bluuebunny/crossref_metadata_2025_split huggingface dataset:
A kernel-based integration of genome-wide data for clinical decision support
Authors: Daemen Anneleen , Gevaert Olivier , Ojeda Fabian , Debucquoy Annelies , Suykens Johan AK , Sempoux Christine , Machiels Jean-Pascal , Haustermans Karin , De Moor Bart 
Published: April 2009

Abstract
Background
Although microarray technology allows the investigation of the transcriptomic make-up of a tumor in one experiment, the transcriptome does not completely reflect the underlying biology due to alternative splicing, post-translational modifications, as well as the influence of pathological conditions (for example, cancer) on transcription and translation. This increases the importance of fusing more than one source of genome-wide data, such as the genome, transcriptome, proteome, and epigenome. The current increase in the amount of available omics data emphasizes the need for a methodological integration framework.

Methods
We propose a kernel-based approach for clinical decision support in which many genome-wide data sources are combined. Integration occurs within the patient domain at the level of kernel matrices before building the classifier. As supervised classification algorithm, a weighted least squares support vector machine is used. We apply this framework to two cancer cases, namely, a rectal cancer data set containing microarray and proteomics data and a prostate cancer data set containing microarray and genomics data. For both cases, multiple outcomes are predicted.

Results
For the rectal cancer outcomes, the highest leave-one-out (LOO) areas under the receiver operating characteristic curves (AUC) were obtained when combining microarray and proteomics data gathered during therapy and ranged from 0.927 to 0.987. For prostate cancer, all four outcomes had a better LOO AUC when combining microarray and genomics data, ranging from 0.786 for recurrence to 0.987 for metastasis.

Conclusions
For both cancer sites the prediction of all outcomes improved when more than one genome-wide data set was considered. This suggests that integrating multiple genome-wide data sources increases the predictive performance of clinical decision support models. This emphasizes the need for comprehensive multi-modal data. We acknowledge that, in a first phase, this will substantially increase costs; however, this is a necessary investment to ultimately obtain cost-efficient models usable in patient tailored therapy.
Coordinate Regulation of Estrogen-Mediated Fibronectin Matrix Assembly and Epidermal Growth Factor Receptor Transactivation by the G Protein-Coupled Receptor, GPR30
Authors: Quinn Jeffrey A. , Graeber C. Thomas , Frackelton A. Raymond , Kim Minsoo , Schwarzbauer Jean E. , Filardo Edward J. 
Published: April 2009

AbstractEstrogen promotes changes in cytoskeletal architecture not easily attributed to the biological action of estrogen receptors, ERα and ERβ. The Gs protein-coupled transmembrane receptor, GPR30, is linked to specific estrogen binding and rapid estrogen-mediated release of heparin-bound epidermal growth factor. Using marker rescue and dominant interfering mutant strategies, we show that estrogen action via GPR30 promotes fibronectin (FN) matrix assembly by human breast cancer cells. Stimulation with 17β-estradiol or the ER antagonist, ICI 182, 780, results in the recruitment of FN-engaged integrin α5β1 conformers to fibrillar adhesions and the synthesis of FN fibrils. Concurrent with this cellular response, GPR30 promotes the formation of Src-dependent, Shc-integrin α5β1 complexes. Function-blocking antibodies directed against integrin α5β1 or soluble Arg-Gly-Asp peptide fragments derived from FN specifically inhibited GPR30-mediated epidermal growth factor receptor transactivation. Estrogen-mediated FN matrix assembly and epidermal growth factor receptor transactivation were similarly disrupted in integrin β1-deficient GE11 cells, whereas reintroduction of integrin β1 into GE11 cells restored these responses. Mutant Shc (317Y/F) blocked GPR30-induced FN matrix assembly and tyrosyl phosphorylation of erbB1. Interestingly, relative to recombinant wild-type Shc, 317Y/F Shc was more readily retained in GPR30-induced integrin α5β1 complexes, yet this mutant did not prevent endogenous Shc-integrin α5β1 complex formation. Our results suggest that GPR30 coordinates estrogen-mediated FN matrix assembly and growth factor release in human breast cancer cells via a Shc-dependent signaling mechanism that activates integrin α5β1.
Mentoring. A Quality Assurance Tool for Dentists Part 3: Building a Successful Mentoring Relationship
Authors: Holt Vernon P , Ladwa Russ 
Published: April 2009

The contribution that the mentor can make to the mentoring relationship is undoubtedly crucial. It revolves around mentor qualities, including honesty, congruence, self-sufficiency, and patience. Mentor attitudes include unconditional positive regard for the mentee and mentee focus. Mentor behaviours include establishing rapport, demonstrating warmth and empathy, and giving constructive feedback. There are also unhelpful mentor positions, which are to be avoided. However, there are enormous rewards for the mentor. Mentees also make a significant contribution to the successful relationship by being open to the process and ready to engage with their mentor in order to discover their own goals and develop their own resources and career. This will help them to serve their patients better in the years to come and thereby to achieve a greater sense of purpose, satisfaction and reward in their professional lives.
Resin-Based Composites and Dentine-Bonding Agents. Which, who and Why? A Study in the East of Scotland
Authors: McFadzean Rhona W , Gibson Emily , Newcombe Ruth F , Nataraja Rajeev , Santini Ario 
Published: April 2009

AimsTo determine which resin-based composite (RBC) and dentine-bonding agent (DBA) systems were most widely used by a random convenience sample of dentists in the East of Scotland, by whom they were used, and what influenced the dentists’ choice when buying/using a particular RBC and DBA.MethodsA cross-sectional questionnaire-based study was conducted from June to December 2006. A questionnaire was compiled and, following a short pilot and revision, 250 questionnaires were randomly distributed to dentists attending vocational training/general professional training study days, continuing education courses and various dental meetings. Data from the completed questionnaires were collated and analysed.ResultsA total of 138 questionnaires were returned, giving a response rate of 55%, of which 101 (73%) were from practitioners working within the General Dental Services, 20 (14%) from Community Dental Service dentists, and 17 (12%) from practitioners in the hospital dental service. The most popular RBC reported by respondents 43 (31%) was Z100™ (3M UK, Bracknell, UK). The most common factors that influenced respondents’ choice when buying an RBC were ease of use and availability, reported by 51 (37%) and 45 (33%) respondents, respectively. Prime & Bond®(DENTSPLY DeTrey, Konstanz, Germany) was reported as the most popular DBA by 58 (42%) respondents. Overall, availability, reported by 61 (44%) respondents, was the most popular reason for choice of a DBA, followed by ease of use, reported by 52 (38%) respondents, and reliability, reported by 23 (17%) respondents.ConclusionsThe most popular RBCs and DBAs used by respondents to this study and common reasons for their use were identified. However, it was found that, among those who responded, there was no discernible relationship between undergraduate training, year of qualification and choice of material. Further research is required to corroborate these findings and to identify the level of understanding of material science by dental clinicians.
The impact of dispositional emotional expressivity and social constraints on distress among prostate cancer patients in Iceland
Authors: Agustsdottir Sjofn , Kristinsdottir Aslaug , Jonsdottir Katrin , Larusdottir Solrun Osk , Smari Jakob , Valdimarsdottir Heiddis B. 
Published: April 2009

ObjectivesThe aim of our study was to identify individual factors that may predict which subset of prostate cancer patients is more likely to experience emotional distress.Design and methodsProstate cancer survivors identified through the Icelandic Cancer Registry (N=184), completed questionnaires measuring emotional distress, dispositional emotional expressivity and social constraints.ResultsA significant positive relationship was observed between perceived social constraints and distress (e.g. anxiety, depression, and intrusive thoughts), but only among prostate cancer survivors with higher levels of dispositional emotional expressivity.ConclusionsThe results of our study suggest that it might be important to assess individual differences as well as social environmental factors in the treatment of distress among prostate cancer survivors.
The Role of the Taxanes in the Treatment of Older Patients with Advanced Stage Non-Small Cell Lung Cancer
Authors: Ramalingam Suresh S. , Khuri Fadlo R. 
Published: April 2009

Abstract
The treatment of older patients with advanced non-small cell lung cancer (NSCLC) represents a considerable challenge for physicians. A patient ’s suitability for chemotherapy is frequently based solely on chronologic age; as a consequence, older patients with NSCLC are less likely to receive standard chemotherapy than younger patients. Although age-related factors, such as comorbid illness, should be taken into consideration when assessing a patient ’s suitability for treatment, fit and functionally independent older patients should be considered candidates for standard chemotherapy. The taxanes are widely used in the treatment of advanced-stage NSCLC and are well tolerated in older patients. The efficacy of both paclitaxel and docetaxel has been studied in older patients and appears to be comparable with that seen in younger patients either as monotherapy or in combination with a platinum compound as first-line therapy. In addition to the available evidence, prospective evaluation of novel agents in elderly-specific or -enriched studies is necessary to guide the treatment of older patients with NSCLC.
Current Treatment Approaches for Infants with Malignant Central Nervous System Tumors
Authors: Lafay-Cousin Lucie , Strother Douglas 
Published: April 2009

Learning Objectives
Evaluate the challenges of identifying very young children with brain tumors so that they can be enrolled in clinical trials. Identify prognostic factors for children with certain brain tumors and assess the influence of these factors on current therapeutic strategies. Outline factors affecting survival and neurocognitive outcome of children with malignant brain tumors.
This article is available for continuing medical education credit at CME.TheOncologist.com.
Immunotherapeutics in Development for Prostate Cancer
Authors: Harzstark Andrea L. , Small Eric J. 
Published: April 2009

AbstractWhereas chemotherapy is the standard of care for metastatic castration-resistant prostate cancer and is associated with a survival benefit, there remains a need for alternative approaches. Extensive work has been done evaluating multiple immunotherapies for the treatment of prostate cancer. This review discusses clinical results for the most promising developments. These include cytokine-based therapy with GM-CSF; vaccines; antibody-based immunotherapies, including anti–cytotoxic T lymphocyte associated antigen 4 therapy and antibodies against additional targets; and dendritic cell-based immunotherapy.
Salvage Therapy in Hodgkin’s Lymphoma
Authors: Mendler Jason H. , Friedberg Jonathan W. 
Published: April 2009

Learning Objectives
Appraise the most important properties of a salvage chemotherapy regimen and name at least three effective regimens. Evaluate poor-risk clinical features pre-HDCT/ASCT that reduce the chance for cure and design a more effective alternative transplant approach. Hypothesize the reasons for the effectiveness of monoclonal antibodies that have shown activity against relapsed HL.
This article is available for continuing medical education credit at CME.TheOncologist.com.
Oil Relative Permeability for Gravity Drainage Based on In-Situ Saturation Measurements
Authors: Naylor P. , Sargent N. C. , Tilsed A. P. , Frorup M. D. 
Published: April 2009

ABSTRACT
A determination of oil relative permeability data during secondary and tertiary, gravity stable, nitrogen injection experiments is described. Four experiments were conducted at high and low pressure using vertical Clashach sandstone cores and a dead oil in the presence of connate brine. The spatial distributions of oil throughout the cores were determined using a radioactive tracer technique and these in-situ saturation measurements were used to determine the oil relative permeability.
The results of two new experiments are presented. A high pressure, secondary, gravity stable, nitrogen injection was conducted in a 1790 mm core with a connate water saturation of 0.25. The residual oil saturation following 12 days of gas flooding was 0.19. A low pressure, tertiary, gravity stable, nitrogen injection was conducted in a 841 mm core with a connate water saturation of 0.19. A residual oil saturation to water flooding of 0.51 was reduced to 0.09 after 37 days of drainage.
The rate of change of oil relative permeabilities with respect to oil saturation was larger in the secondary, gravity stable, nitrogen injection than in the tertiary injection. The predicted residual oil saturation to gas corresponding to an infinite drainage time appears to be finite for secondary gas injection and zero for tertiary gas injection.
The permeability data is consistent with a theoretical model of film drainage which predicts a Corey Exponent of three.
Formation Damage Prevention – Completion of the Most Productive Horizontal Well in Germany in the Mittelplate Offshore Oil Field
Authors: Rappuhn T. , Münch E. , Schuhbauer W. 
Published: April 2009

Abstract
The Mittelplate oil field is located in the Tidelands National Park in the German North Sea. Its location in an ecologically sensitive area was a challenge during well completion planning. The horizontal well A 7a penetrates the Dogger-delta sandstone in the Jurassic trough on the flank of a salt dome. The well's productivity is a very important factor in the economics of field development. The specific reservoir conditions were decisive for well design and completion fluid selection. To retain all options for future production phases, a concept using a cemented liner and subsequent perforation was selected. Formation damage control was supported by short workover time due to new completion techniques. To avoid formation damage during the initial stages of perforation and completion, a non-damaging completion fluid was evaluated in laboratory investigations. The objective was to verify the rheological properties, carrying capacity, and time stability. Minimizing fluid loss during completion guarantees optimum well productivity. A xanthan-based carrier fluid with oil-soluble resins serving as bridging agents was selected. Intensive quality control of the chemicals ensured the use of correct batches in the field, contributing to the positive results of the project.
Cased Hole Exploration: Modern Pulsed Neutron Techniques for Locating By-Passed Hydrocarbons in Old Wells
Authors: Streeter R. W. , Hogan G. P. , Rogers C. B. , Odom R. C. , Barrett D. G. 
Published: April 2009

Abstract
Many Permian Basin fields are considered "mature", with some of these fields almost depleted and/or undergoing water or CO2: flooding. Operators are being faced with decisions to P&A or to recomplete in other zones, often with inadequate data. Unfortunately, many of these wells were logged before modem porosity logs were available. In other wells, for various reasons, the entire well was not logged.
The integration of modem pulsed neutron technologies1 can. however, provide the operator with reservoir parameters from inside casing. For porosity, pulsed neutron systems can make a thermal neutron ratio porosity' (RPHI) similar in response to the compensated neutron. Pulse neutron systems can also be used to make a new type of porosity (IPHI) derived from gamma rays created by inelastic scattering of fast neutrons. IPHI is similar in response to an open hole density and can be crossplotted with RPHI to help identify lithology changes and differentiate tight zones from gas. The crossplotted porosity also helps compensate for lithology and gas effects, and to some extent for some variations in near wellbore environment. The crossplotted porosity can then be used with sigma and/or CATO2 to determine water saturation.
Dealing with Harsh Pumping Conditions in the Dos Cuadras Field, Offshore California
Authors: Krupa Ronald J. , Bebak Ken , Jackson Pat 
Published: April 2009

Abstract
The purpose of this paper is to provide information pertaining to the abrasive pumping conditions and the subsequent corrective action. Additionally, this environment also includes gassy, and corrosive conditions. This paper will describe the characteristics of the harsh environment as well as empirical dataas to the corrective action steps taken to address the application challenges.
The data is an accumulation of computer simulation, field testing, and subsequent evaluation of the equipment upon return to the well.
The results of the paper will show that electrical submersible pump runtimes can be improved by the effective use of abrasion resistant, corrosion resistant, and gas separation technologies. The overall goal of the paper is to share experiences with the industry so that others may benefit from successfully operating submersibles in these harsh conditions.

Introduction
The Dos Cuadras Field is located in the Santa Barbara Channel roughly 7.5miles southeast of Santa Barbara, California, under OCS leases P-0240 and P-0241. Platforms "A", "B", "C" and "Hillhouse"were set in the late 1960's and early 1970's to exploit the reserves in the field. The water depth is 190 feet. The primary zone of interest is the Repetto formation, a Pliocene age sequence of alternating sand and shale intervals. The productive horizons range in depth from about 500 feet below sea level to roughly 4000 feet below sea level. Well conditions are shown on Figure 1.
Original completions consisted of selectively perforated intervals which were produced with electrical submersible pumps. Because of the limited perforation technology applied, relatively high fluid velocities resulted in excessive sand production in the wells. Application of sand control techniques to counter the sand production has been precluded by long producing intervals, limited fluid levels and restricted casing sizes. As a result, to produce the wellbore fluids, it became necessary to produce the sand along with the fluids.
Sol-gel bioactive glass-ceramics Part I: Calcium phosphate silicate/wollastonite glass-ceramics
Authors: Radev Lachezar , Hristov Vladimir , Michailova Irena , Samuneva Bisserka 
Published: April 2009

Abstract
In this work we present experimental results about synthesis, structure evolution and in vitro bioactivity of new calcium phosphate silicate/wollastonite (CPS/W) glass-ceramics. The samples obtained were synthesized via polystep sol-gel process with different Ca/P+Si molar ratio (R). The structure of the materials obtained was studied by XRD, FTIR spectroscopy and SEM. XRD showed the presence of Ca15(PO4)2(SiO4)6, β-CaSiO3 and α-CaSiO3 for the sample with R=1.89 after thermal treatment at 1200°C/2h. The XRD results are in good agreement with FTIR analysis. SEM denotes that apatite formation can be observed after soaking in simulated body fluid (SBF).
Optimal Internal Dissipation of a Damped Wave Equation Using a Topological Approach
Authors: Münch Arnaud 
Published: April 2009

Optimal Internal Dissipation of a Damped Wave Equation Using a Topological ApproachWe consider a linear damped wave equation defined on a two-dimensional domain Ω, with a dissipative term localized in a subset ω. We address the shape design problem which consists in optimizing the shape of ω in order to minimize the energy of the system at a given timeT. By introducing an adjoint problem, we first obtain explicitly the (shape) derivative of the energy at timeTwith respect to the variation in ω. Expressed as a boundary integral on ∂ω, this derivative is then used as an advection velocity in a Hamilton-Jacobi equation for shape changes. We use the level-set methodology on a fixed working Eulerian mesh as well as the notion of the topological derivative. We also consider optimization with respect to the value of the damping parameter. The numerical approximation is presented in detail and several numerical experiments are performed which relate the over-damping phenomenon to the well-posedness of the problem.
Robust Parameter Design Using the Weighted Metric Method—The Case of ‘the Smaller the Better’
Authors: Ardakani Mostafa , Noorossana Rassoul , Akhavan Niaki Seyed , Lahijanian Homayoun 
Published: April 2009

Robust Parameter Design Using the Weighted Metric Method—The Case of ‘the Smaller the Better’In process robustness studies, it is desirable to minimize the influence of noise factors on the system and simultaneously determine the levels of controllable factors optimizing the overall response or outcome. In the cases when a random effects model is applicable and a fixed effects model is assumed instead, an increase in the variance of the coefficient vector should be expected. In this paper, the impacts of this assumption on the results of the experiment in the context of robust parameter design are investigated. Furthermore, two criteria are considered to determine the optimum settings for the control factors. In order to better understand the proposed method and to evaluate its performances, a numerical example for the case of ‘the smaller the better’ is included.
Reachability of Cone Fractional Continuous-Time Linear Systems
Authors: Kaczorek Tadeusz 
Published: April 2009

Reachability of Cone Fractional Continuous-Time Linear SystemsA new class of cone fractional continuous-time linear systems is introduced. Necessary and sufficient conditions for a fractional linear system to be a cone fractional one are established. Sufficient conditions for the reachability of cone fractional systems are given. The discussion is illustrated with an example of linear cone fractional systems.
Positive 2D Discrete-Time Linear Lyapunov Systems
Authors: Przyborowski Przemysław , Kaczorek Tadeusz 
Published: April 2009

Positive 2D Discrete-Time Linear Lyapunov SystemsTwo models of positive 2D discrete-time linear Lyapunov systems are introduced. For both the models necessary and sufficient conditions for positivity, asymptotic stability, reachability and observability are established. The discussion is illustrated with numerical examples.
Changes in the phytoplankton community of a lake restored with phosphorus inactivation (Lake Głęboczek, northern Poland)
Authors: Jaworska Bożena , Gawrońska Helena , Łopata Michał 
Published: April 2009

Abstract
The study applied qualitative and quantitative phytoplankton analysis as a tool for determining algal community characteristics and identifying the directions and general trends of changes caused by the restoration of Lake Głęboczek through phosphorous inactivation before and during its application.
The method applied in the studied lake aimed at reducing phosphorous availability through the chemical precipitation of its excess mineral forms in the water body and limiting their mobility in the bottom sediments. Restoration efforts led to shifts in the phytoplankton domination structure followed by the inhibition of blue-green algae development. In consequence, a significant decrease was recorded in the growth rate of the phytoplankton community.