bluuebunny/crossref_metadata_2025 huggingface dataset:
A model-based regression test selection approach for embedded applications
Authors: Biswas Swarnendu , Mall Rajib , Satpathy Manoranjan , Sukumaran Srihari
Published: July 2009

Regression test selection techniques for embedded programs have scarcely been reported in the literature. In this paper, we propose a model-based regression test selection technique for embedded programs. Our proposed model, in addition to capturing the data and control dependence aspects, also represents several additional program features that are important for regression test case selection of embedded programs. These features include control flow, exception handling, message paths, task priorities, state information and object relations. We select a regression test suite based on slicing our proposed graph model. We also propose a genetic algorithm-based technique to select an optimal subset of test cases from the set of regression test cases selected after slicing our proposed model.
Use case modeling approach for early aspect acquisition
Authors: Kong Leilei , Yuan Tao
Published: July 2009

In the recent years, use cases have been widely applied in software requirement engineering, and use cases have proven particularly valuable as part of the requirements activities of the software process. Use cases play more and more important roles in some modern software processes and methods. Early aspects are defined as crosscutting concerns in the early life cycle phases including the requirements analysis, domain analysis and architecture design phases. Use case modeling approach which supports the acquisition of early aspects is proposed. It accepted the increment and iteration development ideas of Unified Process. The process of use case modeling is divided by five iterative stages which are called initial use case, basic use case, detailed use case, advanced use case and extend use case. The approach supports the early aspects acquisition at requirements level, and early aspect will be captured by analysis the use case properties with aspect features. Modeling processes of this kind of approach is discussed and applying the approach to a case study and analysis are given. We argue that identification of early aspects supports effective determination of their mapping and influence of artifacts at later development stages.
Dependency oriented complexity metrics to detect rippling related design defects
Authors: Reddy K. Reddy , Rao A. Ananda
Published: July 2009

Even though object oriented software development has gained popularity due to its inherent features, it also throws challenges in early detection of defects during design phase. Detection of design defects helps in performing appropriate refactorings in improving the quality of design. Literature indicates that active research is going on in detecting design defects using metrics. The present paper introduces a set of metrics for detecting defects in object oriented designs caused by the presence of shotgun surgery and divergent change bad smells. These metrics are, dependency oriented complexity metric for structure (DOCMS(R)), dependen-cy oriented complexity metric for an artifact causing ripples (DOCMA(CR)), and dependency oriented complexity metric for an artifact affected by ripples (DOCMA(AR)). The proposed me-trics have been computed for four cases. These metrics are used successfully in detecting design defects and complexity. In the present study DOCMA(CR) metric value indicated the presence of shotgun surgery bad smell, whereas DOCMA(AR) metric value indicated the presence of divergent change bad smell. DOCMS(R) metric value indicated the increase in complexity of structure (ar-chitecture) when the design defects are present. Detecting bad smells helps in performing appropriate refactorings to make the software maintainable and to improve the quality of software.
Graph transformation based reduction analysis of PID
Authors: Ren Sheng-bing , Wang Xi-e , Hu Zhi-gang , Hu Ge , Wang Guo-jun
Published: July 2009

The influence of safety risk assessment is being gradually recog-nized along with increasing importance of system safety. In view of the effectiveness of probabilistic influence diagram (PID) in probability reasoning, PID was introduced into system safety risk assessment. Combining the object-oriented method of PID with the traditional risk analysis method, a model of system safety risk probability was successfully constructed. To support the construc-tion and reduction analysis of PID properly, an editor was designed. The syntax and semantics of the editor were detailed in the paper, and its technical feasibility in risk analysis was demonstrated in a case study. Based on graph transformation and reduction algo-rithms of PID, the visualization and describing ability of reduction analysis of PID has been further strengthened, and its semi-automation is achieved by the editor.
State of the art for risk management in software acquisition
Authors: Calvo-Manzano Villalón Jose A. , Agustín Gonzalo Cuevas , Hurtado Gloria Gasca , San Feliu Gilabert Tomás
Published: July 2009

This paper presents the state of the art for risk management in software acquisition. To determine it, a systematic review protocol for Software Engineering is used. Furthermore, the systematic re-view focuses on identifying initiatives and reports of risk manage-ment proposals for software acquisition in small settings. Results show increasing research in risk management and the need for more in-depth studies.
Leadership and management in software architecture workshop 2009 report
Authors: Bass Len , Berenbach Brian
Published: July 2009

This is a report of a workshop on Leadership and Management in Software Architecture held at ICSE on May 19, 2009.
Service level agreement for multithreaded processors
Authors: Gabor Ron , Mendelson Avi , Weiss Shlomo
Published: July 2009

Multithreading is widely used to increase processor throughput. As the number of shared resources increase, managing them while guaranteeing predicted performance becomes a major problem. Attempts have been made in previous work to ease this via different fairness mechanisms. In this article, we present a new approach to control the resource allocation and sharing via a service level agreement (SLA)-based mechanism; that is, via an agreement in which multithreaded processors guarantee a minimal level of service to the running threads. We introduce a new metric,
C
SLA
, for conformance to SLA in multithreaded processors and show that controlling resources using with SLA allows for higher gains than are achievable by previously suggested fairness techniques. It also permits improving one metric (e.g., power) while maintaining SLA in another (e.g., performance). We compare SLA enforcement to schemes based on other fairness metrics, which are mostly targeted at equalizing execution parameters. We show that using SLA rather than fairness based algorithms provides a range of acceptable execution points from which we can select the point that best fits our optimization target, such as maximizing the weighted speedup (sum of the speedups of the individual threads) or reducing power. We demonstrate the effectiveness of the new SLA approach using switch-on-event (coarse-grained) multithreading. Our weighted speedup improvement scheme successfully enforces SLA while improving the weighted speedup by an average of 10% for unbalanced threads. This result is significant when compared with performance losses that may be incurred by fairness enforcement methods. When optimizing for power reduction in unbalanced threads SLA enforcement reduces the power by an average of 15%. SLA may be complemented by other power reduction methods to achieve further power savings
and
maintain the same service level for the threads. We also demonstrate differentiated SLA, where weighted speedup is maximized while each thread may have a different throughput constraint.
Dynamic warp formation
Authors: Fung Wilson W. L. , Sham Ivan , Yuan George , Aamodt Tor M.
Published: July 2009

Recent advances in graphics processing units (GPUs) have resulted in massively parallel hardware that is easily programmable and widely available in today's desktop and notebook computer systems. GPUs typically use single-instruction, multiple-data (SIMD) pipelines to achieve high performance with minimal overhead for control hardware. Scalar threads running the same computing kernel are grouped together into SIMD batches, sometimes referred to as warps. While SIMD is ideally suited for simple programs, recent GPUs include control flow instructions in the GPU instruction set architecture and programs using these instructions may experience reduced performance due to the way branch execution is supported in hardware. One solution is to add a stack to allow different SIMD processing elements to execute distinct program paths after a branch instruction. The occurrence of diverging branch outcomes for different processing elements significantly degrades performance using this approach. In this article, we propose dynamic warp formation and scheduling, a mechanism for more efficient SIMD branch execution on GPUs. It dynamically regroups threads into new warps on the fly following the occurrence of diverging branch outcomes. We show that a realistic hardware implementation of this mechanism improves performance by 13%, on average, with 256 threads per core, 24% with 512 threads, and 47% with 768 threads for an estimated area increase of 8%.
Tolerating process variations in large, set-associative caches
Authors: Koh Cheng-Kok , Wong Weng-Fai , Chen Yiran , Li Hai
Published: July 2009

One important trend in today's microprocessor architectures is the increase in size of the processor caches. These caches also tend to be set associative. As technology scales, process variations are expected to increase the fault rates of the SRAM cells that compose such caches. As an important component of the processor, the parametric yield of SRAM cells is crucial to the overall performance and yield of the microchip. In this article, we propose a microarchitectural solution, called the buddy cache that permits large, set-associative caches to tolerate faults in SRAM cells due to process variations. In essence, instead of disabling a faulty cache block in a set (as is the current practice), it is paired with another faulty cache block in the same set—the buddy. Although both cache blocks are faulty, if the faults of the two blocks do not overlap, then instead of losing two blocks, buddying will yield a functional block from the nonfaulty portions of the two blocks. We found that with buddying, caches can better mitigate the negative impacts of process variations on performance and yield, gracefully downgrading performance as opposed to catastrophic failure. We will describe the details of the buddy cache and give insights as to why it is both more performance and yield resilient to faults.
FEATUREStories that inspire action
Authors: Hirsch Gary , Robertson Brad
Published: July 2009

Editors' Note: Arts-based brand consultancy On Your Feet explores a structure---"Story Plotter"---for organizational stories that help businesses and brands differentiate themselves from their competition and develop a culture of action.
The simulated car racing competition @ CIG-2008
Authors: Togelius Julian
Published: July 2009

The IEEE Symposium on Computational Intelligence and Games was held in Perth, Western Australia on December 15--18 2008. Over the past four years, this symposium has become the focal point for a community of researchers interested in applying computational intelligence techniques (especially evolutionary computation and neural networks) to games. "Games" in the conference title refers to traditional mathematical games studied in game theory, board games and last but absolutely not least video games.
Free, source-code-available, or proprietary
Authors: Wolf Marty J. , Miller Keith W. , Grodzinsky Frances S.
Published: July 2009

We demonstrate that different categories of software raise different ethical concerns with respect to whether software ought to be Free Software or Proprietary Software. We outline the ethical tension between Free Software and Proprietary Software that stems from the two kinds of licenses. For some categories of software we develop support for normative statements regarding the software development landscape. We claim that as society's use of software changes, the ethical analysis for that category of software must necessarily be repeated. Finally, we make a utilitarian argument that the software development environment should encourage both Free Software and Proprietary Software to flourish.
Mechanisms of Growth and Homeostasis in the Drosophila Wing
Authors: Neto-Silva Ricardo M. , Wells Brent S. , Johnston Laura A.
Published: July 2009

Animal shape and size is controlled with amazing precision during development. External factors such as nutrient availability and crowding can alter overall animal size, but individual body parts scale reproducibly to match the body even with challenges from a changing environment. How is such precision achieved? Here, we review selected research from the last few years in Drosophila—arguably the premier genetic model for the study of animal growth—that sheds light on how body and tissue size are regulated by forces intrinsic to individual organs. We focus on two topics currently under intense study: the influence of pattern regulators on organ and tissue growth and the role of local competitive interactions between cells in tissue homeostasis and final size.
Origins of Abnormal Excitability in Biceps Brachii Motoneurons of Spastic-Paretic Stroke Survivors
Authors: Mottram Carol J. , Suresh Nina L. , Heckman C. J. , Gorassini Monica A. , Rymer William Z.
Published: July 2009

Stroke survivors often exhibit abnormal motoneuron excitability, manifested clinically as spasticity with exaggerated stretch reflexes in resting muscles. We examined whether this abnormal excitability is a result of increased activation of intrinsic voltage-dependent persistent inward currents (PICs) or whether it is a result of enhanced synaptic inputs to the motoneuron. This distinction was made by recording firing rate profiles of pairs of motor units during isometric contractions of elbow flexor muscles. To estimate PIC amplitude, the discharge of the lower-threshold (reporter) motor unit of the pair was used to estimate the synaptic input to the higher-threshold (test) motor unit. The estimated synaptic input required to recruit the test unit was compared with the synaptic input when the test unit was derecruited (Δ F) and this served as an estimate of the intrinsic (PIC) contribution to motoneuron firing. We found that PIC estimates were not larger in spastic-paretic motoneurons (Δ F = 4.0 ± 1.6 pps) compared with contralateral (4.6 ± 1.4 pps) and age-matched healthy control motoneurons (3.8 ± 1.7, all P > 0.1). Instead, following the voluntary contractions, the majority of lower-threshold motor units in spastic-paretic muscles (83%) exhibited spontaneous discharge, compared with 14% of contralateral and 0% of control motor units. Furthermore, there was strong co-modulation of simultaneously active units in spastic muscle. The presence of ongoing, correlated unit activity at “rest,” coupled with firing behavior at recruitment unique to lower-threshold motor units in spastic muscles, suggested that firing changes are likely a result of a low-level depolarizing synaptic drive to the resting motoneuron pool.
Kininogen gene (KNG) variation has a consistent effect on aldosterone response to antihypertensive drug therapy: the GERA study
Authors: Barbalic Maja , Schwartz Gary L. , Chapman Arlene B. , Turner Stephen T. , Boerwinkle Eric
Published: July 2009

Recent experimental and clinical studies suggested that apart from playing an essential role in blood pressure homeostasis, aldosterone is involved in the pathophysiology of cardiovascular and renal diseases by inducing structural changes in the heart, kidney, and vessel wall. The interindividual variation of aldosterone response to antihypertensive treatment is considerable, and is at least partially explained by genetic variation. In this study, we investigated aldosterone response to two antihypertensive drugs—a thiazide diuretic and an angiotensin receptor blocker (ARB). Genetic variations in 50 candidate genes were tested for association with aldosterone response in four independent samples: African American (AA) responders to a diuretic ( n = 289), AA responders to an ARB ( n = 252), European American (EA) responders to a diuretic ( n = 295) and EA responders to an ARB ( n = 300). Linear regression was used to test the association with inclusion of age, sex, and body mass index as covariates. The results indicated the existence of one or more variants in the kininogen gene (KNG) that influence interindividual variation in aldosterone response. The significant association was replicated in three of four studied groups. The single nucleotide polymorphism rs4686799 was associated in AA and EA responders to the diuretic ( P = 0.04 and P = 0.07, respectively), and rs5030062 and rs698078 were significantly associated in EA responders to the diuretic ( P = 0.05 and P = 0.01) and EA responders to the ARB ( P = 0.04 and P = 0.02). Although the clinical implication of KNG gene variation to antihypertensive drug response is yet to be determined, this novel candidate locus provides important new insights into drug response physiology.
Liquorice Health Check, Oro-Dental Implications, and a Case Report
Authors: Touyz Louis Z. G.
Published: July 2009

Liquorice has an active substance, Glycyrrhizin which inhibits the conversion of precursor cortisol to cortisone by inhibiting the enzyme11-betahydroxysteroid dehydrogenase. When imbibed, liquorice acts like hyperaldosteronism which presents with typical symptoms including high blood pressure, low blood potassium, and muscle pain and weakness. This article appraises physiological and pharmacological effects on health of liquorice, critiques products containing liquorice, describes a typical case report of liquorice-induced hypertension, and appraises oral effects from consumption of liquorice products.
Testing Metaphorical Educational FPS Games
Authors: Rankin John R. , Sampayo Vargas Sandra , Taylor Paul F.
Published: July 2009

It is widely recognized that there is value in making use of modern Games Technology in Serious Games for educational purposes in the classroom and yet tools that enable teachers to construct such Educational Serious Games (ESGs) with minimal programming, artistic, or GT skills are not yet widely available. In this paper we investigate the feasibility of employing the FPS game genre for teaching purposes in the classroom. This is done by starting with a typical FPS game and constructing metaphorical correspondences with the desired ESG category. This mapping highlights the mentality level of FPS games and what it would take to modify them towards the level for real knowledge acquisition as in ESGs. By changing the game world rules to correspond with a classroom study area, we create a metaphorical educational FPS game. In this paper we describe two metaphorical educational FPS games and report on preliminary testing of their use in education. If testing of these metaphorical educational FPS games indicates that they would be beneficial in school classes then we intend to pursue the design of software tools and tutorials to enable teachers to develop their own metaphorical educational FPS games in two months or less.
A Framework Combining Delta Event‐Related Oscillations (EROs) and Synchronisation Effects (ERD/ERS) to Study Emotional Processing
Authors: Klados Manousos A. , Frantzidis Christos , Vivas Ana B. , Papadelis Christos , Lithari Chrysa , Pappas Costas , Bamidis Panagiotis D.
Published: July 2009

Event‐Related Potentials (ERPs) or Event‐Related Oscillations (EROs) have been widely used to study emotional processing, mainly on the theta and gamma frequency bands. However, the role of the slow (delta) waves has been largely ignored. The aim of this study is to provide a framework that combines EROs with Event‐Related Desynchronization (ERD)/Event‐Related Synchronization (ERS), and peak amplitude analysis of delta activity, evoked by the passive viewing of emotionally evocative pictures. Results showed that this kind of approach is sensitive to the effects of gender, valence, and arousal, as well as, the study of interhemispherical disparity, as the two‐brain hemispheres interplay roles in the detailed discrimination of gender. Valence effects are recovered in both the central electrodes as well as in the hemisphere interactions. These findings suggest that the temporal patterns of delta activity and the alterations of delta energy may contribute to the study of emotional processing. Finally the results depict the improved sensitivity of the proposed framework in comparison to the traditional ERP techniques, thereby delineating the need for further development of new methodologies to study slow brain frequencies.
An Extragradient Method and Proximal Point Algorithm for Inverse Strongly Monotone Operators and Maximal Monotone Operators in Banach Spaces
Authors: Plubtieng Somyot , Sriprad Wanna
Published: July 2009

We introduce an iterative scheme for finding a common element of the solution set of a maximal monotone operator and the solution set of the variational inequality problem for an inverse strongly-monotone operator in a uniformly smooth and uniformly convex Banach space, and then we prove weak and strong convergence theorems by using the notion of generalized projection. The result presented in this paper extend and improve the corresponding results of Kamimura et al. (2004), and Iiduka and Takahashi (2008). Finally, we apply our convergence theorem to the convex minimization problem, the problem of finding a zero point of a maximal monotone operator and the complementary problem.
Bone Morphogenetic Proteins 2 and 5 Are Down-regulated in Adrenocortical Carcinoma and Modulate Adrenal Cell Proliferation and Steroidogenesis
Authors: Johnsen Inga K. , Kappler Roland , Auernhammer Christoph J. , Beuschlein Felix
Published: July 2009

Bone morphogenetic proteins (BMP) have been shown to affect tumorigenesis in a variety of tumors. Quantitative PCR analysis revealed down-regulation of BMP2 and BMP5 in tissue samples from adrenocortical carcinoma and adrenocortical tumor cell lines compared with normal adrenal glands. Integrity of BMP-dependent pathways in these cell lines could be shown by activation of the Smad1/5/8 pathway with subsequent increase of ID protein expression upon incubation with BMP2 or BMP5. On a functional level, BMP treatment resulted in inhibition of cell proliferation and viability in a dose- and time-dependent manner. This growth inhibitory effect was associated with BMP-dependent reduction of AKT phosphorylation under baseline conditions and under insulin-like growth factor costimulation. Furthermore, steroidogenic function, including melanocortin-2 receptor and steroidogenic enzyme expressions, was profoundly reduced. In vitro demethylation treatment and overexpression of GATA6 resulted in reactivation of BMP-dependent pathways with concomitant modulation of steroidogenesis. Taken together, we show that loss of expression of members of the BMP family of ligands is a common finding in adrenocortical tumors and we provide evidence that BMP-dependent pathways are likely to be involved in the modulation of the malignant and functional phenotype of adrenocortical cancer cells. [Cancer Res 2009;69(14):5784–92]
MicroRNA miR-29 Modulates Expression of Immunoinhibitory Molecule B7-H3: Potential Implications for Immune Based Therapy of Human Solid Tumors
Authors: Xu Hong , Cheung Irene Y. , Guo Hong-Fen , Cheung Nai-Kong V.
Published: July 2009

B7-H3, a surface immunomodulatory glycoprotein, inhibits natural killer cells and T cells. The monoclonal antibody (mAb) 8H9 is specific for 4Ig-B7-H3, the long and principal form of B7-H3. Early results from radioimmunotherapy using 8H9 have shown promise in patients with metastatic solid tumors to the central nervous system. Whereas B7-H3 transcript was ubiquitously expressed in a wide spectrum of human solid tumors as well as human normal tissues, B7-H3 protein was preferentially expressed only in tumor tissues. By quantitative reverse transcription-PCR, all three isoforms of microRNA miR-29 (a, b, and c) were highly expressed in normal tissues. However, they were down-regulated in a broad spectrum of solid tumors, including neuroblastoma, sarcomas, brain tumors, and tumor cell lines. B7-H3 protein expression was inversely correlated with miR-29 levels in both cell lines and tumor tissues tested. Using luciferase reporter assay, miR-29a was shown to directly target B7-H3 3′ untranslated region, and knock-in and knockdown of miR-29a led to down-regulation and up-regulation, respectively, of B7-H3 protein expression. The ability of miR-29 to control B7-H3 protein expression has implications in immune escape by solid tumors. Differential modulation of this key immunoinhibitory molecule in tumor versus normal tissues may advance both cell-mediated immunotherapy and antibody-based targeted strategies using the B7-H3–specific mAb 8H9. [Cancer Res 2009;69(15):6275–81]
The Serine Protease Inhibitor Protease Nexin-1 Controls Mammary Cancer Metastasis through LRP-1–Mediated MMP-9 Expression
Authors: Fayard Bérengère , Bianchi Fabrizio , Dey Julien , Moreno Eliza , Djaffer Sabrina , Hynes Nancy E. , Monard Denis
Published: July 2009

Through their ability to degrade the extracellular matrix, proteases mediate cancer cell invasion and metastasis. Paradoxically, some serine protease inhibitors (serpins) are often overexpressed in human tumors. Using computational analysis, we found that the RNA level of protease nexin-1 (PN-1), a serpin that blocks numerous proteases activity, is significantly elevated in estrogen receptor-α-negative and in high-grade breast cancer. The in silico approach was complemented by mechanistic studies on two mammary cancer cell lines, the PN-1-negative 168FARN cells and the PN-1-positive 4T1 cells, both of which form primary mammary tumors, but only 4T1 tumors are able to metastasize to the lungs. We show that treatment of 168FARN cells with PN-1 stimulates extracellular signal-regulated kinase activation via low-density lipoprotein receptor-related protein-1 (LRP-1) binding, resulting in increased matrix metalloproteinase (MMP)-9 RNA, protein, and secreted activity. PN-1–silenced 4T1 cells express low MMP-9 levels. Moreover, injection of PN-1–silenced cells into mice did not affect 4T1 primary mammary tumor outgrowth; however, the tumors had impaired metastatic potential, which could be restored by reexpressing soluble MMP-9 in the PN-1–silenced 4T1 cells. Thus, using mammary tumor models, we describe a novel pathway whereby the serpin PN-1 by binding LRP-1 stimulates extracellular signal-regulated kinase signaling, MMP-9 expression, and metastatic spread of mammary tumors. Importantly, an analysis of 126 breast cancer patients revealed that those whose breast tumors had elevated PN-1 levels had a significantly higher probability to develop lung metastasis, but not metastasis to other sites, on relapse. These results suggest that PN-1 might become a prognostic marker in breast cancer. [Cancer Res 2009;69(14):5690–8]
Transcriptional Output of the Salvador/Warts/Hippo Pathway Is Controlled in Distinct Fashions in Drosophila melanogaster and Mammalian Cell Lines
Authors: Zhang Xiaomeng , Milton Claire C. , Humbert Patrick O. , Harvey Kieran F.
Published: July 2009

The Salvador/Warts/Hippo (SWH) pathway is an important modulator of organ size, and deregulation of pathway activity can lead to cancer. Several SWH pathway components are mutated or expressed at altered levels in different human tumors including NF2, LATS1, LATS2, SAV1, and YAP. The SWH pathway regulates tissue growth by restricting the activity of the transcriptional coactivator protein known as Yorkie (Yki) in Drosophila melanogaster and Yes-associated protein (YAP) in mammals. Yki/YAP drives tissue growth in partnership with the Scalloped (Sd)/TEAD1-4 transcription factors. Yki/YAP also possesses two WW domains, which contact several proteins that have been suggested to either promote or inhibit the ability of Yki to induce transcription. To investigate the regulatory role of the Yki/YAP WW domains, we analyzed the functional consequence of mutating these domains. WW domain mutant YAP promoted transformation and migration of breast epithelial cells with increased potency, suggesting that WW domains mediate the inhibitory regulation of YAP in these cells. By contrast, the WW domains were required for YAP to promote NIH-3T3 cell transformation and for the ability of Yki to drive tissue growth in D. melanogaster and optimally activate Sd. This shows that Yki/YAP WW domains have distinct regulatory roles in different cell types and implies the existence of proteins that promote tissue growth in collaboration with Yki and Sd. [Cancer Res 2009;69(15):6033–41]
Progressive Tumor Formation in Mice with Conditional Deletion of TGF-β Signaling in Head and Neck Epithelia Is Associated with Activation of the PI3K/Akt Pathway
Authors: Bian Yansong , Terse Anita , Du Juan , Hall Bradford , Molinolo Alfredo , Zhang Pin , Chen Wanjun , Flanders Kathleen C. , Gutkind J. Silvio , Wakefield Lalage M. , Kulkarni Ashok B.
Published: July 2009

The precise role of transforming growth factor (TGF)-β signaling in head and neck squamous cell carcinoma (SCC) is not yet fully understood. Here, we report generation of an inducible head- and neck-specific knockout mouse model by crossing TGF-β receptor I (Tgfbr1) floxed mice with K14-CreERtam mice. By applying tamoxifen to oral cavity of the mouse to induce Cre expression, we were able to conditionally delete Tgfbr1 in the mouse head and neck epithelia. On tumor induction with 7,12-dimethylbenz(a)anthracene (DMBA), 45% of Tgfbr1 conditional knockout (cKO) mice (n = 42) developed SCCs in the head and neck area starting from 16 weeks after treatment. However, no tumors were observed in the control littermates. A molecular analysis revealed an enhanced proliferation and loss of apoptosis in the basal layer of the head and neck epithelia of Tgfbr1 cKO mice 4 weeks after tamoxifen and DMBA treatment. The most notable finding of our study is that the phosphoinositide 3-kinase (PI3K)/Akt pathway was activated in SCCs that developed in the Tgfbr1 cKO mice on inactivation of TGF-β signaling through Smad2/3 and DMBA treatment. These observations suggest that activation of Smad-independent pathways may contribute cooperatively with inactivation of Smad-dependent pathways to promote head and neck carcinogenesis in these mice. Our results revealed the critical role of the TGF-β signaling pathway and its cross-talk with the PI3K/Akt pathway in suppressing head and neck carcinogenesis. [Cancer Res 2009;69(14):5918–26]
High Efficacy of a Listeria-Based Vaccine against Metastatic Breast Cancer Reveals a Dual Mode of Action
Authors: Kim Sun Hee , Castro Francisco , Paterson Yvonne , Gravekamp Claudia
Published: July 2009

Most cancer vaccines induce CTL responses to tumor-associated antigens (TAA). Killing of tumor cells occurs through TAA-specific CTL-mediated cytolysis. Here, we show that one preventive followed by two therapeutic immunizations with an attenuated Listeria monocytogenes (LM)–based vaccine eradicates all metastases and almost the entire primary tumor in the syngeneic, aggressive mouse breast tumor model 4T1. We provide strong evidence that this is due to the combined result of direct kill by Listeria infecting the tumor cells and by CTL responses against Listeria antigens. We showed by electron microscopy that LM expressing truncated listeriolysin O (LLO) and amino acid fragments 311 to 660 of TAA Mage-b (LM-LLO-Mage-b311-660) and the control strain LM-LLO infect tumor cells in vitro and in vivo. In vitro data indicate that tumor cell death occurs through activation of NADP+ oxidase and increased intracellular Ca2+ levels, both resulting in the production of high ROS levels. Because both LM-LLO and LM-LLO-Mage-b311-660 showed equally strong efficacies in vivo, we concluded that LM-LLO was crucial and Mage-b was of less importance. We found strong CTL responses to LM-LLO in the spleen, and depletion of CD8 T cells in vivo resulted in significant tumor regrowth (52%) in LM-LLO–vaccinated mice, indicating that LM-LLO–specific CTL indeed partially contributed to tumor cell kill in vivo. This dual mode of action of a Listeria-based vaccine has not been described before and may provide new directions in the development of more effective vaccines against metastatic breast cancer. [Cancer Res 2009;69(14):5860–6]
Biochemical, Cellular, and In vivo Activity of Novel ATP-Competitive and Selective Inhibitors of the Mammalian Target of Rapamycin
Authors: Yu Ker , Toral-Barza Lourdes , Shi Celine , Zhang Wei-Guo , Lucas Judy , Shor Boris , Kim Jamie , Verheijen Jeroen , Curran Kevin , Malwitz David J. , Cole Derek C. , Ellingboe John , Ayral-Kaloustian Semiramis , Mansour Tarek S. , Gibbons James J. , Abraham Robert T. , Nowak Pawel , Zask Arie
Published: July 2009

The mammalian target of rapamycin (mTOR) is centrally involved in cell growth, metabolism, and angiogenesis. While showing clinical efficacy in a subset of tumors, rapamycin and rapalogs are specific and allosteric inhibitors of mTOR complex 1 (mTORC1), but they do not directly inhibit mTOR complex 2 (mTORC2), an emerging player in cancer. Here, we report chemical structure and biological characterization of three pyrazolopyrimidine ATP-competitive mTOR inhibitors, WAY-600, WYE-687, and WYE-354 (IC50, 5–9 nmol/L), with significant selectivity over phosphatidylinositol 3-kinase (PI3K) isofoms (>100-fold). Unlike the rapalogs, these inhibitors acutely blocked substrate phosphorylation by mTORC1 and mTORC2 in vitro and in cells in response to growth factor, amino acids, and hyperactive PI3K/AKT. Unlike the inhibitors of PI3K or dual-pan PI3K/mTOR, cellular inhibition of P-S6K1(T389) and P-AKT(S473) by the pyrazolopyrimidines occurred at significantly lower inhibitor concentrations than those of P-AKT(T308) (PI3K-PDK1 readout), showing mTOR selectivity in cellular setting. mTOR kinase inhibitors reduced AKT downstream function and inhibited proliferation of diverse cancer cell lines. These effects correlated with a strong G1 cell cycle arrest in both the rapamycin-sensitive and rapamycin-resistant cells, selective induction of apoptosis, repression of global protein synthesis, and down-regulation of angiogenic factors. When injected into tumor-bearing mice, WYE-354 inhibited mTORC1 and mTORC2 and displayed robust antitumor activity in PTEN-null tumors. Together, our results highlight mechanistic differentiation between rapalogs and mTOR kinase inhibitors in targeting cancer cell growth and survival and provide support for clinical development of mTOR kinase inhibitors as new cancer therapy. [Cancer Res 2009;69(15):OF6232–9]
Reactivation of Androgen Receptor–Regulated TMPRSS2:ERG Gene Expression in Castration-Resistant Prostate Cancer
Authors: Cai Changmeng , Wang Hongyun , Xu Youyuan , Chen Shaoyong , Balk Steven P.
Published: July 2009

It seems clear that androgen receptor (AR)–regulated expression of the TMPRSS2:ERG fusion gene plays an early role in prostate cancer (PC) development or progression, but the extent to which TMPRSS2:ERG is down-regulated in response to androgen deprivation therapy (ADT) and whether AR reactivates TMPRSS2:ERG expression in castration-resistant PC (CRPC) have not been determined. We show that ERG message levels in TMPRSS2:ERG fusion-positive CRPC are comparable with the levels in fusion gene–positive primary PC, consistent with the conclusion that the TMPRSS2:ERG expression is reactivated by AR in CRPC. To further assess whether TMPRSS2:ERG expression is initially down-regulated in response to ADT, we examined VCaP cells, which express the TMPRSS2:ERG fusion gene, and xenografts. ERG message and protein rapidly declined in response to removal of androgen in vitro and castration in vivo. Moreover, as observed in the clinical samples, ERG expression was fully restored in the VCaP xenografts that relapsed after castration, coincident with AR reactivation. AR reactivation in the relapsed xenografts was also associated with marked increases in mRNA encoding AR and androgen synthetic enzymes. These results show that expression of TMPRSS2:ERG, similarly to other AR-regulated genes, is restored in CRPC and may contribute to tumor progression. [Cancer Res 2009;69(15):6027–32]
Fibulin-5 Suppresses Lung Cancer Invasion by Inhibiting Matrix Metalloproteinase-7 Expression
Authors: Yue Wen , Sun Quanhong , Landreneau Rodney , Wu Chuanyue , Siegfried Jill M. , Yu Jian , Zhang Lin
Published: July 2009

The high mortality rate of lung cancer is largely due to the spread of disease to other organs. However, the molecular changes driving lung cancer invasion and metastasis remain unclear. In this study, we identified fibulin-5, a vascular ligand for integrin receptors, as a suppressor of lung cancer invasion and metastasis. Fibulin-5 was silenced by promoter hypermethylation in a majority of lung cancer cell lines and primary tumors. It inhibited lung cancer cell invasion and down-regulated matrix metalloproteinase-7 (MMP-7), which promoted lung cancer cell invasion. Knockdown of fibulin-5 was sufficient to stimulate cell invasion and MMP-7 expression. The expression levels of fibulin-5 and MMP-7 were inversely correlated in lung tumors. Suppression of MMP-7 expression by fibulin-5 was mediated by an integrin-binding RGD motif via the extracellular signal-regulated kinase (ERK) pathway. Furthermore, overexpression of fibulin-5 in H460 lung cancer cells inhibited metastasis in mice. Collectively, these results suggest that epigenetic silencing of fibulin-5 promotes lung cancer invasion and metastasis by activating MMP-7 expression through the ERK pathway. [Cancer Res 2009;69(15):6339–46]
Cytogenetic and cDNA Microarray Expression Analysis of MCF10 Human Breast Cancer Progression Cell Lines
Authors: Marella Narasimharao V. , Malyavantham Kishore S. , Wang Jianmin , Matsui Sei-ichi , Liang Ping , Berezney Ronald
Published: July 2009

We used a combination of spectral karyotyping, array comparative genomic hybridization, and cDNA microarrays to gain insights into the structural and functional changes of the genome in the MCF10 human breast cancer progression model cell lines. Spectral karyotyping data showed several chromosomal aberrations and array comparative genomic hybridization analysis identified numerous genomic gains and losses that might be involved in the progression toward cancer. Analysis of the expression levels of genes located within these genomic regions revealed a lack of correlation between chromosomal gains and losses and corresponding up-regulation or down-regulation for the majority of the ∼1,000 genes analyzed in this study. We conclude that other mechanisms of gene regulation that are not directly related to chromosomal gains and losses play a major role in breast cancer progression. [Cancer Res 2009;69(14):5946–53]
Epstein-Barr Virus Latent Membrane Protein-1 Effects on Junctional Plakoglobin and Induction of a Cadherin Switch
Authors: Shair Kathy H.Y , Schnegg Caroline I. , Raab-Traub Nancy
Published: July 2009

Latent membrane protein-1 (LMP1) is considered the major oncoprotein of Epstein-Barr virus and is frequently expressed in nasopharyngeal carcinoma (NPC). LMP1 promotes growth and migration of epithelial cells, and the loss of plakoglobin has been identified as a contributing factor to LMP1-induced migration. Plakoglobin is a junctional protein that can also serve as a transcription factor in Tcf/Lef signaling. To determine the effects of LMP1 on the molecular and functional properties of plakoglobin, LMP1 was overexpressed in the NPC cell line C666-1. LMP1 did not affect plakoglobin stability but did decrease plakoglobin transcription. The resultant decreased levels of nuclear plakoglobin did not affect Tcf/Lef activity or the amount of plakoglobin bound to Tcf4. Although LMP1 induced and stabilized β-catenin, a protein with common binding partners to plakoglobin, the loss of plakoglobin did not affect its association with Tcf4. However, LMP1 did induce a cadherin switch from E- to N-cadherin, a process involved in cancer progression, and enhanced the association of junctional β-catenin with N-cadherin. LMP1 decreased overall levels of junctional plakoglobin but the remaining junctional plakoglobin was found associated with the induced N-cadherin. This increased association of junctional plakoglobin with N-cadherin was a distinguishing feature of LMP1-expressing cells that have reduced migration due to restoration of plakoglobin. Low levels of plakoglobin were also detected in human NPC tissues. These findings reveal that the effects of LMP1 on junctional plakoglobin and the initiation of a cadherin switch likely contribute to metastasis of NPC. [Cancer Res 2009;69(14):5734–42]
Tumor Necrosis Factor-α and Interleukin-1 Antagonists Alleviate Inflammatory Skin Changes Associated with Epidermal Growth Factor Receptor Antibody Therapy in Mice
Authors: Surguladze David , Deevi Dhanvanthri , Claros Nidia , Corcoran Erik , Wang Su , Plym Mary Jane , Wu Yan , Doody Jacqueline , Mauro David J. , Witte Larry , Busam Klaus J. , Pytowski Bronek , Rodeck Ulrich , Tonra James R.
Published: July 2009

Cancer patients receiving epidermal growth factor receptor (EGFR) antibody therapy often experience an acneiform rash of uncertain etiology in skin regions rich in pilosebaceous units. Currently, this condition is treated symptomatically with very limited, often anecdotal success. Here, we show that a monoclonal antibody targeting murine EGFR, ME1, caused a neutrophil-rich hair follicle inflammation in mice, similar to that reported in patients. This effect was preceded by the appearance of lipid-filled hair follicle distensions adjacent to enlarged sebaceous glands. The cytokine tumor necrosis factor-α (TNFα), localized immunohistochemically to this affected region of the pilosebaceous unit, was specifically up-regulated by ME1 in skin but not in other tissues examined. Moreover, skin inflammation was reduced by cotreatment with the TNFα signaling inhibitor, etanercept, indicating the involvement of TNFα in this inflammatory process. Interleukin-1, a cytokine that frequently acts in concert with TNFα, is also involved in this process given the efficacy of the interleukin-1 antagonist Kineret. Our results provide a mechanistic framework to develop evidence-based trials for EGFR antibody–induced skin rash in patients with cancer. [Cancer Res 2009;69(14):5643–7]
MicroRNA Classifiers for Predicting Prognosis of Squamous Cell Lung Cancer
Authors: Raponi Mitch , Dossey Lesley , Jatkoe Tim , Wu Xiaoying , Chen Guoan , Fan Hongtao , Beer David G.
Published: July 2009

Non–small cell lung cancer (NSCLC), which is comprised mainly of adenocarcinoma and squamous cell carcinoma (SCC), is the cause of 80% of all lung cancer deaths in the United States. NSCLC is also associated with a high rate of relapse after clinical treatment and, therefore, requires robust prognostic markers to better manage therapy options. The aim of this study was to identify microRNA (miRNA) expression profiles in SCC of the lung that would better predict prognosis. Total RNA from 61 SCC samples and 10 matched normal lung samples was processed for small RNA species and profiled on MirVana miRNA Bioarrays (version 2, Ambion). We identified 15 miRNAs that were differentially expressed between normal lung and SCC, including members of the miR-17-92 cluster and its paralogues. We also identified miRNAs, including miR-155 and let-7, which had previously been shown to have prognostic value in adenocarcinoma. Based on cross-fold validation analyses, miR-146b alone was found to have the strongest prediction accuracy for stratifying prognostic groups at ∼78%. The miRNA signatures were superior in predicting overall survival than a previously described 50-gene prognostic signature. Whereas there was no overlap between the mRNAs targeted by the prognostic miRNAs and the 50-gene expression signature, there was a significant overlap in the corresponding biological pathways, including fibroblast growth factor and interleukin-6 signaling. Our data indicate that miRNAs may have greater clinical utility in predicting the prognosis of patients with squamous cell lung carcinomas than mRNA-based signatures. [Cancer Res 2009;69(14):5776–83]
Modification of Ovarian Cancer Risk by BRCA1/2-Interacting Genes in a Multicenter Cohort of BRCA1/2 Mutation Carriers
Authors: Rebbeck Timothy R. , Mitra Nandita , Domchek Susan M. , Wan Fei , Chuai Shannon , Friebel Tara M. , Panossian Saarene , Spurdle Amanda , Chenevix-Trench Georgia ,   kConFab, Singer Christian F. , Pfeiler Georg , Neuhausen Susan L. , Lynch Henry T. , Garber Judy E. , Weitzel Jeffrey N. , Isaacs Claudine , Couch Fergus , Narod Steven A. , Rubinstein Wendy S. , Tomlinson Gail E. , Ganz Patricia A. , Olopade Olufunmilayo I. , Tung Nadine , Blum Joanne L. , Greenberg Roger , Nathanson Katherine L. , Daly Mary B.
Published: July 2009

Inherited BRCA1/2 mutations confer elevated ovarian cancer risk. Knowledge of factors that can improve ovarian cancer risk assessment in BRCA1/2 mutation carriers is important because no effective early detection for ovarian cancers exists. A cohort of 1,575 BRCA1 and 856 BRCA2 mutation carriers was used to evaluate haplotypes at ATM, BARD1, BRIP1, CTIP, MRE11, NBS1, RAD50, RAD51, and TOPBP1 in ovarian cancer risk. In BRCA1 carriers, no associations were observed with ATM, BARD1, CTIP, RAD50, RAD51, or TOPBP1. At BRIP1, an association was observed for one haplotype with a multiple testing corrected P (Pcorr) = 0.012, although no individual haplotype was significant. At MRE11, statistically significant associations were observed for one haplotype (Pcorr = 0.007). At NBS1, we observed a Pcorr = 0.024 for haplotypes. In BRCA2 carriers, no associations were observed with CTIP, NBS1, RAD50, or TOPBP1. Rare haplotypes at ATM (Pcorr = 0.044) and BARD1 (Pcorr = 0.012) were associated with ovarian cancer risk. At BRIP1, two common haplotypes were significantly associated with ovarian cancer risk (Pcorr = 0.011). At MRE11, we observed a significant haplotype association (Pcorr = 0.012), and at RAD51, one common haplotype was significantly associated with ovarian cancer risk (Pcorr = 0.026). Variants in genes that interact biologically withBRCA1 and/or BRCA2 may be associated with modified ovarian cancer risk in women who carry BRCA1/2 mutations. [Cancer Res 2009;69(14):5801–10]