bluuebunny/crossref_metadata_2025 huggingface dataset:
Algorithm 856
Authors: Gray Genetha A. , Kolda Tamara G.
Published: October 2006

APPSPACK is software for solving unconstrained and bound-constrained optimization problems. It implements an asynchronous parallel pattern search method that has been specifically designed for problems characterized by expensive function evaluations. Using APPSPACK to solve optimization problems has several advantages: No derivative information is needed; the procedure for evaluating the objective function can be executed via a separate program or script; the code can be run serially or in parallel, regardless of whether the function evaluation itself is parallel; and the software is freely available. We describe the underlying algorithm, data structures, and features of APPSPACK version 4.0, as well as how to use and customize the software.
Why spoofing is serious internet fraud
Authors: Dinev Tamara
Published: October 2006

Fake Web sites fool the unwary into divulging personal data, undermining all consumers' trust in e-commerce, no matter how trustworthy the authentic online business truly is.
Who gets spammed?
Authors: Hann Il-Horn , Hui Kai-Lung , Lai Yee-Lin , Lee S.Y.T. , Png I.P.L.
Published: October 2006

Spam is no random event, but specifically targets those with purchasing power.
Upgrading transport protocols using untrusted mobile code
Authors: Patel Parveen , Whitaker Andrew , Wetherall David , Lepreau Jay , Stack Tim
Published: October 2006

In this paper, we present STP, a system in which communicating end hosts use untrusted mobile code to remotely upgrade each other with the transport protocols that they use to communicate. New transport protocols are written in a type-safe version of C, distributed out-of-band, and run in-kernel. Communicating peers select a transport protocol to use as part of a TCP-like connection setup handshake that is backwards-compatible with TCP and incurs minimum connection setup latency. New transports can be invoked by unmodified applications. By providing a late binding of protocols to hosts, STP removes many of the delays and constraints that are otherwise commonplace when upgrading the transport protocols deployed on the Internet. STP is simultaneously able to provide a high level of security and performance. It allows each host to protect itself from untrusted transport code and to ensure that this code does not harm other network users by sending significantly faster than a compliant TCP. It runs untrusted code with low enough overhead that new transport protocols can sustain near gigabit rates on commodity hardware. We believe that these properties, plus compatibility with existing applications and transports, complete the features that are needed to make STP useful in practice.
Model-carrying code
Authors: Sekar R. , Venkatakrishnan V.N. , Basu Samik , Bhatkar Sandeep , DuVarney Daniel C.
Published: October 2006

This paper presents a new approach called
model-carrying code
(MCC) for safe execution of untrusted code. At the heart of MCC is the idea that untrusted code comes equipped with a concise high-level model of its security-relevant behavior. This model helps bridge the gap between high-level security policies and low-level binary code, thereby enabling analyses which would otherwise be impractical. For instance, users can use a fully automated verification procedure to determine if the code satisfies their security policies. Alternatively, an automated procedure can sift through a catalog of acceptable policies to identify one that is compatible with the model. Once a suitable policy is selected, MCC guarantees that the policy will not be violated by the code. Unlike previous approaches, the MCC framework enables code producers and consumers to collaborate in order to achieve safety. Moreover, it provides support for policy selection as well as enforcement. Finally, MCC makes no assumptions regarding the inherent risks associated with untrusted code. It simply provides the tools that enable a consumer to make informed decisions about the risk that he/she is willing to tolerate so as to benefit from the functionality offered by an untrusted application.
Preserving peer replicas by rate-limited sampled voting
Authors: Maniatis Petros , Rosenthal David S. H. , Roussopoulos Mema , Baker Mary , Giuli TJ , Muliadi Yanto
Published: October 2006

The LOCKSS project has developed and deployed in a world-wide test a peer-to-peer system for preserving access to journals and other archival information published on the Web. It consists of a large number of independent, low-cost, persistent web caches that cooperate to detect and repair damage to their content by voting in "opinion polls." Based on this experience, we present a design for and simulations of a novel protocol for voting in systems of this kind. It incorporates rate limitation and intrusion detection to ensure that even some very powerful adversaries attacking over many years have only a small probability of causing irrecoverable damage before being detected.
Samsara
Authors: Cox Landon P. , Noble Brian D.
Published: October 2006

Peer-to-peer storage systems assume that their users consume resources in proportion to their contribution. Unfortunately, users are unlikely to do this without some enforcement mechanism. Prior solutions to this problem require centralized infrastructure, constraints on data placement, or ongoing administrative costs. All of these run counter to the design philosophy of peer-to-peer systems.
Samsara
enforces fairness in peer-to-peer storage systems without requiring trusted third parties, symmetric storage relationships, monetary payment, or certified identities. Each peer that requests storage of another must agree to hold a
claim
in return---a placeholder that accounts for available space. After an exchange, each partner checks the other to ensure faithfulness. Samsara punishes unresponsive nodes
probabilistically
. Because objects are replicated, nodes with transient failures are unlikely to suffer data loss, unlike those that are dishonest or chronically unavailable. Claim storage overhead can be reduced when necessary by forwarding among chains of nodes, and eliminated when cycles are created. Forwarding chains increase the risk of exposure to failure, but such risk is modest under reasonable assumptions of utilization and simultaneous, persistent failure.
Energy-efficient soft real-time CPU scheduling for mobile multimedia systems
Authors: Yuan Wanghong , Nahrstedt Klara
Published: October 2006

This paper presents
GRACE-OS
, an energy-efficient soft real-time CPU scheduler for mobile devices that primarily run multimedia applications. The major goal of GRACE-OS is to support application quality of service and save energy. To achieve this goal, GRACE-OS integrates dynamic voltage scaling into soft real-time scheduling and decides how fast to execute applications in addition to when and how long to execute them. GRACE-OS makes such scheduling decisions based on the probability distribution of application cycle demands, and obtains the demand distribution via online profiling and estimation. We have implemented GRACE-OS in the Linux kernel and evaluated it on an HP laptop with a variable-speed CPU and multimedia codecs. Our experimental results show that (1) the demand distribution of the studied codecs is stable or changes smoothly. This stability implies that it is feasible to perform stochastic scheduling and voltage scaling with low overhead; (2) GRACE-OS delivers soft performance guarantees by bounding the deadline miss ratio under application-specific requirements; and (3) GRACE-OS reduces CPU idle time and spends more busy time in lower-power speeds. Our measurement indicates that compared to deterministic scheduling and voltage scaling, GRACE-OS saves energy by 7% to 72% while delivering statistical performance guarantees.
Implementing an untrusted operating system on trusted hardware
Authors: Lie David , Thekkath Chandramohan A. , Horowitz Mark
Published: October 2006

Recently, there has been considerable interest in providing "trusted computing platforms" using hardware~---~TCPA and Palladium being the most publicly visible examples. In this paper we discuss our experience with building such a platform using a traditional time-sharing operating system executing on XOM~---~a processor architecture that provides copy protection and tamper-resistance functions. In XOM, only the processor is trusted; main memory and the operating system are not trusted.Our operating system (XOMOS) manages hardware resources for applications that don't trust it. This requires a division of responsibilities between the operating system and hardware that is unlike previous systems. We describe techniques for providing traditional operating systems services in this context.Since an implementation of a XOM processor does not exist, we use SimOS to simulate the hardware. We modify IRIX 6.5, a commercially available operating system to create xomos. We are then able to analyze the performance and implementation overheads of running an untrusted operating system on trusted hardware.
Improving the reliability of commodity operating systems
Authors: Swift Michael M. , Bershad Brian N. , Levy Henry M.
Published: October 2006

Despite decades of research in extensible operating system technology, extensions such as device drivers remain a significant cause of system failures. In Windows XP, for example, drivers account for 85% of recently reported failures. This paper describes Nooks, a
reliability subsystem
that seeks to greatly enhance OS reliability by isolating the OS from driver failures. The Nooks approach is practical: rather than guaranteeing complete fault tolerance through a new (and incompatible) OS or driver architecture, our goal is to prevent the
vast majority
of driver-caused crashes with
little or no change
to existing driver and system code. To achieve this, Nooks isolates drivers within lightweight protection domains inside the kernel address space, where hardware and software prevent them from corrupting the kernel. Nooks also tracks a driver's use of kernel resources to hasten automatic clean-up during recovery.To prove the viability of our approach, we implemented Nooks in the Linux operating system and used it to fault-isolate several device drivers. Our results show that Nooks offers a substantial increase in the reliability of operating systems, catching and quickly recovering from many faults that would otherwise crash the system. In a series of 2000 fault-injection tests, Nooks recovered automatically from 99% of the faults that caused Linux to crash.While Nooks was designed for drivers, our techniques generalize to other kernel extensions, as well. We demonstrate this by isolating a kernel-mode file system and an in-kernel Internet service. Overall, because Nooks supports existing C-language extensions, runs on a commodity operating system and hardware, and enables automated recovery, it represents a substantial step beyond the specialized architectures and type-safe languages required by previous efforts directed at safe extensibility.
Review of "The Square Root of 2: A Dialogue Concerning a Number and a Sequence by David Flannery", Copernicus Books, 2006.
Authors: Gasarch William , Kruskal Alexander , Kruskal Justin , Kruskal Rebecca
Published: October 2006

Professor Clyde Kruskal, who works in parallelism, has triplets: Alexander, Justin, and Rebecca Kruskal. They are in 9th grade, have already taken elementary algebra, and are taking Geometry now (this was written in Spring 2006). Professor William Gasarch spoke to them about the square root of 2. What follows is an interpretation of their conversation.
Economic and subjective measures of the perceived value of aesthetics and usability
Authors: Ben-Bassat Tamar , Meyer Joachim , Tractinsky Noam
Published: October 2006

The assessment of the relative value of different design features for users is of great interest for software designers. Users' evaluations are generally measured through questionnaires. We suggest that other evaluation methods, including economic measures, may provide different estimates of the relative value of features. In a laboratory experiment we created four versions of a data-entry application by independently manipulating the system's usability and aesthetics. Users' evaluations of the four experimental systems were obtained in a within-subjects design. In addition, five between-subjects experimental conditions were created, based on the evaluation method (questionnaire alone or auction and questionnaire), monetary incentives (present or absent), and experience in using the system (present or absent). In questionnaire-based responses, the systems' usability affected evaluations of usability as well as aesthetics. Similarly, the systems' aesthetics affected evaluations of both aesthetics and usability. Questionnaire-based evaluations of usability and aesthetics were not affected by experience with the system or by monetary performance incentives. Auction bids were only influenced by the system's usability: bids corresponded to the objective performance levels that could be attained with the different systems. The results suggest that by using economic methods, researchers and practitioners can obtain system evaluations that are strongly related to performance criteria and that may be more valid when the evaluation context favors task-oriented performance.
Reality vs. Perception
Authors: O'Hanlon Charlene
Published: October 2006

October is upon us, the month that celebrates the struggle between perception and reality. Every October 31, children of all ages don costumes and masks in pursuit of receiving treats or playing tricks, trying desperately to fool everyone into thinking they’re a witch or a goblin or a clown instead of a 10-year-old girl or a teenage boy or a middle-aged business executive.
News 2.0
Authors: Stanik John
Published: October 2006

The Mobile Linux Challenge
Calendar
Authors: O'Hanlon Charlene
Published: October 2006

Grace Hopper Celebration of Women in Computing Conference
Automatic rate desynchronization of embedded reactive programs
Authors: Girault Alain , Nicollin Xavier , Pouzet Marc
Published: October 2006

Many embedded reactive programs perform computations at different rates, while still requiring the overall application to satisfy very tight temporal constraints. We propose a method to automatically distribute programs such that the obtained parts can be run at different rates, which we call
rate desynchronization
. We consider general programs whose control structure is a finite state automaton and with a DAG of actions in each state. The motivation is to take into account long-duration tasks inside the programs: these are tasks whose execution time is long compared to the other computations in the application, and whose maximal execution rate is known and bounded. Merely scheduling such a long duration task at a slow rate would not work since the whole program would be slowed down if compiled into sequential code. It would thus be impossible to meet the temporal constraints, unless such long duration tasks could be
desynchronized
from the remaining computations. This is precisely what our method achieves: it distributes the initial program into several parts, so that the parts performing the slow computations can be run at an appropriate rate, therefore not impairing the global reaction time of the program. We present in detail our method, all the involved algorithms, and a small running example. We also compare our method with the related work.
Theory of nearest neighbors indexability
Authors: Shaft Uri , Ramakrishnan Raghu
Published: October 2006

In this article, we consider whether traditional index structures are effective in processing unstable nearest neighbors workloads. It is known that under broad conditions, nearest neighbors workloads become
unstable
---distances between data points become indistinguishable from each other. We complement this earlier result by showing that if the workload for an application is unstable, you are not likely to be able to index it efficiently using (almost all known) multidimensional index structures. For a broad class of data distributions, we prove that these index structures will do no better than a linear scan of the data as dimensionality increases.Our result has implications for how experiments should be designed on index structures such as R-Trees, X-Trees, and SR-Trees: simply put, experiments trying to establish that these index structures scale with dimensionality should be designed to establish
crossover points
, rather than to show that the methods scale to an arbitrary number of dimensions. In other words, experiments should seek to establish the dimensionality of the dataset at which the proposed index structure deteriorates to linear scan, for each data distribution of interest; that linear scan will eventually dominate is a given.An important problem is to analytically characterize the
rate
at which index structures degrade with increasing dimensionality, because the dimensionality of a real data set may well be in the range that a particular method can handle. The results in this article can be regarded as a step toward solving this problem. Although we do not characterize the rate at which a structure degrades, our techniques allow us to reason directly about a broad class of index structures rather than the geometry of the nearest neighbors problem, in contrast to earlier work.
Object feature validation using visual and haptic similarity ratings
Authors: Cooke Theresa , Kannengiesser Sebastian , Wallraven Christian , Bülthoff Heinrich H.
Published: October 2006

The perceived similarity between objects may well vary according to the sensory modality/modalities in which they are experienced, an important consideration for the design of multimodal interfaces. In this study, we present a similarity-based method for comparing the perceptual importance of object properties in touch and in vision and show how the method can also be used to validate computational measures of object properties. Using either vision or touch, human subjects judged the similarity between novel, 3D objects which varied parametrically in shape and texture. Similarities were also computed using a set of state-of-the art 2D and 3D computational measures. Two resolutions of 2D and 3D object data were used for these computations in order to test for scale dependencies. Multidimensional scaling (MDS) was then performed on all similarity data, yielding maps of the stimuli in both perceptual and computational spaces, as well as the relative weight of shape and texture dimensions. For this object set, we found that visual subjects accorded more importance to shape than texture, while haptic subjects weighted them roughly evenly. Fit errors between human and computational maps were then calculated to assess each feature's perceptual validity. Shape-biased features provided good overall fits to the human visual data; however, no single feature yielded a good overall fit to the haptic data, in which we observed large individual differences. This work demonstrates how MDS techniques can be used to evaluate computational object features using the criterion of perceptual similarity. It also demonstrates a way of assessing how the perceptual validity of a feature varies as a function of parameters such as the target modality and the resolution of object data. Potential applications of this method for the design of unimodal and multimodal human---machine interfaces are discussed.
Insulin stimulates muscle protein synthesis in neonates during endotoxemia despite repression of translation initiation
Authors: Orellana Renan A. , Kimball Scot R. , Suryawan Agus , Escobar Jeffery , Nguyen Hanh V. , Jefferson Leonard S. , Davis Teresa A.
Published: October 2006

Skeletal muscle protein synthesis is reduced in neonatal pigs in response to endotoxemia. To examine the role of insulin in this response, neonatal pigs were infused with endotoxin (LPS, 0 and 10 μg·kg−1·h−1), whereas glucose and amino acids were maintained at fasting levels and insulin was clamped at fasting or fed (2 or 10 μU/ml) levels. Fractional rates of protein synthesis and translational control mechanisms were examined in longissimus dorsi muscle and liver. In the presence of fasting insulin, LPS reduced muscle protein synthesis (−29%), and increasing insulin to fed levels accelerated muscle protein synthesis in both groups (controls, +44%; LPS, +64%). LPS, but not insulin, increased liver protein synthesis by +28%. In muscle of fasting neonatal pigs, LPS reduced 4E-BP1 phosphorylation and eIF4E to eIF4G binding. In muscle of controls, but not LPS pigs, raising insulin to fed levels increased 4E-BP1 and S6K1 phosphorylation and eIF4E to eIF4G binding. In muscle and liver, neither LPS nor insulin altered eIF2B activity. eEF2 phosphorylation decreased in response to insulin in both LPS and control animals. The results suggest that, in endotoxemic neonatal animals, the response of protein synthesis to insulin is maintained despite suppression of mTOR-dependent translation initiation and eIF4E availability for eIF4F assembly. Maintenance of an anabolic response to the feeding-induced rise in insulin likely exerts a protective effect for the neonate to the catabolic processes induced by sepsis.
Chronic ethanol feeding to rats decreases adiponectin secretion by subcutaneous adipocytes
Authors: Chen Xiaocong , Sebastian Becky M. , Nagy Laura E.
Published: October 2006

Chronic ethanol feeding to mice and rats decreases serum adiponectin concentration and adiponectin treatment attenuates chronic ethanol-induced liver injury. Although it is clear that lowered adiponectin has pathophysiological importance, the mechanisms by which chronic ethanol decreases adiponectin are not known. Here, we have investigated the impact of chronic ethanol feeding on adiponectin expression and secretion by adipose tissue. Rats were fed a 36% Lieber-DeCarli ethanol-containing liquid diet or pair-fed control diet for 4 wk. Chronic ethanol feeding decreased adiponectin mRNA but had no effect on adiponectin protein in subcutaneous adipose tissue. Chronic ethanol feeding also reduced adiponectin secretion by isolated subcutaneous and retroperitoneal adipocytes despite the maintenance of equivalent intracellular concentrations of adiponectin between subcutaneous adipocytes from ethanol- and pair-fed rats. Treatment with brefeldin A suppressed adiponectin secretion by subcutaneous adipocytes from pair-fed rats but had little effect after ethanol feeding. In subcutaneous adipocytes from pair-fed rats, adiponectin was enriched in endoplasmic reticulum (ER)/Golgi relative to plasma membrane; however, after chronic ethanol feeding, adiponectin was equally distributed between plasma membrane and ER/Golgi fractions. In conclusion, chronic ethanol feeding impaired adiponectin secretion by subcutaneous and retroperitoneal adipocytes; impaired secretion likely contributes to decreased adiponectin concentrations after chronic ethanol feeding.
A threshold exists for the stimulatory effect of insulin on plasmal-carnitine clearance in humans
Authors: Stephens Francis B. , Constantin-Teodosiu Dumitru , Laithwaite David , Simpson Elizabeth J. , Greenhaff Paul L.
Published: October 2006

Maintaining hyperinsulinemia (∼160 mU/l) during steady-state hypercarnitinemia (∼550 μmol/l) increases skeletal muscle total carnitine (TC) content by ∼15% within 5 h. The aim of the present study was to further examine the relationship between serum insulin concentration and skeletal muscle carnitine accumulation by attempting to identify the serum insulin concentration at which this stimulatory effect of insulin on carnitine retention becomes apparent. On four randomized experimental visits, eight healthy men (body mass index 23.8 ± 0.9 kg/m2) underwent a 6-h euglycemic insulin clamp of 5, 30, 55, or 105 mU·m−2·min−1accompanied by a 5-h iv infusion of l-carnitine (15 mg/kg bolus followed by 10 mg·kg−1·h−1). The clamps produced steady-state serum insulin concentrations of 10.1 ± 0.5, 48.8 ± 1.0, 88.9 ± 2.8, and 173.9 ± 6.5 mU/l, respectively. During l-carnitine infusion, plasma TC concentration remained above 450 μmol/l during all four visits. However, there was a significant treatment effect of insulin ( P < 0.001), such that by the end of infusion the plasma TC concentration in the 55- and 105-mU clamps was lower than that seen in the 5- ( P < 0.05 and P < 0.01, respectively) and 30-mU ( P < 0.01) clamps. The findings demonstrate that only high circulating serum insulin concentrations (≥90 mU/l) are capable of stimulating skeletal muscle carnitine accumulation. This is of relevance to athletes, and the treatment of obesity and type 2 diabetes, where increasing skeletal muscle carnitine content may be used as tool to modify skeletal muscle energy metabolism.
Role of noradrenergic pathways in sneeze-induced urethral continence reflex in rats
Authors: Kaiho Yasuhiro , Kamo Izumi , Chancellor Michael B. , Arai Yoichi , de Groat William C. , Yoshimura Naoki
Published: October 2006

To clarify the role of noradrenergic pathways in preventing stress urinary incontinence (SUI) during sneezing, we investigated the effect of the norepinephrine reuptake inhibitor nisoxetine and α-adrenoceptor antagonists phentolamine (nonspecific blocker) and prazosin (α1-receptor-selective blocker) on the neurally evoked urethral continence reflex induced by sneezing in rats. The amplitude of urethral pressure responses during sneezing (A-URS), urethral baseline pressure (UBP) at the midurethra, and sneeze-induced leak point pressure (S-LPP) were measured in normal female adult rats and rats with SUI induced by vaginal distention (VD). In normal rats, intrathecal (it) phentolamine (0.02 nmol) and prazosin (0.02 nmol) decreased A-URS by 11.9 and 15.7%, respectively, without affecting UBP. In both normal and VD rats, intravenous (iv) application of nisoxetine (1 mg/kg) increased A-URS by 17.2 and 18.3% and UBP by 23.7 and 32.7%, respectively. Phentolamine or prazosin (both it) eliminated nisoxetine-induced increases in A-URS, but not the increases in UBP, which were, however, suppressed by iv phentolamine (5 mg/kg) or prazosin (1 mg/kg). Sneezing induced fluid leakage from the urethral orifice in VD rats, but not in normal rats. In VD rats, S-LPP was increased by 30.2% by iv nisoxetine. Application of phentolamine and prazosin (both it) decreased S-LPP by 15.7 and 20.6%, respectively, and nisoxetine induced increases in S-LPP to 13.2 and 12.3%, respectively. These results indicate that activation of the noradrenergic system by a norepinephrine reuptake inhibitor can prevent SUI via α1-adrenoceptors by enhancing the sneeze-induced active urethral closure mechanism at the spinal level and augmenting UBP at the periphery.
HIV infection changes glomerular podocyte cytoskeletal composition and results in distinct cellular mechanical properties
Authors: Tandon R. , Levental I. , Huang C. , Byfield F. J. , Ziembicki J. , Schelling J. R. , Bruggeman L. A. , Sedor J. R. , Janmey P. A. , Miller R. T.
Published: October 2006

In addition to forming the selective filtration barrier for the renal glomerulus, podocytes maintain glomerular capillary architecture by opposing distending hemodynamic forces. To understand the relationship of cytoskeletal properties and the mechanical characteristics of podocytes, we studied filamin expression and distribution and measured cell membrane deformability in conditionally immortalized wild-type (WT) mouse podocytes, and in podocytes derived from a mouse model of HIV-associated nephropathy (HIVAN). In the WT cells, filamin and F-actin were localized at the periphery and in prominent stress fibers. In the HIVAN cells, filamin expression was reduced, and stress fibers were sparse. In a microaspiration assay, HIVAN cells ruptured under minimal negative pressure. Atomic force microscopy demonstrated that the WT cells had a stiffness of 17 kPa, whereas the value for the HIVAN cells was 4 kPa. These results demonstrate that the mechanical properties of WT and HIVAN podocytes are markedly different in a manner that is consistent with differences in the composition and arrangement of their cytoskeletons. The mechanical properties of the WT podocytes suggest that these cells can better maintain capillary integrity than the HIVAN podocytes and implicate pathological assembly of the cytoskeleton as a mechanism of HIVAN.
Identification of calcium-independent phospholipase A2γ in mitochondria and its role in mitochondrial oxidative stress
Authors: Kinsey Gilbert R. , McHowat Jane , Beckett Caroline S. , Schnellmann Rick G.
Published: October 2006

Oxidant-induced lipid peroxidation and cell death mediate pathologies associated with ischemia-reperfusion and inflammation. Our previous work in rabbit renal proximal tubular cells (RPTC) demonstrated that inhibition of Ca2+-independent phospholipase A2(iPLA2) potentiates oxidant-induced lipid peroxidation and necrosis, implicating iPLA2in phospholipid repair. This study was conducted to identify a RPTC mitochondrial PLA2and determine the role of PLA2in oxidant-induced mitochondrial dysfunction. iPLA2activity was detected in Percoll-purified rabbit renal cortex mitochondria (RCM) and in isolated mitochondrial inner membrane fractions from rabbit and human RCM. Immunoblot analysis and inhibitor sensitivity profiles revealed that iPLA2γ is the RCM iPLA2activity. RCM iPLA2activity was enhanced in the presence of ATP and was blocked by the PKCε V1–2 inhibitor. Oxidant-induced mitochondrial lipid peroxidation and swelling were accelerated by pretreatment with R-BEL, but not S-BEL. Furthermore, oxidant treatment of isolated RCM resulted in decreased iPLA2γ activity. These results reveal that RCM iPLA2is iPLA2γ, RCM iPLA2γ is regulated by phosphorylation by PKCε, iPLA2γ protects RCM from oxidant-induced lipid peroxidation and dysfunction, and that a strategy to preserve or enhance iPLA2γ activity may be of therapeutic benefit.
Regulation of Expression of BIK Proapoptotic Protein in Human Breast Cancer Cells: p53-Dependent Induction of BIK mRNA by Fulvestrant and Proteasomal Degradation of BIK Protein
Authors: Hur Jingyung , Bell Daphne W. , Dean Kathleen L. , Coser Kathryn R. , Hilario Pablo C. , Okimoto Ross A. , Tobey Erica M. , Smith Shannon L. , Isselbacher Kurt J. , Shioda Toshi
Published: October 2006

Induction of mRNA for BIK proapoptotic protein by doxorubicin or γ-irradiation requires the DNA-binding transcription factor activity of p53. In MCF7 cells, pure antiestrogen fulvestrant also induces BIK mRNA and apoptosis. Here, we provide evidence that, in contrast to doxorubicin or γ-irradiation, fulvestrant induction of BIK mRNA is not a direct effect of the transcriptional activity of p53, although p53 is necessary for this induction. It is known that p53 up-regulated modulator of apoptosis (PUMA) mRNA is induced directly by the transcriptional activity of p53. Whereas γ-irradiation induced both BIK and PUMA mRNA, only BIK mRNA was induced by fulvestrant. Whereas both fulvestrant and doxorubicin induced BIK mRNA, only doxorubicin enhanced the DNA-binding activity of p53 and induced PUMA mRNA. Small interfering RNA (siRNA) suppression of p53 expression as well as overexpression of dominant-negative p53 effectively inhibited the fulvestrant induction of BIK mRNA, protein, and apoptosis. Transcriptional activity of a 2-kb BIK promoter, which contained an incomplete p53-binding sequence, was not affected by fulvestrant when tested by reporter assay. Fulvestrant neither affected the stability of the BIK mRNA transcripts. Interestingly, other human breast cancer cells, such as ZR75-1, constitutively expressed BIK mRNA even without fulvestrant. In these cells, however, BIK protein seemed to be rapidly degraded by proteasome, and siRNA suppression of BIK in ZR75-1 cells inhibited apoptosis induced by MG132 proteasome inhibitor. These results suggest that expression of BIK in human breast cancer cells is regulated at the mRNA level by a mechanism involving a nontranscriptional activity of p53 and by proteasomal degradation of BIK protein. (Cancer Res 2006; 66(20): 10153-61)
Single-chain Antibodies to the EWS NH2 Terminus Structurally Discriminate between Intact and Chimeric EWS in Ewing's Sarcoma and Interfere with the Transcriptional Activity of EWS In vivo
Authors: Aryee Dave N.T. , Kreppel Michael , Bachmaier Radostina , Üren Aykut , Muehlbacher Karin , Wagner Stefan , Breiteneder Heimo , Ban Jozef , Toretsky Jeffrey A. , Kovar Heinrich
Published: October 2006

The chimeric protein EWS-FLI1, arising from chromosomal translocation in Ewing's sarcoma family tumors (ESFT), acts as an aberrant tumorigenic transcription factor. The transforming activity of EWS-FLI1 minimally requires an ETS DNA binding domain and the EWS NH2 terminus. Proteins interacting with the EWS portion differ between germ-line and chimeric EWS despite their sharing identical sequences in this domain. We explored the use of the phage display technology to isolate anti-EWS-FLI1 specific single-chain antibody fragments (scFvs). Using recombinant EWS-FLI1 as bait, 16 independent specific antibody clones were isolated from combinatorial phage display libraries, of which six were characterized in detail. Despite differing in their complementarity-determining region sequences, all six scFvs bound to the same epitope spanning residues 51 to 75 within the shared minimal transforming EWS domain. Whereas all six scFvs bound efficiently to cellular EWS, reactivity with ESFT-expressed EWS-FLI1 was weak and restricted to denatured protein. One scFv, scFv-I85, when expressed as an intrabody, efficiently suppressed EWS-dependent coactivation of hepatocyte nuclear factor 4– and OCT4-mediated transcription in vivo but no effect on known EWS-FLI1 target genes was observed. These data suggest that a prominent EWS epitope exposed on recombinant EWS-FLI1 structurally differs between germ-line and chimeric EWS in mammalian cells and that this region is functionally involved in the transcriptional activity of EWS. Thus, we have generated a tool that will prove useful to specifically differentiate between normal and rearranged EWS in functional studies. (Cancer Res 2006; 66(20): 9862-9)
Estrogen Receptor-α Phosphorylated at Ser118 Is Present at the Promoters of Estrogen-Regulated Genes and Is Not Altered Due to HER-2 Overexpression
Authors: Weitsman Gregory E. , Li Lin , Skliris George P. , Davie James R. , Ung Kanyarat , Niu Yulian , Curtis-Snell Linda , Tomes Ladislav , Watson Peter H. , Murphy Leigh C.
Published: October 2006

Detection of estrogen receptor (ER)-α phosphorylated at Ser118 (P-Ser118-ER-α) may be an indicator of an intact ligand-dependent ER-α in breast tumors in vivo and may predict responsiveness to endocrine therapy. The current study addresses whether P-Ser118-ER-α is functionally involved in ER target gene transcription and if this is modulated by HER-2 overexpression. Using chromatin immunoprecipitation analysis, P-Ser118-ER-α was found associated with the promoters of several estrogen-regulated genes in MCF-7 breast cancer cells 30 minutes following estrogen treatment. Coactivators AIB1 and p300 were coimmunoprecipitated with P-Ser118-ER-α following estrogen treatment. The overexpression of HER-2 protein in MCF-7 cells did not affect estrogen induction of phosphorylation of Ser118 or its presence at the promoters of several estrogen-regulated genes. U0126, an inhibitor of mitogen-activated protein kinase (MAPK) pathway, had no effect on P-Ser118-ER-α. The lack of effect of HER-2 overexpression on P-Ser118-ER-α expression in cell models is supported by similar levels of expression of P-Ser118-ER-α in ER+/HER-2-overexpressing and ER+/HER-2− breast tumors in vivo. Using inhibitors of cyclin-dependent kinase 7 (Cdk7), [(5,6-dichloro-1-β-d-ribofuranosylbenzimidazole and 2-(R)-1-ethyl-2-hydroxyethylamino)-6-benzylamino-9-isopropylpurine], and IκB kinase-α (IKK-α; BAY-11-7082), we show that IKK-α, but not Cdk7, is at least in part involved in estrogen-mediated phosphorylation at Ser118 in MCF-7 cells. Our data provide direct evidence for a functional role of P-Ser118-ER-α in estrogen-regulated signaling and do not support the hypothesis that resistance of breast tumors to tamoxifen therapy involves ligand independent activation of ER-α due to constitutive phosphorylation of Ser118 by constitutive activation of MAPK pathway. (Cancer Res 2006; 66(20): 10162-70)
A Novel Somatic Mouse Model to Survey Tumorigenic Potential Applied to the Hedgehog Pathway
Authors: Mao Junhao , Ligon Keith L. , Rakhlin Elena Y. , Thayer Sarah P. , Bronson Roderick T. , Rowitch David , McMahon Andrew P.
Published: October 2006

We report a novel mouse model for the generation of sporadic tumors and show the efficiency of this approach by surveying Hedgehog (Hh)–related tumors. Up-regulation of the Hh pathway is achieved by conditionally regulated expression of an activated allele of Smoothened (R26-SmoM2) using either sporadic leakage or global postnatal induction of a ubiquitously expressed inducible Cre transgene (CAGGS-CreER). Following postnatal tamoxifen induction, CAGGS-CreER; R26-SmoM2 mice developed tumors with short latency and high penetrance. All mice exhibited rhabdomyosarcoma and basal cell carcinoma; 40% also developed medulloblastoma. In addition, mice showed a novel pancreatic lesion resembling low-grade mucinous cystic neoplasms in humans. In contrast, widespread activation of SmoM2 in the postnatal prostate epithelium results in no detectable morphologic outcome in 12-month-old mice. Comparison of gene expression profiles among diverse tumors identified several signature genes, including components of platelet-derived growth factor and insulin-like growth factor pathways, which may provide a common mechanistic link to the Hh-related malignancies. This experimental model provides a robust tool for exploring the process of Hh-dependent tumorigenesis and the treatment of such tumors. More generally, this approach provides a genetic platform for identifying tumorigenic potential in putative oncogenes and tumor suppressors and for more effective modeling of sporadic cancers in mice. (Cancer Res 2006; 66(20): 10171-7)
Mutation Accumulation in the Intestine and Colon of Mice Deficient in Two Intracellular Glutathione Peroxidases
Authors: Lee Dong-Hyun , Esworthy R. Steven , Chu Christy , Pfeifer Gerd P. , Chu Fong-Fong
Published: October 2006

Mice deficient in two glutathione peroxidases (GPX), Gpx1 and Gpx2, [Gpx1/2-double knockout (DKO) mice] are prone to ileocolitis on a mixed C57BL/6 and 129S1/SvJ (B6.129) genetic background. We reported previously that ∼25% of B6.129 Gpx1/2-DKO mice develop ileocolonic tumors by 6 to 9 months of age, when their non-DKO littermates [having at least one wild-type (WT) Gpx1 or Gpx2 allele] rarely have inflammation and none have tumors. Because genetic background affects tumor susceptibility, we have generated a B6 Gpx1/2-DKO colony and discovered that these mice have fewer inflammatory cells, milder ileocolitis, and low mortality, and only 2.5% of B6 mice developed tumors. The mutant frequency of a cII reporter gene was about 2- to 3-fold higher in 28-day-old Gpx1/2-DKO and 4-fold higher in 8-month-old Gpx1/2-DKO ileal mucosa than in controls in both genetic backgrounds. In contrast, mutant frequencies in the unaffected B6 liver were not significantly different between WT and Gpx1/2-DKO mice. The mutant frequency of 8-month-old B6.129 Gpx1/2-DKO ileum was 38.94 ± 15.5−5, which was not significantly higher than the age-matched B6 ileum, 25.54 ± 10.33−5. The mutation spectra analysis has shown that B6 Gpx1/2-DKO ileum had a 3-fold increase in small nucleotide deletions at mononucleotide repeats over control B6, which are a signature mutation associated with oxidative stress. Unexpectedly, B6 Gpx1/2-DKO mice had fewer C to T transitions at CpG dinucleotides than the WT B6 (18.0% versus 40.1%; P < 0.001). Our results suggest that inflammation drives gene mutations, which leads to neoplastic transformation of intestinal epithelium in the B6.129 Gpx1/2-DKO mice but rarely in the B6 Gpx1/2-DKO mice. (Cancer Res 2006; 66(20): 9845-51)
Tumor Necrosis Factor–Related Apoptosis-Inducing Ligand Is Required for Tumor Necrosis Factor α–Mediated Sensitization of Human Breast Cancer Cells to Chemotherapy
Authors: Xu Jing , Zhou Jun-Ying , Wu Gen Sheng
Published: October 2006

Tumor necrosis factor α (TNFα) induces apoptosis and sensitizes cancer cells to chemotherapy, but the mechanism underlying its sensitization is not fully understood. Here, we report that TNFα-mediated sensitization of cancer cells to chemotherapy involves activation of the TRAIL pathway. We show that the combined treatment of breast cancer cells with TNFα and Adriamycin significantly increases cell death compared with the treatment with either agent alone. The combined treatment activated both death receptor and mitochondrial apoptotic pathways, whereas Adriamycin alone activated only the mitochondrial pathway, and TNFα failed to activate either. Furthermore, we show that TNFα induces TRAIL through a transcriptional mechanism. Using reporter gene assays in conjunction with chromatin immunoprecipitation assays, we show that TRAIL induction by TNFα is regulated via both nuclear factor-κB and Sp1 binding sites. Importantly, down-regulation of TRAIL by small interfering RNA silencing decreased TNFα-mediated Adriamycin-induced caspase activation and apoptosis, and thus enhanced breast cancer cell resistance to Adriamycin. Collectively, our results suggest that induction of TRAIL by TNFα is critical for sensitization of breast cancer cells to chemotherapy. (Cancer Res 2006; 66(20): 10092-9)
Mammary Stem Cells and Mammopoiesis
Authors: Visvader Jane E. , Lindeman Geoffrey J.
Published: October 2006

The isolation and characterization of mammary stem cells is fundamental to understanding mammary gland development and tissue homeostasis as well as breast oncogenesis. Recent studies have led to the prospective isolation of pluripotential stem cells from the mouse mammary gland through the identification of specific cell-surface markers and transplantation of cells into the mammary stromal microenvironment. A single cell was sufficient to reconstitute a fully developed mammary gland in vivo, indicating that combinatorial activity between independent stem cells is not essential to generate an outgrowth. Here we review the characteristics of mouse mammary stem cells, their estrogen receptor status, and the potential cellular hierarchy that exists within the mammary gland. (Cancer Res 2006; 66(20): 9798-801)
The Farnesoid X Receptor Is Expressed in Breast Cancer and Regulates Apoptosis and Aromatase Expression
Authors: Swales Karen E. , Korbonits Márta , Carpenter Robert , Walsh Desmond T. , Warner Timothy D. , Bishop-Bailey David
Published: October 2006

Bile acids are present at high concentrations in breast cysts and in the plasma of postmenopausal women with breast cancer. The farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily that regulates bile acid homeostasis. FXR was detected in normal and tumor breast tissue, with a high level of expression in ductal epithelial cells of normal breast and infiltrating ductal carcinoma cells. FXR was also present in the human breast carcinoma cells, MCF-7 and MDA-MB-468. Activation of FXR by high concentrations of ligands induced MCF-7 and MDA-MB-468 apoptosis. At lower concentrations that had no direct effect on viability, the FXR agonist GW4064 induced expression of mRNA for the FXR target genes, small heterodimer partner (SHP), intestinal bile acid binding protein, and multidrug resistance–associated protein 2 (MRP-2), and repressed the expression of the SHP target gene aromatase. In contrast to MRP-2, mRNA for the breast cancer target genes MDR-3, MRP-1, and solute carrier transporter 7A5 were decreased. Although multidrug resistance transporters were regulated and are known FXR target genes, GW4064 had no effect on the cell death induced by the anticancer drug paclitaxel. Our findings show for the first time that FXR is expressed in breast cancer tissue and has multiple properties that could be used for the treatment of breast cancer. (Cancer Res 2006; 66(20): 10120-6)
Bromodomain and Histone Acetyltransferase Domain Specificities Control Mixed Lineage Leukemia Phenotype
Authors: Santillan Donna A. , Theisler Catherine M. , Ryan Amanda S. , Popovic Relja , Stuart Tara , Zhou Ming-Ming , Alkan Serhan , Zeleznik-Le Nancy J.
Published: October 2006

A critical unanswered question about mixed lineage leukemia (MLL) is how specific MLL fusion partners control leukemia phenotype. The MLL-cyclic AMP-responsive element binding protein–binding protein (CBP) fusion requires both the CBP bromodomain and histone acetyltransferase (HAT) domain for transformation and causes acute myelogenous leukemia (AML), often preceded by a myelodysplastic phase. We did domain-swapping experiments to define whether unique specificities of these CBP domains drive this specific MLL phenotype. Within MLL-CBP, we replaced the CBP bromodomain or HAT domain with P300/CBP-associated factor (P/CAF) or TAFII250 bromodomains or the P/CAF or GCN5 HAT domains. HAT, but not bromodomain, substitutions conferred enhanced proliferative capacity in vitro but lacked expression of myeloid cell surface markers normally seen with MLL-CBP. Mice reconstituted with domain-swapped hematopoietic progenitors developed different disease from those with MLL-CBP. This included development of lymphoid disease and lower frequency of the myelodysplastic phase in those mice developing AML. We conclude that both the CBP bromodomain and HAT domain play different but critical roles in determining the phenotype of MLL-CBP leukemia. Our results support an important role for MLL partner genes in determining the leukemia phenotype besides their necessity in leukemogenesis. Here, we find that subtleties in MLL fusion protein domain specificity direct cells toward a specific disease phenotype. (Cancer Res 2006; 66(20):10032-9)
p63 Overexpression Induces the Expression of Sonic Hedgehog
Authors: Caserta Tina M. , Kommagani Ramakrishna , Yuan Ziqiang , Robbins David J. , Mercer Carol A. , Kadakia Madhavi P.
Published: October 2006

p63 and p73 are members of the p53 protein family and have been shown to play an important role in cell death, development, and tumorigenesis. In particular, p63 has been shown to be involved in the maintenance of epidermal stem cells and in the stratification of the epidermis. Sonic Hedgehog (Shh) is a morphogen that has also been implicated to play a role in epithelial stem cell proliferation and in the development of organs. Recently, Shh has also been shown to play an important role in the progression of a variety of cancers. In this report, we show that p63 and p73 but not p53 overexpression induces Shh expression. In particular, p63γ and p63β (both TA and ΔN isoforms) and TAp73β isoform induce Shh. Expression of Shh was found to be significantly reduced in mouse embryo fibroblasts obtained from p63−/− mice. The naturally occurring p63 mutant TAp63γ(R279H) and the tumor suppressor protein p14ARF inhibited the TAp63γ-mediated transactivation of Shh. The region −228 to −102 bp of Shh promoter was found to be responsive to TAp63γ-induced transactivation and TAp63γ binds to regions within the Shh promoter in vivo. The results presented in this study implicate p63 in the regulation of the Shh signaling pathway. (Mol Cancer Res 2006;4(10):759–68)