bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome Analyses of Icelandic Strains ofSulfolobus islandicus, Model Organisms for Genetic and Virus-Host Interaction Studies
Authors: Guo Li , Brügger Kim , Liu Chao , Shah Shiraz A. , Zheng Huajun , Zhu Yongqiang , Wang Shengyue , Lillestøl Reidun K. , Chen Lanming , Frank Jeremy , Prangishvili David , Paulin Lars , She Qunxin , Huang Li , Garrett Roger A.
Published: January 2011

The genomes of twoSulfolobus islandicusstrains obtained from Icelandic solfataras were sequenced and analyzed. Strain REY15A is a host for a versatile genetic toolbox. It exhibits a genome of minimal size, is stable genetically, and is easy to grow and manipulate. Strain HVE10/4 shows a broad host range for exceptional crenarchaeal viruses and conjugative plasmids and was selected for studying their life cycles and host interactions. The genomes of strains REY15A and HVE10/4 are 2.5 and 2.7 Mb, respectively, and each genome carries a variable region of 0.5 to 0.7 Mb where major differences in gene content and gene order occur. These include gene clusters involved in specific metabolic pathways, multiple copies of VapBC antitoxin-toxin gene pairs, and in strain HVE10/4, a 50-kb region rich in glycosyl transferase genes. The variable region also contains most of the insertion sequence (IS) elements and high proportions of the orphanorfBelements and SMN1 miniature inverted-repeat transposable elements (MITEs), as well as the clustered regular interspaced short palindromic repeat (CRISPR)-based immune systems, which are complex and diverse in both strains, consistent with them having been mobilized both intra- and intercellularly. In contrast, the remainder of the genomes are highly conserved in their protein and RNA gene syntenies, closely resembling those of otherS. islandicusandSulfolobus solfataricusstrains, and they exhibit only minor remnants of a few genetic elements, mainly conjugative plasmids, which have integrated at a few tRNA genes lacking introns. This provides a possible rationale for the presence of the introns.
EAL Domain Protein YdiV Acts as an Anti-FlhD
4
C
2
Factor Responsible for Nutritional Control of the Flagellar Regulon in
Salmonella enterica
Serovar Typhimurium
Authors: Wada Takeo , Morizane Tomoe , Abo Tatsuhiko , Tominaga Akira , Inoue-Tanaka Kanako , Kutsukake Kazuhiro
Published: January 2011

Flagellar operons are divided into three classes with respect to their transcriptional hierarchy in
Salmonella enterica
serovar Typhimurium. The class 1 gene products FlhD and FlhC act together in an FlhD
4
C
2
heterohexamer, which binds upstream of the class 2 promoters to facilitate binding of RNA polymerase. In this study, we showed that flagellar expression was much reduced in the cells grown in poor medium compared to those grown in rich medium. This nutritional control was shown to be executed at a step after class 1 transcription. We isolated five Tn
5
insertion mutants in which the class 2 expression was derepressed in poor medium. These insertions were located in the
ydiV
(
cdgR
) gene or a gene just upstream of
ydiV
. The
ydiV
gene is known to encode an EAL domain protein and to act as a negative regulator of flagellar expression. Gene disruption and complementation analyses revealed that the
ydiV
gene is responsible for nutritional control. Expression analysis of the
ydiV
gene showed that its translation, but not transcription, was enhanced by growth in poor medium. The
ydiV
mutation did not have a significant effect on either the steady-state level of
flhDC
mRNA or that of FlhC protein. Purified YdiV protein was shown
in vitro
to bind to FlhD
4
C
2
through interaction with FlhD subunit and to inhibit its binding to the class 2 promoter, resulting in inhibition of FlhD
4
C
2
-dependent transcription. Taking these data together, we conclude that YdiV is a novel anti-FlhD
4
C
2
factor responsible for nutritional control of the flagellar regulon.
Genome Sequence of
Taylorella equigenitalis
MCE9, the Causative Agent of Contagious Equine Metritis
Authors: Hébert Laurent , Moumen Bouziane , Duquesne Fabien , Breuil Marie-France , Laugier Claire , Batto Jean-Michel , Renault Pierre , Petry Sandrine
Published: January 2011

Taylorella equigenitalis
is the causative agent of contagious equine metritis (CEM), a sexually transmitted infection of horses. We herein report the genome sequence of
T. equigenitalis
strain MCE9, isolated in 2005 from the urethral fossa of a 4-year-old stallion in France.
Does Acupuncture Help in Helping the Ones you Cannot Help? The Role of Acupuncture in Facilitating Adaptive Processes
Authors: Foell Jens
Published: January 2011

In the public funded healthcare arena, acupuncture is delivered with ‘disease’ as the defining label that grants access to funding. This funding process is regulated by recommendations derived from systematic reviews and meta-analyses of randomised controlled trials. However, ‘off-label’ use of acupuncture, outside established indications like pain or nausea, happens frequently, though there is a paucity of data about this situation. The case of a young man with weakness and fatigue as residuum of relapsing-remitting multiple sclerosis highlights the situation. His treatment goal was well defined. Specific and non-specific needling effects and the provider-patient relationship are explored. The role of technological and adaptive processes in the treatment of long-term conditions, the effect of somatosensory stimulation on different levels and the implication for funding are discussed.
The development and evolution of a tertiary pancreaticobiliary endoscopic ultrasound service: lessons learned
Authors: Oppong K W , Richardson D L , Charnley R M , Nayar M K
Published: January 2011

This article reviews the development of the hepatopancreatobiliary (HPB) endoscopic ultrasound (EUS) service at Freeman Hospital and seeks to identify from our experience learning points for good practice and pitfalls to avoid. The Freeman HPB EUS service has expanded rapidly over the past 10 years in response to the consolidation of cancer care and aligned to the needs of the cancer network. Effective multidisciplinary teamwork and increased subspecialisation by the endosonographers has allowed the efficient use of capacity and development of skills. Mechanisms for monitoring diagnostic performance put in place at the outset of the EUS–fine needle aspiration programme have helped to identify interventions that have led to improved test performance. An excellent working relationship between all stakeholders is critical to the success of such a service as is a preparedness to seek and respond to the views of patients and referrers.
Prevalence of depression in granted and refused requests for euthanasia and assisted suicide: a systematic review
Authors: Levene Ilana , Parker Michael
Published: January 2011

Background

There is an established link between depression and interest in hastened death in patients who are seriously ill. Concern exists over the extent of depression in patients who actively request euthanasia/physician-assisted suicide (PAS) and those who have their requests granted.

Objectives

To estimate the prevalence of depression in refused and granted requests for euthanasia/PAS and discuss these findings.

Methods

A systematic review was performed in MEDLINE and PsycINFO in July 2010, identifying studies reporting rates of depression in requests for and cases of euthanasia/PAS. One author critically appraised the strength of the data using published criteria.

Results

21 studies were included covering four countries. There was considerable heterogeneity in methods of assessing depression and selecting patients. In the highest quality studies, in the Netherlands and Oregon, 8–47% of patients requesting euthanasia/PAS had depressive symptoms and 2–17% of completed euthanasia/PAS cases had depressive symptoms. In the Netherlands, depression was significantly higher in refused than granted requests, and there was no significant difference in the rate of depression between euthanasia cases and similar patients who had not made a request for euthanasia.

Conclusion

It is unclear whether depression increases the probability of making a request for euthanasia/PAS, but in the Netherlands most requests in depressed patients are rejected, leaving a depression rate in cases that is similar to the surrounding population. Less evidence is available elsewhere, but some level of depression has been identified in patients undergoing euthanasia/PAS in all the countries studied. Whether the presence of depression is ever compatible with an ethical decision on euthanasia/PAS is discussed.
SELDI-TOF derived serum biomarkers failed to differentiate between patients with beryllium sensitisation and patients with chronic beryllium disease
Authors: Tooker B C , Bowler R P , Orcutt J M , Maier L A , Christensen H M , Newman L S
Published: January 2011

Background

People exposed to beryllium may develop beryllium sensitisation (BeS) and, in some cases, progress to chronic beryllium disease (CBD).

Objectives

The objective of this study was to test the ability of proteomic technology to identify patterns of serum protein biomarkers that allow differentiation between BeS and CBD and thus remove the need for invasive bronchoscopic procedures.

Methods

Initially, SELDI-TOF methodology and analysis was performed on serum samples from 30 CBD and 31 BeS patients.

Results

This ‘starter set’ yielded two distinct biomarker pattern sets with eight candidate proteins. The first set differentiated between BeS and CBD with 83.3% sensitivity and 82.3% specificity, with 10-fold cross-validation of 75% and 79%, respectively. The second set of biomarkers yielded higher sensitivity (90.0%) and higher specificity (90.3%), with 10-fold cross-validation of 71.7% and 82.3%, respectively. Due to its greater sensitivity and specificity, the second set of biomarkers was used as the framework for differentiating between CBD and BeS in a second set of serum samples from 450 patients with BeS and CBD. When this larger set of samples was subjected to the biomarker framework in a blinded fashion, it yielded a sensitivity of 43.53% and a specificity of 38.93%.

Conclusions

Due to these low sensitivity and specificity values, we have concluded that, currently, the unique set of SELDI-TOF derived biomarkers does not possess the qualities that would allow it to differentiate between a CBD patient and a BeS patient using serum protein biomarkers. Future refinements in sample collection or proteomic technology may be needed to improve biomarker discovery.
Combining syntactic and semantic bidirectionalization
Authors: Voigtländer Janis , Hu Zhenjiang , Matsuda Kazutaka , Wang Meng
Published: February 2011

Matsuda et al. [2007, ICFP] and Voigtländer [2009, POPL] introduced two techniques that given a source-to-view function provide an update propagation function mapping an original source and an updated view back to an updated source, subject to standard consistency conditions. Being fundamentally different in approach, both techniques have their respective strengths and weaknesses. Here we develop a synthesis of the two techniques to good effect. On the intersection of their applicability domains we achieve more than what a simple union of applying the techniques side by side delivers.
Experience report
Authors: Pop Iustin
Published: February 2011

In system administration, the languages of choice for solving automation tasks are scripting languages, owing to their flexibility, extensive library support and quick development cycle. Functional programming is more likely to be found in software development teams and the academic world.

This separation means that system administrators cannot use the most effective tool for a given problem; in an ideal world, we should be able to mix and match different languages, based on the problem at hand.

This experience report details our initial introduction and use of Haskell in a mature, medium size project implemented in Python. We also analyse the interaction between the two languages, and show how Haskell has excelled at solving a particular type of real-world problems
G-Finder
Authors: Li Wei , Zhang Charles , Hu Songlin
Published: February 2011

Programming forums are becoming the primary tools for programmers to find answers for their programming problems. Our empirical study of popular programming forums shows that the forum users experience long waiting period for answers and a small number of experts are often overloaded with questions. To improve the usage experience, we have designed and implemented G-Finder, both an algorithm and a tool that makes intelligent routing decisions as to which participant is the expert for answering a particular programming question. Our main approach is to leverage the source code information of the software systems that forums are dedicated to, and discover latent relationships between forums users. Our algorithms construct the concept networks and the user networks from the program source and the forum data.We use programming questions to dynamically integrate these two networks and present an adaptive ranking of the potential experts. Our evaluation of G-Finder, using the data from three large programming forums, takes a retrospective view to check if G-Finder can correctly predict the experts who provided answers to programming questions. The evaluation results show that G-Finder improves the prediction precision by 25% to 74%, compared to related approaches.
Hera-JVM
Authors: McIlroy Ross , Sventek Joe
Published: February 2011

Heterogeneous multi-core processors, such as the IBM Cell processor, can deliver high performance. However, these processors are notoriously difficult to program: different cores support different instruction set architectures, and the processor as a whole does not provide coherence between the different cores' local memories.

We present Hera-JVM, an implementation of the Java Virtual Machine which operates over the Cell processor, thereby making this platforms more readily accessible to mainstream developers. Hera-JVM supports the full Java language; threads from an unmodified Java application can be simultaneously executed on both the main PowerPC-based core and on the additional
SPE
accelerator cores. Migration of threads between these cores is transparent from the point of view of the application, requiring no modification to Java source code or bytecode. Hera-JVM supports the existing Java Memory Model, even though the underlying hardware does not provide cache coherence between the different core types.

We examine Hera-JVM's performance under a series of real-world Java benchmarks from the SpecJVM, Java Grande and Dacapo benchmark suites. These benchmarks show a wide variation in relative performance on the different core types of the Cell processor, depending upon the nature of their workload. Execution of these benchmarks on Hera-JVM can achieve speedups of up to 2.25x by using one of the Cell processor's SPE accelerator cores, compared to execution on the main PowerPC-based core. When all six SPE cores are exploited, parallel workloads can achieve speedups of up to 13x compared to execution on the single PowerPC core.
What can the GC compute efficiently?
Authors: Reichenbach Christoph , Immerman Neil , Smaragdakis Yannis , Aftandilian Edward E. , Guyer Samuel Z.
Published: February 2011

We present the DeAL language for heap assertions that are efficiently evaluated during garbage collection time. DeAL is a rich, declarative, logic-based language whose programs are guaranteed to be executable with good whole-heap locality, i.e., within a single traversal over every live object on the heap and a finite neighborhood around each object. As a result, evaluating DeAL programs incurs negligible cost: for simple assertion checking at each garbage collection, the end-to-end execution slowdown is below 2%. DeAL is integrated into Java as a VM extension and we demonstrate its efficiency and expressiveness with several applications and properties from the past literature.

Compared to past systems for heap assertions, DeAL is distinguished by its very attractive expressiveness/efficiency tradeoff: it o ers a significantly richer class of assertions than what past systems could check with a single traversal. Conversely, past systems that can express the same (or more) complex assertions as DeAL do so only by su ering orders-of-magnitude higher costs.
Parallel inclusion-based points-to analysis
Authors: Méndez-Lojo Mario , Mathew Augustine , Pingali Keshav
Published: February 2011

Inclusion-based points-to analysis provides a good trade-off between precision of results and speed of analysis, and it has been incorporated into several production compilers including gcc. There is an extensive literature on how to speed up this algorithm using heuristics such as detecting and collapsing cycles of pointer-equivalent variables. This paper describes a complementary approach based on exploiting parallelism. Our implementation exploits two key insights. First, we show that inclusion-based points-to analysis can be formulated entirely in terms of graphs and graph rewrite rules. This exposes the amorphous data-parallelism in this algorithm and makes it easier to develop a parallel implementation. Second, we show that this graph-theoretic formulation reveals certain key properties of the algorithm that can be exploited to obtain an efficient parallel implementation. Our parallel implementation achieves a scaling of up to 3x on a 8-core machine for a suite of ten large C programs. For all but the smallest benchmarks, the parallel analysis outperforms a state-of-the-art, highly optimized, serial implementation of the same algorithm. To the best of our knowledge, this is the first parallel implementation of a points-to analysis.
Random testing for higher-order, stateful programs
Authors: Klein Casey , Flatt Matthew , Findler Robert Bruce
Published: February 2011

Testing is among the most effective tools available for finding bugs. Still, we know of no automatic technique for generating test cases that expose bugs involving a combination of mutable state and callbacks, even though objects and method overriding set up exactly that combination. For such cases, a test generator must create callbacks or subclasses that aggressively exercise side-effecting operations using combinations of generated objects.

This paper presents a new algorithm for randomly testing programs that use state and callbacks. Our algorithm exploits a combination of contracts and environment bindings to guide the test-case generator toward interesting inputs. Our prototype implementation for Racket (formerly PLT Scheme) - which has a Java-like class system, but with first-class classes as well as gbeta-like augmentable methods - uncovered dozens of bugs in a well-tested and widely used text-editor library.

We describe our approach in a precise, formal notation, borrowing the techniques used to describe operational semantics and type systems. The formalism enables us to provide a compact and self-contained explanation of the core of our technique without the ambiguity usually present in pseudo-code descriptions.
Refactoring references for library migration
Authors: Kapur Puneet , Cossette Brad , Walker Robert J.
Published: February 2011

Automated refactoring is a key feature of modern IDEs. Existing refactorings rely on the transformation of source code declarations, in which references may also be transformed as a side effect. However, there exist situations in which a declaration is not available for refactoring or would be inappropriate to transform, for example, in the presence of dangling references or where a set of references should be retargeted to a different declaration.

We investigate the problem of dangling references through a detailed study of three open source libraries. We find that the introduction of dangling references during library migration is a significant real problem, and characterize the specific issues that arise. Based on these findings we provide and test a prototype tool, called Trident, that allows programmers to refactor references. Our results suggest that supporting the direct refactoring of references is a significant improvement over the state-of-the-art.
Programming with time
Authors: Sorensen Andrew , Gardner Henry
Published: February 2011

The act of computer programming is generally considered to be temporally removed from a computer program's execution. In this paper we discuss the idea of programming as an activity that takes place within the temporal bounds of a real-time computational process and its interactions with the physical world. We ground these ideas within the con- text of livecoding -- a live audiovisual performance practice. We then describe how the development of the programming environment "Impromptu" has addressed our ideas of programming with time and the notion of the programmer as an agent in a cyber-physical system.
Restoring leptin signaling reduces hyperlipidemia and improves vascular stiffness induced by chronic intermittent hypoxia
Authors: Yang Ronghua , Sikka Gautam , Larson Jill , Watts Vabren L. , Niu Xiaolin , Ellis Carla L. , Miller Karen L. , Camara Andre , Reinke Christian , Savransky Vladimir , Polotsky Vsevolod Y. , O'Donnell Christopher P. , Berkowitz Dan E. , Barouch Lili A.
Published: January 2011

Chronic intermittent hypoxia (IH) during sleep can result from obstructive sleep apnea (OSA), a disorder that is particularly prevalent in obesity. OSA is associated with high levels of circulating leptin, cardiovascular dysfunction, and dyslipidemia. Relationships between leptin and cardiovascular function in OSA and chronic IH are poorly understood. We exposed lean wild-type (WT) and obese leptin-deficient ob/ob mice to IH for 4 wk, with and without leptin infusion, and measured cardiovascular indices including aortic vascular stiffness, endothelial function, cardiac myocyte morphology, and contractile properties. At baseline, ob/ob mice had decreased vascular compliance and endothelial function vs. WT mice. We found that 4 wk of IH decreased vascular compliance and endothelial relaxation responses to acetylcholine in both WT and leptin-deficient ob/ob animals. Recombinant leptin infusion in both strains restored IH-induced vascular abnormalities toward normoxic WT levels. Cardiac myocyte morphology and function were unaltered by IH. Serum cholesterol and triglyceride levels were significantly decreased by leptin treatment in IH mice, as was hepatic stearoyl-Coenzyme A desaturase 1 expression. Taken together, these data suggest that restoring normal leptin signaling can reduce vascular stiffness, increase endothelial relaxation, and correct dyslipidemia associated with IH.
Suppression of cerebral hemodynamics is associated with reduced functional capacity in patients with heart failure
Authors: Fu Tieh-Cheng , Wang Chao-Hung , Hsu Chih-Chin , Cherng Wen-Jin , Huang Shu-Chun , Wang Jong-Shyan
Published: January 2011

This investigation elucidated the underlying mechanisms of functional impairments in patients with heart failure (HF) by simultaneously comparing cardiac-cerebral-muscle hemodynamic and ventilatory responses to exercise among HF patients with various functional capacities. One hundred one patients with HF [New York Heart Association HF functional class II (HF-II, n = 53) and functional class III (HF-III, n = 48) patients] and 71 normal subjects [older control (O-C, n = 39) and younger control (Y-C, n = 32) adults] performed an incremental exercise test using a bicycle ergometer. A recently developed noninvasive bioreactance device was adopted to measure cardiac hemodynamics, and near-infrared spectroscopy was employed to assess perfusions in the frontal cerebral lobe (Δ[THb]FC) and vastus lateralis muscle (Δ[THb]VL). The results demonstrated that the Y-C group had higher levels of cardiac output, Δ[THb]FC, and Δ[THb]VL during exercise than the O-C group. Moreover, these cardiac/peripheral hemodynamic responses to exercise in HF-III group were smaller than those in both HF-II and O-C groups. Although the change of cardiac output caused by exercise was normalized, the amounts of blood distributed to frontal cerebral lobe and vastus lateralis muscle in the HF-III group significantly declined during exercise. The HF-III patients had lower oxygen-uptake efficiency slopes (OUES) and greater V̇e-V̇o2 slopes than the HF-II patients and age-matched controls. However, neither hemodynamic nor ventilatory response to exercise differed significantly between the HF-II and O-C groups. Cardiac output, Δ[THb]FC, and Δ[THb]VL during exercise were directly related to the OUES and V̇o2peak and inversely related to the V̇e-V̇co2 slope. Moreover, cardiac output or Δ[THb]FC was an effect modifier, which modulated the correlation status between Δ[THb]VL and V̇e-V̇co2 slope. We concluded that the suppression of cerebral/muscle hemodynamics during exercise is associated with ventilatory abnormality, which reduces functional capacity in patients with HF.
Characterization of potentialS-nitrosylation sites in the myocardium
Authors: Kohr Mark J. , Aponte Angel M. , Sun Junhui , Wang Guanghui , Murphy Elizabeth , Gucek Marjan , Steenbergen Charles
Published: January 2011

S-nitrosylation (SNO) is a reversible protein modification that has the ability to alter the activity of target proteins. However, only a small number of SNO proteins have been found in the myocardium, and even fewer specific sites of SNO have been identified. Therefore, this study aims to characterize potential SNO sites in the myocardium. We utilized a modified version of the SNO-resin-assisted capture technique in tandem with mass spectrometry. In brief, a modified biotin switch was performed using perfused mouse heart homogenates incubated with or without the S-nitrosylating agent S-nitrosoglutathione. Our modified SNO-resin-assisted capture protocol identified 116 unique SNO-modified proteins under basal conditions, and these represent the constitutive SNO proteome. These constitutive SNO proteins are likely to be physiologically relevant targets, since nitric oxide has been shown to play an important role in the regulation of normal cardiovascular physiology. Following S-nitrosoglutathione treatment, we identified 951 unique SNO proteins, many of which contained multiple SNO sites. These proteins show the potential for SNO. This study provides novel information regarding the constitutive SNO proteome of the myocardium, as well as potential myocardial SNO sites, and yields additional information on the SNO sites for many key proteins involved in myocardial contraction, metabolism, and cellular signaling.
Interplay between RAGE, CD44, and focal adhesion molecules in epithelial-mesenchymal transition of alveolar epithelial cells
Authors: Buckley Stephen T. , Medina Carlos , Kasper Michael , Ehrhardt Carsten
Published: January 2011

Fibrosis of the lung is characterized by the accumulation of myofibroblasts, a key mediator in the fibrogenic reaction. Cumulative evidence indicates that epithelial-mesenchymal transition (EMT), a process whereby epithelial cells become mesenchyme-like, is an important contributing source for the myofibroblast population. Underlying this phenotypical change is a dramatic alteration in cellular structure. The receptor for advanced glycation end-products (RAGE) has been suggested to maintain lung homeostasis by mediating cell adhesion, while the family of ezrin/radixin/moesin (ERM) proteins, on the other hand, serve as an important cross-linker between the plasma membrane and cytoskeleton. In the present investigation, we tested the hypothesis that RAGE and ERM interact and play a key role in regulating EMT-associated structural changes in alveolar epithelial cells. Exposure of A549 cells to inflammatory cytokines resulted in phosphorylation and redistribution of ERM to the cell periphery and localization with EMT-related actin stress fibers. Simultaneously, blockade of Rho kinase (ROCK) signaling attenuated these cytokine-induced structural changes. Additionally, RAGE expression was diminished after cytokine stimulation, with release of its soluble isoform via a matrix metalloproteinase (MMP)-9-dependent mechanism. Immunofluorescence microscopy and coimmunoprecipitation revealed association between ERM and RAGE under basal conditions, which was disrupted when challenged with inflammatory cytokines, as ERM in its activated state complexed with membrane-linked CD44. Dual-fluorescence immunohistochemistry of patient idiopathic pulmonary fibrosis (IPF) tissues highlighted marked diminution of RAGE in fibrotic samples, together with enhanced levels of CD44 and double-positive cells for CD44 and phospho (p)ERM. These data suggest that dysregulation of the ERM-RAGE complex might be an important step in rearrangement of the actin cytoskeleton during proinflammatory cytokine-induced EMT of human alveolar epithelial cells.
Influence of DMT1 and iron status on inflammatory responses in the lung
Authors: Kim Jonghan , Molina Ramon M. , Donaghey Thomas C. , Buckett Peter D. , Brain Joseph D. , Wessling-Resnick Marianne
Published: January 2011

Divalent metal transporter 1 (DMT1) is the major iron transporter responsible for duodenal dietary iron absorption and is required for erythropoiesis. Recent studies suggest that loss of DMT1 activity could be involved in metal-related lung injury, but little is known about the effects of iron status and DMT1 function on pulmonary inflammation. To better define the role of DMT1 and iron status in pulmonary inflammatory responses, we performed bronchoalveolar lavage (BAL) following intratracheal instillation of lipopolysaccharide (LPS) to the Belgrade rat, an animal model deficient in DMT1 function. In the basal state, the BAL fluid of Belgrade rats had more macrophages and higher lactate dehydrogenase, myeloperoxidase, albumin, and hemoglobin levels compared with heterozygote control rats. Following LPS instillation, the macrophage fraction relative to total BAL cell content and levels of albumin and IgM were increased in Belgrade rats compared with controls. In contrast, heterozygote Belgrade rats made anemic by diet-induced iron deficiency exhibited attenuated inflammatory responses to LPS. These combined results show that pulmonary inflammation can be modified by both DMT1 and iron status. Loss of DMT1 alters pulmonary responses necessary for lung homeostasis in the basal state and enhances LPS-induced inflammation and therefore would contribute to progression of lung injury.
CARM1 Is an Important Determinant of ERα-Dependent Breast Cancer Cell Differentiation and Proliferation in Breast Cancer Cells
Authors: Al-Dhaheri Mariam , Wu Jiacai , Skliris Georgios P. , Li Jun , Higashimato Ken , Wang Yidan , White Kevin P. , Lambert Paul , Zhu Yuerong , Murphy Leigh , Xu Wei
Published: February 2011

Breast cancers with estrogen receptor α (ERα) expression are often more differentiated histologically than ERα-negative tumors, but the reasons for this difference are poorly understood. One possible explanation is that transcriptional cofactors associated with ERα determine the expression of genes which promote a more differentiated phenotype. In this study, we identify one such cofactor as coactivator-associated arginine methyltransferase 1 (CARM1), a unique coactivator of ERα that can simultaneously block cell proliferation and induce differentiation through global regulation of ERα-regulated genes. CARM1 was evidenced as an ERα coactivator in cell-based assays, gene expression microarrays, and mouse xenograft models. In human breast tumors, CARM1 expression positively correlated with ERα levels in ER-positive tumors but was inversely correlated with tumor grade. Our findings suggest that coexpression of CARM1 and ERα may provide a better biomarker of well-differentiated breast cancer. Furthermore, our findings define an important functional role of this histone arginine methyltransferase in reprogramming ERα-regulated cellular processes, implicating CARM1 as a putative epigenetic target in ER-positive breast cancers. Cancer Res; 71(6); 2118–28. ©2011 AACR.
NRF2 Blockade Suppresses Colon Tumor Angiogenesis by Inhibiting Hypoxia-Induced Activation of HIF-1α
Authors: Kim Tae-Hyoung , Hur Eu-gene , Kang Su-Jin , Kim Jung-Ae , Thapa Dinesh , Lee You Mie , Ku Sae Kwang , Jung Yunjin , Kwak Mi-Kyoung
Published: January 2011

Transcription factor NRF2 is an important modifier of cellular responses to oxidative stress. Although its cytoprotective effects are firmly established, recent evidence suggesting important roles in cancer pathobiology has yet to be mechanistically developed. In the current study, we investigated the role of NRF2 in colon tumor angiogenesis. Stable RNAi-mediated knockdown of NRF2 in human colon cancer cells suppressed tumor growth in mouse xenograft settings with a concomitant reduction in blood vessel formation and VEGF expression. Similar antiangiogenic effects of NRF2 knockdown were documented in chick chorioallantoic membrane assays and endothelial tube formation assays. Notably, NRF2-inhibited cancer cells failed to accumulate HIF-1α protein under hypoxic conditions, limiting expression of VEGF and other HIF-1α target genes. In these cells, HIF-1α was hydroxylated but pharmacological inhibition of PHD domain-containing prolyl hydroxylases was sufficient to restore hypoxia-induced accumulation of HIF-1α. Mechanistic investigations demonstrated that reduced mitochondrial O2 consumption in NRF2-inhibited cells was probably responsible for HIF-1α degradation during hypoxia; cellular O2 consumption and ATP production were lower in NRF2 knockdown cells than in control cells. Our findings offer novel insights into how cellular responses to O2 and oxidative stress are integrated in cancer cells, and they highlight NRF2 as a candidate molecular target to control tumor angiogenesis by imposing a blockade to HIF-1α signaling. Cancer Res; 71(6); 2260–75. ©2011 AACR.
Suppression of Glucosylceramide Synthase Restores p53-Dependent Apoptosis in Mutant p53 Cancer Cells
Authors: Liu Yong-Yu , Patwardhan Gauri A. , Bhinge Kaustubh , Gupta Vineet , Gu Xin , Jazwinski S. Michal
Published: January 2011

Tumor suppressor p53 plays an essential role in protecting cells from malignant transformation by inducing cell-cycle arrest and apoptosis. Mutant p53 that is detected in more than 50% of cases of cancers loses its role in suppression of tumors but gains in oncogenic function. Strategies to convert mutant p53 into wild-type p53 have been suggested for cancer prevention and treatment, but they face a variety of challenges. Here, we report an alternative approach that involves suppression of glucosylceramide synthase (GCS), an enzyme that glycosylates ceramide and blunts its proapoptotic activity in cancer cells. Human ovarian cancer cells expressing mutant p53 displayed resistance to apoptosis induced by DNA damage. We found that GCS silencing sensitized these mutant p53 cells to doxorubicin but did not affect the sensitivity of cells with wild-type p53. GCS silencing increased the levels of phosphorylated p53 and p53-responsive genes, including p21Waf1/Cip1, Bax, and Puma, consistent with a redirection of the mutant p53 cells to apoptosis. Reactivated p53-dependent apoptosis was similarly verified in p53-mutant tumors where GCS was silenced. Inhibition of ceramide synthase with fumonisin B1 prevented p53 reactivation induced by GCS silencing, whereas addition of exogenous C6-ceramide reactivated p53 function in p53-mutant cells. Our findings indicate that restoring active ceramide to cells can resuscitate wild-type p53 function in p53-mutant cells, offering preclinical support for a novel type of mechanism-based therapy in the many human cancers harboring p53 mutations. Cancer Res; 71(6); 2276–85. ©2011 AACR.
Identification of a Tumor Suppressor Relay between the FOXP3 and the Hippo Pathways in Breast and Prostate Cancers
Authors: Li Weiquan , Wang Lizhong , Katoh Hiroto , Liu Runhua , Zheng Pan , Liu Yang
Published: January 2011

Defective expression of LATS2, a negative regulator of YAP oncoprotein, has been reported in cancer of prostate, breast, liver, brain, and blood origins. However, no transcriptional regulators for the LATS2 gene have been identified. Here we report that spontaneous mutation of the transcription factor FOXP3 reduces expression of the LATS2 gene in mammary epithelial cells. shRNA-mediated silencing of FOXP3 in normal or malignant mammary epithelial cells of mouse and human origin repressed LATS2 expression and increased YAP protein levels. LATS2 induction required binding of FOXP3 to a specific sequence in the LATS2 promoter, and this interaction contributed to FOXP3-mediated growth inhibition of tumor cells. In support of these results, reduced expression and somatic mutations of FOXP3 correlated strongly with defective LATS2 expression in microdissected prostate cancer tissues. Thus, defective expression of LATS2 is attributable to FOXP3 defects and may be a major independent determinant of YAP protein elevation in cancer. Our findings identify a novel mechanism of LATS2 downregulation in cancer and reveal an important tumor suppressor relay between the FOXP3 and HIPPO pathways which are widely implicated in human cancer. Cancer Res; 71(6); 2162–71. ©2011 AACR.
A Phase I Study of the Heat Shock Protein 90 Inhibitor Alvespimycin (17-DMAG) Given Intravenously to Patients with Advanced Solid Tumors
Authors: Pacey Simon , Wilson Richard H. , Walton Mike , Eatock Martin M. , Hardcastle Anthea , Zetterlund Anna , Arkenau Hendrik-Tobias , Moreno-Farre Javier , Banerji Udai , Roels Belle , Peachey Heidi , Aherne Wynne , de Bono Johan S. , Raynaud Florence , Workman Paul , Judson Ian
Published: January 2011

Purpose: A phase I study to define toxicity and recommend a phase II dose of the HSP90 inhibitor alvespimycin (17-DMAG; 17-dimethylaminoethylamino-17-demethoxygeldanamycin). Secondary endpoints included evaluation of pharmacokinetic profile, tumor response, and definition of a biologically effective dose (BED).

Patients and Methods: Patients with advanced solid cancers were treated with weekly, intravenous (i.v.) 17-DMAG. An accelerated titration dose escalation design was used. The maximum tolerated dose (MTD) was the highest dose at which ≤1/6 patients experienced dose limiting toxicity (DLT). Dose de-escalation from the MTD was planned with mandatory, sequential tumor biopsies to determine a BED. Pharmacokinetic and pharmacodynamic assays were validated prior to patient accrual.

Results: Twenty-five patients received 17-DMAG (range 2.5–106 mg/m2). At 106 mg/m2 of 17-DMAG 2/4 patients experienced DLT, including one treatment-related death. No DLT occurred at 80 mg/m2. Common adverse events were gastrointestinal, liver function changes, and ocular. Area under the curve and mean peak concentration increased proportionally with 17-DMAG doses 80 mg/m2 or less. In peripheral blood mononuclear cells significant (P < 0.05) HSP72 induction was detected (≥20 mg/m2) and sustained for 96 hours (≥40 mg/m2). Plasma HSP72 levels were greatest in the two patients who experienced DLT. At 80 mg/m2 client protein (CDK4, LCK) depletion was detected and tumor samples from 3 of 5 patients confirmed HSP90 inhibition. Clinical activity included complete response (castration refractory prostate cancer, CRPC 124 weeks), partial response (melanoma, 159 weeks), and stable disease (chondrosarcoma, CRPC, and renal cancer for 28, 59, and 76 weeks, respectively).

Couclusions: The recommended phase II dose of 17-DMAG is 80 mg/m2 weekly i.v. Clin Cancer Res; 17(6); 1561–70. ©2011 AACR.
Expression of p16 and Retinoblastoma Determines Response to CDK4/6 Inhibition in Ovarian Cancer
Authors: Konecny Gottfried E. , Winterhoff Boris , Kolarova Teodora , Qi Jingwei , Manivong Kanthinh , Dering Judy , Yang Guorong , Chalukya Meenal , Wang He-Jing , Anderson Lee , Kalli Kimberly R. , Finn Richard S. , Ginther Charles , Jones Siân , Velculescu Victor E. , Riehle Darren , Cliby William A. , Randolph Sophia , Koehler Maria , Hartmann Lynn C. , Slamon Dennis J.
Published: January 2011

Purpose: PD-0332991 is a selective inhibitor of the CDK4/6 kinases with the ability to block retinoblastoma (Rb) phosphorylation in the low nanomolar range. Here we investigate the role of CDK4/6 inhibition in human ovarian cancer.

Experimental Design: We examined the effects of PD-0332991 on proliferation, cell-cycle, apoptosis, and Rb phosphorylation using a panel of 40 established human ovarian cancer cell lines. Molecular markers for response prediction, including p16 and Rb, were studied using gene expression profiling, Western blot, and array CGH. Multiple drug effect analysis was used to study interactions with chemotherapeutic drugs. Expression of p16 and Rb was studied using immunohistochemistry in a large clinical cohort of ovarian cancer patients.

Results: Concentration-dependent antiproliferative effects of PD-0332991 were seen in all ovarian cancer cell lines, but varied significantly between individual lines. Rb-proficient cell lines with low p16 expression were most responsive to CDK4/6 inhibition. Copy number variations of CDKN2A, RB, CCNE1, and CCND1 were associated with response to PD-0332991. CDK4/6 inhibition induced G0/G1 cell cycle arrest, blocked Rb phosphorylation in a concentration-and time-dependent manner, and enhanced the effects of chemotherapy. Rb-proficiency with low p16 expression was seen in 97/262 (37%) of ovarian cancer patients and was independently associated with poor progression-free survival (adjusted relative risk 1.49, 95% CI 1.00–2.24, P = 0.052).

Conclusions: PD-0332991 shows promising biologic activity in ovarian cancer cell lines. Assessment of Rb and p16 expression may help select patients most likely to benefit from CDK4/6 inhibition in ovarian cancer. Clin Cancer Res; 17(6); 1591–602. ©2011 AACR.
TGF-β Blockade Controls Ascites by Preventing Abnormalization of Lymphatic Vessels in Orthotopic Human Ovarian Carcinoma Models
Authors: Liao Shan , Liu Jieqiong , Lin Peichun , Shi Tony , Jain Rakesh K. , Xu Lei
Published: January 2011

Purpose: Ovarian cancer patients with malignant ascites have poor prognosis. The accumulation of ascites is caused by an imbalance between fluid extravasation from the blood vessels and reabsorption by lymphatic vessels. Whereas, the role of TGF-β in tumor progression has been well studied, the role of TGF-β in lymphatic vessel function is far from understood. Here, we sought to dissect the role of TGF-β blockade in the formation of ascites.

Experimental Design: We used soluble TGF-β Receptor II (sTβRII) to block TGF-β signaling in two orthotopic human ovarian carcinoma models: SKOV3ip1 and Hey-A8. We measured tumor proliferation, apoptosis, lymphangiogenesis, and angiogenesis by immunohistochemical staining, and examined diaphragm lymphatic vessel network by intraperitoneal injection of a fluorescent dye. Diaphragm lymphatic vessel function was assessed by tracking fluorescent beads in the diaphragm and measuring their drainage rate.

Results: TGF-β blockade impaired tumor growth in both models, accompanied by a decreased tumor cell proliferation and angiogenesis. More strikingly, TGF-β blockade almost completely abolished ascites formation. TGF-β blockade significantly inhibited the expression of VEGF, which is the major contributor to ascites formation. At the same time, TGF-β blockade prevent ‘abnormalization’ of diaphragm lymphatic vessels and improved ascites drainage.

Conclusions: TGF-β blockade decreased ascites by both inhibiting ascites formation and improving ascites drainage. Based on our finding, it is reasonable to consider the use of TGF-β blockade as a palliative treatment for symptomatic ascites. Clin Cancer Res; 17(6); 1415–24. ©2011 AACR.
Genomic and Epigenomic Integration Identifies a Prognostic Signature in Colon Cancer
Authors: Yi Joo Mi , Dhir Mashaal , Van Neste Leander , Downing Stephanie R. , Jeschke Jana , Glöckner Sabine C. , de Freitas Calmon Marilia , Hooker Craig M. , Funes Juan M. , Boshoff Chris , Smits Kim M. , van Engeland Manon , Weijenberg Matty P. , Iacobuzio-Donahue Christine A. , Herman James G. , Schuebel Kornel E. , Baylin Stephen B. , Ahuja Nita
Published: January 2011

Purpose: The importance of genetic and epigenetic alterations maybe in their aggregate role in altering core pathways in tumorigenesis.

Experimental Design: Merging genome-wide genomic and epigenomic alterations, we identify key genes and pathways altered in colorectal cancers (CRC). DNA methylation analysis was tested for predicting survival in CRC patients using Cox proportional hazard model.

Results: We identified 29 low frequency-mutated genes that are also inactivated by epigenetic mechanisms in CRC. Pathway analysis showed the extracellular matrix (ECM) remodeling pathway is silenced in CRC. Six ECM pathway genes were tested for their prognostic potential in large CRC cohorts (n = 777). DNA methylation of IGFBP3 and EVL predicted for poor survival (IGFBP3: HR = 2.58, 95% CI: 1.37–4.87, P = 0.004; EVL: HR = 2.48, 95% CI: 1.07–5.74, P = 0.034) and simultaneous methylation of multiple genes predicted significantly worse survival (HR = 8.61, 95% CI: 2.16–34.36, P < 0.001 for methylation of IGFBP3, EVL, CD109, and FLNC). DNA methylation of IGFBP3 and EVL was validated as a prognostic marker in an independent contemporary-matched cohort (IGFBP3 HR = 2.06, 95% CI: 1.04–4.09, P = 0.038; EVL HR = 2.23, 95% CI: 1.00–5.0, P = 0.05) and EVL DNA methylation remained significant in a secondary historical validation cohort (HR = 1.41, 95% CI: 1.05–1.89, P = 0.022). Moreover, DNA methylation of selected ECM genes helps to stratify the high-risk stage 2 colon cancers patients who would benefit from adjuvant chemotherapy (HR: 5.85, 95% CI: 2.03–16.83, P = 0.001 for simultaneous methylation of IGFBP3, EVL, and CD109).

Conclusions: CRC that have silenced genes in ECM pathway components show worse survival suggesting that our finding provides novel prognostic biomarkers for CRC and reflects the high importance of integrative analyses linking genetic and epigenetic abnormalities with pathway disruption in cancer. Clin Cancer Res; 17(6); 1535–45. ©2011 AACR.
Chinese Red Yeast Rice Inhibition of Prostate Tumor Growth in SCID Mice
Authors: Hong Mee Young , Henning Susanne , Moro Aune , Seeram Navindra P. , Zhang Yanjun , Heber David
Published: January 2011

Prostate cancer is a slowly developing but very common cancer in males that may be amenable to preventive strategies that are not toxic. Chinese red yeast rice (RYR), a food herb made by fermenting Monascus purpureus Went yeast on white rice, contains a mixture of eight different monacolins that inhibit cholesterogenesis in addition to red pigments with antioxidant properties. Monacolin K is identical to lovastatin (LV), but LV unlike RYR can be used in individuals intolerant to statins due to muscle pain. Both LV and RYR inhibit de novo cholesterogenesis, which is critical to the growth of tumor cells. Long-term use of statin drugs has been associated with a reduced risk of prostate cancer. We have previously shown that RYR inhibited androgen-dependent and androgen receptor–overexpressing androgen-independent prostate cancer cell proliferation in vitro. This study was designed to determine whether RYR and LV inhibit prostate tumor growth in SCID mice. RYR significantly reduced tumor volumes of androgen-dependent and androgen-independent prostate xenograft tumors compared with animals receiving vehicle alone (P < 0.05). Inhibition by RYR was greater than that observed with LV at the dose found in RYR, showing that other compounds in RYR contributed to the antiproliferative effect. There was a significant correlation of tumor volume to serum cholesterol (P < 0.001). RYR decreased gene expression of androgen synthesizing enzymes (HSD3B2, AKR1C3, and SRD5A1) in both type of tumors (P < 0.05). Clinical studies of RYR for prostate cancer prevention in the increasing population of men undergoing active surveillance should be considered. Cancer Prev Res; 4(4); 608–15. ©2011 AACR.