bluuebunny/crossref_metadata_2025 huggingface dataset:
SIMPLE AND EFFECTIVE C++ MATRIX–VECTOR LIBRARY FOR NONPROFESSIONALS IN COMPUTER SCIENCE
Authors: BRČIĆ STANKO , ŽUGIĆ-ZORNIJA LJILJANA
Published: April 2009

This paper presents a matrix–vector computational library written in the C++ language. Effective matrix–vector manipulation is an essential aspect of scientific numerical modeling, especially while using the finite element method. Even though there are a lot of matrix libraries written in C++ which are freely or commercially available on the Internet, most of them are either too complicated or too simple, i.e. with very limited capabilities. Therefore, the main idea is to develop a reliable matrix library, as part of the computer code in C++, which will be, at the same time, as simple as possible and as complex as possible. Consequently, the basic motto of the library, which is called SMV++, is "Simple and effective" and it is meant to be of use to researchers dedicated to reliable obtained results and not to the "beauty of programming." The library is developed without use of the template concept and inheritance, with the purpose of understanding it easily and of extending it easily with new possibilities and algorithms. Last but not least, it is aimed at having a simple and intuitive user interface. The bottom line is that the SMV++ is not meant to be of use to someone who is in the software development business. Rather, it is oriented to the user who has a modest programming knowledge (e.g. a Ph.D. student) and who is basically concerned about how to obtain the solution to the considered problem, for which he has to do some "homemade programming," because the available commercial software cannot be applied for all of his/her needs. Consequently, as mentioned, the motto of the library is "Simple and effective"; the effectiveness is in the sense of complexity of possibilities, rather than computational efficiency. However, if one is forced to choose between the two in the development of the library, having in mind the target users, priority is given to simplicity of use.
HEGDE'S INTERFACE NUMERICAL TECHNIQUE FOR RESOLVING QUASI-ONE-DIMENSIONAL NOZZLE FLOWS
Authors: HEGDE GANESH S. , MADHU G. M.
Published: April 2009

Faster convergence, better accuracy and improved stability of the solutions to fluid flow and heat transfer problems in CFD reduce the computational cost and time. The numerical solutions to partial differential equations governing the physical flow and heat phenomena, using computer software and hardware, have been obtained by various techniques which have been refined over the years. The numerical techniques have obtained the base in finite difference method (FDM) approximations derived from Taylor series expansion. Because of linearization, FDM approximations have truncation error creeping into the values of the partial derivatives, which projects an unrealistic picture of the final outcome of results in terms of accuracy, convergence and stability. As the prime objective of this paper, the minimization of truncation error is attempted with the aid of the interface theory (briefly described in the appendix) used as a computational treatment tool. In simple terms, the interface theory provides an optimal solution to all variables in a linear indeterminate system with redundancy in unknowns. The effort has converged in the form of Hegde's interface numerical technique (HINT), which is demonstrated on a quasi-one-dimensional nozzle flow, the physical behavior of which is described by the Navier–Stokes equation considered specific to the said case. HINT could successfully match the results of MacCormack's predictor–corrector method as far as the accuracy is concerned, but with less computational effort and higher productivity. To the knowledge of the authors, HINT may be considered both original and different for its kind in the vast developments in CFD.
ON THE CONVERGENCE OF THE KRIGING-BASED FINITE ELEMENT METHOD
Authors: WONG F. T. , KANOK-NUKULCHAI W.
Published: April 2009

An enhancement of the FEM using Kriging interpolation (K-FEM) was recently proposed. This method offers advantages over the conventional FEM and mesh-free methods. With Kriging interpolation, the approximated field over an element is influenced not only by its own element nodes but also by a set of satellite nodes outside the element. This results in incompatibility along interelement boundaries. Consequently, the convergence of the solutions is questionable. In this paper, the convergence is investigated through several numerical tests. It is found that the solutions of the K-FEM with an appropriate range of parameters converge to the corresponding exact solutions.
Community Ecology of Fungal Pathogens Causing Wheat Head Blight
Authors: Xu Xiangming , Nicholson Paul
Published: April 2009

Research on the pathogen components involved in Fusarium head blight (FHB) along with the effects of their interactions on disease development and mycotoxin accumulation is reviewed. The fungal components within the FHB complex differ significantly in different environments. Individual species may respond differently to, and be differentially influenced by, particular disease control measures. Almost all published co-inoculation studies on wheat spikes or grains show that competitive interactions among FHB pathogens are the rule when fungal/disease development is considered. However, the fungi with the competitive advantage do not usually gain any advantage from the presence of other weaker competing fungi. Total mycotoxin production in mixed inoculations may decrease, increase, or remain unchanged compared with single-isolate inoculations, depending on the fungal species concerned and environmental conditions. A few recent studies, where each individual fungal component was quantified using molecular methods, suggest that mycotoxin productivity in mixed inoculations generally increases.
Plant Disease Diagnostic Capabilities and Networks
Authors: Miller Sally A. , Beed Fen D. , Harmon Carrie Lapaire
Published: April 2009

Emerging, re-emerging and endemic plant pathogens continue to challege our ability to safeguard plant health worldwide. Further, globalization, climate change, increased human mobility, and pathogen and vector evolution have combined to increase the spread of invasive plant pathogens. Early and accurate diagnoses and pathogen surveillance on local, regional, and global scales are necessary to predict outbreaks and allow time for development and application of mitigation strategies. Plant disease diagnostic networks have developed worldwide to address the problems of efficient and effective disease diagnosis and pathogen detection, engendering cooperation of institutions and experts within countries and across national borders. Networking maximizes impact in the face of shrinking government investments in agriculture and diminishing human resource capacity in diagnostics and applied pathology. New technologies promise to improve the speed and accuracy of disease diagnostics and pathogen detection. Widespread adoption of standard operating procedures and diagnostic laboratory accreditation serve to build trust and confidence among institutions. Case studies of national, regional, and international diagnostic networks are presented.
Diversity, Pathogenicity, and Management of Verticillium Species
Authors: Klosterman Steven J. , Atallah Zahi K. , Vallad Gary E. , Subbarao Krishna V.
Published: April 2009

The genus Verticillium encompasses phytopathogenic species that cause vascular wilts of plants. In this review, we focus on Verticillium dahliae, placing emphasis on the controversy surrounding the elevation of a long-spored variant as a new species, recent advances in the analysis of compatible and incompatible interactions, highlighted by the use of strains expressing fluorescent proteins, and the genetic diversity among Verticillium spp. A synthesis of the approaches to explore genetic diversity, gene flow, and the potential for cryptic recombination is provided. Control of Verticillium wilt has relied on a panoply of chemical and nonchemical strategies, but is beset with environmental or site-specific efficacy problems. Host resistance remains the most logical choice, but is unavailable in most crops. The genetic basis of resistance to Verticillium wilt is unknown in most crops, as are the subcellular signaling mechanisms associated with Ve-mediated, race-specific resistance. Increased understanding in each of these areas promises to facilitate management of Verticillium wilts across a broad range of crops.
Look Before You Leap: Memoirs of a “Cell Biological” Plant Pathologist
Authors: Heath Michèle C.
Published: April 2009

In this article, I recount how I became a plant pathologist and used clues derived from light and electron microscopy to direct my research on the interactions between plants and biotrophic fungi. Examples of the value of microscopic examination are described for investigations of host compatibility, the hypersensitive response, nonhost resistance, and the evolution of host-parasite specificity.
The Importance of History for Economic Development
Authors: Nunn Nathan
Published: April 2009

This article provides a survey of a growing body of empirical evidence that points toward the important long-term effects that historic events can have on economic development. The most recent studies, using microlevel data and more sophisticated identification techniques, have moved beyond testing whether history matters and attempt to identify exactly why history matters. The most commonly examined channels include institutions, culture, knowledge and technology, and movements between multiple equilibria. The article concludes with a discussion of the questions that remain and the direction of current research in the literature.
School Vouchers and Student Achievement: Recent Evidence and Remaining Questions
Authors: Rouse Cecilia Elena , Barrow Lisa
Published: April 2009

In this article, we review the empirical evidence on the impact of education vouchers on student achievement and briefly discuss the evidence from other forms of school choice. The best research to date finds relatively small achievement gains for students offered education vouchers, most of which are not statistically different from zero. Furthermore, what little evidence exists regarding the potential for public schools to respond to increased competitive pressure generated by vouchers suggests that one should remain wary that large improvements would result from a more comprehensive voucher system. The evidence from other forms of school choice is also consistent with this conclusion. Many questions remain unanswered, however, including whether vouchers have longer-run impacts on outcomes such as graduation rates, college enrollment, or even future wages, and whether vouchers might nevertheless provide a cost-neutral alternative to our current system of public education provision at the elementary and secondary school level.
Regulation of Translation Initiation by RNA Binding Proteins
Authors: Babitzke Paul , Baker Carol S. , Romeo Tony
Published: April 2009

RNA binding proteins are capable of regulating translation initiation by a variety of mechanisms. Although the vast majority of these regulatory mechanisms involve translational repression, one example of translational activation has been characterized in detail. The RNA recognition targets of these regulatory proteins exhibit a wide range in structural complexity, with some proteins recognizing complex pseudoknot structures and others binding to simple RNA hairpins and/or short repeated single-stranded sequences. In some instances the bound protein directly competes with ribosome binding, and in other instances the bound protein promotes formation of an RNA structure that inhibits ribosome binding. Examples also exist in which the bound protein traps the ribosome in a complex that is incapable of initiating translation.
Effects of 7 days of exercise training on insulin sensitivity and responsiveness in type 2 diabetes mellitus
Authors: Kirwan John P. , Solomon Thomas P. J. , Wojta Daniel M. , Staten Myrlene A. , Holloszy John O.
Published: April 2009

The objectives of this study were to determine whether 1) the improvement in insulin action induced by short-term exercise training in patients with type 2 diabetes is due to an improvement in insulin sensitivity, an improvement in insulin responsiveness, or a combination of improved insulin sensitivity and responsiveness and 2) short-term exercise training results in improved suppression of hepatic glucose production by insulin. Fourteen obese patients with type 2 diabetes, age 64 ± 2 yr, underwent a two-stage hyperinsulinemic euglycemic clamp procedure, first stage 40 mU·m−2·min−1insulin infusion, second stage 1,000 mU·m−2·min−1insulin infusion, together with a [3-3H]glucose infusion, before and after 7 days of exercise. The training consisted of 30 min of cycling and 30 min of treadmill walking at ∼70% of maximal aerobic capacity daily for 7 days. The exercise program resulted in improvements in insulin action in the absence of weight loss. Glucose disposal rates during the euglycemic clamp were significantly increased at both hyperinsulinemic stages after training (40 mU: 1.84 ± 0.32 to 2.67 ± 0.37 mg·kg−1·min−1, P < 0.0001; 1,000 mU: 7.57 ± 0.61 to 8.84 ± 0.56 mg·kg−1·min−1, P = 0.008). Hepatic glucose production, both in the basal state (3.17 ± 0.43 vs. 2.54 ± 0.26 mg·kg−1·min−1, P = 0.05) and during the 40-mU clamp stage (1.15 ± 0.41 vs. 0.46 ± 0.20 mg·kg−1·min−1, P = 0.03), was significantly reduced after training. One week of vigorous exercise training can induce significant improvements in insulin action in type 2 diabetes. These improvements include increased peripheral insulin sensitivity and responsiveness as well as enhanced suppression of hepatic glucose production.
High glucose concentration in cell culture medium does not acutely affect human mesenchymal stem cell growth factor production or proliferation
Authors: Weil Brent R. , Abarbanell Aaron M. , Herrmann Jeremy L. , Wang Yue , Meldrum Daniel R.
Published: April 2009

Optimizing the function and proliferative capacity of stem cells is essential to maximize their therapeutic benefits. High glucose concentrations are known to have detrimental effects on many cell types. We hypothesized that human mesenchymal stem cells (hMSCs) cultured in high glucose-containing media would exhibit diminished proliferation and attenuated production of VEGF, hepatocyte growth factor (HGF), and FGF2 in response to treatment with TNF-α, LPS, or hypoxia. hMSCs were plated in medium containing low (5.5 mM) and high (20 mM or 30 mM) glucose concentrations and treated with TNF-α, LPS, or hypoxia. Supernatants were collected at 24 and 48 h and assayed via ELISA for VEGF, HGF, and FGF2. In addition, hMSCs were cultured on 96-well plates at the above glucose concentrations, and proliferation at 48 h was determined via bromo-2′-deoxy-uridine (BrdU) incorporation. At 24 and 48 h, TNF-α, LPS, and hypoxia-treated hMSCs produced significantly higher VEGF, HGF, and FGF2 compared with control. Hypoxia-induced VEGF production by hMSCs was the most pronounced change over baseline. At both 24 and 48 h, glucose concentration did not affect production of VEGF, HGF, or FGF2 by untreated hMSCs and those treated with TNF-α, LPS, or hypoxia. Proliferation of hMSCs as determined via BrdU incorporation was unaffected by glucose concentration of the media. Contrary to what has been observed with other cells, hMSCs may be resistant to the short-term effects of high glucose. Ongoing efforts to characterize and optimize ex vivo and in vivo conditions are critical if the therapeutic benefits of MSCs are to be maximized.
Regulation of Cation Channel Voltage and Ca2+ Dependence by Multiple Modulators
Authors: Gardam Kate E. , Magoski Neil S.
Published: April 2009

Ion channel regulation is key to controlling neuronal excitability. However, the extent that modulators and gating factors interact to regulate channels is less clear. For Aplysia, a nonselective cation channel plays an essential role in reproduction by driving an afterdischarge in the bag cell neurons to elicit egg-laying hormone secretion. We examined the regulation of cation channel voltage and Ca2+ dependence by protein kinase C (PKC) and inositol trisphosphate (IP3)—two prominent afterdischarge signals. In excised, inside-out patches, the channel remained open longer and reopened more often with depolarization from −90 to +30 mV. As previously reported, PKC could closely associate with the channel and increase activity at −60 mV. We now show that, following the effects of PKC, voltage dependence was shifted to the left (essentially enhanced), particularly at more negative voltages. Conversely, the voltage dependence of channels lacking PKC was shifted to the right (essentially suppressed). Predictably, activity was increased at all Ca2+ concentrations following the effects of PKC; nevertheless, Ca2+ dependence was actually shifted to the right. Moreover, whereas IP3 did not alter activity at −60 mV, it drastically shifted Ca2+ dependence to the right—an outcome largely reversed by PKC. With respect to the afterdischarge, these data suggest PKC initially upregulates the channel by direct gating and shifting voltage dependence to the left. Subsequently, PKC and IP3 attenuate the channel by suppressing Ca2+ dependence. This ensures hormone delivery by allowing afterdischarge initiation and maintenance but also prevents interminable bursting. Similar regulatory interactions may be used by other neurons to achieve diverse outputs.
Expression profiling of skeletal muscle in young bulls treated with steroidal growth promoters
Authors: Carraro L. , Ferraresso S. , Cardazzo B. , Romualdi C. , Montesissa C. , Gottardo F. , Patarnello T. , Castagnaro M. , Bargelloni L.
Published: April 2009

Dexamethasone (Dex), alone or in association with estrogens, is often illegally administered per os at very low dosage as a growth promoter in beef cattle, with effects that are opposite to the muscle wasting and atrophy induced by repeated administration at therapeutic dosages. In vitro and in vivo studies have investigated the catabolic effects of Dex at therapeutic doses on skeletal muscle, demonstrating an increase in the expression of GDF8 (myostatin) gene, a well-known negative regulator of skeletal muscle mass, in a dose-dependent way. This suggested a direct role of myostatin in Dex-induced muscle wasting. In the present study, an oligonucleotide microarray platform was used to compare expression profiles of beef cattle muscle in animals treated with either Dex or Dex plus 17-β estradiol (Estr) administered at subtherapeutic dosage, against untreated controls. Data analysis demonstrates that the expression profiles were strongly affected by Dex treatment with hundreds of genes upregulated with relevant fold-change, whereas seven genes were downregulated including the myostatin gene. On the contrary, the number of differentially regulated genes was lower in response to the addition of Estr to the Dex treatment. Differentially regulated genes were analyzed to describe the effects of these treatments on muscle physiology, highlighting the importance of specific pathways (e.g., Wnt or cytokine signaling) and cellular processes (e.g., cell shape and motility). Finally, the observed differences in the expression profile will allow the development of indirect bio-markers to detect illegal Dex treatments in beef cattle using quantitative RT-PCR.
Simple Spectrophotometric Method for Determination of Paroxetine in Tablets Using 1,2‐Naphthoquinone‐4‐Sulphonate as a Chromogenic Reagent
Authors: Darwish Ibrahim A. , Abdine Heba H. , Amer Sawsan M. , Al-Rayes Lama I.
Published: April 2009

Simple and rapid spectrophotometric method has been developed and validated for the determination of paroxetine (PRX) in tablets. The proposed method was based on nucleophilic substitution reaction of PRX with 1,2‐naphthoquinone‐4‐sulphonate (NQS) in an alkaline medium to form an orange‐colored product of maximum absorption peak (λmax) at 488 nm. The stoichiometry and kinetics of the reaction were studied, and the reaction mechanism was postulated. Under the optimized reaction conditions, Beer′s law correlating the absorbance (A) with PRX concentration (C) was obeyed in the
range of 1–8 μg mL−1. The regression equation for the calibration data was: A = 0.0031 + 0.1609 C, with good correlation coefficients (0.9992).
The molar absorptivity (ε) was 5.9 × 105 L mol−1 1 cm−1. The limits of detection and quantitation were 0.3 and 0.8 μg mL−1, respectively. The precision of the method was satisfactory; the values of relative standard deviations did not exceed 2%. The proposed method was successfully applied to the determination of PRX in its pharmaceutical tablets with good accuracy and precisions; the label claim percentage was 97.17 ± 1.06
%. The results obtained by the proposed method were comparable with those obtained by the official method.
Device and Circuit Design Challenges in the Digital Subthreshold
Region for Ultralow-Power Applications
Authors: Vaddi Ramesh , Dasgupta S. , Agarwal R. P.
Published: April 2009

In recent years, subthreshold operation has gained a lot of attention due to ultra low-power consumption in applications requiring low to medium performance. It has also been shown that by optimizing the device structure, power consumption of digital subthreshold
logic can be further minimized while improving its performance. Therefore, subthreshold circuit design is very promising for future ultra low-energy sensor applications as well as high-performance parallel processing. This paper deals with various device and circuit design challenges associated with the state of the art in optimal digital subthreshold circuit design and reviews device design methodologies and circuit topologies for optimal digital subthreshold operation. This paper identifies the suitable candidates for subthreshold operation at device and circuit levels for optimal subthreshold circuit design and provides an effective roadmap for digital designers interested to work with ultra low-power applications.
Convergence of Batch Split‐Complex Backpropagation Algorithm for Complex‐Valued Neural Networks
Authors: Zhang Huisheng , Zhang Chao , Wu Wei
Published: April 2009

The batch split‐complex backpropagation (BSCBP) algorithm for training complex‐valued neural networks is considered. For constant learning rate, it is proved that the error function of BSCBP algorithm is monotone during the training iteration process, and the gradient of the error function tends to zero. By adding a moderate condition, the weights sequence itself is also proved to be convergent. A numerical example is given to support the theoretical analysis.
A Tumor-Protective Role for Human Kallikrein-Related Peptidase 6 in Breast Cancer Mediated by Inhibition of Epithelial-to-Mesenchymal Transition
Authors: Pampalakis Georgios , Prosnikli Evangelia , Agalioti Theodora , Vlahou Antonia , Zoumpourlis Vassilis , Sotiropoulou Georgia
Published: April 2009

Human kallikrein-related peptidase 6 (KLK6) was cloned as a putative class II tumor suppressor based on its inactivated expression in metastatic breast cancer. Here, we investigated the mechanism(s) underlying the silencing of KLK6 gene in metastatic breast cancer and its putative implications for tumor progression. We present evidence that tumor-specific loss of KLK6 expression is due to hypermethylation of specific CpGs located in the KLK6 proximal promoter. Methylation-dependent binding of methyl CpG-binding protein 2 and the formation of repressive chromatin mediated by localized histone deacetylation are critical components of KLK6 silencing in breast tumors. Re-expression of KLK6 in nonexpressing MDA-MB-231 breast tumor cells by stable cDNA transfection resulted in marked reversal of their malignant phenotype, manifested by lower proliferation rates and saturation density, marked inhibition of anchorage-independent growth, reduced cell motility, and their dramatically reduced ability to form tumors when implanted in severe combined immunodeficiency mice. Interestingly, inhibition of tumor growth was observed at physiologic concentrations of KLK6, but not when KLK6 was highly overexpressed, as observed in a subset of breast tumors. Differential proteomic profiling revealed that KLK6 re-expression results in significant down-regulation of vimentin which represents an established marker of epithelial-to-mesenchymal transition of tumor cells and in concomitant up-regulation of calreticulin and epithelial markers cytokeratin 8 and 19, indicating that KLK6 may play a protective role against tumor progression that is likely mediated by inhibition of epithelial-to-mesenchymal transition. We suggest that KLK6 is an epigenetically regulated tumor suppressor in human breast cancer and provide ways of pharmacologic modulation. [Cancer Res 2009;69(9):3779–87]
Doxorubicin and Paclitaxel-Loaded Lipid-Based Nanoparticles Overcome Multidrug Resistance by Inhibiting P-Glycoprotein and Depleting ATP
Authors: Dong Xiaowei , Mattingly Cynthia A. , Tseng Michael T. , Cho Moo J. , Liu Yang , Adams Val R. , Mumper Russell J.
Published: April 2009

To test the ability of nanoparticle formulations to overcome P-glycoprotein (P-gp)–mediated multidrug resistance, several different doxorubicin and paclitaxel-loaded lipid nanoparticles were prepared. Doxorubicin nanoparticles showed 6- to 8-fold lower IC50 values in P-gp–overexpressing human cancer cells than those of free doxorubicin. The IC50 value of paclitaxel nanoparticles was over 9-fold lower than that of Taxol in P-gp–overexpressing cells. A series of in vitro cell assays were used including quantitative studies on uptake and efflux, inhibition of calcein acetoxymethylester efflux, alteration of ATP levels, membrane integrity, mitochondrial membrane potential, apoptosis, and cytotoxicity. Enhanced uptake and prolonged retention of doxorubicin were observed with nanoparticle-based formulations in P-gp–overexpressing cells. Calcein acetoxymethylester and ATP assays confirmed that blank nanoparticles inhibited P-gp and transiently depleted ATP. I.v. injection of pegylated paclitaxel nanoparticles showed marked anticancer efficacy in nude mice bearing resistant NCI/ADR-RES tumors versus all control groups. Nanoparticles may be used to target both drug and biological mechanisms to overcome multidrug resistance via P-gp inhibition and ATP depletion. [Cancer Res 2009;69(9):3918–26]
Antitumor Activity of γδ T Cells Reactive against Cytomegalovirus-Infected Cells in a Mouse Xenograft Tumor Model
Authors: Devaud Christel , Bilhere Eric , Loizon Séverine , Pitard Vincent , Behr Charlotte , Moreau Jean-François , Dechanet-Merville Julie , Capone Myriam
Published: April 2009

γδ T cells recognize stress-induced autoantigens and contribute to immunity against infections and cancer. Our previous study revealed that Vδ2-negative (neg) γδ T lymphocytes isolated from transplant recipients infected by cytomegalovirus (CMV) killed both CMV-infected cells and HT29 colon cancer cells in vitro. To investigate the antitumor effects of Vδ2neg clones in vivo, we generated hypodermal HT29 tumors in immunodeficient mice. Concomitant injections of Vδ2negclones, in contrast to Vδ2+ cells, prevented the development of HT29 tumors. Vδ2neg clones expressed chemokine C-C motif receptor 3 (CCR3) and migrated in vitro in response to chemokines secreted by HT29 cells, among which were the CCR3 ligands macrophage inflammatory protein-1δ and monocyte chemoattractant protein-4. More importantly, a systemic i.p. treatment with Vδ2neg clones delayed the growth of HT29 s.c. tumors. The effect of in vivo γδ T-cell passive immunotherapy on tumor growth could be reverted by addition of a blocking anti-CCR3 antibody. γδ T-cell passive immunotherapy was dependent on the cytotoxic activity of the γδ effectors toward their targets because Vδ2neg clones were not able to inhibit the growth of A431 hypodermal tumors. Our findings suggest that CMV-specific Vδ2neg cells could target in vivo cancer cells, making them an attractive candidate for antitumor immunotherapy. [Cancer Res 2009;69(9):3971–8]
Neoadjuvant Vaccination Provides Superior Protection against Tumor Relapse following Surgery Compared with Adjuvant Vaccination
Authors: Grinshtein Natalie , Bridle Byram , Wan Yonghong , Bramson Jonathan L.
Published: April 2009

Tumors that recur following surgical resection of melanoma are typically metastatic and associated with poor prognosis. Using the murine B16F10 melanoma and a robust antimelanoma vaccine, we evaluated immunization as a tool to improve tumor-free survival following surgery. We investigated the utility of vaccination in both neoadjuvant and adjuvant settings. Surprisingly, neoadjuvant vaccination was far superior and provided ∼100% protection against tumor relapse. Neoadjuvant vaccination was associated with enhanced frequencies of tumor-specific T cells within the tumor and the tumor-draining lymph nodes following resection. We also observed increased infiltration of antigen-specific T cells into the area of surgery. This method should be amenable to any vaccine platform and can be readily extended to the clinic. [Cancer Res 2009;69(9):3979–85]
Relationship of Deregulated Signaling Converging onto mTOR with Prognosis and Classification of Lung Adenocarcinoma Shown by Two Independent In silico Analyses
Authors: Ebi Hiromichi , Tomida Shuta , Takeuchi Toshiyuki , Arima Chinatsu , Sato Takahiko , Mitsudomi Tetsuya , Yatabe Yasushi , Osada Hirotaka , Takahashi Takashi
Published: April 2009

There is marked disparity with a slight overlap among prognosis-predictive signatures reported thus far for lung cancers. In this study, we aimed at linking poor prognosis with particular pathways and/or functions of the gene sets involved to better understand the underlying molecular characteristics associated with the prognosis of lung adenocarcinomas. Gene set enrichment analysis identified a gene set down-regulated by rapamycin as the most significant, whereas several others responsive to withdrawal of glucose or amino acids, which are related to signaling converging onto mammalian target of rapamycin (mTOR), were also shown to be significantly associated, in addition to those related to DNA damage response and cell cycle progression. We also used connectivity map (C-MAP) analysis, an independent bioinformatics approach, to search for Food and Drug Administration–approved drugs that potentially transform an unfavorable signature to a favorable one. Those results identified inhibitors of phosphatidylinositol 3-kinase (PI3K) and mTOR, as well as unexpected drugs such as phenothiazine antipsychotics and resveratrol as potential candidates. Experimental validation revealed that the latter unexpected agents also inhibited signaling converging onto mTOR and exhibited antitumor activities. In addition, deregulation of multiple signaling converging onto mTOR was shown to be significantly associated with sensitivity to PI-103, a dual specificity PI3K/mTOR inhibitor that is not contained in the C-MAP database, lending further support for the connection. Our results clearly show the existence of gene set–definable, intrinsic heterogeneities in lung adenocarcinomas, which seem to be related to both clinical behavior and sensitivity to agents affecting the identified pathways. [Cancer Res 2009;69(9):4027–35]
eIF4E Activation Is Commonly Elevated in Advanced Human Prostate Cancers and Significantly Related to Reduced Patient Survival
Authors: Graff Jeremy R. , Konicek Bruce W. , Lynch Rebecca L. , Dumstorf Chad A. , Dowless Michele S. , McNulty Ann M. , Parsons Stephen H. , Brail Leslie H. , Colligan Bruce M. , Koop Jonathan W. , Hurst Bernadette M. , Deddens James A. , Neubauer Blake L. , Stancato Louis F. , Carter Harry W. , Douglass Larry E. , Carter Julia H.
Published: April 2009

Elevated eukaryotic translation initiation factor 4E (eIF4E) function induces malignancy in experimental models by selectively enhancing translation of key malignancy-related mRNAs (c-myc and BCL-2). eIF4E activation may reflect increased eIF4E expression or phosphorylation of its inhibitory binding proteins (4E-BP). By immunohistochemical analyses of 148 tissues from 89 prostate cancer patients, we now show that both eIF4E expression and 4E-BP1 phosphorylation (p4E-BP1) are increased significantly, particularly in advanced prostate cancer versus benign prostatic hyperplasia tissues. Further, increased eIF4E and p4E-BP1 levels are significantly related to reduced patient survival, whereas uniform 4E-BP1 expression is significantly related to better patient survival. Both immunohistochemistry and Western blotting reveal that elevated eIF4E and p4E-BP1 are evident in the same prostate cancer tissues. In two distinct prostate cancer cell models, the progression to androgen independence also involves increased eIF4E activation. In these prostate cancer cells, reducing eIF4E expression with an eIF4E-specific antisense oligonucleotide currently in phase I clinical trials robustly induces apoptosis, regardless of cell cycle phase, and reduces expression of the eIF4E-regulated proteins BCL-2 and c-myc. Collectively, these data implicate eIF4E activation in prostate cancer and suggest that targeting eIF4E may be attractive for prostate cancer therapy. [Cancer Res 2009;69(9):3866–73]
Expansion of Highly Cytotoxic Human Natural Killer Cells for Cancer Cell Therapy
Authors: Fujisaki Hiroyuki , Kakuda Harumi , Shimasaki Noriko , Imai Chihaya , Ma Jing , Lockey Timothy , Eldridge Paul , Leung Wing H. , Campana Dario
Published: April 2009

Infusions of natural killer (NK) cells are an emerging tool for cancer immunotherapy. The development of clinically applicable methods to produce large numbers of fully functional NK cells is a critical step to maximize the potential of this approach. We determined the capacity of the leukemia cell line K562 modified to express a membrane-bound form of interleukin (IL)-15 and 41BB ligand (K562-mb15-41BBL) to generate human NK cells with enhanced cytotoxicity. Seven-day coculture with irradiated K562-mb15-41BBL induced a median 21.6-fold expansion of CD56+CD3- NK cells from peripheral blood (range, 5.1- to 86.6-fold; n = 50), which was considerably superior to that produced by stimulation with IL-2, IL-12, IL-15, and/or IL-21 and caused no proliferation of CD3+ lymphocytes. Similar expansions could also be obtained from the peripheral blood of patients with acute leukemia undergoing therapy (n = 11). Comparisons of the gene expression profiles of the expanded NK cells and their unstimulated or IL-2–stimulated counterparts showed marked differences. The expanded NK cells were significantly more potent than unstimulated or IL-2–stimulated NK cells against acute myeloid leukemia cells in vitro. They could be detected for >1 month when injected into immunodeficient mice and could eradicate leukemia in murine models of acute myeloid leukemia. We therefore adapted the K562-mb15-41BBL stimulation method to large-scale clinical-grade conditions, generating large numbers of highly cytotoxic NK cells. The results that we report here provide rationale and practical platform for clinical testing of expanded and activated NK cells for cell therapy of cancer. [Cancer Res 2009;69(9):4010–7]
FOXP3 Defines Regulatory T Cells in Human Tumor and Autoimmune Disease
Authors: Kryczek Ilona , Liu Rebecca , Wang Guobin , Wu Ke , Shu Xiaogong , Szeliga Wojciech , Vatan Linhua , Finlayson Emily , Huang Emina , Simeone Diane , Redman Bruce , Welling Theodore H. , Chang Alfred , Zou Weiping
Published: April 2009

Activated T cells may express FOXP3. It is thought that FOXP3 is not a specific marker to determine regulatory T cells (Treg) in humans. Here, we examined the functional phenotype and cytokine profile of the in vitro induced FOXP3+ T cells, primary FOXP3+ and FOXP3- T cells in patients with ulcerative colitis and tumors including colon carcinoma, melanoma, hepatic carcinoma, ovarian carcinoma, pancreatic cancer, and renal cell carcinoma. We observed similar levels of suppressive capacity of primary FOXP3+ T cells in blood, tumors, and colitic tissues. Compared with primary FOXP3- T cells in the same microenvironment, these primary FOXP3+ T cells expressed minimal levels of effector cytokines, negligible amount of cytotoxic molecule granzyme B, and levels of suppressive molecules interleukin-10 and PD-1. Although the in vitro activated T cells expressed FOXP3, these induced FOXP3+ T cells expressed high levels of multiple effector cytokines and were not functionally suppressive. The data reinforce the fact that FOXP3 remains an accurate marker to define primary Tregs in patients with cancer and autoimmune disease. We suggest that the combination of FOXP3 and cytokine profile is useful for further functionally distinguishing primary Tregs from activated conventional T cells. [Cancer Res 2009;69(9):3995–4000]
Analysis of DNA Copy Number Alterations in Ovarian Serous Tumors Identifies New Molecular Genetic Changes in Low-Grade and High-Grade Carcinomas
Authors: Kuo Kuan-Ting , Guan Bin , Feng Yuanjian , Mao Tsui-Lien , Chen Xu , Jinawath Natini , Wang Yue , Kurman Robert J. , Shih Ie-Ming , Wang Tian-Li
Published: April 2009

Ovarian serous carcinoma, the most common and lethal type of ovarian cancer, is thought to develop from two distinct molecular pathways. High-grade (HG) serous carcinomas contain frequent TP53 mutations, whereas low-grade (LG) carcinomas arise from serous borderline tumors (SBT) and harbor mutations in KRAS/BRAF/ERBB2 pathway. However, the molecular alterations involved in the progression from SBT to LG carcinoma remain unknown. In addition, the extent of deletion of tumor suppressors in ovarian serous carcinomas has not been well studied. To further address these two issues, we assessed DNA copy number changes among affinity-purified tumor cells from 37 ovarian serous neoplasms including SBT, LG, and HG tumors using high-density 250K single nucleotide polymorphism arrays. Chromosomal instability index as measured by changes in DNA copy number was significantly higher in HG than in LG serous carcinomas. Hemizygous ch1p36 deletion was common in LG serous carcinomas but was rarely seen in SBT. This region contains several candidate tumor suppressors including miR-34a. In contrast, in HG serous carcinomas, significant numbers of amplifications and deletions, including homozygous deletions, were identified. Among homozygous deletions, loci containing Rb1, CDKN2A/B, CSMD1, and DOCK4 were most common, being present in 10.6%, 6.4%, 6.4%, and 4.3%, respectively, in independent 47 affinity-purified HG serous carcinomas. Except for the CDKN2A/B region, these homozygous deletions were not present in either SBT or LG tumors. Our study provides a genome-wide homozygous deletion profile in HG serous carcinomas, which can serve as a molecular foundation to study tumor suppressors in ovarian cancer. [Cancer Res 2009;69(9):4036–42]
Identification of Smyd4 as a Potential Tumor Suppressor Gene Involved in Breast Cancer Development
Authors: Hu Liping , Zhu Yiwei Tony , Qi Chao , Zhu Yi-Jun
Published: April 2009

To identify genes involved in breast tumorigenesis, we applied the retroviral LoxP-Cre system to a nontumorigenic mouse mammary epithelial cell line NOG8 to create random chromosome deletion/translocation. We found that the disruption of one allele of Smyd4 (SET and MYND domain containing 4) gene through chromosome translocation led to tumorigenesis. The expression of Smyd4 was markedly decreased in tumor cells. Re-expression of Smyd4 resulted in growth suppression of tumor cells and inhibition of tumor formation in nude mice. Furthermore, the RNA interference–mediated suppression of Smyd4 expression in human MCF10A mammary epithelial cells caused their growth in soft agar. Microarray studies revealed that platelet-derived growth factor receptor α polypeptide (Pdgfr-α) was highly expressed in tumor cells compared with NOG8 cells. Re-expression of Smyd4 significantly reduced the expression of Pdgfr-α in tumor cells. In human breast cancers, reverse transcription-PCR results revealed that Smyd4 expression was totally silenced in 2 of 10 specimens. These findings indicate that Smyd4, as a potential tumor suppressor, plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of Pdgfr-α, and could be a novel target for improving treatment of breast cancer. [Cancer Res 2009;69(9):4067–72]
CD38/CD31, the CCL3 and CCL4 Chemokines, and CD49d/Vascular Cell Adhesion Molecule-1 Are Interchained by Sequential Events Sustaining Chronic Lymphocytic Leukemia Cell Survival
Authors: Zucchetto Antonella , Benedetti Dania , Tripodo Claudio , Bomben Riccardo , Dal Bo Michele , Marconi Daniela , Bossi Fleur , Lorenzon Debora , Degan Massimo , Rossi Francesca Maria , Rossi Davide , Bulian Pietro , Franco Vito , Del Poeta Giovanni , Deaglio Silvia , Gaidano Gianluca , Tedesco Francesco , Malavasi Fabio , Gattei Valter
Published: April 2009

CD38 and CD49d are associated negative prognosticators in chronic lymphocytic leukemia (CLL). Despite evidence that both molecules are involved in interactions occurring between CLL and normal cells in the context of CLL-involved tissues, a functional link is still missing. Using gene expression profiles comparing CD38+CD49d+ versus CD38−CD49d− CLL cells, we showed overexpression of the CCL3 and CCL4 chemokines in cells from the former group. These chemokines were also up-regulated by CD38 signals in CLL; moreover, CCL3 was expressed by CLL cells from bone marrow biopsies (BMB) of CD38+CD49d+ but not CD38−CD49d− cases. High levels of CCR1 and, to a lesser extent, CCR5, the receptors for CCL3 and CCL4, were found in CLL-derived monocyte-macrophages. Consistently, CCL3 increased monocyte migration, and CD68+ macrophage infiltration was particularly high in BMB from CD38+CD49d+ CLL. Conditioned media from CCL3-stimulated macrophages induced endothelial cells to express vascular cell adhesion molecule-1 (VCAM-1), the CD49d ligand, likely through tumor necrosis factor α overproduction. These effects were apparent in BMB from CD38+CD49d+ CLL, where lymphoid infiltrates were characterized by a prominent meshwork of VCAM-1+ stromal/endothelial cells. Lastly, CD49d engagement by VCAM-1 transfectants increased viability of CD38+CD49d+ CLL cells. Altogether, CD38 and CD49d can be thought of as parts of a consecutive chain of events ultimately leading to improved survival of CLL cells. [Cancer Res 2009;69(9):4001–9]
The Steroid Receptor Coactivator-1 Regulates Twist Expression and Promotes Breast Cancer Metastasis
Authors: Qin Li , Liu Zhaoliang , Chen Hongwu , Xu Jianming
Published: April 2009

In breast cancer, steroid receptor coactivator-1 (SRC-1) expression positively correlates with HER2 expression and poor prognosis. In mouse mammary tumor virus–polyoma middle T (PyMT) breast cancer mouse model, SRC-1 strongly promotes mammary tumor metastasis. However, the molecular targets and mechanisms that mediate the role of SRC-1 in metastasis are unknown. In this study, SRC-1 wild-type (WT) and knockout (KO) cell lines were developed from the mammary tumors of WT/PyMT and KO/PyMT mice. WT cells exhibited strong migration and invasion capabilities, reduced E-cadherin and β-catenin epithelial markers, gained N-cadherin and vimentin mesenchymal markers, and formed undifferentiated invasive structures in three-dimensional culture. In contrast, KO cells showed slow migration and invasion, retained E-cadherin, had less N-cadherin and vimentin, and developed partially differentiated three-dimensional structures. Importantly, WT cells expressed Twist, a master regulator of metastasis, at significantly higher levels versus KO cells. SRC-1 knockdown in WT cells reduced Twist expression, whereas SRC-1 restoration in KO cells also rescued Twist expression. Furthermore, SRC-1 was found to coactivate Twist transcription through physical interaction with the transcription factor PEA3 at the proximal Twist promoter. Accordingly, Twist knockdown in WT cells increased E-cadherin and reduced cell invasion and metastasis, and Twist expression in KO cells decreased E-cadherin and increased cell invasion. SRC-1 knockdown in human breast cancer cells also decreased Twist, cell migration, and invasion. Therefore, SRC-1 promotes breast cancer invasiveness and metastasis by coactivating PEA3-mediated Twist expression. Intervention of SRC-1 function may provide new strategies to inhibit breast cancer metastasis. [Cancer Res 2009;69(9):3819–27]
Development of a Multiplex Quantitative PCR Signature to Predict Progression in Non–Muscle-Invasive Bladder Cancer
Authors: Wang Rou , Morris David S. , Tomlins Scott A. , Lonigro Robert J. , Tsodikov Alexander , Mehra Rohit , Giordano Thomas J. , Kunju L. Priya , Lee Cheryl T. , Weizer Alon Z. , Chinnaiyan Arul M.
Published: April 2009

In bladder cancer, clinical grade and stage fail to capture outcome. We developed a clinically applicable quantitative PCR (QPCR) gene signature to predict progression in non–muscle-invasive bladder cancer. Comparative metaprofiling of 12 DNA microarray data sets (comprising 631 samples and 241,298 probe sets) identified 96 genes, which showed differential expression in seven clinical outcome categories, or were identified as outliers, historic markers, or housekeeping genes. QPCR was done to determine mRNA expression from 96 bladder tumors. Fifty-seven genes differentiated T2 from non-T2 tumors (P < 0.05). Principal components analysis and Cox regression models were used to predict probability of T2 progression for non-T2 patients, placing them into high- and low-risk groups based on their gene expression. At 2 years, high-risk patients exhibited greater T2 progression (45% for high-risk patients versus 12% for low-risk patients; P = 0.003, log-rank test). This difference remained significant within T1 tumors (61% for high-risk patients versus 22% for low-risk patients; P = 0.02) and Ta tumors (29% for high-risk patients versus 0% for low-risk patients; P = 0.03). The best multivariate Cox model included stage and gender, and this signature provided predictive improvement over both (P = 0.002, likelihood ratio test). Immunohistochemistry was done for two genes in the signature not previously described in bladder cancer, ACTN1 and CDC25B, corroborating their up-regulation at the protein level with disease progression. Thus, we identified a 57-gene QPCR panel to help predict progression of non–muscle-invasive bladder cancers and delineate a systematic, generalizable approach to converting microarray data into a multiplex assay for cancer progression. [Cancer Res 2009;69(9):3810–8]