptotic cells modulate macrophage function and result in Treg generation/increase. This may be involved in inhibition of inflammation and amelioration of arthritis. This highlights and confirms previous studies showing that in vivo generation of Tregs using apoptotic cell injection may be a useful tool to prevent and treat inflammatory autoimmune responses.
The extracellular domain of CD11d regulates its cell surface expression
Authors: McKillop William M , Barrett John W , Pasternak Stephen H , Chan Bosco M C , Dekaban Gregory A 
Published: July 2009

Abstract
CD11d’s extracellular domain is responsible for intracellular retention of the protein to the Golgi apparatus, a restriction which is relieved upon CD11d/CD18 heterodimerization resulting in release of the integrin to the cell surface.
A mAb targeting the CD11d subunit of the leukocyte integrin CD11d/CD18 decreases intraspinal inflammation and oxidative damage leading to improved neurological outcomes in rodent models of SCI. CD11d/CD18 is the fourth member of the β2-integrin family. Current evidence indicates that CD11d/CD18 is regulated differently than other β2-integrins, suggesting that CD11d+ leukocytes play a distinct role in inflammation. Although the transcriptional control of CD11d expression has been evaluated, control of the intracellular distribution of CD11d has not been addressed. For this reason and as a result of the potential of CD11d as a therapeutic target for SCI and possibly other CNS injuries, we investigated the intracellular localization and surface expression of CD11d in cultured cells. CD11d and CD18 were fused at their C-termini with YFP and mRFP, respectively. Flow cytometry and confocal microscopy demonstrated that rCD11d-YFP is expressed on the cell surface of leukocyte cell lines expressing CD18. In contrast, in heterologous cell lines, CD11d-YFP is retained intracellularly in the TGN. Coexpression of CD11d-YFP and CD18-mRFP relieves this intracellular restriction and allows the CD11d/CD18 heterodimer to be surface-expressed. Based on domain-swapping experiments with CD25, the extracellular domain of CD11d is required and sufficient for the observed intracellular retention in heterologous cells. Furthermore, the transmembrane and C-terminus are also required for proper heterodimerization with CD18 and localization to the plasma membrane. These findings suggest that multiple CD11d domains play a role in controlling intracellular location and association with CD18.
The trainer, the trainee and the surgeons’ assistant
Authors: Palan J. , Gulati A. , Andrew J. G. , Murray D. W. , Beard D. J. 
Published: June 2009

Balancing service provision and surgical training is a challenging issue that affects all healthcare systems. A multicentre prospective study of 1501 total hip replacements was undertaken to investigate whether there is an association between surgical outcome and the grade of the operating surgeon, and whether there is any difference in outcome if surgeons’ assistants assist with the operation, rather than orthopaedic trainees. The primary outcome measure was the change in the Oxford hip score (OHS) at five years. Secondary outcomes included the rate of revision and dislocation, operating time, and length of hospital stay. There was no significant difference in ΔOHS or complication rates between operations undertaken by trainers and trainees, or those at which surgeons’ assistants and trainees were the assistant. However, there was a significant difference in the duration of surgery, with a mean reduction of 28 minutes in those in which a surgeons’ assistant was the assistant. This study provides evidence that total hip replacements can be performed safely and effectively by appropriately trained surgeons in training, and that there are potential benefits of using surgeons’ assistants in orthopaedic surgery.
Dioxin Assessment in a River Flood Plain: Soil and Sediment Contamination
Authors: VanHouten J. W. 
Published: July 2009

AbstractDioxins are a group of 210 chemicals with similar properties and structures that are usually found as a “mixture” in the environment. Dioxins are found at low levels in air, soil, water, and sediment as well in foods such meat, dairy, fish, and shellfish. The highest levels are usually found in sediments soil and animal fats. The most toxic chemical in the group is 2,3,7,8-tetrachlorodibenzo-para-dioxin, which is the “standard” to which other dioxins are compared. This paper examines the Michigan Department of Environmental Quality (MDEQ) assessment and remediation efforts in the Tittabawassee River (Michigan, USA) flood plain. Soil and sediment samples indicate higher than “normal” (background) levels of dioxins for soil and sediment, which exceed the Center for Disease Control (CDC) and U.S. Agency for Toxic Substances and Diseases Registry (ATSDR) action level of 1000 parts per trillion. Data presented indicates the difficulties associated with assessing historical dioxin levels in environments such as soil and sediments. Activities associated with these efforts such as dioxin and furan exposure studies, animal toxicology assessments, U.S. Environmental Protection Agency (EPA) enforcement, MDEQ efforts to expedite remediation, as well as future directions for this on-going project are discussed.
Growth and development of tadpoles (Xenopus laevis) exposed to selective serotonin reuptake inhibitors, fluoxetine and sertraline, throughout metamorphosis
Authors: Conners Deanna E. , Rogers Emily D. , Armbrust Kevin L. , Kwon Jeong-Wook , Black Marsha C. 
Published: July 2009

Abstract
Selective serotonin reuptake inhibitors (SSRIs) are widely prescribed drugs that are present in sewage effluents and surface waters. The objective of the present study was to determine whether low environmentally relevant concentrations of the SSRIs fluoxetine and sertraline could impair growth and development in tadpoles of the African clawed frog (Xenopus laevis) and to evaluate if such effects may be caused by a disruption of the neuroendocrine system. Tadpoles were exposed to SSRIs at concentrations of 0.1, 1, and 10 μL for 70 d throughout metamorphosis. No effects on deformities were observed. Tadpoles exposed to fluoxetine (10 μL) and sertraline (0.1, 1, and 10 μL) exhibited reduced growth at metamorphosis. Tadpoles exposed to sertraline (0.1 and 1 μL) exhibited an acceleration of development as indicated by an increase in the time to tail resorption. The effects of SSRIs on growth and development in tadpoles were likely driven by reduced food intake. Reduced feeding rates were observed in SSRI-exposed tadpoles, and nutritional status can influence growth and development in amphibians via effects on the neuroendocrine system. Only sertraline was capable of causing developmental toxicity in tadpoles at environmentally relevant concentrations. These data warrant additional research to characterize the risks to human health and wildlife from pharmaceutical exposures.
Estrogen Concentration Affects its Biodegradation Rate in Activated Sludge
Authors: Xu Nan , Johnson Andrew C. , Jürgens Monika D. , Llewellyn Neville R. , Hankins Nick P. , Darton Richard C. 
Published: July 2009

Abstract
The effect of concentration on the biodegradation rate of the steroid estrogens, estrone (E1) and 17-α-ethinylestradiol (EE2), was studied in batch and continuous-flow reactor systems using fresh activated sludge from two sewage treatment plants. Between the concentrations of 0.03 and 10 μg/L in the batch system, no consistent difference was found in the biodegradation rates for either estrogen. The biodegradation half-life was 0.3 to 0.7 h for E1 and 1.5 to 4.4 h for EE2 at 15 to 20°C. However, at 100 μg/L, biodegradation rates for both estrogens decreased, with the half-life prolonged to approximately 2.5 h for E1 and 12 to 18 h for EE2. In continuous-flow experiments, over a 2-h residence time, 95% of E1 and 48% of EE2 were removed on average at 0.1 μg/L while 52% of E1 and 20% of EE2 were removed at 100 μg/L. In general, spiking concentration of estrogens did not appear to affect biodegradation rates between the nanogram per liter to low microgram per liter levels in activated sludge; however, the rates greatly slowed when the concentration increased up to 100 μg/L. The results suggest activated sludge biodegradation studies with estrogens in the high microgram per liter levels could give misleading results and should be avoided.
Evaluation of acute copper toxicity to juvenile freshwater mussels (fatmucket, Lampsilis siliquoidea) in natural and reconstituted waters
Authors: Wang Ning , Mebane Christopher A. , Kunz James L. , Ingersoll Christopher G. , May Thomas W. , Arnold W. Ray , Santore Robert C. , Augspurger Tom , Dwyer F. James , Barnhart M. Chris 
Published: July 2009

Abstract
The influence of dissolved organic carbon (DOC) and water composition on the toxicity of copper to juvenile freshwater mussels (fatmucket, Lampsilis siliquoidea) were evaluated in natural and reconstituted waters. Acute 96-h copper toxicity tests were conducted at four nominal DOC concentrations (0, 2.5, 5, and 10 mg/L as carbon [C]) in dilutions of natural waters and in American Society for Testing and Materials (ASTM) reconstituted hard water. Toxicity tests also were conducted in ASTM soft, moderately hard, hard, and very hard reconstituted waters (nominal hardness 45–300 mg/L as CaCO3). Three natural surface waters (9.5–11 mg/L DOC) were diluted to obtain a series of DOC concentrations with diluted well water, and an extract of natural organic matter and commercial humic acid was mixed with ASTM hard water to prepare a series of DOC concentrations for toxicity testing. Median effective concentrations (EC50s) for dissolved copper varied &gt;40-fold (9.9 to &gt;396 μg Cu/L) over all 21 treatments in various DOC waters. Within a particular type of DOC water, EC50s increased 5- to 12-fold across DOC concentrations of 0.3 to up to 11 mg C/L. However, EC50s increased by only a factor of 1.4 (21–30 μg Cu/L) in the four ASTM waters with wide range of water hardness (52–300 mg CaCO3/L). Predictions from the biotic ligand model (BLM) for copper explained nearly 90% of the variability in EC50s. Nearly 70% of BLM-normalized EC50s for fatmucket tested in natural waters were below the final acute value used to derive the U.S. Environmental Protection Agency acute water quality criterion for copper, indicating that the criterion might not be protective of fatmucket and perhaps other mussel species.
Effect of Activated Carbon on Microbial Bioavailability of Phenanthrene in Soils
Authors: Yang Yu , Hunter Wesley , Tao Shu , Crowley David , Gan Jay 
Published: July 2009

Abstract
Bioavailability is a governing factor that controls the rate of biological degradation of hydrophobic organic contaminants in soil. Among the solid phases that can adsorb hydrophobic organic contaminants in soil, black carbon (BC) exerts a particularly significant effect on phase distribution. However, knowledge on the effect of BC on the microbial availability of polycyclic aromatic hydrocarbons in soil is still limited. In the present study, the effect of a coal-derived activated carbon on the bioavailability of phenanthrene (PHE) during its degradation by Mycobacterium vanbaalenii PYR-1 was measured in three soils. The freely dissolved concentration of PHE was concurrently determined in soil solutions using disposable polydimethylsiloxane fibers. The results showed that PHE mineralization was significantly inhibited after addition of activated carbon in all test soils. After 216 h, only 5.20, 5.83, and 6.85% of PHE was degraded in the 0.5% BC-amended soils initially containing organic carbon at 0.23, 2.1, and 7.1%, respectively. Significant correlation was found between PHE degradability and freely dissolved concentration, suggesting that BC affected PHE bioavailability by decreasing chemical activity. The effect of activated carbon in the amended soils was attributed to its enhancement of soil surface areas and pore volumes. Results from the present study clearly highlighted the importance of BC for influencing the microbial availability of polycyclic aromatic hydrocarbons in soils.
Hydraulic-Fracture Predictions With a Fully Coupled Geomechanical Reservoir Simulator
Authors: Dean R. H. , Schmidt J. H. 
Published: July 2009

Summary
A new geomechanical reservoir simulator has been developed that combines hydraulic fracture growth, multiphase/multicomponent Darcy/nonDarcy porous flow, heat convection and conduction, solids deposition, and poroelastic/poroplastic deformation in a single application. The equations for the different mechanisms such as fracture-width changes, laminar-channel flow in the fracture, porous flow in the reservoir, heat convection and conduction, and poroelastic/poroplastic deformations are combined to produce an implicit fully coupled formulation. The nonlinear system of equations is solved through use of a full Newton-Raphson expansion of all solution variables, which enhances solution stability and allows second-order convergence rates for the nonlinear iterations.
The program contains two separate criteria that one can use to model fracture propagation. Fracture-growth computations can be based on critical stress-intensity factors or can use cohesive elements that exhibit strain-softening behavior. The critical stress-intensity factor is based on the asymptotic stress/strain state at the tip of a fracture and is limited to linear poroelastic applications or applications in which the plastic zone is small relative to the fracture length; while cohesive elements are based on energy-release rates and cohesive stresses and can be used for both poroelastic and poro-plastic applications. In addition to the fracture-propagation logic, the program allows a dry zone to develop at the fracture tip as a natural part of the solution process. It is shown in sample simulation that a dry zone may develop naturally at the tip of a propagating fracture when there is a large pressure drop down the fracture.
The new geomechanical simulator is described and several examples are included to demonstrate the predictive capability of the application. Examples are also included to highlight the differences between the two fracture-propagation models and to illustrate when a dry zone may be expected to develop at the fracture tip. The examples also allow one to compare the program's predictions with analytic solutions validating the fracture propagation algorithms used in the application.
Does handling reduce the winter body mass of the European hare?
Authors: Takacs Viktoria , Zduniak Piotr , Panek Marek , Tryjanowski Piotr 
Published: July 2009

AbstractWinter body mass of the European hare Lepus europaeus Pallas 1778 was analyzed with a special focus on changes induced by handling. Data were obtained from large scale translocation (net catchments) during 1960–1980 in Poland. The influence of handling was compared using the mass of first-time captured and repeatedly-captured hares, and, in case of repeated capture, individuals’ mass changes were investigated. The average body mass ranged from 2.1 kg to 5.0 kg. Generally, fewer factors influenced the hare’s body mass than expected. Body mass was related to age and winter precipitation, while the date of catching, sex and temperature did not have an effect. Body mass of first-captured hares were significantly higher than the re-captured ones (3.99±0.42 vs. 3.88±0.48, mean ±SD). Body mass change between captures was related to the date of the first capture, and the duration between the first capture and re-capture. Following the initial capture, a slight (2.8±2.6), but significant decrease in body weight occurred. Thus, the handling of hares should be used with caution during studies or management of the species.
Portable electro-optic device for performing serviceability check on IR guided missiles
Authors: Maini A. , Agrawal V. 
Published: July 2009

AbstractElectro-optically guided weapons are the most potent and widely used munitions on land-based, aerial and ship-borne platforms because of their proven precision strike capability. Two such guided weapon categories include the IR guided surface-to-air and air-to-air missiles and laser guided bombs and missiles. The efficacy of the mission is critically dependent on the successful deployment of the weapon. This not only necessitates that periodic functionality check be carried out on these weapons, it should also be possible to perform functionality check also known as serviceability check even after they are strapped on to the launch platform. Serviceability check in the strap-on condition ensures a much higher hit probability. This paper presents the design and development of a portable electro-optic device that generates IR signatures in 3–5-µm band having the desired amplitude and spectral shape to match the IR signatures of target aircraft. A prototype was built using the proposed concept. The prototype was characterized in terms of its output amplitude and wavelength spectrum. The prototype was used to perform serviceability check on IR seekers of foreign origin. Test results are presented in the paper.
Simplified coupling power model for fibers fusion
Authors: Saktioto J. , Ali J. , Fadhali M. 
Published: July 2009

AbstractFiber coupler fabrication used for an optical waveguide requires lossless power for an optimal application. The previous research coupled fibers were successfully fabricated by injecting hydrogen flow at 1 bar and fused slightly by unstable torch flame in the range of 800–1350°C. Optical parameters may vary significantly over wide range physical properties. Coupling coefficient and refractive index are estimated from the experimental result of the coupling ratio distribution from 1% to 75%. The change of geometrical fiber affects the normalized frequency V even for single mode fibers. V is derived and some parametric variations are performed on the left and right hand side of the coupling region. A partial power is modelled and derived using V, normalized lateral phase constant u, and normalized lateral attenuation constant, w through the second kind of modified Bessel function of the l order, which obeys the normal mode and normalized propagation constant b. Total power is maintained constant in order to comply with the energy conservation law. The power is integrated through V, u, and w over the pulling length of 7500 µm for 1-D. The core radius of a fiber significantly affects V and power partially at coupling region rather than wavelength and refractive index of core and cladding. This model has power phenomena in transmission and reflection for an optical switch and tunable filter.