bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catching Cancer by the Tail: New Perspectives on the Use of Kinase Inhibitors
Authors: Khanna Chand , Gordon Ira 
Published: May 2009

Abstract
In this issue of Clinical Cancer Research, London and colleagues evaluate a small molecule multiple-targeted tyrosine kinase inhibitor in dogs with c-kit driven skin cancer. The study represents another example of opportunities to include pet dogs in studies that improve our understanding of human cancer biology and therapy.
The Effects of Varying Dietary Carbohydrate and Fat Content on Survival in a Murine LNCaP Prostate Cancer Xenograft Model
Authors: Mavropoulos John C. , Buschemeyer W. Cooper , Tewari Alok K. , Rokhfeld Dmitriy , Pollak Michael , Zhao Yunhua , Febbo Phillip G. , Cohen Pinchas , Hwang David , Devi Gayathri , Demark-Wahnefried Wendy , Westman Eric C. , Peterson Bercedis L. , Pizzo Salvatore V. , Freedland Stephen J. 
Published: May 2009

Abstract
Purpose: Numerous dietary factors elevate serum levels of insulin and insulin-like growth factor I (IGF-I), both potent prostate cancer mitogens. We tested whether varying dietary carbohydrate and fat, without energy restriction relative to comparison diets, would slow tumor growth and reduce serum insulin, IGF-I, and other molecular mediators of prostate cancer in a xenograft model.
Experimental Design: Individually caged male severe combined immunodeficient mice (n = 130) were randomly assigned to one of three diets (described as percent total calories): very high-fat/no-carbohydrate ketogenic diet (NCKD: 83% fat, 0% carbohydrate, 17% protein), low-fat/high-carbohydrate diet (LFD: 12% fat, 71% carbohydrate, 17% protein), or high-fat/moderate-carbohydrate diet (MCD: 40% fat, 43% carbohydrate, 17% protein). Mice were fed to maintain similar average body weights among groups. Following a preliminary feeding period, mice were injected with 1 × 106 LNCaP cells (day 0) and sacrificed when tumors were ≥1,000 mm3.
Results: Two days before tumor injection, median NCKD body weight was 2.4 g (10%) and 2.1 g (8%) greater than the LFD and MCD groups, respectively (P &lt; 0.0001). Diet was significantly associated with overall survival (log-rank P = 0.004). Relative to MCD, survival was significantly prolonged for the LFD (hazard ratio, 0.49; 95% confidence interval, 0.29-0.79; P = 0.004) and NCKD groups (hazard ratio, 0.59; 95% confidence interval, 0.37-0.93; P = 0.02). Median serum insulin, IGF-I, IGF-I/IGF binding protein-1 ratio, and IGF-I/IGF binding protein-3 ratio were significantly reduced in NCKD relative to MCD mice. Phospho-AKT/total AKT ratio and pathways associated with antiapoptosis, inflammation, insulin resistance, and obesity were also significantly reduced in NCKD relative to MCD tumors.
Conclusions: These results support further preclinical exploration of carbohydrate restriction in prostate cancer and possibly warrant pilot or feasibility testing in humans.
The Owl in Phoenician Mortuary Practice
Authors: Schmitz Philip 
Published: May 2009

AbstractRecent excavations in the Iron Age necropolis of Tyre (al-Bass district) allow a substantial reconstruction of the Phoenician ritual of cremation burial. Among the faunal remains from Tyre al-Bass Tomb 8 are two talons from a species of owl. The talons had been charred and perhaps boiled before placement with the grave goods. This paper examines ancient Near Eastern and biblical cultural interpretations of the owl and suggests a range of possible explanations for the presence of owl remains in this Phoenician burial.
Navigating International River Disputes to Avert Conflict
Authors: Gerlak Andrea , Zawahri Neda 
Published: May 2009

AbstractBuilding on the findings from the International Negotiation's 2000 issue on negotiations in international watercourses and the major advances in the field during the past nine years, this issue seeks to advance our knowledge about the management of international river disputes. Collectively, the articles in this issue move beyond the simple dichotomy of conflict and cooperation to suggest the possibility that both are often simultaneously present within a basin and should be studied as such. Using a diversity of methodological approaches from comparative case studies to single case studies to quantitative analysis, the articles also illustrate the growth of institutionalization within river basins and their contribution to conflict management. Moreover, the articles advance our knowledge of the role of the relative distribution of power within the basin on the resolution of water disputes and management of resources. Some scholars find power asymmetry important for treaty formation, while others suggest that issue linkages and side payments can provide weaker riparians with the means to gain from cooperation.
Asymmetric Power: Negotiating Water in the Euphrates and Tigris
Authors: Daoudy Marwa 
Published: May 2009

AbstractThis article addresses the conflict over the Euphrates and Tigris waters from the perspective of negotiation theories, by examining the role of power in upstream/downstream negotiations. Conceptual and empirical links are established between water, negotiation (structure, process), power (asymmetries, coalition dynamics, strategies, development of alternatives) and security (direct/indirect interests such as national security, border security, territorial claims, economic development and environmental concerns). The study concludes that asymmetries in power have favored upstream/downstream interactions towards bilateral if not basin-wide arrangements. The framework shows that traditional elements of power, such as upstream positions, military and economic resources, do not constitute the only sources of power. Bargaining power can also determine the dynamics between respective riparians. Time constitutes an important source of power, and interests vary over time when political settings and security concerns shift. Downstream or more vulnerable riparians can invert situations of power asymmetry by acting on the basin-dominant riparian's interests and thus reduce its alternatives. Syria's use of 'issue-linkage' in its interactions with Turkey over water and wider security issues serves as the primary example.
Peaceful Management of International River Claims
Authors: Hensel Paul , Brochmann Marit 
Published: May 2009

AbstractAs global water scarcity increases, both scholars and leaders have suggested that water will be a leading cause of future armed conflict. Yet other scholars argue that states typically cooperate rather than fight to manage their shared water resources. We address these arguments by examining the management of internationally shared rivers in the Americas, Western Europe, and the Middle East from 1900–2001. We propose hypotheses on the factors that lead states to become involved in disagreements over shared rivers as well as the factors that lead them to negotiate over these disagreements. Heckman probit analysis suggests that water scarcity – found by past work to be an important influence on armed conflict over rivers – is also an important influence on peaceful efforts to settle river problems; river claims are more likely where water supply is lower and demand is greater, but negotiations are also generally more likely in these same situations. Furthermore, while the existence of river treaties does not prevent the emergence of river claims, the presence of at least one treaty over the specific subject of the claim provides an important starting point that greatly increases the likelihood of negotiations over such claims. We conclude that the more pessimistic views of water management are missing an important part of the story. States are much more likely to negotiate in the most dangerous situations, and institutionalization of river resources can make an important contribution to negotiations over any disagreements that do emerge.
Estimating Higher-Order Moments of Nonlinear Time Series
Authors: Gluhovsky Alexander , Agee Ernest 
Published: May 2009

Abstract
This study extends the authors’ earlier work that addresses the importance of bootstrap methods in computing statistical characteristics of meteorological and climatological datasets. Subsampling confidence intervals for the skewness and kurtosis are developed for nonlinear datasets, for which traditional time series techniques are not applicable. It also provides an example of how to apply subsampling to real data when only a single record of limited length is available: aircraft observations of vertical velocity in the wintertime convective boundary layer over Lake Michigan. This demonstrates the value of bootstrap methods in obtaining reliable confidence intervals for turbulent flows with coherent structures (characterized by non-Gaussian skewness and kurtosis).
Eddy Formation in the Tropical Atlantic Induced by Abrupt Changes in the Meridional Overturning Circulation
Authors: Goes Marlos , Marshall David P. , Wainer Ilana 
Published: May 2009

Abstract
The variability of the meridional overturning circulation (MOC) in the upper tropical Atlantic basin is investigated using a reduced-gravity model in a simplified domain. Four sets of idealized numerical experiments are performed: (i) switch-on of the MOC until a fixed value when a constant northward flow is applied along the western boundary; (ii) MOC with a variable flow; (iii) MOC in a quasi-steady flow; and (iv) shutdown of the MOC in the Northern Hemisphere. Results from experiments (i) show that eddies are generated at the equatorial region by shear instability and detached northward; eddies are responsible for an enhancement of the mean flow and the variability of the MOC. Results from experiments (ii) show a transitional behavior of the MOC related to the eddy generation in interannual–decadal time scales as the Reynolds number varies due to the variations in the MOC. In experiments (iii), a critical Reynolds number Rec around 30 is found, above which eddies are generated. Experiments (iv) demonstrate that even after the collapse of MOC in the Northern Hemisphere, eddies can still be generated and carry energy across the equator into the Northern Hemisphere; these eddies act to attenuate the impact of the MOC shutdown on short time scales. The results described here may be particularly pertinent to ocean general circulation models in which the Reynolds number lies close to the bifurcation point separating the laminar and turbulent regimes.
Improving Global Model Precipitation Forecasts over India Using Downscaling and the FSU Superensemble. Part I: 1–5-Day Forecasts
Authors: Krishnamurti T. N. , Mishra A. K. , Chakraborty A. , Rajeevan M. 
Published: May 2009

Abstract
The availability of daily observed rainfall estimates at a resolution of 0.5° × 0.5° latitude–longitude from a collection of over 2100 rain gauge sites over India provided the possibility for carrying out 5-day precipitation forecasts using a downscaling and a multimodel superensemble methodology. This paper addresses the forecast performances and regional distribution of predicted monsoon rains from the downscaling and from the addition of a multimodel superensemble. The extent of rainfall prediction improvements that arise above those of a current suite of operational models are discussed. The design of two algorithms one for downscaling and the other for the construction of multimodel superensembles are both based on the principle of least squares minimization of errors. That combination is shown to provide a robust forecast product through day 5 of the forecast for regional rains over the Indian monsoon region. The equitable threat scores from the downscaled superensemble over India well exceed those noted from the conventional superensemble and member models at current operational large-scale resolution.
On the Deterministic Observation Impact Guidance: A Geometrical Perspective
Authors: Daescu Dacian N. 
Published: May 2009

Abstract
An optimal use of the atmospheric data in numerical weather prediction requires an objective assessment of the value added by observations to improve the analyses and forecasts of a specific data assimilation system (DAS). This research brings forward the issue of uncertainties in the assessment of observation values based on deterministic observation impact (OBSI) estimations using observing system experiments (OSEs) and the adjoint-DAS framework. The state-to-observation space uncertainty propagation as a result of the errors in the verification state is investigated. For a quadratic forecast error measure, a geometrical perspective is used to provide insight and to convey some of the key aspects of this research. The study is specialized to a DAS implementing a linear analysis scheme and numerical experiments are presented using the Lorenz 40-variable model.
An MJO Simulated by the NICAM at 14- and 7-km Resolutions
Authors: Liu Ping , Satoh Masaki , Wang Bin , Fudeyasu Hironori , Nasuno Tomoe , Li Tim , Miura Hiroaki , Taniguchi Hiroshi , Masunaga Hirohiko , Fu Xiouhua , Annamalai H. 
Published: May 2009

Abstract
This study discloses detailed Madden–Julian oscillation (MJO) characteristics in the two 30-day integrations of the global cloud-system-resolving Nonhydrostatic Icosahedral Atmospheric Model (NICAM) using the all-season real-time multivariate MJO index of Wheeler and Hendon. The model anomaly is derived by excluding the observed climatology because the simulation is sufficiently realistic. Results show that the MJO has a realistic evolution in amplitude pattern, geographical locations, eastward propagation, and baroclinic- and westward-tilted structures. In the central Indian Ocean, convection develops with the low-level easterly wind anomaly then matures where the low-level easterly and westerly anomalies meet. Anomalous moisture tilts slightly with height. In contrast, over the western Pacific, the convection grows with a low-level westerly anomaly. Moisture fluctuations, leading convection in eastward propagation, tilt clearly westward with height. The frictional moisture convergence mechanism operates to maintain the MJO. Such success can be attributed to the explicit representation of the interactions between convection and large-scale circulations. The simulated event, however, grows faster in phases 2 and 3, and peaks with 30% higher amplitude than that observed, although the 7-km version shows slight improvement. The fast-growth phases are induced by the fast-growing low-level convergence in the Indian Ocean and the strongly biased ITCZ in the west Pacific when the model undergoes a spinup. The simulated OLR has a substantial bias in the tropics. Possible solutions to the deficiencies are discussed.
Gait adjustments in obstacle crossing, gait initiation and gait termination after a recent lower limb amputation
Authors: Vrieling Aline H , van Keeken Helco G , Schoppen Tanneke , Hof At L , Otten Bert , Halbertsma Jan PK , Postema Klaas 
Published: May 2009

Objective: To describe the adjustments in gait characteristics of obstacle crossing, gait initiation and gait termination that occur in subjects with a recent lower limb amputation during the rehabilitation process. Design: Prospective and descriptive study. Subjects: Fourteen subjects with a recent transfemoral, knee disarticulation or transtibial amputation. Methods: Subjects stepped over an obstacle and initiated and terminated gait at four different times during the rehabilitation process. Outcome measures: Success rate, gait velocity and lower limb joint angles in obstacle crossing, centre of pressure shift and peak anteroposterior ground reaction force in gait initiation and termination. Results: In obstacle crossing amputees increased success rate, gait velocity and swing knee flexion of the prosthetic limb. Knee flexion in transfemoral and knee disarticulation amputees was not sufficient for safe obstacle crossing, which resulted in a circumduction strategy. In gait initiation and termination amputees increased the anteroposterior ground reaction force and the centre of pressure shift in the mediolateral direction in both tasks. Throughout the rehabilitation process the centre of pressure was shifted anteriorly before single-limb stance on the trailing prosthetic limb in gait initiation, whereas in gait termination the centre of pressure in single-limb stance remained posterior when leading with the prosthetic limb. Conclusion: Subjects with a recent amputation develop adjustment strategies to improve obstacle crossing, gait initiation and gait termination. Innovations in prosthetic design or training methods may ease the learning process of these tasks.
Follicular lymphomas with and without translocation t(14;18) differ in gene expression profiles and genetic alterations
Authors: Leich Ellen , Salaverria Itziar , Bea Silvia , Zettl Andreas , Wright George , Moreno Victor , Gascoyne Randy D. , Chan Wing-Chung , Braziel Rita M. , Rimsza Lisa M. , Weisenburger Dennis D. , Delabie Jan , Jaffe Elaine S. , Lister Andrew , Fitzgibbon Jude , Staudt Louis M. , Hartmann Elena M. , Mueller-Hermelink Hans-Konrad , Campo Elias , Ott German , Rosenwald Andreas 
Published: May 2009

AbstractFollicular lymphoma (FL) is genetically characterized by the presence of the t(14;18)(q32;q21) chromosomal translocation in approximately 90% of cases. In contrast to FL carrying the t(14;18), their t(14;18)-negative counterparts are less well studied about their immunohistochemical, genetic, molecular, and clinical features. Within a previously published series of 184 FLs grades 1 to 3A with available gene expression data, we identified 17 FLs lacking the t(14;18). Comparative genomic hybridization and high-resolution single nucleotide polymorphism (SNP) array profiling showed that gains/amplifications of the BCL2 gene locus in 18q were restricted to the t(14;18)-positive FL subgroup. A comparison of gene expression profiles showed an enrichment of germinal center B cell–associated signatures in t(14;18)-positive FL, whereas activated B cell–like, NFκB, proliferation, and bystander cell signatures were enriched in t(14;18)-negative FL. These findings were confirmed by immunohistochemistry in an independent validation series of 84 FLs, in which 32% of t(14;18)-negative FLs showed weak or absent CD10 expression and 91% an increased Ki67 proliferation rate. Although overall survival did not differ between FL with and without t(14;18), our findings suggest distinct molecular features of t(14;18)-negative FL.
Emerging potential of transposons for gene therapy and generation of induced pluripotent stem cells
Authors: VandenDriessche Thierry , Ivics Zoltán , Izsvák Zsuzsanna , Chuah Marinee K. L. 
Published: May 2009

AbstractEffective gene therapy requires robust delivery of the desired genes into the relevant target cells, long-term gene expression, and minimal risks of secondary effects. The development of efficient and safe nonviral vectors would greatly facilitate clinical gene therapy studies. However, nonviral gene transfer approaches typically result in only limited stable gene transfer efficiencies in most primary cells. The use of nonviral gene delivery approaches in conjunction with the latest generation transposon technology based on Sleeping Beauty (SB) or piggyBac transposons may potentially overcome some of these limitations. In particular, a large-scale genetic screen in mammalian cells yielded a novel hyperactive SB transposase, resulting in robust and stable gene marking in vivo after hematopoietic reconstitution with CD34+ hematopoietic stem/progenitor cells in mouse models. Moreover, the first-in-man clinical trial has recently been approved to use redirected T cells engineered with SB for gene therapy of B-cell lymphoma. Finally, induced pluripotent stem cells could be generated after genetic reprogramming with piggyBac transposons encoding reprogramming factors. These recent developments underscore the emerging potential of transposons in gene therapy applications and induced pluripotent stem generation for regenerative medicine.
GAGE: generally applicable gene set enrichment for pathway analysis
Authors: Luo Weijun , Friedman Michael S , Shedden Kerby , Hankenson Kurt D , Woolf Peter J 
Published: May 2009

AbstractBackgroundGene set analysis (GSA) is a widely used strategy for gene expression data analysis based on pathway knowledge. GSA focuses on sets of related genes and has established major advantages over individual gene analyses, including greater robustness, sensitivity and biological relevance. However, previous GSA methods have limited usage as they cannot handle datasets of different sample sizes or experimental designs.ResultsTo address these limitations, we present a new GSA method called Generally Applicable Gene-set Enrichment (GAGE). We successfully apply GAGE to multiple microarray datasets with different sample sizes, experimental designs and profiling techniques. GAGE shows significantly better results when compared to two other commonly used GSA methods of GSEA and PAGE. We demonstrate this improvement in the following three aspects: (1) consistency across repeated studies/experiments; (2) sensitivity and specificity; (3) biological relevance of the regulatory mechanisms inferred.GAGE reveals novel and relevant regulatory mechanisms from both published and previously unpublished microarray studies. From two published lung cancer data sets, GAGE derived a more cohesive and predictive mechanistic scheme underlying lung cancer progress and metastasis. For a previously unpublished BMP6 study, GAGE predicted novel regulatory mechanisms for BMP6 induced osteoblast differentiation, including the canonical BMP-TGF beta signaling, JAK-STAT signaling, Wnt signaling, and estrogen signaling pathways–all of which are supported by the experimental literature.ConclusionGAGE is generally applicable to gene expression datasets with different sample sizes and experimental designs. GAGE consistently outperformed two most frequently used GSA methods and inferred statistically and biologically more relevant regulatory pathways. The GAGE method is implemented in R in the "gage" package, available under the GNU GPL fromhttp://sysbio.engin.umich.edu/~luow/downloads.php.