bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomics and Proteomics of Bone Cancer
Authors: Marguiles Aaron G. , Klimberg V. Suzanne , Bhattacharrya Sudeepa , Gaddy Dana , Suva Larry J. 
Published: October 2006

Abstract
Although the control of bone metastasis has been the focus of intensive investigation, relatively little is known about the molecular mechanisms that regulate or predict the process, even though widespread skeletal dissemination is an important step in the progression of many tumors. As a result, understanding the complex interactions contributing to the metastatic behavior of tumor cells is essential for the development of effective therapies. Using a state-of-the-art combination of gene expression profiling and functional annotation of human tumor cells, and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry of patient serum, we have shown that changes in tumor biochemistry correlate with disease progression and help to define the aggressive tumor phenotype. Based on these approaches, it is apparent that the metastatic phenotype of tumor cells is extremely complex. The identification of the phenotype of tumor cells has benefited greatly from the application of gene expression profiling (microarray analysis). This technology has been used by many investigators to identify changes in gene expression and cytokine and growth factor elaboration (such as interleukin 8). The tumor phenotype(s) presumably also include changes in the cell surface carbohydrate profile (via altered glycosyltransferase expression) and heparan sulfate expression (via increased heparanase activity), to name but a few. These specific alterations in gene expression, identified by functional annotation of accumulated microarray data, have been validated using a variety of approaches. Collectively, the data described here suggest that each of these activities is associated with distinct aspects of the aggressive tumor cell phenotype. Collectively, the data suggest that multiple factors constitute the complex phenotype of metastatic tumor cells. In particular, the differences observed in gene expression profiles and serum protein biomarkers play a critical role in defining the mechanisms responsible for bone-specific colonization and growth of tumors in bone. Future studies will identify the mechanisms that participate in the formation of secondary tumor growths of cancers in bone.
Hoosier Oncology Group Randomized Phase II Study of Docetaxel, Vinorelbine, and Estramustine in Combination in Hormone-Refractory Prostate Cancer with Pharmacogenetic Survival Analysis
Authors: Hahn Noah M. , Marsh Sharon , Fisher William , Langdon Robert , Zon Robin , Browning Mark , Johnson Cynthia S. , Scott-Horton Tiffany J. , Li Lang , McLeod Howard L. , Sweeney Christopher J. 
Published: October 2006

Abstract
Purpose: To determine the safety and efficacy of two docetaxel doublets in hormone-refractory prostate cancer (HRPC) patients and to examine the prognostic role of polymorphisms in host genes important to docetaxel metabolism and transport.
Experimental Design: Sixty-four chemotherapy-naive patients with HRPC were randomized to docetaxel and vinorelbine (D, 20 mg/m2 i.v. days 1 and 8; V, 25 mg/m2 i.v. days 1 and 8) or docetaxel and estramustine phosphate (D, 60-70 mg/m2 i.v. day 1; E, 280 mg oral thrice daily days 1-5) administered q21d. Primary end point was clinically significant toxicity. A pharmacogenetic analysis of host genes was done in patients who received at least one cycle of docetaxel therapy.
Results: Grade 3/4 toxicity occurred in 15.6% of DV patients and in 28.6% DE patients. Neither arm exceeded the threshold of clinically significant toxicity. In the DV arm, objective response rate was 33%, prostate-specific antigen response rate was 20%, and median survival was 16.2 months. In the DE arm, objective response rate was 67%, prostate-specific antigen response rate was 43%, and median survival was 19.7 months. Pharmacogenetic analyses showed a significant association between survival beyond 15 months and the ABCG2 421 C&gt;A (Q141K) polymorphism compared with the wild-type (C/C) genotype (66% versus 27%; P = 0.05).
Conclusions: DV and DE doublets are active with a tolerable toxicity profile in patients with HRPC; however, efficacy does not seem superior to standard single-agent docetaxel. The ABCG2 421 C&gt;A (Q141K) polymorphism may be an important predictor of response and survival in HRPC patients treated with docetaxel-based chemotherapy.
Extra-pair copulations in common murres I: a mate attraction strategy?
Authors: Cameron-Macmillan Maureen L. , Walsh Carolyn J. , Wilhelm Sabina I. , Storey Anne E. 
Published: October 2006

AbstractWe investigated the behavioural context of pair (PCs) and extra-pair copulations (EPCs) in individually-marked socially-monogamous, long-lived seabirds, common murres (Uria aalge). Since forced EPCs have been documented for this species, we first examined which sex controls successful (cloacal contact achieved) copulation. The finding that all successful copulations required female cooperation and crouching suggested that benefits of successful EPCs accrue primarily to females. In a group of murres for which paternity analyses indicated no extra-pair paternity, behavioural observations over five breeding seasons showed that individual females engaged in EPCs primarily under two circumstances: (1) before they were reunited with their mates, and (2) when they were in the process of re-pairing. There was no such relationship between EPCs and re-pairing for males. Successful EPCs occurred with familiar neighboring males of apparent high quality, indicated by their high ledge attendance and prior reproductive success rates. Thus, EPCs may be used by females to attract potential high quality mates in situations where females are attempting to re-pair as a result of divorce or mate death.
Use of chemical cues during shell fights in the hermit crab Pagurus bernhardus
Authors: Briffa Mark , Williams Rebecca 
Published: October 2006

AbstractChemical communication is likely to play an important role during agonistic encounters in aquatic crustaceans but the use of chemical signals is difficult to observe. An alternative approach to direct observation is to collect water that has contained fighting animals and then expose a focal animal of the same species to the cue water and monitor its behaviour. Here we investigate the possibility of the use of chemical cues during 'shell fights' in the hermit crab Pagurus bernhardus. Focal crabs exposed to the fighting cue spent more time withdrawn into their gastropod shell, less time on locomotion and less time searching for food than did those exposed to cues from non-fighting hermit crabs or those treated with plain sea water. At the end of the observation period we used a novel stimulus to induce a startle response in order to probe the focal crab's motivational state for this exploratory behaviour. Those exposed to the fighting cue water took longer to recover than crabs in the other groups, indicating that their motivation was lower. These findings provide clear evidence that chemical cues are a feature of these contests.
Risk factors and escape strategy in the grasshopper Dissosteira carolina
Authors: Cooper William E. 
Published: October 2006

AbstractTo determine aspects of escape strategy by the Carolina grasshopper, Dissosteira carolina, and applicability of models of escape behavior applied primarily to vertebrates, I conducted three field experiments by simulating an approaching predator. Escape theory predicts that flight initiation distance (distance from predator when escape begins) and distance fled increase as predation risk increases. Some aspects of escape are not predicted, and theory does not identify escape strategies including several components. I examined effects of risk factors (predator approach speed, directness of approach, and repeated approach) on flight initiation distance, distance fled, and the initial direction of escape. Flight initiation distance and distance fled were predicted to increase with approach speed. Because predators approaching directly may bypass prey without detecting it, probability of fleeing and flight initiation distance were predicted to increase with directness of approach. Because a persistent predator poses greater threat, flight initiation distance and distance fled were predicted to be greater for the second of two successive approaches. All findings were consistent with predictions of the Ydenberg & Dill (1986) model, suggesting that risk assessment and escape decisions by visually oriented insects may be similar to those of vertebrates. Although escape directly away from the predator might be expected to minimize risk, most grasshoppers escaped by flying at nearly right angles to the approach path. Lateral escape may be part of an escape strategy in which dark wing colour during flight rapidly disappears upon landing. With sudden change in colour and movement, the grasshopper becomes cryptic and difficult to relocate. Lateral escape may increase difficulty of maintaining visual contact with the grasshopper until it lands. It also avoids need for further escape from a predator that continues in its initial direction.
Amplification and Suppression of Internal Waves by Tides over Variable Bottom Topography
Authors: Vlasenko Vasiliy , Stashchuk Nataliya 
Published: October 2006

Abstract
The energy exchange between internal waves and barotropic currents over inclined bottom topography is studied theoretically and in the framework of the numerical model. The energy balance equation derived for a continuously stratified fluid predicts that energy can either be transferred toward or away from the internal wave depending on the direction of propagation of both the wave and current. Four scenarios of wave–flow interaction over the inclined bottom were identified. An internal wave extracts energy from the background tidal flow during its propagation upslope–upstream or downslope–downstream and its amplitude grows. The wave loses energy propagating downslope–upstream or upslope–downstream and reduces in amplitude. This mechanism of suppression or amplification of internal waves by a current over an inclined bottom is verified numerically. When applied to the area of the Knight Inlet sill, a high-resolution fully nonlinear, nonhydrostatic model reproduces the packets of internal waves generated by supercritical tidal flow over the sill. Careful inspection of the wave fields revealed the presence of an irregular wave structure within wave packets—namely, internal waves are not arranged by amplitude. This phenomenon, obtained numerically and observed in situ, is treated in terms of the mechanism of wave–flow interaction: the energy exchange between the tidal current and generated internal waves over the inclined bottom topography is the reason for the absence of traditional rank-ordered waves in the packet.
Employee characteristics and participation in a worksite wellness programme
Authors: Joslin Beth , Lowe John B , Peterson N Andrew 
Published: October 2006

Objective The purpose of this study was to explore the underlying structure of participation in a worksite wellness programme, and to examine the relationship between the demographic and quality of life (QOL) characteristics of employees, and the wellness programme offerings in which they choose to participate. Design The cross-sectional design of this study involved gathering data from individuals at one point in time, following their decision to participate (or not participate) in a worksite wellness programme. Setting This study involved county government employees in a Midwestern United States community. Method Surveys were mailed to a random sample of 329 county government employees. The survey included demographics and measured QOL via the Short Form-36 (SF-36). One-week and three-week follow-ups were conducted in attempt to increase the survey response rate. Results Two dimensions of wellness programme participation were identified to exist among wellness programme participants: (1) medical offerings; and (2) health education offerings. Certain employee characteristics were associated with participation in each of the two dimensions of participation. Conclusion Findings suggest demographic and QOL characteristics may predict the type of employees a programme might expect to participate in wellness offerings. Results may be useful for worksite wellness programme coordinators regarding tailoring programme offerings, participant recruitment, and education efforts, based on the characteristics of the employee population.
Experiences and challenges in data monitoring for clinical trials within an international tropical disease research network
Authors: Chen-Mok M , VanRaden M J , Higgs E S , Dominik R 
Published: October 2006

Background Models for the structure and procedures of data and safety monitoring boards (DSMBs) continue to evolve in response to issues of new and of old concern. Some authors have called for an open dialogue on these questions through publication of the experiences of DSMBs in addressing them. Purpose The goal of this paper is to add to the current discussion about acceptable models for establishing, serving on, and reporting to monitoring committees, particularly those that oversee multiple studies in less developed countries. The paper seeks to do so by describing the establishment and subsequent operation of one such multi-trial DSMB over a five-year period. This DSMB was formed to monitor trials conducted by members of the International Centers for Tropical Disease Research (ICTDR) network of the National Institute of Allergy and Infectious Diseases (NIAID). Methods The operational model and experiences are summarized by the authors, who had immediate responsibilities for directing the DSMB's activities. Results The board played an active, traditional role in assuring that patient safety was maintained and that current standards for clinical research were met. In addition, both NIAID and the board members viewed education of investigators to be an important role for the board to play in this particular setting. This affected the threshold for identifying which trials would be monitored, and it impacted several procedures adopted by the board. Limitations This report reflects the observations of those involved in managing the DSMB, including comments offered by the DSMB and by investigators, but not data gathered in a systematic way. Conclusions The operational model described here has allowed the DSMB to fulfill its role in the oversight of the trials. We hope that the ideas we present may help others facing similar situations and may stimulate further critical thinking about DSMB structure and function.
Consent for genetics studies among clinical trial participants: findings from Action for Health in Diabetes (Look AHEAD)
Authors: Espeland M A , Dotson K , Jaramillo S A , Kahn S E , Harrison B , Montez M , Foreyt J P , Montgomery B , Knowler W C ,   Look AHEAD Research Group
Published: October 2006

Background Increasingly, genetic specimens are collected to expand the value of clinical trials through study of genetic effects on disease incidence, progression or response to interventions. Purpose and methods We describe the experience obtaining IRB-approved DNA consent forms across the 19 institutions in the Action for Health in Diabetes (Look AHEAD), a clinical trial examining the effect of a lifestyle intervention for weight loss on the risk of serious cardiovascular events among individuals with type 2 diabetes. We document the rates participants provided consent for DNA research, identify participant characteristics associated with consent, and discuss implications for genetics research. Results IRB approval to participate was obtained from 17 of 19 institutions. The overall rate of consent was 89.6% among the 15 institutions that had completed consenting at the time of our analysis, which was higher than reported for other types of cohort studies. Consent rates were associated with factors expected to be associated with weight loss and cardiovascular disease and to affect the distribution of candidate genes. Non-consent occurred more frequently among participants grouped as African-American, Hispanic, female, more highly educated or not dyslipidemic. Limitations The generalizabilty of results is limited by the inclusion/exclusion criteria of the trial. Conclusions Barriers to obtaining consent to participate in genetic studies may differ from other recruitment settings. Because of the potentially complex associations between personal characteristics related to adherence, outcomes and gene distributions, differential rates of consent may introduce biases in estimates of genetic relationships.
Imputation strategies for blood pressure data nonignorably missing due to medication use
Authors: Cook N R 
Published: October 2006

Background Underlying or untreated blood pressure (BP) is often an outcome of interest, but is unobservable when study participants are on anti-hypertensive medications. Untreated levels are not missing at random but would be higher among those on such medication. In such cases, standard methods of analysis may lead to bias. Purpose BPs obtained at the private physician's office (out-of-study BPs) at the time of prescription of anti-hypertensive medications were available from Phase II of the Trials of Hypertension Prevention (TOHP) and were used to adjust for the potential bias. Methods Observed out-of-study BPs were used to estimate the conditional expectation and variance of the unobserved unmedicated study BPs. For those with no physician data, imputation from bootstrap samples of out-of-study BPs was used. An iterative method based on the EM algorithm was used to estimate the unknown study parameters in a random-effects model using multiple imputations. This was compared to an alternative model for the out-of-study BPs based on a theoretical truncated normal distribution, and to standard analyses, including both multivariate repeated measures and last-observation-carried-forward (LOCF) analyses, using data from Phase II of TOHP. Results Differences between methods were seen in the decline in BP over time in the reference group, where the changes from baseline to 36 months were 3.0 in univariate analyses, 2.4 using LOCF, and 2.6 in the multivariate analysis, compared to 2.0 or 1.7 in the imputation analyses, depending on the number of physician visits. Estimated intervention effects tended to be slightly larger using the imputation methods. Limitations out-of-study measures may not be available for other studies. Conclusions Because the proposed strategy was based on an empirically observed distribution for out-of-study BP, fewer assumptions about the missing data were made. These data may be useful in suggesting imputation strategies for other studies.
Species sensitivity of zeolite minerals for uptake of mercury solutes
Authors: Campbell L. S. , Chimedtsogzol A. , Dyer A. 
Published: October 2006

AbstractThe uptake of inorganic Hg2+and organometallic CH3Hg+from aqueous solutions by 11 different natural zeolites has been investigated using a batch distribution coefficient(Kd) method and supported by a preliminary voltammetric study. The effect of mercury concentration on theKdresponse is shown over an environmentally appropriate concentration range of 0.1–5 ppm inorganic and organometallic Hg using a batch factor of 100 ml g-1and 20 h equilibration. Analcime and a Na-chabazite displayed the greatest methylmercury uptakes(Kdvalues at 1.5 ppm of 4023 and 3456, respectively), with mordenite as the smallest at 578. All uptake responses were greater for methylmercury than for the inorganic mercuric nitrate solutions, suggesting a distinctive sensitivity of zeolites to reaction with different types of solute species. It is likely that this sensitivity is attributable to the precise nature of the resultant Hg-zeolite bonds. Additionally, both the Si-Al ratio and the Na content of the initial natural zeolite samples are shown to influence theKdresponses, with positive correlations betweenKdand Na content for all zeolites excluding mordenite.
Orientation relationships of carlsbergite in schreibersite and kamacite in the north Chile iron meteorite
Authors: Nolze G. , Wagner G. , Saliwan Neumann R. , Skála R. , Geist V. 
Published: October 2006

AbstractThe crystallographic orientation of carlsbergite (CrN) in the north Chile meteorite (hexahedrite) was investigated using electron backscatter diffraction and transmission electron microscopy. These studies examined the CrN crystals in the rhabdites (idiomorphic schreibersite) and in kamacite. It was found that the CrN crystals embedded in rhabdite show a number of different orientation relationships with the host crystals. These orientations can be explained based on the lattice dimensions of both coexisting crystalline materials. It was also found that both carlsbergite and kamacite are characterized by a high dislocation density (≥ l09 cm-2) while rhabdite is free of dislocations. It is supposed that in spite of the deformed metallic matrix, a general connection between the orientation relation of all the phases involved exists.
A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database
Authors: Katz Simon , Irizarry Rafael A , Lin Xue , Tripputi Mark , Porter Mark W 
Published: October 2006

Abstract

Background
Many of the most popular pre-processing methods for Affymetrix expression arrays, such as RMA, gcRMA, and PLIER, simultaneously analyze data across a set of predetermined arrays to improve precision of the final measures of expression. One problem associated with these algorithms is that expression measurements for a particular sample are highly dependent on the set of samples used for normalization and results obtained by normalization with a different set may not be comparable. A related problem is that an organization producing and/or storing large amounts of data in a sequential fashion will need to either re-run the pre-processing algorithm every time an array is added or store them in batches that are pre-processed together. Furthermore, pre-processing of large numbers of arrays requires loading all the feature-level data into memory which is a difficult task even with modern computers. We utilize a scheme that produces all the information necessary for pre-processing using a very large training set that can be used for summarization of samples outside of the training set. All subsequent pre-processing tasks can be done on an individual array basis. We demonstrate the utility of this approach by defining a new version of the Robust Multi-chip Averaging (RMA) algorithm which we refer to as refRMA.

Results
We assess performance based on multiple sets of samples processed over HG U133A Affymetrix GeneChip® arrays. We show that the refRMA workflow, when used in conjunction with a large, biologically diverse training set, results in the same general characteristics as that of RMA in its classic form when comparing overall data structure, sample-to-sample correlation, and variation. Further, we demonstrate that the refRMA workflow and reference set can be robustly applied to naïve organ types and to benchmark data where its performance indicates respectable results.

Conclusion
Our results indicate that a biologically diverse reference database can be used to train a model for estimating probe set intensities of exclusive test sets, while retaining the overall characteristics of the base algorithm. Although the results we present are specific for RMA, similar versions of other multi-array normalization and summarization schemes can be developed.