bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving modularity by refactoring code clones
Authors: Yu Liguo , Ramaswamy Srini
Published: April 2008

Modularity is an important principle of software design. It is directly associated with software understandability, maintainability, and reusability. However, as software systems evolve, old code segments are modified / removed and new code segments are added, the original modular design of the program might be distorted. One of the factors that can affect the modularity of the system is the introduction of code clones --- a portion of source code that is identical or similar to another --- in the software evolution process. This paper applies clone detection techniques to study the modularity of Linux. The code clones are first identified using an automatic tool. Then each clone set is analyzed by a domain expert to classify it into one of the three clone concern categories: singular concern, crosscutting concern, and partial concern. Different approaches to dealing with these different categories of code clones are suggested in order to improve modularity.
Optimistic parallelism benefits from data partitioning
Authors: Kulkarni Milind , Pingali Keshav , Ramanarayanan Ganesh , Walter Bruce , Bala Kavita , Chew L. Paul
Published: April 2008

Recent studies of irregular applications such as finite-element mesh generators and data-clustering codes have shown that these applications have a generalized data parallelism arising from the use of iterative algorithms that perform computations on elements of worklists. In some irregular applications, the computations on different elements are independent. In other applications, there may be complex patterns of dependences between these computations.

The Galois system was designed to exploit this kind of irregular data parallelism on multicore processors. Its main features are (i) two kinds of set iterators for expressing worklist-based data parallelism, and (ii) a runtime system that performs optimistic parallelization of these iterators, detecting conflicts and rolling back computations as needed. Detection of conflicts and rolling back iterations requires information from class implementors.

In this paper, we introduce mechanisms to improve the execution efficiency of Galois programs: data partitioning, data-centric work assignment, lock coarsening, and over-decomposition. These mechanisms can be used to exploit locality of reference, reduce mis-speculation, and lower synchronization overhead. We also argue that the design of the Galois system permits these mechanisms to be used with relatively little modification to the user code. Finally, we present experimental results that demonstrate the utility of these mechanisms.
With
Mathematica
and J
Authors: Reiter Cliff
Published: April 2008

Computational exercises and demonstrations appear frequently in the classes that I teach at Lafayette College. The software that I use for in-class demonstrations is usually
Mathematica
[4] or J [3]. I focus on one language or the other throughout the course when I expect the students to develop the ability to make substantial explorations and do independent experimentation. There is an ongoing expectation at Lafayette that
Mathematica
be used in Calculus Classes [2]; I also use
Mathematica
for my Numerical Analysis and Techniques of Math Modeling classes. I use J for teaching Number Theory and Linear Algebra and it is central to my mathematical visualization course that follows the text [6]. However, I always have interest in how the explorations that I do in one language would be done in the other.
Client-server HTTP communications made easy
Authors: Kutinsky Vladimir
Published: April 2008

This article covers the problem of making client requests to Web servers over HTTP. More specifically, this article addresses two interrelated problems, sending data to a Web server using the POST method and processing the request with a CGI script at the server side. The purpose of this work is to provide a basis for understanding how these tasks can be performed in APL. While the proposed solutions are of a general form, the discussion is oriented around working examples, instead of simply providing reference material.

The APL code discussed in the article uses a number of .Net libraries that greatly assist the task of programming and do most of the drudgery work for us, hence the name of the article.
Automatic generation of APL programs
Authors: Alfonseca Manuel
Published: April 2008

This paper describes the use of grammatical evolution to generate APL programs which perform some pre-required function.
A generic language for application-specific flow sampling
Authors: Madhyastha Harsha V. , Krishnamurthy Balachander
Published: April 2008

Flow records gathered by routers provide valuable coarse-granularity traffic information for several measurement-related network applications. However, due to high volumes of traffic, flow records need to be sampled before they are gathered. Current techniques for producing sampled flow records are either focused on selecting flows from which statistical estimates of traffic volume can be inferred, or have simplistic models for applications. Such sampled flow records are not suitable for many applications with more specific needs, such as ones that make decisions across flows

As a first step towards tailoring the sampling algorithm to an application's needs, we design a generic language in which any particular application can express the classes of traffic of its interest. Our evaluation investigates the expressive power of our language, and whether flow records have sufficient information to enable sampling of records of relevance to applications. We use templates written in our custom language to instrument sampling tailored to three different applications--BLINC, Snort, and Bro. Our study, based on month-long datasets gathered at two different network locations, shows that by learning local traffic characteristics we can sample relevant flow records near-optimally with low false negatives in diverse applications
On BGP communities
Authors: Donnet Benoit , Bonaventure Olivier
Published: April 2008

This paper focuses on BGP communities, a particular BGP attribute that has not yet been extensively studied by the research community. It allows an operator to group destinations in a single entity to which the same routing decisions might be applied. In this paper, we show that the usage of this attribute has increased and that it also contributes to routing table growth. In addition, we propose a taxonomy of BGP community attributes to allow operators to better document their communities. We further manually collect information on BGP communities and tag it according to our taxonomy. We show that a large proportion of the BGP communities are used for traffic engineering purposes
You must be joking...
Authors: Faloutsos Michalis
Published: April 2008

For those of us in academia, tenure is great. Unless you don't have it, in which case it pretty much sucks. In fact, it goes beyond sucking: it kills. Mainly your personal life, sometimes your spirit. I claim that assistant professors are an endangered species. Are we heading towards an environmental disaster that is going to destabilize the academic ecosystem or did I just have too much to drink last night? Either way, I think I deserve the Noble prize for Peace.
The CoNEXT shadow TPC
Authors: Bonaventure Olivier , Chaintreau Augustin , Mathy Laurent , Owezarski Philippe
Published: April 2008

This paper claims that Shadow Technical Program Committee (TPC) should be organized on a regular basis for attractive conferences in the networking domain. It helps ensuring that young generations of researchers have experience with the process of reviewing and selecting papers before they actually become part of regular TPCs. We highlight several reasons why a shadow TPC offers a unique educational experience, as compared with the two most traditional learning process: "delegated review" and "learn on the job". We report examples taken from the CoNEXT 2007 shadow TPC and announce the CoNEXT 2008 Shadow TPC
Compact Weighted Composition Operators and Multiplication Operators between Hardy Spaces
Authors: Ueki Sei-Ichiro , Luo Luo
Published: March 2008

We estimate the essential norm of a compact weighted composition operator uCφ acting between different Hardy spaces of the unit ball in ℂN. Also we will discuss a compact multiplication operator between Hardy spaces.
Nicotine Enemas for Active Crohn's Colitis: An Open Pilot Study
Authors: Ingram J. R. , Rhodes J. , Evans B. K. , Thomas G. A. O.
Published: March 2008

Background. Smoking has a detrimental effect in Crohn's disease (CD), but this may be due to factors in smoking other than nicotine. Given that transdermal nicotine benefits ulcerative colitis (UC), and there is a considerable overlap in the treatment of UC and CD, the possible beneficial effect of nicotine has been examined in patients with Crohn's colitis.Aims. To assess the efficacy and safety of nicotine enemas in active Crohn's colitis.Patients. Thirteen patients with active rectosigmoid CD; 3 patients were excluded because they received antibiotics.Methods. Subjects were given 6 mg nicotine enemas, each day for 4 weeks, in an open pilot study. At the beginning and end of the trial, a Crohn's disease activity index (CDAI) score was calculated, sigmoidoscopy was performed, and haematological inflammatory markers measured.Results. Mean CDAI decreased from 202 to 153—the score was reduced in 6 patients, unchanged in 3, and increased in one. Frequency of bowel movements decreased in 8 patients and the sigmoidoscopy grade was reduced in 7. Mean C-reactive protein decreased from 22.0 to 12.3 mg/L. There were no withdrawals due to adverse events.Conclusions. In this relatively small study of patients with active Crohn's colitis, 6 mg nicotine enemas appeared to be of clinical benefit in most patients. They were well tolerated and safe.
The Effect of Tb and Sm Ions on the Photochromic Behavior of Two Spiropyrans of Benzoxazine Series in Solution
Authors: Bakeir Esam , Attia G. M. , Lukyanova Maria , Lukyanov Boris , Abdel-Mottaleb M. S. A.
Published: March 2008

The photochromism of [7′-hydroxy-8′-formyl-3-methyl-4-oxospiro[1,3-benzoxazin-2,2′-[2H-1]benzopyran],SP(I),[7′-hydroxy-8′-formyl-3-benzyl-4-oxospiro[1,3-benzoxazin-2,2′-[2H-1]benzopyran] SP(II) and their coordination with Tb3+and Sm3+ ions have been studied in DMF. UV/vis induced-color development due to heterolytic bond cleavage of SP(I) and SP(II) is greatly influenced by complexation with
the lanthanide ions. The irradiation-induced color enhancement due to ring opening and thermal decoloration of the open forms of SP(I), SP(II) follows first-order kinetics. Physical characteristics of the studied systems such as colorability and relaxation time of thermal bleaching parameters were determined. Moreover, light-energy transfer-induced luminescence of lanthanide ions via coordination with the two
spirobenzoxazines was monitored.
Competition of Lactobacillus paracasei with Salmonella enterica for Adhesion to Caco‐2 Cells
Authors: Jankowska Alicja , Laubitz Daniel , Antushevich Hanna , Zabielski Romuald , Grzesiuk Elżbieta
Published: March 2008

Competition of commensal and probiotic bacteria with pathogens for adhesion and colonization is one of the important protective mechanisms of gastrointestinal tract. In this study, we examined the ability of Lactobacillus paracasei to inhibit the adhesion of pathogenic Salmonella enterica to human colon adenocarcinoma Caco‐2 cells. Caco‐2 cells were grown for 6 or 21 days to obtain nondifferentiated or well‐differentiated cells, respectively. In adhesion experiments, bacteria were added to the cells for 2 or 4 hours. The number of attached bacteria was expressed as colony‐forming units (CFUs), Caco‐2 cells were counted in hematocytometer. Both bacterial strains used adhered better to well‐differentiated than to nondifferentiated Caco‐2 cells, however, the amount of Salmonella adhered to Caco‐2 after 2 hours of contact was 12‐fold higher in comparison to L. paracasei and almost 27‐fold higher after 4 hours of contact. Two types of experiments were done: coincubation (both bacteria were added to Caco‐2 cells simultaneously), and preincubation (L. paracasei was incubated with Caco‐2 cells first, and then S. enterica was added). In coincubation experiment, the presence of L. paracasei decreased S. enterica adhesion by 4‐fold and in preincubation experiment even 7‐fold. Generally, Lactobacillus spent culture supernatants (SCSs) acted weaker as inhibitors of Salmonella adhesion in comparison to the whole L. paracasei culture in coincubation experiment. In conclusion, the displacement of pathogens by lactic acid bacteria and its secretions showed here depends on the time of bacteria‐epithelial cell contact, and also on the stage of Caco‐2 differentiation.
PPAR Genomics and Pharmacogenomics: Implications for Cardiovascular Disease
Authors: Cresci Sharon
Published: March 2008

The peroxisome proliferator‐activated receptors (PPARs) consist of three related transcription factors that serve to regulate a number of cellular processes that are central to cardiovascular health and disease. Numerous pharmacologic studies have assessed the effects of specific PPAR agonists in clinical trials and have provided insight into the clinical effects of these genes while genetic studies have demonstrated clinical associations between PPAR polymorphisms and abnormal cardiovascular phenotypes. With the abundance of data available from these studies as a background, PPAR pharmacogenetics has become a promising and rapidly advancing field. This review focuses on summarizing the current state of understanding of PPAR genetics and pharmacogenetics and the important implications for the individualization of therapy for patients with cardiovascular diseases.
Extension of The Best Approximation Operator in Orlicz Spaces
Authors: Carrizo Ivana , Favier Sergio , Zó Felipe
Published: March 2008

Let (Ω, 𝒜, μ) be a probability space and ℒ ⊂ 𝒜 a sub‐σ‐lattice of the σ‐algebra 𝒜. We study an extension of the best ϕ‐approximation operator from an Orlicz space Lϕ to the space , where ϕ′ denotes the derivative of the convex, but not necessarily a strictly convex function ϕ. We obtain convergence results when a sequence of σ‐algebras ℬn converges to ℬ∞ in a suitable way.
On Optimal Bit Allocation for Classification‐Based Source‐Dependent Transform Coding
Authors: Akopian David
Published: March 2008

An optimal bit allocation is presented for
classification‐based source‐dependent transform coding. A vector
of transform coefficients is considered to have been produced by
a mixture of processes. The available bit resource is distributed
optimally in two stages: (1) bit allocation is performed for each
class of coefficient vectors, and (2) bit allocation is performed for
each vector coefficient. The solution for low bit rates imposing
nonnegative bit resource is also presented. The rate‐distortion
bound of the classification‐based source coding is
derived.
Potential Therapeutic Targets for PPARγ after Spinal Cord Injury
Authors: McTigue Dana M.
Published: March 2008

Traumatic injury to the spinal cord results in multiple anatomical, physiological, and functional deficits as a result of local neuronal and glial cell death as well as loss of descending and ascending axons traversing the injury site. The many different mechanisms thought to contribute to protracted secondary cell death and dysfunction after spinal cord injury (SCI) are potential therapeutic targets. Agents that bind and activate the transcription factor peroxisome proliferator‐activated receptor‐γ (PPAR‐γ) show great promise for minimizing or preventing these deleterious cascades in other models of CNS disorders. This review will summarize the major secondary injury cascades occurring after SCI and discuss data from experimental CNS injury and disease models showing the exciting potential for PPARγ therapies after SCI.
A Real‐Time Facial Expression Recognition System for Online Games
Authors: Zhan Ce , Li Wanqing , Ogunbona Philip , Safaei Farzad
Published: March 2008

Multiplayer online games (MOGs) have become increasingly popular because of the opportunity they provide for
collaboration, communication, and interaction. However, compared with ordinary human communication, MOG still has
several limitations, especially in communication using facial expressions. Although detailed facial animation has already been achieved in a number of MOGs, players have to use text commands to control the expressions of avatars. In this paper, we propose an automatic expression recognition system that can be integrated into an MOG to control the facial expressions of avatars. To meet the specific requirements of such a system, a number of algorithms are studied, improved, and extended. In particular, Viola and Jones face‐detection method is extended to detect small‐scale key facial components; and fixed facial landmarks are used to reduce the computational load with little performance degradation in the recognition accuracy.
Characterization for the Convergence of Krasnoselskij Iteration for Non‐Lipschitzian Operators
Authors: Şoltuz Ştefan M. , Rhoades B. E.
Published: March 2008

We establish the convergence of Krasnoselskij iteration for various
classes of non‐Lipschitzian operators.
Fixed Point Methods for the Generalized Stability of Functional Equations in a Single Variable
Authors: Cădariu Liviu , Radu Viorel
Published: March 2008

We discuss on the generalized Ulam-Hyers stability for functional equations in a single variable, including the nonlinear functional equations, the linear functional equations, and a generalization of functional equation for the square root spiral. The stability results have been obtained by a fixed point method. This method introduces a metrical context and shows that the stability is related to some fixed point of a suitable operator.
Influence of C‐Peptide on Glucose Utilisation
Authors: Wilhelm B. , Kann P. , Pfützner A.
Published: March 2008

During the recent years, multiple studies demonstrated that C‐peptide is not an inert peptide, but exerts important physiological effects. C‐peptide binds to cell membranes, stimulates the Na,K‐ATPase and the endothelial nitric oxide (NO) synthase. Moreover, there is evidence that C‐peptide decreases glomerular hyperfiltration and increases glucose utilisation. Nevertheless, there is still limited knowledge concerning mechanisms leading to an increased glucose utilisation either in rats or in humans. The aim of this paper is to give an overview over the published studies regarding C‐peptide and glucose metabolism from in vitro studies to longer lasting studies in humans.
A Multiband Diversity Antenna System for Compact Mobile/Wireless Devices: Modeling and Performance Evaluation
Authors: Karaboikis M. , Papamichael V. , Soras C. , Makios V.
Published: March 2008

A novel compact multiband diversity antenna system appropriate for integration onto space‐limited devices is
presented. It comprises three pairs of printed fractal Minkowski and Koch monopole antennas which resonate in the
1.67–2, 2.3–2.56 and 4.55–5.55 GHz bands, respectively, supporting thus a large variety of wireless technologies for mobile
and wireless local area networks (WLANs) applications. The operational characteristics of the antenna system were
extracted by simulation using a method‐of‐moment‐ (MoM‐) based electromagnetic field solver. The diversity performance
in a uniform multipath environment under the maximal‐ratio combining (MRC) scheme is also evaluated for the two extreme
modes of operation, that is, when all three antenna pairs operate simultaneously (worst case) and when only one pair is active while the others being open‐circuited (best case). The calculated effective diversity gain (EDG) for the worst/best case
is 5.8/6.4, 5.8/7.2 and 7.1/7.5 dB for the 1.8, 2.4 and 5.2 GHz frequencies, respectively.
Synthesis and Elastic Characterization of Zinc Oxide Nanowires
Authors: Manoharan M. P. , Desai A. V. , Neely G. , Haque M. A.
Published: March 2008

Zinc oxide nanowires, nanobelts, and nanoneedles were synthesized using the vapor‐liquid‐solid technique. Young′s modulus of the nanowires was measured by performing cantilever bending experiments on individual nanowires in situ inside a scanning electron microscope. The nanowires tested had diameters in the range of 200–750 nm. The average Young′s modulus, measured to be 40 GPa, is about 30% of that reported at the bulk scale. The experimental results are discussed in light of the pronounced electromechanical coupling due to the piezoelectric nature of the material.
Hypoxia Down-regulates CCAAT/Enhancer Binding Protein-α Expression in Breast Cancer Cells
Authors: Seifeddine Ramzi , Dreiem Anne , Blanc Etienne , Fulchignoni-Lataud Marie-Claude , Belda Marie-Aude Le Frère , Lecuru Fabrice , Mayi Thérèse Hervèe , Mazure Nathalie , Favaudon Vincent , Massaad Charbel , Barouki Robert , Massaad-Massade Liliane
Published: April 2008

The transcription factor CCAAT/enhancer binding protein-α (C/EBPα) is involved in the control of cell differentiation and proliferation, and has been suggested to act as a tumor suppressor in several cancers. By using microarray analysis, we have previously shown that hypoxia and estrogen down-regulate C/EBPα mRNA in T-47D breast cancer cells. Here, we have examined the mechanism by which the down-regulation by hypoxia takes place. Using the specific RNA polymerase II inhibitor 5,6-dichlorobenzimidazole-1-β-d-ribofuranoside, the mRNA stability was analyzed under normoxia or hypoxia by quantitative reverse transcription-PCR. Hypoxia reduced the half-life of C/EBPα mRNA by ∼30%. C/EBPα gene promoter studies indicated that hypoxia also repressed the transcription of the gene and identified a hypoxia-responsive element (−522; −527 bp), which binds to hypoxia-inducible factor (HIF)-1α, as essential for down-regulation of C/EBPα transcription in hypoxia. Immunocytochemical analysis showed that C/EBPα was localized in the nucleus at 21% O2, but was mostly cytoplasmic under 1% O2. Knockdown of HIF-1α by RNAi restored C/EBPα to normal levels under hypoxic conditions. Immunohistochemical studies of 10 tumor samples did not show any colocalization of C/EBPα and glucose transporter 1 (used as a marker for hypoxia). Taken together, these results show that hypoxia down-regulates C/EBPα expression in breast cancer cells by several mechanisms, including transcriptional and posttranscriptional effects. The down-regulation of C/EBPα in hypoxia is mediated by HIF-1. [Cancer Res 2008;68(7):2158–65]
Conjugation of Human Topoisomerase 2α with Small Ubiquitin-like Modifiers 2/3 in Response to Topoisomerase Inhibitors: Cell Cycle Stage and Chromosome Domain Specificity
Authors: Agostinho Marta , Santos Vera , Ferreira Fernando , Costa Rafael , Cardoso Joana , Pinheiro Inês , Rino José , Jaffray Ellis , Hay Ronald T. , Ferreira João
Published: April 2008

Type 2 topoisomerases, in particular the α isoform in human cells, play a key role in cohesion and sister chromatid separation during mitosis. These enzymes are thus vital for cycling cells and are obvious targets in cancer chemotherapy. Evidence obtained in yeast and Xenopus model systems indicates that conjugation of topoisomerase 2 with small ubiquitin-like modifier (SUMO) proteins is required for its mitotic functions. Here, we provide biochemical and cytologic evidence that topoisomerase 2α is conjugated to SUMO-2/3 during interphase and mitosis in response to topoisomerase 2 inhibitors and “poisons” (ICRF-187, etoposide, doxorubicin) that stabilize catalytic intermediates (cleavage complexes, closed clamp forms) of the enzyme onto target DNA. During mitosis, SUMO-2/3–modified forms of topoisomerase 2α localize to centromeres and chromosome cores/axes. However, centromeres are unresponsive to inhibitors during interphase. Furthermore, formation of topoisomerase 2α–SUMO-2/3 conjugates within mitotic chromosomes strongly correlates with incomplete chromatid decatenation and decreases progressively as cells approach the metaphase-anaphase transition. We also found that the PIASy protein, an E3 ligase for SUMO proteins, colocalizes with SUMO-2/3 at the mitotic chromosomal cores/axes and is necessary for both formation of SUMO-2/3 conjugates and proper chromatid segregation. We suggest that the efficacy of topoisomerase inhibitors to arrest cells traversing mitosis may relate to their targeting of topoisomerase 2α–SUMO-2/3 conjugates that concentrate at mitotic chromosome axes and are directly involved in chromatid arm separation. [Cancer Res 2008;68(7):2409–18]
MCF7 Side Population Cells with Characteristics of Cancer Stem/Progenitor Cells Express the Tumor Antigen MUC1
Authors: Engelmann Katja , Shen Hongmei , Finn Olivera J.
Published: April 2008

Chemotherapy, radiation, and growth inhibitory drugs preferentially eliminate actively growing cancer cells. Cancer recurrence is currently thought to be due to nondividing cancer stem/progenitor cells that are resistant to these therapies. Different therapeutic approaches need to be considered for the elimination of the cancer stem cell population. Immunotherapy is one such approach. In addition to specificity and lack of toxicity, immunotherapy targets cancer cells irrespective of their state of proliferation, as long as they express particular tumor antigens. For that reason, it is important to examine if the tumor antigens that are currently being tested as immunotherapeutic agents are also present on cancer stem cells. This study aimed to determine if one well-known tumor antigen, MUC1, which is being tested as an immunotherapy target on tumor cells, is also expressed on the quiescent cancer stem/progenitor cells. We used the so-called side population (SP) cells found in the MCF7 breast cancer cell line, which we first confirmed by cell surface markers and gene profiling to be highly enriched in cells that fulfill specific functional, phenotypic, and molecular criteria for being tumor stem/progenitor cells. We show that these cells express MUC1 and give rise to MUC1+ tumors in vivo, which maintain the MUC1+ SP population. MUC1 on SP cells is hypoglycosylated and heavily sialylated; the characteristics of the tumor-specific form were expressed on mature cancer cells and recognized by tumor-specific T cells and antibodies. This suggests that stem/progenitor cells, like mature tumor cells, would be targets of MUC1-directed immunotherapy. [Cancer Res 2008;68(7):2419–26]
DNA Damage Signaling in Hematopoietic Cells: A Role for Mre11 Complex Repair of Topoisomerase Lesions
Authors: Morales Monica , Liu Yan , Laiakis Evagelia C. , Morgan William F. , Nimer Stephen D. , Petrini John H.J.
Published: April 2008

The Mre11 complex promotes DNA double-strand break repair and regulates DNA damage signaling via activation of the ataxia-telangiectasia mutated (ATM) kinase. The hypermorphic Rad50S allele encodes a variant of Rad50, a member of the Mre11 complex. Cells expressing Rad50S experience constitutive ATM activation, which leads to precipitous apoptotic attrition in hematopoietic cells. In this study, we show that ATM activation by the Rad50S-containing Mre11 complex enhances the proliferation of LSK cells, a population consisting of hematopoietic stem cells and multipotent progenitor cells. In Rad50S/S mice, enhanced LSK proliferation triggers apoptotic attrition. This phenotype is mitigated when Rad50S/S is combined with mutations that alter either LSK cell quiescence (myeloid elf-1–like factor/ELF4–deficient mice) or hematopoietic differentiation (p21- and p27-deficient mice), indicating that the LSK population is a primary target of Rad50S pathology. We show that cells from Rad50S/S mice are hypersensitive to camptothecin, a topoisomerase I inhibitor that causes DNA damage primarily during DNA replication. On this basis, we propose that apoptotic attrition of Rad50S/S hematopoietic cells results from enhanced proliferation in the context of topoisomerase-associated DNA damage. Impairment of apoptosis in Rad50S/S mice promotes hematopoietic malignancy, suggesting that primitive hematopoietic cells serve as a reservoir of potentially oncogenic lesions in Rad50S/S mice. These data provide compelling evidence that the Mre11 complex plays a role in the metabolism of topoisomerase lesions in mammals, and further suggest that such lesions can accumulate in primitive hematopoietic cells and confer significant oncogenic potential. [Cancer Res 2008;68(7):2186–93]
A Cryptic Vascular Endothelial Growth Factor T-Cell Epitope: Identification and Characterization by Mass Spectrometry and T-Cell Assays
Authors: Weinzierl Andreas O. , Maurer Dominik , Altenberend Florian , Schneiderhan-Marra Nicole , Klingel Karin , Schoor Oliver , Wernet Dorothee , Joos Thomas , Rammensee Hans-Georg , Stevanović Stefan
Published: April 2008

Vascular endothelial growth factor (VEGF) is involved in various physiologic processes, such as angiogenesis or wound healing, but is also crucial in pathologic events, such as tumor growth. Thus, clinical anti-VEGF treatments have been developed that could already show beneficial effects for cancer patients. In this article, we describe the first VEGF-derived CD8+ T-cell epitope. The natural HLA ligand SRFGGAVVR was identified by differential mass spectrometry in two primary renal cell carcinomas (RCC) and was significantly overpresented on both tumor tissues. SRFGGAVVR is derived from a cryptic translated region of VEGF presumably by initiation of translation at the nonclassic start codon CUG499. SRFGGAVVR-specific T cells were generated in vitro using peptide-loaded dendritic cells or artificial antigen-presenting cells. SRFGGAVVR-specific CD8+ T cells, identified by HLA tetramer analysis after in vitro stimulation, were fully functional T effector cells, which were able to secrete IFN-γ on stimulation and killed tumor cells in vitro. Additionally, we have quantitatively analyzed VEGF mRNA and protein levels in RCC tumor and normal tissue samples by gene chip analysis, quantitative reverse transcription-PCR, in situ hybridization, and bead-based immunoassay. In the future, T cells directed against VEGF as a tumor-associated antigen may represent a possible way of combining peptide-based anti-VEGF immunotherapy with already existent anti-VEGF cancer therapies. [Cancer Res 2008;68(7):2447–54]
FGFR2-Amplified Gastric Cancer Cell Lines Require FGFR2 and Erbb3 Signaling for Growth and Survival
Authors: Kunii Kaiko , Davis Lenora , Gorenstein Julie , Hatch Harold , Yashiro Masakazu , Di Bacco Alessandra , Elbi Cem , Lutterbach Bart
Published: April 2008

We have identified a critical role for amplified FGFR2 in gastric cancer cell proliferation and survival. In a panel of gastric cancer cell lines, fibroblast growth factor receptor 2 (FGFR2) was overexpressed and tyrosine phosphorylated selectively in FGFR2-amplified cell lines KatoIII, Snu16, and OCUM-2M. FGFR2 kinase inhibition by a specific small-molecule inhibitor resulted in selective and potent growth inhibition in FGFR2-amplified cell lines, resulting in growth arrest in KatoIII cells and prominent induction of apoptosis in both Snu16 and OCUM-2M cells. FGFR2-amplified cell lines also contained elevated phosphotyrosine in EGFR, Her2, and Erbb3, but the elevated phosphorylation in EGFR could not be inhibited by gefitinib or erlotinib. We show that the elevated EGFR, Her2, and Erbb3 phosphotyrosine is dependent on FGFR2, revealing EGFR family kinases to be downstream targets of amplified FGFR2. Moreover, shRNA to Erbb3 resulted in a loss of proliferation, confirming a functional role for the activated EGFR signaling pathway. These results reveal that both the FGFR2 and EGFR family signaling pathways are activated in FGFR2-amplified gastric cancer cell lines to drive cell proliferation and survival. Inhibitors of FGFR2 or Erbb3 signaling may have therapeutic efficacy in the subset of gastric cancers containing FGFR2 amplification. [Cancer Res 2008;68(7):2340–8]
Skewing the T-Cell Repertoire by Combined DNA Vaccination, Host Conditioning, and Adoptive Transfer
Authors: Jorritsma Annelies , Bins Adriaan D. , Schumacher Ton N.M. , Haanen John B.A.G.
Published: April 2008

Approaches for T-cell–based immunotherapy that have shown substantial effects in clinical trials are generally based on the adoptive transfer of high numbers of antigen-specific cells, and the success of these approaches is thought to rely on the high magnitude of the tumor-specific T-cell responses that are induced. In this study, we aimed to develop strategies that also yield a T-cell repertoire that is highly skewed toward tumor recognition but do not rely on ex vivo generation of tumor-specific T cells. To this end, the tumor-specific T-cell repertoire was first expanded by DNA vaccination and then infused into irradiated recipients. Subsequent vaccination of the recipient mice with the same antigen resulted in peak CD8+ T-cell responses of ∼50%. These high T-cell responses required the presence of antigen-experienced tumor-specific T cells within the graft because only mice that received cells of previously vaccinated donor mice developed effective responses. Tumor-bearing mice treated with this combined therapy showed a significant delay in tumor outgrowth, compared with mice treated by irradiation or vaccination alone. Furthermore, this antitumor effect was accompanied by an increased accumulation of activated and antigen-specific T cells within the tumor. In summary, the combination of DNA vaccination with host conditioning and adoptive transfer generates a marked, but transient, skewing of the T-cell repertoire toward tumor recognition. This strategy does not require ex vivo expansion of cells to generate effective antitumor immunity and may therefore easily be translated to clinical application. [Cancer Res 2008;68(7):2455–62]
Methylation Silencing of Transforming Growth Factor-β Receptor Type II in Rat Prostate Cancers
Authors: Yamashita Satoshi , Takahashi Satoru , McDonell Nathalie , Watanabe Naoko , Niwa Tohru , Hosoya Kosuke , Tsujino Yoshimi , Shirai Tomoyuki , Ushijima Toshikazu
Published: April 2008

To identify methylation-silenced genes in prostate cancers, a microarray analysis for genes up-regulated by treatment with a demethylating agent, 5-aza-2′-deoxycytidine, was performed using three rat prostate cancer cell lines. Eight genes (Aebp1, Dysf, Gas6, LOC361288, Nnat, Ocm, RGD1308119, and Tgfbr2) were re-expressed at 16-fold or more, and their promoter CpG islands were shown to be densely methylated in the cancer cell lines. From the eight genes, Tgfbr2, a key mediator of transforming growth factor-β (TGF-β) signaling that has been strongly implicated in human and rat prostate carcinogenesis, was selected, and its silencing in primary samples was analyzed further. Tgfbr2 was methylated and markedly down-regulated in three of seven 3,2′-dimethyl-4-aminobiphenyl–induced invasive adenocarcinomas in the dorsolateral lobe of the rat prostate. In humans, marked down-regulation of TGFBR2 protein was observed in 12 of 20 high-grade prostatic intraepithelial neoplasia and 36 of 60 prostate cancers. DNA methylation of the human TGFBR2 promoter CpG islands repressed transcription, if present, but neither methylation nor mutation were detected in 27 human prostate cancers analyzed. Methylation silencing of rat Tgfbr2 was associated with histone H3 lysine 9 trimethylation, whereas decreased expression of human TGFBR2 was mainly due to decreased transcription activity, sometimes in concert with histone deacetylation and H3 lysine 27 trimethylation. The identification of methylation silencing of Tgfbr2 in rat prostate cancers, in accordance with TGFBR2 down-regulation in human prostate cancers, will enable us to analyze how aberrant methylation is induced in vivo and identify factors that promote and suppress the induction of aberrant methylation. [Cancer Res 2008;68(7):2112–21]
Antitumor Effects of Mucin 1/sec Involves the Modulation of Urokinase-Type Plasminogen Activator and Signal Transducer and Activator of Transcription 1 Expression in Tumor Cells
Authors: Ilkovitch Dan , Handel-Fernandez Mary Ellen , Herbert Lynn M. , Lopez Diana M.
Published: April 2008

Expression of the transmembrane isoform of Mucin 1 (MUC1/TM) in an aggressive murine mammary tumor line, DA-3, does not alter tumor development and metastasis, leading to death of the host. However, tumor cells expressing a secreted isoform of MUC1 (MUC1/sec) fail to develop tumors in immunocompetent mice. The rejection of MUC1/sec-expressing tumor cells is immunologically mediated, as, initially, innate cells and, ultimately, T cells are required. After gene array analysis, and confirmation at the protein level, it was discovered that MUC1/sec-expressing tumor cells (DA-3/sec) have a significant reduction in expression of urokinase-type plasminogen activator (uPA) relative to the parental tumor line and tumor cells expressing MUC1/TM. The serine protease uPA has been found to be involved in growth-promoting signaling, angiogenesis, and induction of matrix remodeling leading to metastasis. Although the tumor-promoting Stat3 transcription factor was unaltered in these tumor cells, the tumor-suppressive and IFN-responsive signal transducer and activator of transcription 1 (Stat1) is dramatically up-regulated in DA-3/sec cells. In addition, treatment of various murine and human cell lines with conditioned medium containing MUC1/sec results in up-regulation of Stat1. DA-3/sec tumor cells are also sensitized to the antiproliferative effects of IFN-γ. Furthermore, transfection of the Stat1 gene into DA-3 tumor cells leads to a down-regulation of uPA and delays tumor progression. Thus, Stat1 up-regulation in DA-3/sec cells seems to play a significant role in the mechanism(s) by which rejection of tumor cells expressing MUC1/sec may be occurring. [Cancer Res 2008;68(7):2427–35]
Immunity to Growth Factor Receptor–Bound Protein 10, a Signal Transduction Molecule, Inhibits the Growth of Breast Cancer in Mice
Authors: O-Sullivan InSug , Chopra Amla , Carr Janai , Kim Tae Sung , Cohen Edward P.
Published: April 2008

This study describes the application of a unique strategy to identify breast cancer antigens [tumor-associated antigen (TAA)]. In a mouse model, the strategy led to the identification of growth factor receptor–bound protein 10 (Grb10) as a newly identified TAA. Grb10 is a signal transduction molecule associated with multiple transmembrane tyrosine kinase receptors. It was discovered by comparing microarrays of cellular breast cancer vaccines highly enriched for cells that induced breast cancer immunity in tumor-bearing mice with nonenriched vaccines. The vaccines were prepared by transferring a cDNA expression library derived from SB5b cells, a breast cancer cell line C3H/He origin (H-2k), into LM mouse fibroblasts (H-2k). As the transferred cDNA integrates spontaneously into the genome of the recipient cells, replicates as the cells divide, and is expressed, the vaccine could be prepared from microgram amounts of tumor tissue. Relatively few cells in the transduced cell population, however, incorporated cDNA fragments that included genes specifying TAA. (The vast majority specified normal cellular constituents.) A unique strategy was used, therefore, to enrich the vaccine for immunotherapeutic cells. Twenty genes were overrepresented in the enriched vaccines. One, the gene for Grb10, was ∼100-fold overrepresented. To determine if Grb10 in the enriched vaccine was partly responsible for its therapeutic benefits, the gene was transferred into the fibroblast cell line, which was then used as a vaccine. Mice with established breast cancer treated solely by immunization with the modified fibroblasts developed robust immunity to the breast cancer cells, which, in some instances, was sufficient to result in tumor rejection. [Cancer Res 2008;68(7):2463–70]
Characterization of an Akt Kinase Inhibitor with Potent Pharmacodynamic and Antitumor Activity
Authors: Rhodes Nelson , Heerding Dirk A. , Duckett Derek R. , Eberwein Derek J. , Knick Victoria B. , Lansing Timothy J. , McConnell Randy T. , Gilmer Tona M. , Zhang Shu-Yun , Robell Kimberly , Kahana Jason A. , Geske Robert S. , Kleymenova Elena V. , Choudhry Anthony E. , Lai Zhihong , Leber Jack D. , Minthorn Elisabeth A. , Strum Susan L. , Wood Edgar R. , Huang Pearl S. , Copeland Robert A. , Kumar Rakesh
Published: April 2008

Akt kinases 1, 2, and 3 are important regulators of cell survival and have been shown to be constitutively active in a variety of human tumors. GSK690693 is a novel ATP-competitive, low-nanomolar pan-Akt kinase inhibitor. It is selective for the Akt isoforms versus the majority of kinases in other families; however, it does inhibit additional members of the AGC kinase family. It causes dose-dependent reductions in the phosphorylation state of multiple proteins downstream of Akt, including GSK3β, PRAS40, and Forkhead. GSK690693 inhibited proliferation and induced apoptosis in a subset of tumor cells with potency consistent with intracellular inhibition of Akt kinase activity. In immune-compromised mice implanted with human BT474 breast carcinoma xenografts, a single i.p. administration of GSK690693 inhibited GSK3β phosphorylation in a dose- and time-dependent manner. After a single dose of GSK690693, >3 μmol/L drug concentration in BT474 tumor xenografts correlated with a sustained decrease in GSK3β phosphorylation. Consistent with the role of Akt in insulin signaling, treatment with GSK690693 resulted in acute and transient increases in blood glucose level. Daily administration of GSK690693 produced significant antitumor activity in mice bearing established human SKOV-3 ovarian, LNCaP prostate, and BT474 and HCC-1954 breast carcinoma xenografts. Immunohistochemical analysis of tumor xenografts after repeat dosing with GSK690693 showed reductions in phosphorylated Akt substrates in vivo. These results support further evaluation of GSK690693 as an anticancer agent. [Cancer Res 2008;68(7):2366–74]
Cell Cycle–Dependent Ciliogenesis and Cancer
Authors: Plotnikova Olga V. , Golemis Erica A. , Pugacheva Elena N.
Published: April 2008

In mammals, most cell types have primary cilia, protruding structures involved in sensing mechanical and chemical signals from the extracellular environment that act as major communication hubs for signaling controlling cell differentiation and polarity. The list of clinical disorders associated with ciliary dysfunction has expanded from polycystic kidney disease to include many others. Transformed cells commonly lack cilia, but whether this lack is cause or consequence of transformation is not well understood. Here we discuss work addressing recently identified actions of the cancer-promoting proteins Aurora A and HEF1/NEDD9/CAS-L at cilia. Together with older studies, this work suggests that loss of cilia in cancer may contribute to the insensitivity of cancer cells to environmental repressive signals, based in part on derangement of cell cycle checkpoints governed by cilia and centrosomes. [Cancer Res 2008;68(7):2058–61]
Effect of Caffeine on the ATR/Chk1 Pathway in the Epidermis of UVB-Irradiated Mice
Authors: Lu Yao-Ping , Lou You-Rong , Peng Qing-Yun , Xie Jian-Guo , Nghiem Paul , Conney Allan H.
Published: April 2008

Administration of caffeine was shown in earlier studies to enhance UVB-induced apoptosis and inhibit UVB-induced carcinogenesis in hairless SKH-1 mice. Here, we describe a potential mechanism for these in vivo effects. A single irradiation of mouse skin with UVB activated the ataxia-telangiectasia mutated– and Rad3-related (ATR) pathway, causing a severalfold increase in keratinocytes with phospho-Chk1 (Ser345) and a marked decrease in mitotic keratinocytes with cyclin B1 compared with baseline. When given in the drinking water for 1 to 2 weeks before UVB, caffeine (0.4 mg/mL) markedly inhibited the UVB-induced phosphorylation of Chk1 on Ser345 and caused premature expression of cyclin B1 in the epidermis. Normal keratinocytes had delayed mitotic entry for >10 h following UVB. Caffeine administration reduced this mitotic delay to only 4 h and caused markedly increased apoptosis by 6 to 10 h after UVB. p53 knockout mice were used to determine the role of p53 in these processes. Irradiation with UVB markedly decreased the number of mitotic keratinocytes with cyclin B1 in p53 knockout mice, and topical caffeine immediately after UVB abrogated this response and increased UVB-induced apoptosis severalfold. These effects of caffeine in knockout mice were substantially greater than in wild-type mice. The ability of caffeine to promote the deletion of p53−/− keratinocytes may be relevant to its inhibitory effect on UVB-induced skin cancer. Our studies indicate that administration of caffeine enhances the removal of DNA-damaged cells by inhibiting the ATR-mediated phosphorylation of Chk1 and prematurely increasing the number of cyclin B1–containing cells that undergo lethal mitosis. [Cancer Res 2008;68(7):2523–9]
Gli Activity Correlates with Tumor Grade in Platelet-Derived Growth Factor–Induced Gliomas
Authors: Becher Oren J. , Hambardzumyan Dolores , Fomchenko Elena I. , Momota Hiroyuki , Mainwaring Lori , Bleau Anne-Marie , Katz Amanda M. , Edgar Mark , Kenney Anna M. , Cordon-Cardo Carlos , Blasberg Ron G. , Holland Eric C.
Published: April 2008

Gli signaling is critical for central nervous system development and is implicated in tumorigenesis. To monitor Gli signaling in gliomas in vivo, we created platelet-derived growth factor–induced gliomas in a Gli-luciferase reporter mouse. We find that Gli activation is found in gliomas and correlates with grade. In addition, we find that sonic hedgehog (SHH) is expressed in these tumors and also correlates with grade. We identify microvascular proliferation and pseudopalisades, elements that define high-grade gliomas as SHH-producing microenvironments. We describe two populations of SHH-producing stromal cells that reside in perivascular niche (PVN), namely low-cycling astrocytes and endothelial cells. Using the Ptc-LacZ knock-in mouse as a second Gli responsive reporter, we show β-galactosidase activity in the PVN and in some tumors diffusely throughout the tumor. Lastly, we observe that SHH is similarly expressed in human gliomas and note that an intact tumor microenvironment or neurosphere conditions in vitro are required for Gli activity. [Cancer Res 2008;68(7):2241–49]
Regulation of Id1 Expression by Src: Implications for Targeting of the Bone Morphogenetic Protein Pathway in Cancer
Authors: Gautschi Oliver , Tepper Clifford G. , Purnell Phillip R. , Izumiya Yoshihiro , Evans Christopher P. , Green Tim P. , Desprez Pierre Y. , Lara Primo N. , Gandara David R. , Mack Philip C. , Kung Hsing-Jien
Published: April 2008

Deregulated activation of the Src tyrosine kinase and heightened Id1 expression are independent mediators of aggressive tumor biology. The present report implicates Src signaling as a critical regulator of Id1 gene expression. Microarray analyses showed that Id family genes were among the most highly down-regulated by incubation of A549 lung carcinoma cells with the small-molecule Src inhibitor AZD0530. Id1 transcript and protein levels were potently reduced in a dose-dependent manner concomitantly with the reduction of activated Src levels. These effects were conserved across a panel of lung, breast, prostate, and colon cancer cell lines and confirmed by the ability of PP2, Src siRNA, and Src-blocking peptides to suppress Id1 expression. PP2, AZD0530, and dominant-negative Src abrogated Id1 promoter activity, which was induced by constitutively active Src. The Src-responsive region of the Id1 promoter was mapped to a region 1,199 to 1,360 bps upstream of the translation start site and contained a Smad-binding element. Src was also required for bone morphogenetic protein-2 (BMP-2)–induced Id1 expression and promoter activity, was moderately activated by BMP-2, and complexed with Smad1/5. Conversely, Src inhibitors blocked Smad1/5 nuclear translocation and binding to the Src-responsive region of the Id1 promoter. Consistent with a role for Src and Id1 in cancer cell invasion, Src inhibitors and Id1 siRNA decreased cancer cell invasion, which was increased by Id1 overexpression. Taken together, these results reveal that Src positively interacts with the BMP-Smad-Id pathway and provide new ways for targeted inhibition of Id1. [Cancer Res 2008;68(7):2250–8]