bluuebunny/crossref_metadata_2025 huggingface dataset:
Dial a Ride from
k
-forest
Authors: Gupta Anupam , Hajiaghayi Mohammadtaghi , Nagarajan Viswanath , Ravi R.
Published: April 2010

The
k-forest problem
is a common generalization of both the
k-MST
and the
dense-k-subgraph
problems. Formally, given a metric space on
n
vertices
V
, with
m
demand pairs ⊆
V
×
V
and a “target”
k
≤
m
, the goal is to find a minimum cost subgraph that connects
at least
k
pairs. In this paper, we give an
O
(min{√
n
⋅log
k
,√
k
})-approximation algorithm for
k
-forest, improving on the previous best ratio of
O
(min {
n
2/3
,√
m
}log
n
) by Segev and Segev.

We then apply our algsorithm for
k
-forest to obtain approximation algorithms for several
Dial-a-Ride
problems. The basic Dial-a-Ride problem is the following: given an
n
point metric space with
m
objects each with its own source and destination, and a vehicle capable of carrying
at most
k
objects at any time, find the minimum length tour that uses this vehicle to move each object from its source to destination. We want that the tour be
non-preemptive
: that is, each object, once picked up at its source, is dropped only at its destination. We prove that an α-approximation algorithm for the
k
-forest problem implies an
O
(α⋅log
2
n
)-approximation algorithm for Dial-a-Ride. Using our results for
k
-forest, we get an
O
(min{√
n
,√
k
}⋅log
2
n
)-approximation algorithm for Dial-a-Ride. The only previous result known for Dial-a-Ride was an
O
(√
k
log
n
)-approximation by Charikar and Raghavachari; our results give a different proof of a similar approximation guarantee—in fact, when the vehicle capacity
k
is large, we give a slight improvement on their results. The reduction from Dial-a-Ride to the
k
-forest problem is fairly robust, and allows us to obtain approximation algorithms (with the same guarantee) for some interesting generalizations of Dial-a-Ride.
A fast algorithm to generate open meandric systems and meanders
Authors: Bobier Bruce , Sawada Joe
Published: April 2010

An open meandric system is a planar configuration of acyclic curves crossing an infinite horizontal line in the plane such that the curves may extend in both horizontal directions. We present a fast, recursive algorithm to exhaustively generate open meandric systems with
n
crossings. We then illustrate how to modify the algorithm to generate unidirectional open meandric systems (the curves extend only to the right) and nonisomorphic open meandric systems where equivalence is taken under horizontal reflection. Each algorithm can be modified to generate systems with exactly
k
curves. In the unidirectional case when
k
= 1, we can apply a minor modification along with some additional optimization steps to yield the first fast and simple algorithm to generate open meanders.
Predicting and preventing inconsistencies in deployed distributed systems
Authors: Yabandeh Maysam , Knežević Nikola , Kostić Dejan , Kuncak Viktor
Published: April 2010

We propose a new approach for developing and deploying distributed systems, in which nodes predict distributed consequences of their actions and use this information to detect and avoid errors. Each node continuously runs a state exploration algorithm on a recent consistent snapshot of its neighborhood and predicts possible future violations of specified safety properties. We describe a new state exploration algorithm, consequence prediction, which explores causally related chains of events that lead to property violation.

This article describes the design and implementation of this approach, termed CrystalBall. We evaluate CrystalBall on RandTree, BulletPrime, Paxos, and Chord distributed system implementations. We identified new bugs in mature Mace implementations of three systems. Furthermore, we show that if the bug is not corrected during system development, CrystalBall is effective in steering the execution away from inconsistent states at runtime.
DDoS defense by offense
Authors: Walfish Michael , Vutukuru Mythili , Balakrishnan Hari , Karger David , Shenker Scott
Published: April 2010

This article presents the design, implementation, analysis, and experimental evaluation of
speak-up
, a defense against
application-level
distributed denial-of-service (DDoS), in which attackers cripple a server by sending legitimate-looking requests that consume computational resources (e.g., CPU cycles, disk). With speak-up, a victimized server encourages all clients, resources permitting,
to automatically send higher volumes of traffic
. We suppose that attackers are already using most of their upload bandwidth so cannot react to the encouragement. Good clients, however, have spare upload bandwidth so can react to the encouragement with drastically higher volumes of traffic. The intended outcome of this traffic inflation is that the good clients crowd out the bad ones, thereby capturing a much larger fraction of the server's resources than before. We experiment under various conditions and find that speak-up causes the server to spend resources on a group of clients in rough proportion to their aggregate upload bandwidths, which is the intended result.
Schubmehl-Prein essay competition
Authors: Bowyer Kevin W.
Published: April 2010

The 2009 competition was the fifth year of the Schubmehl-Prein contest for the Best Essay on Social Impact of Computing. The competition is open to high school juniors each year, with a submission deadline at the end of May. The essay topic varies each year, with the 2009 topic being, "What are the potential social and ethical implications of the $100 laptop?" The 2009 competition attracted a number of essays that strongly engaged with the topic. The 2009 First Place winner is Katherine Heit (Saint Thomas Aquinas High School, Kansas), the Second Place winner is Danielle Harris (Mayfield Senior School, California), and the Third Place winner is David Purington (Damien High School, California). In addition, this year, for the first time, two Honorable Mention winners were also selected: Bryan Dongre (Brookfield Central High School, Wisconsin) and Erica Smith (St. Agnes Academy, Texas). Revised versions of the First, Second and Third Place essays appear in this issue of Computers and Society. Congratulations to all of this year's winners. Thanks to all of the students who prepared and submitted an entry to the competition. And thanks as well to all of the teachers and school counselors who worked with all of the students.
A nice attempt
Authors: Heit Katherine
Published: April 2010

Throughout history, one focus of society has been expanding and educating its less fortunate or less advanced. This has not change in the twenty-first century. It seems to be a topic in every political election: what are you going to do to help the poor? What are you going to do to help the poor in other countries? The mistreatment of others is all over the media. It fills the home and the head. The squalor of poorer countries is featured on the nightly news. People typically say, send food. Send medicine. One man had a different idea. Send education in the form of inexpensive laptops.
Attitudes of sixth form female students toward the IT field
Authors: Leiviskä Katja , Siponen Mikko
Published: April 2010

It is well known that girls are not interested in computer science, information systems (IS), and software engineering studies. While the underlying reasons for this phenomenon have been studied in the US, Canada, and Australia, only a few studies have been carried out in Europe and in Scandinavia. To fill this gap in the research, we have analyzed the qualitative responses of 64 female sixth form students concerning their attitudes towards studying information technology (IT), including computer science, information systems, and software engineering disciplines, and their views about IT as a profession.

The results suggest that the IT field is seen in quite a positive light by the girls. Although many of the respondents do not consider IT to be their profession, they nevertheless have positive attitudes towards the field. According to the respondents, the field is growing and developing; it is respected, and seen as the field of the future. Girls who want to become IT professionals see that the profession entails good employment possibilities and benefits and is respected. Some girls have negative views towards the field. These views illustrate the underlying reasons why these girls do not want to study IT. The girls did not perceive the field to be human-related (the work is only computer-related, according to the respondents). The need for skills in mathematics and physics are also listed as key reasons why some girls do not want to become IT students.

The results of the study suggest that there is a need to clarify among sixth form students the fact that IT jobs can be divided into computer science, information systems, and software engineering, all of which require different competences.
A survey of buffer management policies for packet switches
Authors: Goldwasser Michael H.
Published: April 2010

Over the past decade, there has been great interest in the study of buffer management policies in the context of packet transmission for network switches. In a typical model, a switch receives packets on one or more input ports, with each packet having a designated output port through which it should be transmitted. An online policy must consider bandwidth limits on the rate of transmission, memory constraints impacting the buffering of packets within a switch, and variations in packet properties used to differentiate quality of service. With so many constraints, a switch may not be able to deliver all packets, in which case some will be dropped

In the online algorithms community, researchers have used competitive analysis to evaluate the quality of an online policy in maximizing the value of those packets it is able to transmit. In this article, we provide a detailed survey of the field, describing various models of the problem that have been studied, and summarizing the known results.
How to Turn an Online Course into a Book
Authors: Hedden Heather
Published: April 2010

It's not unusual for online course instructors to write books based on their courses. Online courses have an advantage in this regard, since much of the course material is already written down in narrative form. Creating a book, though, is quite a different endeavor from creating an online course. If you're considering converting your online course to a book, at the outset you need to ask yourself certain interrelated questions...
Bronchial epithelial damage after a half-marathon in nonasthmatic amateur runners
Authors: Chimenti Laura , Morici Giuseppe , Paternò Alessandra , Santagata Roberta , Bonanno Anna , Profita Mirella , Riccobono Loredana , Bellia Vincenzo , Bonsignore Maria R.
Published: April 2010

High neutrophil counts in induced sputum have been found in nonasthmatic amateur runners at rest and after a marathon, but the pathogenesis of airway neutrophilia in athletes is still poorly understood. Bronchial epithelial damage may occur during intense exercise, as suggested by investigations conducted in endurance-trained mice and competitive human athletes studied under resting conditions. To gain further information on airway changes acutely induced by exercise, airway cell composition, apoptosis, IL-8 concentration in induced sputum, and serum CC-16 level were measured in 15 male amateur runners at rest (baseline) and shortly after a half-marathon. Different from results obtained after a marathon, neutrophil absolute counts were unchanged, whereas bronchial epithelial cell absolute counts and their apoptosis increased significantly ( P < 0.01). IL-8 in induced sputum supernatants almost doubled postrace compared with baseline ( P < 0.01) and correlated positively with bronchial epithelial cell absolute counts ( R2 = 0.373, P < 0.01). Serum CC-16 significantly increased after all races ( P < 0.01). These data show mild bronchial epithelial cell injury acutely induced by intense endurance exercise in humans, extending to large airways the data obtained in peripheral airways of endurance-trained mice. Therefore, neutrophil influx into the airways of athletes may be secondary to bronchial epithelial damage associated with intense exercise.
Frequency-Dependent Spatiotemporal Tuning Properties of Non–Eye Movement Related Vestibular Neurons to Three-Dimensional Translations in Squirrel Monkeys
Authors: Chen-Huang Chiju , Peterson Barry W.
Published: April 2010

Responses of vestibular-only translation sensitive (VOTS) neurons in vestibular nuclei of two squirrel monkeys were studied at multiple frequencies to three-dimensional translations and rotations. A novel frequency-dependent spatiotemporal analysis examined in each neuron whether complex models, with unrestricted response dynamics in three-dimensional (3D) space, provided significantly better fits than restricted models following simple, cosine rule. Subsequently, the statistically selected optimal model was used to predict the maximum translation direction, expressed as a unitary vector, Vtmax, and its associated sensitivity and phase across frequencies. Simple models were sufficient to quantify the 3D translational responses of 66% of neurons. Most VOTS neurons, complex or simple, exhibited flat-gain or low-pass response dynamics. The Vtmax of simple neurons was fixed, whereas that of complex neurons changed with frequency. The spatial distribution of Vtmax in simple neurons, which fell within 30° of either the horizontal plane or/and the sagittal plane, was closely aligned with Vtmax of vestibular afferents. In contrast, the frequency-dependent Vtmax of most complex neurons migrated from the dorsoventral axis at higher frequency toward the horizontal plane, especially the interaural axis, at lower frequency. When the maximum rotation direction was estimated from responses of the same VOTS neurons to 1.2 Hz yaw, pitch, and roll rotations, complex neurons were more likely to respond to rotations activating vertical canals. Responses to 0.15–0.3 Hz linear accelerations produced by inertial or gravitational forces were indistinguishable in most complex neurons but significantly different in most simple neurons. These observations suggest that simple and complex VOTS neurons constitute distinctive vestibular pathways where complex neurons, exhibiting a novel spatiotemporal filtering mechanism in processing otolith-related signals, are well suited to drive tilt-related responses, whereas simple neurons probably mediate pure translation related responses.
A New Method to Prove and Find Analytic Inequalities
Authors: Zhang Xiao-Ming , Xi Bo-Yan , Chu Yu-Ming
Published: April 2010

We present a new method to study analytic inequalities. As for its applications, we prove the well‐known Hölder inequality and establish several new analytic inequalities.
Evidence for Maternal-Fetal Genotype Incompatibility as a Risk Factor for Schizophrenia
Authors: Palmer Christina G. S.
Published: April 2010

Prenatal/obstetric complications are implicated in schizophrenia susceptibility. Some complications may arise from maternal-fetal genotype incompatibility, a term used to describe maternal-fetal genotype combinations that produce an adverse prenatal environment. A review of maternal-fetal genotype incompatibility studies suggests that schizophrenia susceptibility is increased by maternal-fetal genotype combinations at theRHDandHLA-Bloci. Maternal-fetal genotype combinations at these loci are hypothesized to have an effect on the maternal immune system during pregnancy which can affect fetal neurodevelopment and increase schizophrenia susceptibility. This article reviews maternal-fetal genotype incompatibility studies and schizophrenia and discusses the hypothesized biological role of these ‘‘incompatibility genes’’. It concludes that research is needed to further elucidate the role ofRHDandHLA-Bmaternal-fetal genotype incompatibility in schizophrenia and to identify other genes that produce an adverse prenatal environment through a maternal-fetal genotype incompatibility mechanism. Efforts to develop more sophisticated study designs and data analysis techniques for modeling maternal-fetal genotype incompatibility effects are warranted.
Genome Sizes in Hepatica Mill: (Ranunculaceae) Show a Loss of DNA, Not a Gain, in Polyploids
Authors: Zonneveld B. J. M.
Published: April 2010

Genome size (C-value) was applied anew to investigate the relationships within the genus Hepatica (Ranunculaceae). More than 50 samples representing all species (except H. falconeri), from wild and cultivated material, were investigated. Species of Hepatica turn out to be diploid (), tetraploid (
), and a possible pentaploid. The somatic nuclear DNA contents (2C-value), as measured by flow cytometry with propidium iodide, were shown to range from 33 to 80 pg. The Asiatic and American species, often considered subspecies of H. nobilis, could be clearly distinguished from European H. nobilis. DNA content confirmed the close relationships in the Asiatic species, and these are here considered as subspecies of H. asiatica. Parents for the allotetraploid species could be suggested based on their nuclear DNA content. Contrary to the increase in genome size suggested earlier for Hepatica, a significant (6%–14%) loss of nuclear DNA in the natural allopolyploids was found.
Functional Differences between the N-Terminal Domains of Mouse and Human Myosin Binding Protein-C
Authors: Shaffer Justin F. , Wong Peony , Bezold Kristina L. , Harris Samantha P.
Published: April 2010

The N-terminus of cMyBP-C can activate actomyosin interactions in the absence ofCa2+, but it is unclear which domains are necessary. Prior studies suggested that the Pro-Ala rich region of human cMyBP-C activated force in permeabilized human cardiomyocytes, whereas the C1 and M-domains of mouse cMyBP-C activated force in permeabilized rat cardiac trabeculae. Because the amino acid sequence of the P/A region differs between human and mouse cMyBP-C isoforms (46% identity), we investigated whether species-specific differences in the P/A region could account for differences in activating effects. Using chimeric fusion proteins containing combinations of human and mouse C0, Pro-Ala, and C1 domains, we demonstrate here that the human P/A and C1 domains activate actomyosin interactions, whereas the same regions of mouse cMyBP-C are less effective. These results suggest that species-specific differences between homologous cMyBP-C isoforms confer differential effects that could fine-tune cMyBP-C function in hearts of different species.
Flexible Human Behavior Analysis Framework for Video Surveillance Applications
Authors: Lao Weilun , Han Jungong , de With Peter H. N.
Published: April 2010

We study a flexible framework for semantic analysis of human motion from surveillance video. Successful trajectory estimation and human-body modeling facilitate the semantic analysis of human activities in video sequences. Although human motion is widely investigated, we have extended such research in three aspects. By adding a second camera, not only more reliable behavior analysis is possible, but it also enables to map the ongoing scene events onto a 3D setting to facilitate further semantic analysis. The second contribution is the introduction of a 3D reconstruction scheme for scene understanding. Thirdly, we perform a fast scheme to detect different body parts and generate a fitting skeleton model, without using the explicit assumption of upright body posture. The extension of multiple-view fusion improves the event-based semantic analysis by 15%–30%. Our proposed framework proves its effectiveness as it achieves a near real-time performance (13–15 frames/second and 6–8 frames/second) for monocular and two-view video sequences.
Expression of p21 Protein Predicts Clinical Outcome in DLBCL Patients Older than 60 Years Treated with R-CHOP but not CHOP: A Prospective ECOG and Southwest Oncology Group Correlative Study on E4494
Authors: Winter Jane N. , Li Shuli , Aurora Vikas , Variakojis Daina , Nelson Beverly , Krajewska Maryla , Zhang Lijun , Habermann Thomas M. , Fisher Richard I. , Macon William R. , Chhanabhai Mukesh , Felgar Raymond E. , Hsi Eric D. , Medeiros L. Jeffrey , Weick James K. , Weller Edie A. , Melnick Ari , Reed John C. , Horning Sandra J. , Gascoyne Randy D.
Published: April 2010

Purpose: To prospectively investigate the prognostic significance of p21 and p53 expression in diffuse large B-cell lymphoma in the context of the U.S. Intergroup trial comparing conventional cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) chemotherapy to rituximab-CHOP (R-CHOP) induction, with or without maintenance rituximab.

Experimental Design: Immunohistochemical staining of 197 paraffin-embedded biopsy specimens was scored by an independent panel of experts.

Results: The cyclin-dependent kinase inhibitor, p21, was expressed in 55% of cases examined. In a multivariable analysis adjusting for International Prognostic Index score and BCL2 status, p21 expression was a significant, independent, favorable predictive factor for failure-free survival (relative risk, 0.3; P = 0.001) and overall survival (relative risk, 0.3; P = 0.003) for patients treated with R-CHOP. Expression of p21 was not predictive of outcome for CHOP-treated patients.

Only p21-positive cases benefited from the addition of rituximab to CHOP. Among p21-positive patients, treatment with R-CHOP was associated with a higher failure-free survival rate at 5 years compared with CHOP (61% versus 24%; P = 0.01). In contrast, no significant differences were detected in failure-free survival according to treatment arm for p21-negative patients. Expression of p53, alone or in combination with p21, did not predict for outcome in univariable or multivariable analyses.

Conclusions: In this study, p21 protein expression emerged as an important independent predictor of a favorable clinical outcome when rituximab was added to CHOP therapy. These data suggest that rituximab-related effects on lymphoma survival pathways may be functionally linked to p21 activity. Clin Cancer Res; 16(8); 2435–42. ©2010 AACR.
A Novel Prognostic Model for Malignant Mesothelioma Incorporating Quantitative FDG-PET Imaging with Clinical Parameters
Authors: Nowak Anna K. , Francis Roslyn J. , Phillips Michael J. , Millward Michael J. , van der Schaaf Agatha A. , Boucek Jan , Musk Arthur W. , McCoy Melanie J. , Segal Amanda , Robins Peter , Byrne Michael J.
Published: April 2010

Purpose: Existing prognostic systems for malignant pleural mesothelioma do not incorporate imaging information. We aimed to identify the contribution of quantitative fluorodeoxyglucose positron emission tomography (FDG-PET) analysis to other prognostic variables in this disease.

Experimental Design: Patients with malignant pleural mesothelioma underwent helical thoracoabdominal computed tomography and FDG-PET scans at baseline. Patients were treated as clinically indicated and followed for survival. FDG-PET variables derived included total glycolytic volume, a composite of tumor volume and glycolytic activity.

Results: Ninety-three patients were accrued from 2003 to 2006. Of 89 eligible assessable patients, 28 had undergone pleurodesis before enrolment. Seventeen patients remained alive at analysis; median survival is 15.4 months. On univariate analysis, significant prognostic factors were: total glycolytic volume on FDG-PET (P = 0.003), sarcomatoid histology (P < 0.0005), weight loss (P = 0.031), computed tomography stage (P = 0.015), and European Organization for Research and Treatment of Cancer good prognostic score (P = 0.049). In patients with epithelioid or biphasic histology, baseline total glycolytic volume remained predictive of survival in patients with (P = 0.01) or without (P = 0.018) previous pleurodesis. In multivariate analysis, no variable other than histology contributed to the model in patients with sarcomatoid histology; total glycolytic volume and weight loss contributed to the models in patients with nonsarcomatoid histology. computed tomography–assessed tumor-node-metastasis stage did not contribute to the model. A nomogram, which incorporates quantitative PET parameters and pleurodesis into prognostic information, is presented.

Conclusions: Sarcomatoid histology remains the strongest prognostic factor. In patients with non sarcomatoid disease, volumetric FDG-PET parameters are more predictive of survival than tumor-node-metastasis staging, suggesting that tumor volume and glycolytic activity may be more important determinants of prognosis in malignant pleural mesothelioma than anatomic extent of disease. Clin Cancer Res; 16(8); 2409–17. ©2010 AACR.
Selective Cytotoxicity to HER2-Positive Tumor Cells by a Recombinant e23sFv-TD-tBID Protein Containing a Furin Cleavage Sequence
Authors: Wang Fang , Ren Jing , Qiu Xiu-Chun , Wang Li-Feng , Zhu Qing , Zhang Ying-Qi , Huan Yi , Meng Yan-Ling , Yao Li-Bo , Chen Si-Yi , Xu Yan-Ming , Yang An-Gang
Published: April 2010

Purpose: The HER2 antigen is a recognized target on breast cancer cells for immunotherapy. To overcome the immunogenicity and systemic toxicity of traditional immunotoxins, a novel human immunoproapoptotic molecule was developed and its antitumor activity was investigated.

Experimental Design: Recombinant e23sFv-TD-tBID, consisting of a single-chain anti-HER2 antibody fragment linked to a human active truncated Bid by a 10–amino acid residue furin cleavage sequence, was bacterially expressed. Purified e23sFv-TD-tBID was tested for binding, internalization, and cytotoxic activity in cell and for tumor localization and antitumor activity in athymic nude mice bearing established human tumor xenografts.

Results: e23sFv-TD-tBID selectively binds to HER2-positive cells and induces apoptotic cell death in vitro and in vivo. An investigation of its mechanism of action has revealed that e23sFv-TD-tBID was internalized on binding to the surface of HER2-positive tumor cells, proteolytically cleaved and transported directly to cytosol. The antitumor activity of e23sFv-TD-tBID was shown in a dose-dependent manner when injected i.p. into immunodeficient mice bearing human breast carcinomas. Moreover, this immunoproapoptotic protein, either given as a single dose or in combination with chemotherapy agents, significantly inhibited tumor growth without any observed toxic side effects on mice. Magnetic resonance imaging further showed the specific targeting and good penetration of tumors by e23sFv-TD-tBID in vivo. The therapeutic value of e23sFv-TD-tBID to human was shown by its cytotoxic effects on primary patient-derived breast tumor cells but not on endothelial cells.

Conclusion: These data suggest that recombinant e23sFv-TD-tBID has therapeutic potential for HER2-positive tumors and warrant further testing for clinical applications. Clin Cancer Res; 16(8); 2284–94. ©2010 AACR.
ERBB2 and TOP2A in Breast Cancer: A Comprehensive Analysis of Gene Amplification, RNA Levels, and Protein Expression and Their Influence on Prognosis and Prediction
Authors: Brase Jan C. , Schmidt Marcus , Fischbach Thomas , Sültmann Holger , Bojar Hans , Koelbl Heinz , Hellwig Birte , Rahnenführer Jörg , Hengstler Jan G. , Gehrmann Mathias C.
Published: April 2010

Purpose: The prognostic and predictive relevance of epidermal growth factor receptor 2 (ERBB2) and topoisomerase II α (TOP2A) have long been a matter of debate. However, the correlation of DNA amplification, RNA levels, and protein expression and their prognostic role and association with anthracycline responses in node-negative breast cancer have not yet been evaluated.

Experimental Design: We first analyzed TOP2A and ERBB2 at the levels of gene amplification, and RNA and protein expression, and studied their correlations. Additionally, TOP2A and ERBB2 were analyzed in 782 node-negative breast carcinomas in patients who did not receive systemic therapy and in 80 patients treated with epirubicin and cyclophosphamide (EC) prior to surgery.

Results: TOP2A gene amplification did not correlate with protein expression (P = 0.283) and showed an association with gene expression with only borderline significance (P = 0.047). By contrast, TOP2A RNA levels correlated with protein expression (P < 0.001). TOP2A gene expression was significantly associated with the metastasis-free interval (MFI; P < 0.001) and was associated with complete remission in patients treated with EC (P = 0.002). In contrast to TOP2A, ERBB2 gene amplification correlated with RNA level (P < 0.001) and protein expression (P < 0.001). ERBB2 gene expression was associated with the MFI only in estrogen receptor–positive carcinomas, whereas ERBB2 protein expression (P = 0.032) was associated with MFI in the entire cohort.

Conclusions: Overall, our study indicates that the TOP2A RNA level is a good prognostic marker and is also associated with a favorable response to anthracyclin-based therapy. By contrast, ESR1 was associated with poorer responses to anthracyclin-based therapy, whereas the association with ERBB2 RNA was not significant. Clin Cancer Res; 16(8); 2391–401. ©2010 AACR.
Development of a Functional Assay for Homologous Recombination Status in Primary Cultures of Epithelial Ovarian Tumor and Correlation with Sensitivity to Poly(ADP-Ribose) Polymerase Inhibitors
Authors: Mukhopadhyay Asima , Elattar Ahmed , Cerbinskaite Aiste , Wilkinson Sarah J. , Drew Yvette , Kyle Suzanne , Los Gerrit , Hostomsky Zdenek , Edmondson Richard J. , Curtin Nicola J.
Published: April 2010

Purpose: Poly(ADP-ribose) polymerase (PARP) inhibitors selectively target homologous recombination (HR)–defective cells and show good clinical activity in hereditary breast and ovarian cancer associated with BRCA1 or BRCA2 mutations. A high proportion (up to 50%) of sporadic epithelial ovarian cancers (EOC) could be deficient in HR due to genetic or epigenetic inactivation of BRCA1/BRCA2 or other HR genes. Therefore, there is a potential for extending the use of PARP inhibitors to these patients if HR status can be identified. We developed a functional assay of HR status in primary cultures of EOCs based on Rad51 focus formation that correlates well with sensitivity to the potent PARP inhibitor AG014699.

Experimental Design: Primary cultures were derived from ascitic fluid from patients with EOCs. HR status was investigated by γH2AX and Rad51 focus formation by immunofluorescence. Cytotoxicity to PARP inhibitors was tested by sulforhodamine B and survival assay.

Results: Twenty-five cultures were evaluated for HR status and cytotoxicity to PARP inhibitor. Following exposure to AG014699, there was an increase in Rad51 foci (HR competent) in 9 of 24 (36%) but no increase (HR deficient) in 16 of 24 (64%) cultures. Cytotoxicity was observed in 15 of 16 (93%) HR-deficient samples but not in 9 of 9 HR-competent samples following 24-hour exposure to 10 μmol/L AG014699.

Conclusion: HR status can be determined in primary cancer samples by Rad51 focus formation, and this correlates with in vitro response to PARP inhibition. Use of this assay as a biomarker now needs testing in the setting of a clinical trial. Clin Cancer Res; 16(8); 2344–51. ©2010 AACR.
Long Interspersed Nuclear Element 1 Hypomethylation Is a Marker of Poor Prognosis in Stage IA Non–Small Cell Lung Cancer
Authors: Saito Kenichiro , Kawakami Kazuyuki , Matsumoto Isao , Oda Makoto , Watanabe Go , Minamoto Toshinari
Published: April 2010

Purpose: Global hypomethylation and the hypermethylation of gene promoter regions are common events in tumor DNA. The aim of this study was to evaluate the prognostic significance of both global hypomethylation and gene promoter hypermethylation in DNA from non–small cell lung cancer (NSCLC).

Experimental Design: Genomic DNA was obtained from the tumor tissue of 379 NSCLC patients who underwent surgery. Methylation levels were measured by real-time PCR following bisulfite modification of DNA and were correlated with clinicopathologic parameters and patient prognosis. Methylation of long interspersed nuclear element 1 (LINE-1) was used as a surrogate marker for global methylation. Hypermethylation of the APC, CDH13, and RASSF1 promoter regions was also evaluated.

Results: Tumor tissue showed significantly higher CDH13 and RASSF1 methylation levels compared with normal lung tissue, but lower LINE-1 methylation levels. APC, RASSF1, and LINE-1 methylation levels were significant prognostic factors in univariate analysis of an initial cohort of 234 cases. APC and LINE-1 methylation remained significant prognostic factors in multivariate analysis that included age, gender, smoking history, histologic type, and pathologic stage. LINE-1 methylation showed marginally significant prognostic value in stage IA and IB disease. Expansion of the study cohort to 364 cases revealed that LINE-1 methylation had significant prognostic value for stage IA NSCLC patients in multivariate analysis.

Conclusions: LINE-1 hypomethylation was an independent marker of poor prognosis in stage IA NSCLC. Validation of this finding in additional tumor cohorts could have clinical relevance for the management of early-stage NSCLC. Clin Cancer Res; 16(8); 2418–26. ©2010 AACR.
Targeted Cytosine Deaminase-Uracil Phosphoribosyl Transferase Suicide Gene Therapy Induces Small Cell Lung Cancer–Specific Cytotoxicity and Tumor Growth Delay
Authors: Christensen Camilla L. , Gjetting Torben , Poulsen Thomas T. , Cramer Frederik , Roth Jack A. , Poulsen Hans S.
Published: April 2010

Purpose: Small cell lung cancer (SCLC) is a highly malignant cancer for which there is no curable treatment. Novel therapies are therefore in great demand. In the present study we investigated the therapeutic effect of transcriptionally targeted suicide gene therapy for SCLC based on the yeast cytosine deaminase (YCD) gene alone or fused with the yeast uracil phosphoribosyl transferase (YUPRT) gene followed by administration of 5-fluorocytosine (5-FC) prodrug.

Experimental design: The YCD gene or the YCD-YUPRT gene was placed under regulation of the SCLC-specific promoter insulinoma-associated 1 (INSM1). Therapeutic effect was evaluated in vitro in SCLC cell lines and in vivo in SCLC xenografted nude mice using the nonviral nanoparticle DOTAP/cholesterol for transgene delivery.

Results: INSM1-YCD/5-FC and INSM1-YCD-YUPRT/5-FC therapy induced high cytotoxicity in a range of SCLC cell lines. The highest therapeutic effect was obtained from the YCD-YUPRT fusion gene strategy. No cytotoxicity was induced after treatment of cell lines of other origin than SCLC. In addition the INSM1-YCD-YUPRT/5-FC therapy was superior to an established suicide gene system consisting of the herpes simplex virus thymidine kinase (HSVTK) gene and the prodrug ganciclovir. The superior effect was in part due to massive bystander cytotoxicity of YCD-YUPRT-produced toxins. Finally, INSM1-YCD-YUPRT/5-FC therapy induced significant tumor growth delay in SCLC xenografts compared with control-treated xenografts.

Conclusions: The current study is the first to test cytosine deaminase-based suicide gene therapy for SCLC and the first to show an antitumor effect from the delivery of suicide gene therapeutics for SCLC in vivo. Clin Cancer Res; 16(8); 2308–19. ©2010 AACR.
Antitumor Efficacy Profile of PKI-402, a Dual Phosphatidylinositol 3-Kinase/Mammalian Target of Rapamycin Inhibitor
Authors: Mallon Robert , Hollander Irwin , Feldberg Larry , Lucas Judy , Soloveva Veronica , Venkatesan Aranapakam , Dehnhardt Christoph , Delos Santos Efren , Chen Zecheng , dos Santos Osvaldo , Ayral-Kaloustian Semiramis , Gibbons Jay
Published: April 2010

PKI-402 is a selective, reversible, ATP-competitive, equipotent inhibitor of class I phosphatidylinositol 3-kinases (PI3K), including PI3K-α mutants, and mammalian target of rapamycin (mTOR; IC50 versus PI3K-α = 2 nmol/L). PKI-402 inhibited growth of human tumor cell lines derived from breast, brain (glioma), pancreas, and non–small cell lung cancer tissue and suppressed phosphorylation of PI3K and mTOR effector proteins (e.g., Akt at T308) at concentrations that matched those that inhibited cell growth. In MDA-MB-361 [breast: Her2+ and PIK3CA mutant (E545K)], 30 nmol/L PKI-402 induced cleaved poly(ADP-ribose) polymerase (PARP), a marker for apoptosis. In vivo, PKI-402 inhibited tumor growth in MDA-MB-361, glioma (U87MG), and lung (A549) xenograft models. In MDA-MB-361, PKI-402 at 100 mg/kg (daily for 5 days, one round) reduced initial tumor volume of 260 mm3 to 129 mm3 and prevented tumor regrowth for 70 days. In MDA-MB-361 tumors, PKI-402 (100 mg/kg, single dose) suppressed Akt phosphorylation (at T308) and induced cleaved PARP. Suppression of phosphorylated Akt (p-Akt) was complete at 8 hours and still evident at 24 hours. Cleaved PARP was evident at 8 and 24 hours. In normal tissue (heart and lung), PKI-402 (100 mg/kg) had minimal effect on p-Akt, with no detectable cleaved PARP. Preferential accumulation of PKI-402 in tumor tissue was observed. Complete, sustained suppression of Akt phosphorylation may cause tumor regression in MDA-MB-361 and other xenograft models. We are testing whether dual PI3K/mTOR inhibitors can durably suppress p-Akt, induce cleaved PARP, and cause tumor regression in a diverse set of human tumor xenograft models. Mol Cancer Ther; 9(4); 976–84. ©2010 AACR.
SIRT Inhibitors Induce Cell Death and p53 Acetylation through Targeting Both SIRT1 and SIRT2
Authors: Peck Barrie , Chen Chun-Yuan , Ho Ka-Kei , Di Fruscia Paolo , Myatt Stephen S. , Coombes R. Charles , Fuchter Matthew J. , Hsiao Chwan-Deng , Lam Eric W.-F.
Published: April 2010

SIRT proteins play an important role in the survival and drug resistance of tumor cells, especially during chemotherapy. In this study, we investigated the potency, specificity, and cellular targets of three SIRT inhibitors, Sirtinol, Salermide, and EX527. Cell proliferative and cell cycle analyses showed that Sirtinol and Salermide, but not EX527, were effective in inducing cell death at concentrations of 50 μmol/L or over in MCF-7 cells. Instead, EX527 caused cell cycle arrest at G1 at comparable concentrations. In vitro SIRT assays using a p53 peptide substrate showed that all three compounds are potent SIRT1/2 inhibitors, with EX527 having the highest inhibitory activity for SIRT1. Computational docking analysis showed that Sirtinol and Salermide have high degrees of selectivity for SIRT1/2, whereas EX527 has high specificity for SIRT1 but not SIRT2. Consistently, Sirtinol and Salermide, but not EX527, treatment resulted in the in vivo acetylation of the SIRT1/2 target p53 and SIRT2 target tubulin in MCF-7 cells, suggesting that EX527 is ineffective in inhibiting SIRT2 and that p53 mediates the cytotoxic function of Sirtinol and Salermide. Studies using breast carcinoma cell lines and p53-deficient mouse fibroblasts confirmed that p53 is essential for the Sirtinol and Salermide-induced apoptosis. Further, we showed using small interfering RNA that silencing both SIRTs, but not SIRT1 and SIRT2 individually, can induce cell death in MCF-7 cells. Together, our results identify the specificity and cellular targets of these novel inhibitors and suggest that SIRT inhibitors require combined targeting of both SIRT1 and SIRT2 to induce p53 acetylation and cell death. Mol Cancer Ther; 9(4); 844–55. ©2010 AACR.
Treatment with Panobinostat Induces Glucose-Regulated Protein 78 Acetylation and Endoplasmic Reticulum Stress in Breast Cancer Cells
Authors: Rao Rekha , Nalluri Srilatha , Kolhe Ravindra , Yang Yonghua , Fiskus Warren , Chen Jianguang , Ha Kyungsoo , Buckley Kathleen M. , Balusu Ramesh , Coothankandaswamy Veena , Joshi Atul , Atadja Peter , Bhalla Kapil N.
Published: April 2010

Increased levels of misfolded polypeptides in the endoplasmic reticulum (ER) triggers the dissociation of glucose-regulated protein 78 (GRP78) from the three transmembrane ER-stress mediators, i.e., protein kinase RNA-like ER kinase (PERK), activating transcription factor-6 (ATF6), and inositol-requiring enzyme 1α, which results in the adaptive unfolded protein response (UPR). In the present studies, we determined that histone deacetylase-6 (HDAC6) binds and deacetylates GRP78. Following treatment with the pan-histone deacetylase inhibitor panobinostat (Novartis Pharmaceuticals), or knockdown of HDAC6 by short hairpin RNA, GRP78 is acetylated in 11 lysine residues, which dissociates GRP78 from PERK. This is associated with the activation of a lethal UPR in human breast cancer cells. Coimmunoprecipitation studies showed that binding of HDAC6 to GRP78 requires the second catalytic and COOH-terminal BUZ domains of HDAC6. Treatment with panobinostat increased the levels of phosphorylated-eukaryotic translation initiation factor (p-eIF2α), ATF4, and CAAT/enhancer binding protein homologous protein (CHOP). Panobinostat treatment also increased the proapoptotic BIK, BIM, BAX, and BAK levels, as well as increased the activity of caspase-7. Knockdown of GRP78 sensitized MCF-7 cells to bortezomib and panobinostat-induced UPR and cell death. These findings indicate that enforced acetylation and decreased binding of GRP78 to PERK is mechanistically linked to panobinostat-induced UPR and cell death of breast cancer cells. Mol Cancer Ther; 9(4); 942–52. ©2010 AACR.
Organic Cation Transporters Modulate the Uptake and Cytotoxicity of Picoplatin, a Third-Generation Platinum Analogue
Authors: More Swati S. , Li Shuanglian , Yee Sook Wah , Chen Ligong , Xu Zhidong , Jablons David M. , Giacomini Kathleen M.
Published: April 2010

Picoplatin, a third-generation platinum agent, is efficacious against lung cancers that are otherwise resistant or become refractory during platinum treatment. This effort was aimed at the determination of the influence of organic cation transporters 1, 2, and 3 (OCT1, OCT2, and OCT3) and their genetic variants on cellular uptake of picoplatin and on the individual components of the ensuing cytotoxicity such as DNA adduct formation. The effect of OCT1 on picoplatin pharmacokinetics and antitumor efficacy was determined using OCT knockout mice and HEK293 xenografts stably expressing OCT1. The uptake and DNA adduct formation of picoplatin were found to be significantly enhanced by the expression of the OCTs. Expression of OCT1 and OCT2, but not OCT3, significantly enhanced picoplatin cytotoxicity, which was reduced in the presence of an OCT inhibitor. Common reduced functional variants of OCT1 and OCT2 led to reduction in uptake and DNA adduct formation of picoplatin in comparison with the reference OCT1 and OCT2. Pharmacokinetic parameters of picoplatin in Oct1−/− and Oct1+/+ mice were not significantly different, suggesting that the transporters do not influence the disposition of the drug. In contrast, the volume of OCT1-expressing xenografts in mice was significantly reduced by picoplatin treatment, suggesting that OCT1 may enhance the antitumor efficacy of picoplatin. These studies provide a basis for follow-up clinical studies that would seek to examine the relationship between the anticancer efficacy of picoplatin and expression levels of OCTs and their genetic variants in tumors. Mol Cancer Ther; 9(4); 1058–69. ©2010 AACR.
Garcinol Potentiates TRAIL-Induced Apoptosis through Modulation of Death Receptors and Antiapoptotic Proteins
Authors: Prasad Sahdeo , Ravindran Jayaraj , Sung Bokyung , Pandey Manoj K. , Aggarwal Bharat B.
Published: April 2010

Whether garcinol, the active component of Garcinia indica, can modulate the sensitivity of cancer cells to TRAIL, a cytokine currently in phase II clinical trial, was investigated. We found that garcinol potentiated TRAIL-induced apoptosis of cancer cells as indicated by intracellular esterase activity, DNA strand breaks, accumulation of the membrane phospholipid phosphatidylserine, mitochondrial activity, and activation of caspase-8, -9, and -3. We found that garcinol, independent of the cell type, induced both of the TRAIL receptors, death receptor 4 (DR4) and DR5. Garcinol neither induced the receptors on normal cells nor sensitized them to TRAIL. Deletion of DR5 or DR4 by small interfering RNA significantly reduced the apoptosis induced by TRAIL and garcinol. In addition, garcinol downregulated various cell survival proteins including survivin, bcl-2, XIAP, and cFLIP, and induced bid cleavage, bax, and cytochrome c release. Induction of death receptors by garcinol was found to be independent of modulation of CCAAT/enhancer-binding protein-homologous protein, p53, bax, extracellular signal-regulated kinase, or c-Jun-NH2-kinase. The effect of garcinol was mediated through the generation of reactive oxygen species, in as much as induction of both death receptors, modulation of antiapoptotic and proapoptotic proteins, and potentiation of TRAIL-induced apoptosis were abolished by N-acetyl cysteine and glutathione. Interestingly, garcinol also converted TRAIL-resistant cells into TRAIL-sensitive cells. Overall, our results indicate that garcinol can potentiate TRAIL-induced apoptosis through upregulation of death receptors and downregulation of antiapoptotic proteins. Mol Cancer Ther; 9(4); 856–68. ©2010 AACR.
Nutlin-3a Induces Cytoskeletal Rearrangement and Inhibits the Migration and Invasion Capacity of p53 Wild-Type Cancer Cells
Authors: Moran Diarmuid M. , Maki Carl G.
Published: April 2010

MDM2 is an E3 ubiquitin ligase that binds and ubiquitinates the tumor suppressor protein p53, leading to its proteasomal degradation. Nutlin-3a (Nutlin) is a preclinical drug that binds MDM2 and prevents the interaction between MDM2 and p53, leading to p53 stabilization and activation of p53 signaling events. Previous studies have reported that Nutlin promotes growth arrest and/or apoptosis in cancer cells that express wild-type p53. In the current study, Nutlin treatment caused a cytoskeletal rearrangement in p53 wild-type human cancer cells from multiple etiologies. Specifically, Nutlin decreased actin stress fibers and reduced the size and number of focal adhesions in treated cells. This process was dependent on p53 expression but was independent of p21 expression and growth arrest. Consistent with this, Nutlin-treated cells failed to form filamentous actin–based motility structures (lamellipodia) and displayed significantly decreased directional persistence in response to migratory cues. Finally, chemotactic assays showed a p53-dependent/p21-independent decrease in migratory and invasive capacity of Nutlin-treated cells. Taken together, these findings reveal that Nutlin treatment can inhibit the migration and invasion capacity of p53 wild-type cells, adding to the potential therapeutic benefit of Nutlin and other small molecule MDM2 inhibitors. Mol Cancer Ther; 9(4); 895–905. ©2010 AACR.
Preclinical Antitumor Activity of the Orally Available Heat Shock Protein 90 Inhibitor NVP-BEP800
Authors: Massey Andrew J. , Schoepfer Joseph , Brough Paul A. , Brueggen Josef , Chène Patrick , Drysdale Martin J. , Pfaar Ulrike , Radimerski Thomas , Ruetz Stephan , Schweitzer Alain , Wood Mike , Garcia-Echeverria Carlos , Jensen Michael Rugaard
Published: April 2010

Heat shock protein 90 (Hsp90) is a ubiquitously expressed molecular chaperone with ATPase activity involved in the conformational maturation and stability of key signaling molecules involved in cell proliferation, survival, and transformation. Through its ability to modulate multiple pathways involved in oncogenesis, Hsp90 has generated considerable interest as a therapeutic target. NVP-BEP800 is a novel, fully synthetic, orally bioavailable inhibitor that binds to the NH2-terminal ATP-binding pocket of Hsp90. NVP-BEP800 showed activity against a panel of human tumor cell lines and primary human xenografts in vitro at nanomolar concentrations. In A375 melanoma and BT-474 breast cancer cell lines, NVP-BEP800 induced client protein degradation (including ErbB2, B-RafV600E, Raf-1, and Akt) and Hsp70 induction. Oral administration of NVP-BEP800 was well tolerated and induced robust antitumor responses in tumor xenograft models, including regression in the BT-474 breast cancer model. In these tumor models, NVP-BEP800 modulated Hsp90 client proteins and downstream signaling pathways at doses causing antitumor activity. NVP-BEP800 showed in vivo activity in a variety of dosing regimens covering daily to weekly schedules, potentially providing a high degree of flexibility in dose and schedule within the clinical setting. Overall, given the mechanism of action, preclinical activity profile, tolerability, and pharmaceutical properties, NVP-BEP800 is an exciting new oral Hsp90 inhibitor warranting further development. Mol Cancer Ther; 9(4); 906–19. ©2010 AACR.