bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modal Interpretation for the Ekman Destabilization of Inviscidly Stable Baroclinic Flow in the Phillips Model
Authors: Swaters Gordon E. 
Published: December 2009

Abstract
Ekman boundary layers can lead to the destabilization of baroclinic flow in the Phillips model that, in the absence of dissipation, is nonlinearly stable in the sense of Liapunov. It is shown that the Ekman-induced instability of inviscidly stable baroclinic flow in the Phillips model occurs if and only if the kinematic phase velocity associated with the dissipation lies outside the interval bounded by the greatest and least neutrally stable Rossby wave phase velocities. Thus, Ekman-induced destabilization does not correspond to a coalescence of the barotropic and baroclinic Rossby modes as in classical inviscid baroclinic instability. The differing modal mechanisms between the two instability processes is the reason why subcritical baroclinic shears in the classical theory can be destabilized by an Ekman layer, even in the zero dissipation limit of the theory.
Stable Shallow Water Vortices over Localized Topography
Authors: Iacono Roberto 
Published: December 2009

Abstract
It is shown that a sufficient condition for stability by P. Ripa, based on the monotonicity of the flow potential vorticity (PV), can be used to prove linear stability of isolated shallow water vortices over localized topographic features. Stable axisymmetric vortices over axisymmetric topography that satisfy Ripa’s condition are explicitly constructed by using a simple two-step, fully analytic approach. First, for a given velocity profile, the topography is found that yields a steady-state, constant-PV solution of the shallow water equations. Then, this topography is slightly modified to obtain new steady solutions, with monotonic PV, that satisfy Ripa’s stability criterion. Application of this procedure shows that modest depressions (elevations) can stabilize cyclones (anticyclones) with small Rossby and large Burger numbers and velocity profiles similar to those observed in mesoscale oceanic vortices. The stabilizing topographic features have radial sizes comparable with that of the vortex (about twice the radius of maximum speed) and maximum vertical size, normalized to the unperturbed fluid depth, from 2 to 3.3 times the Rossby number for the profiles considered. The upper limit corresponds to a Gaussian profile, whereas the lower limit is approached by a velocity profile that is linear inside the vortex core and a cubic polynomial outside.
Finally, it is argued that a similar stabilization mechanism holds for two-dimensional (2D) flows, and a method for the construction of stable 2D shallow water vortices over 2D topography is outlined that is analogous to that used for the axisymmetric problem. In the 2D case, however, it is generally not possible to obtain stable equilibria analytically.
Improving Policy for Stormwater Management: Implications for Climate Change Adaptation
Authors: Tryhorn Lee 
Published: December 2009

Abstract
Lack of local information on climate change impacts is increasingly recognized as an important barrier to progress in adaptation. However, simply providing decision makers with higher-resolution climate information will not ensure successful adaptation. In order for there to be appropriate information uptake and use, it is essential to understand the political constraints and conditions under which decision makers operate. A detailed examination of the current regulatory context in relation to climate and weather impacts can provide insight into the barriers and obstacles affecting decision makers in adaptation endeavors.
This study examines the experiences of the municipalities of Tompkins County, New York, as they attempt to manage stormwater in compliance with federally mandated regulations. The current policies fail to adequately address the fundamental problems affecting local government in New York: fragmented jurisdiction, interagency communication, inability to cope with unfunded mandates, enforcement, and the promotion of informed decision making. The way forward may be the adaptive governance approach for the management of complex environmental issues. This article is intended to serve as an initial model for other university-based researchers that are interested in serving their local communities with weather, climate, and policy research and are willing to engage in the complexities involved.
Constitutively active AKT depletes hematopoietic stem cells and induces leukemia in mice
Authors: Kharas Michael G. , Okabe Rachel , Ganis Jared J. , Gozo Maricel , Khandan Tulasi , Paktinat Mahnaz , Gilliland D. Gary , Gritsman Kira 
Published: December 2009

Abstract
Human cancers, including acute myeloid leukemia (AML), commonly display constitutive phosphoinositide 3-kinase (PI3K) AKT signaling. However, the exact role of AKT activation in leukemia and its effects on hematopoietic stem cells (HSCs) are poorly understood. Several members of the PI3K pathway, phosphatase and tensin homolog (Pten), the forkhead box, subgroup O (FOXO) transcription factors, and TSC1, have demonstrated functions in normal and leukemic stem cells but are rarely mutated in leukemia. We developed an activated allele of AKT1 that models increased signaling in normal and leukemic stem cells. In our murine bone marrow transplantation model using a myristoylated AKT1 (myr-AKT), recipients develop myeloproliferative disease, T-cell lymphoma, or AML. Analysis of the HSCs in myr-AKT mice reveals transient expansion and increased cycling, associated with impaired engraftment. myr-AKT–expressing bone marrow cells are unable to form cobblestones in long-term cocultures. Rapamycin, an inhibitor of the mammalian target of rapamycin (mTOR) rescues cobblestone formation in myr-AKT–expressing bone marrow cells and increases the survival of myr-AKT mice. This study demonstrates that enhanced AKT activation is an important mechanism of transformation in AML and that HSCs are highly sensitive to excess AKT/mTOR signaling.
Graphle: Interactive exploration of large, dense graphs
Authors: Huttenhower Curtis , Mehmood Sajid O , Troyanskaya Olga G 
Published: December 2009

Abstract

Background
A wide variety of biological data can be modeled as network structures, including experimental results (e.g. protein-protein interactions), computational predictions (e.g. functional interaction networks), or curated structures (e.g. the Gene Ontology). While several tools exist for visualizing large graphs at a global level or small graphs in detail, previous systems have generally not allowed interactive analysis of dense networks containing thousands of vertices at a level of detail useful for biologists. Investigators often wish to explore specific portions of such networks from a detailed, gene-specific perspective, and balancing this requirement with the networks' large size, complex structure, and rich metadata is a substantial computational challenge.

Results
Graphle is an online interface to large collections of arbitrary undirected, weighted graphs, each possibly containing tens of thousands of vertices (e.g. genes) and hundreds of millions of edges (e.g. interactions). These are stored on a centralized server and accessed efficiently through an interactive Java applet. The Graphle applet allows a user to examine specific portions of a graph, retrieving the relevant neighborhood around a set of query vertices (genes). This neighborhood can then be refined and modified interactively, and the results can be saved either as publication-quality images or as raw data for further analysis. The Graphle web site currently includes several hundred biological networks representing predicted functional relationships from three heterogeneous data integration systems: S. cerevisiae data from bioPIXIE, E. coli data using MEFIT, and H. sapiens data from HEFalMp.

Conclusions
Graphle serves as a search and visualization engine for biological networks, which can be managed locally (simplifying collaborative data sharing) and investigated remotely. The Graphle framework is freely downloadable and easily installed on new servers, allowing any lab to quickly set up a Graphle site from which their own biological network data can be shared online.
A changing picture of shigellosis in southern Vietnam: shifting species dominance, antimicrobial susceptibility and clinical presentation
Authors: Vinh Ha , Nhu Nguyen Thi Khanh , Nga Tran Vu Thieu , Duy Pham Thanh , Campbell James I , Hoang Nguyen Van Minh , Boni Maciej F , My Phan Vu Tra , Parry Christopher , Nga Tran Thi Thu , Van Minh Pham , Thuy Cao Thu , Diep To Song , Phuong Le Thi , Chinh Mai Thu , Loan Ha Thi , Tham Nguyen Thi Hong , Lanh Mai Ngoc , Mong Bui Li , Anh Vo Thi Cuc , Bay Phan Van Be , Chau Nguyen Van Vinh , Farrar Jeremy , Baker Stephen 
Published: December 2009

Abstract

Background
Shigellosis remains considerable public health problem in some developing countries. The nature of Shigellae suggests that they are highly adaptable when placed under selective pressure in a human population. This is demonstrated by variation and fluctuations in serotypes and antimicrobial resistance profile of organisms circulating in differing setting in endemic locations. Antimicrobial resistance in the genus Shigella is a constant threat, with reports of organisms in Asia being resistant to multiple antimicrobials and new generation therapies.

Methods
Here we compare microbiological, clinical and epidemiological data from patients with shigellosis over three different periods in southern Vietnam spanning14 years.

Results
Our data demonstrates a shift in dominant infecting species (S. flexneri to S. sonnei) and resistance profile of the organisms circulating in southern Vietnam. We find that there was no significant variation in the syndromes associated with either S. sonnei or S. flexneri, yet the clinical features of the disease are more severe in later observations.

Conclusions
Our findings show a change in clinical presentation of shigellosis in this setting, as the disease may be now more pronounced, this is concurrent with a change in antimicrobial resistance profile. These data highlight the socio-economic development of southern Vietnam and should guide future vaccine development and deployment strategies.

Trial Registration
Current Controlled Trials ISRCTN55945881
Nuclear receptor coregulator SNP discovery and impact on breast cancer risk
Authors: Hartmaier Ryan J , Tchatchou Sandrine , Richter Alexandra S , Wang Jay , McGuire Sean E , Skaar Todd C , Rae Jimmy M , Hemminki Kari , Sutter Christian , Ditsch Nina , Bugert Peter , Weber Bernhard HF , Niederacher Dieter , Arnold Norbert , Varon-Mateeva Raymonda , Wappenschmidt Barbara , Schmutzler Rita K , Meindl Alfons , Bartram Claus R , Burwinkel Barbara , Oesterreich Steffi 
Published: December 2009

Abstract

Background
Coregulator proteins are "master regulators", directing transcriptional and posttranscriptional regulation of many target genes, and are critical in many normal physiological processes, but also in hormone driven diseases, such as breast cancer. Little is known on how genetic changes in these genes impact disease development and progression. Thus, we set out to identify novel single nucleotide polymorphisms (SNPs) within SRC-1 (NCoA1), SRC-3 (NCoA3, AIB1), NCoR (NCoR1), and SMRT (NCoR2), and test the most promising SNPs for associations with breast cancer risk.

Methods
The identification of novel SNPs was accomplished by sequencing the coding regions of these genes in 96 apparently normal individuals (48 Caucasian Americans, 48 African Americans). To assess their association with breast cancer risk, five SNPs were genotyped in 1218 familial BRCA1/2-mutation negative breast cancer cases and 1509 controls (rs1804645, rs6094752, rs2230782, rs2076546, rs2229840).

Results
Through our resequencing effort, we identified 74 novel SNPs (30 in NCoR, 32 in SMRT, 10 in SRC-3, and 2 in SRC-1). Of these, 8 were found with minor allele frequency (MAF) >5% illustrating the large amount of genetic diversity yet to be discovered. The previously shown protective effect of rs2230782 in SRC-3 was strengthened (OR = 0.45 [0.21-0.98], p = 0.04). No significant associations were found with the other SNPs genotyped.

Conclusions
This data illustrates the importance of coregulators, especially SRC-3, in breast cancer development and suggests that more focused studies, including functional analyses, should be conducted.
Evaluation of single-nucleotide polymorphism imputation using random forests
Authors: Schwarz Daniel F , Szymczak Silke , Ziegler Andreas , König Inke R 
Published: December 2009

Abstract
Genome-wide association studies (GWAS) have helped to reveal genetic mechanisms of complex diseases. Although commonly used genotyping technology enables us to determine up to a million single-nucleotide polymorphisms (SNPs), causative variants are typically not genotyped directly. A favored approach to increase the power of genome-wide association studies is to impute the untyped SNPs using more complete genotype data of a reference population.
Random forests (RF) provides an internal method for replacing missing genotypes. A forest of classification trees is used to determine similarities of probands regarding their genotypes. These proximities are then used to impute genotypes of untyped SNPs.
We evaluated this approach using genotype data of the Framingham Heart Study provided as Problem 2 for Genetic Analysis Workshop 16 and the Caucasian HapMap samples as reference population. Our results indicate that RFs are faster but less accurate than alternative approaches for imputing untyped SNPs.
The adequacy of policy responses to the treatment needs of South Africans living with HIV (1999‐2008): a case study
Authors: Gow Jeff A 
Published: December 2009

IntroductionSouth Africa has the largest HIV/AIDS epidemic of any country in the world.Case descriptionNational antiretroviral therapy (ART) policy is examined over the period of 1999 to 2008, which coincided with the government of President Thabo Mbeki and his Minister of Health, Dr Manto Tshabalala‐Msimang. The movement towards a national ART programme in South Africa was an ambitious undertaking, the likes of which had not been contemplated before in public health in Africa.Discussion and evaluationOne million AIDS‐ill individuals were targeted to be enrolled in the ART programme by 2007/08. Fewer than 50% of eligible individuals were enrolled. This failure resulted from lack of political commitment and inadequate public health system capacity. The human and economic costs of this failure are large and sobering.ConclusionsThe total lost benefits of ART not reaching the people who need it are estimated at 3.8 million life years for the period, 2000 to 2005. The economic cost of those lost life years over this period has been estimated at more than US$15 billion.
Efficacy and Safety of Pazopanib in Patients With Metastatic Renal Cell Carcinoma
Authors: Hutson Thomas E. , Davis Ian D. , Machiels Jean-Pascal H. , De Souza Paul L. , Rottey Sylvie , Hong Bao-fa , Epstein Richard J. , Baker Katherine L. , McCann Lauren , Crofts Theresa , Pandite Lini , Figlin Robert A. 
Published: December 2009

Purpose Inactivation of the von Hippel-Lindau gene in clear-cell renal cell carcinomas (RCC) leads to overexpression of hypoxia inducible factor, a transcription factor regulating vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) gene expression. Pazopanib, an angiogenesis inhibitor targeting VEGF receptor, PDGF receptor, and c-KIT, was evaluated in patients with RCC. Patients and Methods This phase II study was designed as a randomized discontinuation study but was revised to an open-label study on the recommendation of the data monitoring committee (based on week 12 response rate [RR] of 38% in the first 60 patients). The primary end point was changed from progressive disease rate at 16 weeks postrandomization to RR. Pazopanib 800 mg was administered orally once daily. Pazopanib 800 mg was administered orally once daily. Results The study enrolled 225 patients with metastatic RCC; 155 patients (69%) were treatment naïve, and 70 patients (31%) had received one prior cytokine- or bevacizumab-containing regimen. Overall RR was 35%; median duration of response was 68 weeks. Median progression-free survival (PFS) was 52 weeks. Eastern Cooperative Oncology Group performance status of 0 and time from diagnosis to treatment of more than 1 year were correlated with prolonged PFS. Pazopanib was generally well tolerated. The most common adverse events were diarrhea, fatigue, and hair depigmentation. The most common laboratory abnormalities were elevated AST and ALT. Conclusion Pazopanib demonstrated durable activity in patients with advanced RCC and was generally well tolerated in this population. These findings support the further development of pazopanib in advanced RCC.
Older Breast Cancer Survivors: Geriatric Assessment Domains Are Associated With Poor Tolerance of Treatment Adverse Effects and Predict Mortality Over 7 Years of Follow-Up
Authors: Clough-Gorr Kerri M. , Stuck Andreas E. , Thwin Soe Soe , Silliman Rebecca A. 
Published: December 2009

Purpose To evaluate geriatric assessment (GA) domains in relation to clinically important outcomes in older breast cancer survivors. Methods Six hundred sixty women diagnosed with primary breast cancer in four US geographic regions (Los Angeles, CA; Minnesota; North Carolina; and Rhode Island) were selected with disease stage I to IIIA, age ≥ 65 years at date of diagnosis, and permission from attending physician to contact. Data were collected over 7 years of follow-up from consenting patients' medical records, telephone interviews, physician questionnaires, and the National Death Index. Outcomes included self-reported treatment tolerance and all-cause mortality. Four GA domains were described by six individual measures, as follows: sociodemographic by adequate finances; clinical by Charlson comorbidity index (CCI) and body mass index; function by number of physical function limitations; and psychosocial by the five-item Mental Health Index (MHI5) and Medical Outcomes Study Social Support Survey (MOS-SSS). Associations were evaluated using t tests, χ2 tests, and regression analyses. Results In multivariable regression including age and stage, three measures from two domains (clinical and psychosocial) were associated with poor treatment tolerance; these were CCI ≥ 1 (odds ratio [OR] = 2.49; 95% CI, 1.18 to 5.25), MHI5 score less than 80 (OR = 2.36; 95% CI, 1.15 to 4.86), and MOS-SSS score less than 80 (OR = 3.32; 95% CI, 1.44 to 7.66). Four measures representing all four GA domains predicted mortality; these were inadequate finances (hazard ratio [HR] = 1.89; 95% CI, 1.24 to 2.88; CCI ≥ 1 (HR = 1.38; 95% CI, 1.01 to 1.88), functional limitation (HR = 1.40; 95% CI, 1.01 to 1.93), and MHI5 score less than 80 (HR = 1.34; 95% CI, 1.01 to 1.85). In addition, the proportion of women with these outcomes incrementally increased as the number of GA deficits increased. Conclusion This study provides longitudinal evidence that GA domains are associated with poor treatment tolerance and predict mortality at 7 years of follow-up, independent of age and stage of disease.
Impact of Environmental Tobacco Smoke on the Incidence of Mutations in Epidermal Growth Factor Receptor Gene in Never-Smoker Patients With Non–Small-Cell Lung Cancer
Authors: Lee Young Joo , Cho Byoung Chul , Jee Sun Ha , Moon Jin Wook , Kim Se Kyu , Chang Joon , Chung Kyung Young , Park In Kyu , Choi Sung Ho , Kim Joo-Hang 
Published: December 2009

PurposeActive tobacco smoking has been associated with the incidence of epidermal growth factor receptor (EGFR) mutations. However, the impact of environmental tobacco smoke (ETS) on EGFR mutations has been unknown. We investigated an association between ETS exposure and EGFR mutations in never smokers with non–small-cell lung cancer (NSCLC).Patients and MethodsWe enrolled 179 consecutive never smokers who were newly diagnosed with NSCLC. The history of ETS exposure was obtained with a standardized questionnaire that included exposure period, place, and duration. The nucleotide sequences of exons 18 to 21 on EGFR gene were determined using nested polymerase chain reaction amplification.ResultsThe incidence of EGFR mutations was significantly lower in patients with ETS exposure than in those without (38.5% v 61.4%; P = .008). In a logistic regression model that adjusted for sex and histology, an adjusted odds ratio (AOR) for the risk of EGFR mutations with exposure to ETS was 0.40 (95% CI, 0.20 to 0.81; P = .011). In quartile groups based on total smoker-year, the AORs for the lowest- to highest-quartile groups were 0.59 (95% CI, 0.23 to 1.49), 0.50 (95% CI, 0.17 to 1.50), 0.48 (95% CI, 0.20 to 1.18), and 0.22 (95% CI, 0.08 to 0.62; Ptrend= .028). Among the types of ETS exposure, adulthood ETS and household ETS were significantly associated with the incidence of EGFR mutations. Patients with ETS exposure showed a lower response rate to EGFR tyrosine kinase inhibitors than did patients without ETS exposure (24.6% v 44.8%; P = .053).ConclusionETS exposure is negatively associated with EGFR mutations in never smokers with NSCLC.
Filming Resistance
Authors: el Houri Walid , Saber Dima 
Published: December 2009

The article focuses on Hezbollah's filmed operations as key media texts in the group's discourse of resistance. In 1986 Hezbollah surprised the public with an innovation in their strategies of resistance: their fighters filmed one of their armed operations in the occupied southern Lebanon and broadcast it to the public. This video, followed by numerous others, had an impact on the growing popularity of the movement and, even more so, on the construction of their image in the minds of both their public and the Israeli one.
First broadcast by national media, these videos are now in online archives accessible to anyone at any time through Hezbollah's Internet sites. Stemming from Michel Foucault's and Edward Said's notions of power and knowledge, the article reads these videos as a strategy of resistance and as an attempt at self-representation that defies and inverts the prevalent relation of power and domination. The videos act as a metaphor of empowerment of a dominated self being presented as the “one who sees,” the “one who allows to see,” and the “one who is seen.” Thus they become what Daniel Dayan calls “monstration”: a reality that exists only through the way it is shown.
Metallo-supramolecular Systems for Synergistic Functions Based on Unique Arrangement of Ligation Sites
Authors: Nabeshima Tatsuya , Akine Shigehisa , Ikeda Chusaku , Yamamura Masaki 
Published: December 2009

Abstract
Pseudomacrocyclic compounds with 2,2′-bipyridine subunits and multimetal-assisting functional molecules with salamo and dipyrrin moieties as the N2O2 ligation moieties are described. The unique and suitable arrangement of these ligation units results in highly synergistic functions in the metallo-supramolecular systems.
Gold Nanoclusters as a Catalyst for Intramolecular Addition of Primary Amines to Unactivated Alkenes under Aerobic Conditions
Authors: Kitahara Hiroaki , Sakurai Hidehiro 
Published: December 2009

Abstract
Gold nanoclusters stabilized by the poly(N-vinyl-2-pyrrolidone) hydrophilic polymer (Au:PVP) catalyzed the intramolecular cycloaddition of primary amines to unactivated alkenes in the presence of formic acid derivatives. The reaction proceeded under neutral to slightly acidic conditions in air.