bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative Detection of p53 Mutations in Plasma DNA from Tobacco Smokers
Authors: Hagiwara Nobutoshi , Mechanic Leah E. , Trivers Glenwood E. , Cawley Helen L. , Taga Masataka , Bowman Elise D. , Kumamoto Kensuke , He Peijun , Bernard Mark , Doja Saira , Miyashita Masao , Tajiri Takashi , Sasajima Koji , Nomura Tsutomu , Makino Hiroshi , Takahashi Ken , Hussain S. Perwez , Harris Curtis C.
Published: August 2006

In lung tumors, the p53 tumor suppressor gene is commonly mutated with a characteristic mutation spectrum. The amount of and alterations in plasma DNA, such as mutations in p53, were associated with several cancers. Few studies used quantitative methods of high sensitivity. Previously, we observed p53 mutations in the noncancerous tissue that differed from those in lung tumors using the highly sensitive p53 mutation load assay. Based on our observation of an increased p53 mutation load in nontumorous lung tissue in smokers, we hypothesized that plasma DNA may contain mutant p53 indicative of tobacco smoke exposure and will be an effective biomarker of lung cancer or smoking exposure. We modified the p53 mutation load assay to detect mutations at p53 codons 248 and 249, common mutations in lung cancer, in plasma DNA samples with a sensitivity of 1:5,000. The assay was applied to a set of lung cancer cases (n = 39), hospital controls (n = 21), and population controls (n = 20) from a larger study. Controls were selected to consist of equal numbers of both ever and never smokers. The p53 mutation load (mutated p53 copies per total number of p53 copies) was associated with smoking (P = 0.06), but not with lung cancer (P = 0.59). Most of the individuals with p53 mutations observed in plasma DNA were ever smokers and the p53 mutation load was higher in those who smoked for longer durations (P = 0.04). In summary, we were able to detect p53 mutations in plasma DNA from healthy individuals and our data suggest that p53 mutations in plasma DNA may be a marker of carcinogen exposure from tobacco smoke. (Cancer Res 2006; 66(16): 8309-17)
Assessment of Endostatin Gene Therapy for Familial Adenomatous Polyposis–Related Desmoid Tumors
Authors: Martinico Sandra C.M. , Jezzard Sarah , Sturt N. Julian H. , Michils Genevieve , Tejpar Sabine , Phillips Robin K. , Vassaux Georges
Published: August 2006

Constitutive activation of the Wnt signaling pathway is a hallmark of many cancers, including familial adenomatous polyposis (FAP)–related desmoid tumors. Endostatin is a well-known antiangiogenic protein that has been described recently as a potential inhibitor of this signaling pathway. Here, we show that endostatin directly induces apoptosis and inhibits the Wnt signaling pathway in colorectal cancer cell lines bearing mutations on the adenomatous polyposis coli (APC) gene as a model of FAP-related malignant cells. We then explore the relationship between apoptosis and inhibition of this pathway and show that they are not correlated. These results seem to contradict a well-recognized study, showing that reintroduction of the APC cDNA in APC-deficient cells leads to apoptosis. To reconcile our conclusions with the literature, we further show that a truncated fragment of APC capable of inhibiting the Wnt signaling pathway in SW480 cells is incapable of inducing apoptosis in these cells, confirming that APC-mediated apoptosis is uncoupled to the inhibition of the Wnt signaling pathway. Finally, we show that endostatin directly induces cell death on primary FAP-related desmoid tumor cells in culture. This phenomenon is also independent of the inhibition of the Wnt signaling pathway. Considering the current lack of effective treatment against desmoid tumors, we advocate that endostatin gene therapy represents an attractive new therapeutic approach for this disease. (Cancer Res 2006; 66(16): 8233-40)
Tyrosine Kinase Etk/BMX Is Up-regulated in Human Prostate Cancer and Its Overexpression Induces Prostate Intraepithelial Neoplasia in Mouse
Authors: Dai Bojie , Kim Oekyung , Xie Yingqiu , Guo Zhiyong , Xu Kexin , Wang Bin , Kong Xiangtian , Melamed Jonathan , Chen Hegang , Bieberich Charles J. , Borowsky Alexander D. , Kung Hsing-Jien , Wei Guo , Ostrowski Michael C. , Brodie Angela , Qiu Yun
Published: August 2006

The nonreceptor tyrosine kinase Etk/BMX was originally identified from the human prostate xenograft CWR22. Here, we report that Etk is up-regulated in human prostate tumor specimens surveyed. Knocking down Etk expression by a specific small interfering RNA (siRNA) in prostate cancer cells attenuates cell proliferation, suggesting an essential role of Etk for prostate cancer cell survival and growth. Targeted expression of Etk in mouse prostate epithelium results in pathologic changes resembling human prostatic intraepithelial neoplasia, indicating that up-regulation of Etk may contribute to prostate cancer development. A marked increase of luminal epithelial cell proliferation was observed in the Etk transgenic prostate, which may be attributed in part to the elevated activity of Akt and signal transducers and activators of transcription 3 (STAT3). More interestingly, the expression level of acetyltransferase cyclic AMP–responsive element binding protein–binding protein (CBP) is also increased in the Etk transgenic prostate as well as in a prostate cancer cell line overexpressing Etk, concomitant with elevated histone 3 acetylation at lysine 18 (H3K18Ac). Down-modulation of Etk expression by a specific siRNA leads to a decrease of H3 acetylation in prostate cancer cell lines. Our data suggest that Etk may also modulate chromatin remodeling by regulating the activity of acetyltransferases, such as CBP. Given that Etk may exert its effects in prostate through modulation of multiple signaling pathways altered in human prostate cancer, the Etk transgenic mouse model may be a useful tool for studying the functions of Etk and identification of new molecular markers and drug targets relevant to human diseases. (Cancer Res 2006; 66(16): 8058-64)
Imaging Steps of Lymphatic Metastasis Reveals That Vascular Endothelial Growth Factor-C Increases Metastasis by Increasing Delivery of Cancer Cells to Lymph Nodes: Therapeutic Implications
Authors: Hoshida Tohru , Isaka Naohide , Hagendoorn Jeroen , di Tomaso Emmanuelle , Chen Yen-Lin , Pytowski Bronislaw , Fukumura Dai , Padera Timothy P. , Jain Rakesh K.
Published: August 2006

Preclinical and clinical studies positively correlate the expression of vascular endothelial growth factor (VEGF)-C in tumors and the incidence of lymph node metastases. However, how VEGF-C regulates individual steps in the transport of tumor cells from the primary tumor to the draining lymph nodes is poorly understood. Here, we image and quantify these steps in tumors growing in the tip of the mouse ear using intravital microscopy of the draining lymphatic vessels and lymph node, which receives spontaneously shed tumor cells. We show that VEGF-C overexpression in cancer cells induces hyperplasia in peritumor lymphatic vessels and increases the volumetric flow rate in lymphatics at the base of the ear by 40%. The increases in lymph flow rate and peritumor lymphatic surface area enhance the rate of tumor cell delivery to lymph nodes, leading to a 200-fold increase in cancer cell accumulation in the lymph node and a 4-fold increase in lymph node metastasis. In our model, VEGF-C overexpression does not confer any survival or growth advantage on cancer cells. We also show that an anti-VEGF receptor (VEGFR)-3 antibody reduces both lymphatic hyperplasia and the delivery of tumor cells to the draining lymph node, leading to a reduction in lymph node metastasis. However, this treatment is unable to prevent the growth of tumor cells already seeded in lymph nodes. Collectively, our results indicate that VEGF-C facilitates lymphatic metastasis by increasing the delivery of cancer cells to lymph nodes and therapies directed against VEGF-C/VEGFR-3 signaling target the initial steps of lymphatic metastasis. (Cancer Res 2006; 66(16): 8065-75)
Functional Interaction of the Retinoblastoma and Ini1/Snf5 Tumor Suppressors in Cell Growth and Pituitary Tumorigenesis
Authors: Guidi Cynthia J. , Mudhasani Rajini , Hoover Kathleen , Koff Andrew , Leav Irwin , Imbalzano Anthony N. , Jones Stephen N.
Published: August 2006

The Ini1 subunit of the SWI/SNF chromatin remodeling complex suppresses formation of malignant rhabdoid tumors in humans and mice. Transduction of Ini1 into Ini1-deficient tumor-derived cell lines has indicated that Ini1 arrests cell growth, controls chromosomal ploidy, and suppresses tumorigenesis by regulating components of the retinoblastoma (Rb) signaling pathway. Furthermore, conditional inactivation of Ini1 in mouse fibroblasts alters the expression of various Rb-E2F-regulated genes, indicating that endogenous Ini1 levels may control Rb signaling in cells. We have reported previously that loss of one allele of Ini1 in mouse fibroblasts results only in a 15% to 20% reduction in total Ini1 mRNA levels due to transcriptional compensation by the remaining Ini1 allele. Here, we examine the effects of Ini1 haploinsufficiency on cell growth and immortalization in mouse embryonic fibroblasts. In addition, we examine pituitary tumorigenesis in Rb-Ini1 compound heterozygous mice. Our results reveal that heterozygosity for Ini1 up-regulates cell growth and immortalization and that exogenous Ini1 down-regulates the growth of primary cells in a Rb-dependent manner. Furthermore, loss of Ini1 is redundant with loss of Rb function in the formation of pituitary tumors in Rb heterozygous mice and leads to the formation of large, atypical Rb+/− tumor cells lacking adrenocorticotropic hormone expression. These results confirm in vivo the relationship between Rb and Ini1 in tumor suppression and indicate that Ini1 plays a role in maintaining the morphologic and functional differentiation of corticotrophic cells. (Cancer Res 2006; 66(16): 8076-82)
Multiple Acquired Renal Carcinoma Tumor Capabilities Abolished upon Silencing of ADAM17
Authors: Franovic Aleksandra , Robert Isabelle , Smith Karlene , Kurban Ghada , Pause Arnim , Gunaratnam Lakshman , Lee Stephen
Published: August 2006

Malignancy is a manifestation of acquired defects in regulatory circuits that direct normal cell proliferation and homeostasis. Most of these circuits operate through cell autonomous pathways, whereas others potentially involve the neighboring microenvironment. We report that the metalloprotease ADAM17 plays a pivotal role in several acquired tumor cell capabilities by mediating the availability of soluble transforming growth factor-α, an epidermal growth factor receptor (EGFR) ligand, and thus the establishment of a key autocrine signaling pathway. Silencing of ADAM17 in human renal carcinoma cell lines corrects critical features associated with cancer cells, including growth autonomy, tumor inflammation, and tissue invasion. Highly malignant renal carcinoma cancer cells fail to form in vivo tumors in the absence of ADAM17, confirming the essential function of this molecule in tumorigenesis. These data show that ligand shedding is a crucial step in endogenous EGFR activation and endorse prospective therapeutic strategies targeting ADAM17 in human cancer. (Cancer Res 2006; 66(16): 8083-90)
Acute Reduction of Blood Pressure by Nitroglycerin Does Not Normalize Large Artery Stiffness in Essential Hypertension
Authors: Stewart Andrew D. , Jiang Benyu , Millasseau Sandrine C. , Ritter James M. , Chowienczyk Philip J.
Published: August 2006

Stiffness of large elastic arteries is elevated in subjects with hypertension, an effect that could potentially be explained by increased distending pressure. We examined effects of an acute change in blood pressure on carotid-femoral pulse wave velocity and carotid artery distensibility (inversely related to stiffness) in normotensive control subjects (n=20, mean age 42) with mean arterial pressure (MAP) 84±1.7 mm Hg (mean±SE) and subjects with essential hypertension (n=20, mean age 45, MAP 104±2.0 mm Hg). Normotensive subjects received intravenous nitroglycerin (NTG) and angiotensin II to lower/increase blood pressure. Hypertensive subjects received NTG to lower blood pressure. Pulse wave velocity was 24% (95% CI: 12% to 35%) higher and carotid distensibility 47% (95% CI: 32% to 63%) lower in hypertensive subjects compared with controls. In normotensive subjects, acute changes in blood pressure produced expected changes in stiffness. However, in hypertensive subjects, despite reducing MAP by 22 mm Hg to the same level as in normotensive subjects, there was no detectable reduction in arterial stiffness: pulse wave velocity remained 24% (95% CI: 10% to 38%) higher and carotid distensibility 48% (95% CI: 31% to 63%) lower in hypertensive compared with normotensive subjects. Because blood pressure–independent effects of NTG are, if anything, to reduce stiffness, these results indicate that elevated carotid and aortic stiffness in hypertensive subjects is not explained by elevated blood pressure but relates to structural change in the arterial wall.
Endogenous Endothelin-1 Is Required for Cardiomyocyte Survival In Vivo
Authors: Zhao Xiao-Song , Pan Wentong , Bekeredjian Raffi , Shohet Ralph V.
Published: August 2006

Background—

Endothelin-1 (ET-1) has potent vasoconstrictor and hypertrophic actions. Pharmacological antagonists of endothelin receptors attenuate cardiac hypertrophy, have been approved for treatment of pulmonary hypertension, and are under investigation for treatment of heart failure. To investigate the role of ET-1 in the heart, we created mice with cardiomyocyte deletion of ET-1.

Methods and Results—

Mice with cardiomyocyte-specific deletion of ET-1 are phenotypically normal when young. Remarkably, as the mice age or when young animals are subjected to aortic banding, they develop an unexpected phenotype of progressive systolic dysfunction and cardiac dilation. Echocardiography, necropsy, histology, and molecular phenotype confirm a dilated cardiomyopathy. Terminal deoxynucleotidyl transferase–mediated dUTP nick-end-labeling analysis reveals greater abundance of apoptotic nuclei in the ET-1–deficient hearts. Transcriptional and Western analyses suggest enhanced tumor necrosis factor (TNF)–mediated apoptosis with increases in caspase-8 activity. These ET-1–deficient hearts also have diminished nuclear factor (NF)-κB activity, resulting in diminution of downstream inhibitors of TNF signaling.

Conclusions—

Local ET-1 gene expression is necessary to maintain normal cardiac function and cardiomyocyte survival in mice with both age and hemodynamic stress. This cardiac-protective effect is mediated by paracrine ET-1 modulation of TNF-related apoptosis, in part through upregulation of NF-κB signaling.
β2-Adrenergic Agonists Suppress Rat Autoimmune Myocarditis
Authors: Nishii Mototsugu , Inomata Takayuki , Niwano Hiroe , Takehana Hitoshi , Takeuchi Ichiro , Nakano Hironari , Shinagawa Hisahito , Naruke Takashi , Koitabashi Toshimi , Nakahata Jun-ichi , Izumi Tohru
Published: August 2006

Background—

The therapeutic potential of β2-adrenergic receptor (AR) agonists in the treatment of autoimmune diseases has been reported. However, the role of these drugs in the myocardial structure–induced autoimmune process, which is thought to play a crucial role in the progression of myocarditis to subsequent complications, has not been elucidated.

Methods and Results—

Experimental autoimmune myocarditis (EAM) was induced in rats by immunization with cardiac myosin. On daily administration from day 0 after immunization, the β2-selective AR agonists formoterol or salbutamol ameliorated EAM on day 21 and increased myocardial interleukin-10/interferon-γ mRNA levels. Propranolol, a nonselective β-AR antagonist, aggravated EAM on day 21 and decreased mRNA levels, whereas metoprolol, a β1-selective AR antagonist, showed no effect. These results were reflected in vivo by the proliferation of cardiac myosin–primed lymph node cells from drug-treated rats. In vitro addition of β2-selective AR agonists inhibited the activation of cardiac myosin fragment–specific myocarditogenic T lymphocytes, and this effect was reversed by ICI118,551, a β2-selective AR antagonist. Furthermore, treatment with 2 different β2-selective AR agonists starting on day 14 also ameliorated EAM on day 21.

Conclusions—

β2-AR stimulation suppressed the development of EAM by inhibiting cardiac myosin–specific T-lymphocyte activation in lymphoid organs and by shifting the imbalance in Th1/Th2 cytokine toward Th2 cytokine. Furthermore, it also ameliorated established myocardial inflammation. β2-AR–stimulating agents may represent important immunomodulators of the cardiac myosin–induced autoimmune process and have potential as a new therapy for myocarditis.
Primary Stenting of Totally Occluded Native Coronary Arteries II (PRISON II)
Authors: Suttorp Maarten J. , Laarman Gert J. , Rahel Braim M. , Kelder Johannes C. , Bosschaert Mike A.R. , Kiemeneij Ferdinand , ten Berg Jur M. , Bal Egbert T. , Rensing Benno J. , Eefting Frank D. , Mast E. Gijs
Published: August 2006

Background—

Sirolimus-eluting stents markedly reduce the risk of restenosis compared with bare metal stents. However, it is not known whether there are differences in effectiveness between bare metal and sirolimus-eluting stents in patients with total coronary occlusions.

Methods and Results—

In a prospective, randomized, single-blind, 2-center trial, we enrolled 200 patients with total coronary occlusions: Half (n=100) were randomly assigned to receive bare metal BxVelocity stents and half (n=100) to receive sirolimus-eluting Cypher stents. The primary end point was angiographic binary in-segment restenosis rate at 6-month follow-up. Secondary end points were a composite of major adverse cardiac events, target vessel failure, binary in-stent restenosis rate, in-stent and in-segment minimal lumen diameter, percent diameter stenosis, and late luminal loss at 6-month follow-up. The sirolimus stent group showed a significantly lower in-stent binary restenosis rate of 7% compared with 36% in the bare metal stent group (
P
<0.001). The in-segment binary restenosis rate was 11% in the group receiving a sirolimus stent versus 41% in the bare metal stent group (
P
<0.0001), resulting in a target lesion revascularization rate of 4% in the sirolimus group versus 19% in the bare metal group (
P
<0.001). Patients who received the drug-eluting stent also had significantly lower rates of target vessel revascularization, target vessel failure, and all major adverse cardiac events.

Conclusions—

In patients with total coronary occlusions, use of the sirolimus-eluting stents are superior to the bare metal stents with significant reduction in angiographic binary restenosis, resulting in significantly less need for target lesion and target vessel revascularization.
Clinical Phenotype and Functional Characterization of
CASQ2
Mutations Associated With Catecholaminergic Polymorphic Ventricular Tachycardia
Authors: di Barletta Marina Raffaele , Viatchenko-Karpinski Serge , Nori Alessandra , Memmi Mirella , Terentyev Dmitry , Turcato Federica , Valle Giorgia , Rizzi Nicoletta , Napolitano Carlo , Gyorke Sandor , Volpe Pompeo , Priori Silvia G.
Published: August 2006

Background—

Four distinct mutations in the human cardiac calsequestrin gene (
CASQ2
) have been linked to catecholaminergic polymorphic ventricular tachycardia (CPVT). The mechanisms leading to the clinical phenotype are still poorly understood because only 1
CASQ2
mutation has been characterized in vitro.

Methods and Results—

We identified a homozygous 16-bp deletion at position 339 to 354 leading to a frame shift and a stop codon after 5aa (CASQ2
G112+5X
) in a child with stress-induced ventricular tachycardia and cardiac arrest. The same deletion was also identified in association with a novel point mutation (CASQ2
L167H
) in a highly symptomatic CPVT child who is the first CPVT patient carrier of compound heterozygous
CASQ2
mutations. We characterized in vitro the properties of
CASQ2
mutants: CASQ2
G112+5X
did not bind Ca
2+
, whereas CASQ2
L167H
had normal calcium-binding properties. When expressed in rat myocytes, both mutants decreased the sarcoplasmic reticulum Ca
2+
-storing capacity and reduced the amplitude of
I
Ca
-induced Ca
2+
transients and of spontaneous Ca
2+
sparks in permeabilized myocytes. Exposure of myocytes to isoproterenol caused the development of delayed afterdepolarizations in CASQ2
G112+5X
.

Conclusions—

CASQ2
L167H
and CASQ2
G112+5X
alter CASQ2 function in cardiac myocytes, which leads to reduction of active sarcoplasmic reticulum Ca
2+
release and calcium content. In addition, CASQ2
G112+5X
displays altered calcium-binding properties and leads to delayed afterdepolarizations. We conclude that the 2
CASQ2
mutations identified in CPVT create distinct abnormalities that lead to abnormal intracellular calcium regulation, thus facilitating the development of tachyarrhythmias.
Angiotensin II Induces Premature Senescence of Vascular Smooth Muscle Cells and Accelerates the Development of Atherosclerosis via a p21-Dependent Pathway
Authors: Kunieda Takeshige , Minamino Tohru , Nishi Jun-ichiro , Tateno Kaoru , Oyama Tomomi , Katsuno Taro , Miyauchi Hideyuki , Orimo Masayuki , Okada Sho , Takamura Masayuki , Nagai Toshio , Kaneko Shuichi , Komuro Issei
Published: August 2006

Background—

Angiotensin II (Ang II) has been reported to contribute to the pathogenesis of various human diseases including atherosclerosis, and inhibition of Ang II activity has been shown to reduce the morbidity and mortality of cardiovascular diseases. We have previously demonstrated that vascular cell senescence contributes to the pathogenesis of atherosclerosis; however, the effects of Ang II on vascular cell senescence have not been examined.

Methods and Results—

Ang II significantly induced premature senescence of human vascular smooth muscle cells (VSMCs) via the p53/p21-dependent pathway in vitro. Inhibition of this pathway effectively suppressed induction of proinflammatory cytokines and premature senescence of VSMCs by Ang II. Ang II also significantly increased the number of senescent VSMCs and induced the expression of proinflammatory molecules and of p21 in a mouse model of atherosclerosis. Loss of p21 markedly ameliorated the induction of proinflammatory molecules by Ang II, thereby preventing the development of atherosclerosis. Replacement of
p21
-deficient bone marrow cells with wild-type cells had little influence on the protective effect of
p21
deficiency against the progression of atherogenesis induced by Ang II.

Conclusions—

We demonstrated that Ang II promotes vascular inflammation by inducing premature senescence of VSMCs both in vitro and in vivo. Our results suggest a critical role of p21-dependent premature senescence of VSMCs in the pathogenesis of atherosclerosis.
‘High Theology’/‘Popular Theology’? The Arts, Popular Culture and the Contemporary Theological Task
Authors: Marsh Clive
Published: August 2006

This article asks how theology is to be done in a media age, when definitions of ‘culture’ are expanding and life is lived in the context of extensive and diverse media consumption. The impact on theology is considered with respect to definitions of ‘high’ and ‘popular’ culture, and to how religion is like and unlike forms of entertainment.
Armour-bearers of Christ (Mark 10:33-40)?
Authors: Derrett J. D. M.
Published: August 2006

James and John hoped to obtain posts superior to squires when they accepted the prospect of martyrdom. To ‘follow in death’ their Master entitled them to survival with him, but not an automatic promotion.
Recognition Memory and the Evolution of Cooperation: How Simple Strategies Succeed in an Agent-Based World
Authors: Aktipis C. Athena
Published: August 2006

Recent approaches to understanding the cognitive mechanisms underlying decision processes sug gest that simple strategies can result in successful and adaptive behaviors. Here, the evolutionary suc cess of simple recognition memory is investigated. Agents have a limited memory capacity for either agents who have previously cooperated (C-Mem) or those that have previously defected (D-Mem). Various aspects of the ecological and social environment influence the success of each of these strat egies. These findings suggest that recognition memory can play a role in promoting the evolution of cooperation, but that the effectiveness of such a simple recognition memory strategy depends on the fit between that strategy and the (ecological and social) environment in which that strategy is employed. The D-Mem strategy is able to invade only when the memory size of these agents is close to the total number of defectors in the population. However, the C-Mem strategy can invade a popula tion of defectors when memory size is one, as long as the population size is relatively small and the ecological environment promotes longer intervals between each reproductive opportunity.
Whispering Down the Lane: The Economics of Vicarious Information Transfer
Authors: De Backer Charlotte J. S. , Gurven Michael
Published: August 2006

This article presents a model of the use of communication about personal experience or experiences of third parties (gossip) in the context of cooperation. To date, previous research on the effect of gossip on cooperation has focused primarily on the manipulation of reputations. We present a formal model of vicarious information transfer, as a social learning strategy, between (potential) cooperative and competitive group members. We build on theories that have shown how effective communication can solve the adaptive problem of the high costs of individual learning. By communicating about the strat egies of others, individuals can vicariously learn at faster rates and lower cost. The costs and benefits of social versus individual learning have been modeled extensively. In this article, we focus on the unexplored and more basic question of when an individual should initiate the sharing of vicarious infor mation that can potentially affect the fitness of a cooperative or competitive receiver.
Crossing Large Gaps: A Simulation Study of Stick Insect Behavior
Authors: Bläsing Bettina
Published: August 2006

The motor behavior of stick insects climbing over large gaps has already been the subject of many experimental studies. The searching movement of the legs after stepping into the gap is analyzed in the first part of this study. Based on these and earlier biological results, a simulation study is carried out using WALKNET, a neural network model of the stick insect walking system. Five new modules are implemented into the model in the form of a unit assembly system. The performance of the enhanced model is evaluated in a series of tests designed based on previous biological experiments. The simu lation study shows that with only four new modules (for searching movements, velocity control, a load effect and short steps), the performance of the model in a simulated gap crossing situation can be improved beyond the performance of the biological system under comparable conditions.
Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays
Authors: Wang Xujing , Jia Shuang , Meyer Lisa , Xiang Bixia , Chen Li-Yen , Jiang Nan , Moreno Carol , Jacob Howard J , Ghosh Soumitra , Hessner Martin J
Published: August 2006

Background

Gene expression profiling using microarrays has become an important genetic tool. Spotted arrays prepared in academic labs have the advantage of low cost and high design and content flexibility, but are often limited by their susceptibility to quality control (QC) issues. Previously, we have reported a novel 3-color microarray technology that enabled array fabrication QC. In this report we further investigated its advantage in spot-level data QC.

Results

We found that inadequate amount of bound probes available for hybridization led to significant, gene-specific compression in ratio measurements, increased data variability, and printing pin dependent heterogeneities. The impact of such problems can be captured through the definition of quality scores, and efficiently controlled through quality-dependent filtering and normalization. We compared gene expression measurements derived using our data processing pipeline with the known input ratios of spiked in control clones, and with the measurements by quantitative real time RT-PCR. In each case, highly linear relationships (R2>0.94) were observed, with modest compression in the microarray measurements (correction factor<1.17).

Conclusion

Our microarray analytical and technical advancements enabled a better dissection of the sources of data variability and hence a more efficient QC. With that highly accurate gene expression measurements can be achieved using the cDNA microarray technology.
Validation and functional annotation of expression-based clusters based on gene ontology
Authors: Steuer Ralf , Humburg Peter , Selbig Joachim
Published: August 2006

Background

The biological interpretation of large-scale gene expression data is one of the paramount challenges in current bioinformatics. In particular, placing the results in the context of other available functional genomics data, such as existing bio-ontologies, has already provided substantial improvement for detecting and categorizing genes of interest. One common approach is to look for functional annotations that are significantly enriched within a group or cluster of genes, as compared to a reference group.

Results

In this work, we suggest the information-theoretic concept of mutual information to investigate the relationship between groups of genes, as given by data-driven clustering, and their respective functional categories. Drawing upon related approaches (Gibbons and Roth, Genome Research 12:1574-1581, 2002), we seek to quantify to what extent individual attributes are sufficient to characterize a given group or cluster of genes.

Conclusion

We show that the mutual information provides a systematic framework to assess the relationship between groups or clusters of genes and their functional annotations in a quantitative way. Within this framework, the mutual information allows us to address and incorporate several important issues, such as the interdependence of functional annotations and combinatorial combinations of attributes. It thus supplements and extends the conventional search for overrepresented attributes within a group or cluster of genes. In particular taking combinations of attributes into account, the mutual information opens the way to uncover specific functional descriptions of a group of genes or clustering result. All datasets and functional annotations used in this study are publicly available. All scripts used in the analysis are provided as additional files.
Cell organisation, sulphur metabolism and ion transport-related genes are differentially expressed in Paracoccidioides brasiliensis mycelium and yeast cells
Authors: Andrade Rosângela V , Paes Hugo C , Nicola André M , de Carvalho Maria José A , Fachin Ana Lúcia , Cardoso Renato S , Silva Simoneide S , Fernandes Larissa , Silva Silvana P , Donadi Eduardo A , Sakamoto-Hojo Elza T , Passos Geraldo AS , Soares Célia MA , Brígido Marcelo M , Felipe Maria Sueli S
Published: August 2006

Background

Mycelium-to-yeast transition in the human host is essential for pathogenicity by the fungus Paracoccidioides brasiliensis and both cell types are therefore critical to the establishment of paracoccidioidomycosis (PCM), a systemic mycosis endemic to Latin America. The infected population is of about 10 million individuals, 2% of whom will eventually develop the disease. Previously, transcriptome analysis of mycelium and yeast cells resulted in the assembly of 6,022 sequence groups. Gene expression analysis, using both in silico EST subtraction and cDNA microarray, revealed genes that were differential to yeast or mycelium, and we discussed those involved in sugar metabolism. To advance our understanding of molecular mechanisms of dimorphic transition, we performed an extended analysis of gene expression profiles using the methods mentioned above.

Results

In this work, continuous data mining revealed 66 new differentially expressed sequences that were MIPS(Munich Information Center for Protein Sequences)-categorised according to the cellular process in which they are presumably involved. Two well represented classes were chosen for further analysis: (i) control of cell organisation – cell wall, membrane and cytoskeleton, whose representatives were hex (encoding for a hexagonal peroxisome protein), bgl (encoding for a 1,3-β-glucosidase) in mycelium cells; and ags (an α-1,3-glucan synthase), cda (a chitin deacetylase) and vrp (a verprolin) in yeast cells; (ii) ion metabolism and transport – two genes putatively implicated in ion transport were confirmed to be highly expressed in mycelium cells – isc and ktp, respectively an iron-sulphur cluster-like protein and a cation transporter; and a putative P-type cation pump (pct) in yeast. Also, several enzymes from the cysteine de novo biosynthesis pathway were shown to be up regulated in the yeast form, including ATP sulphurylase, APS kinase and also PAPS reductase.

Conclusion

Taken together, these data show that several genes involved in cell organisation and ion metabolism/transport are expressed differentially along dimorphic transition. Hyper expression in yeast of the enzymes of sulphur metabolism reinforced that this metabolic pathway could be important for this process. Understanding these changes by functional analysis of such genes may lead to a better understanding of the infective process, thus providing new targets and strategies to control PCM.
An examination of factors influencing the choice of therapy for patients with coronary artery disease
Authors: Hirani Shashivadan P , Hyam Jonathan A , Shaefi Shahzad , Walker John M , Walesby Robin K , Newman Stanton P
Published: August 2006

Background

A diverse range of factors influence clinicians' decisions regarding the allocation of patients to different treatments for coronary artery disease in routine cardiology clinics. These include demographic measures, risk factors, co-morbidities, measures of objective cardiac disease, symptom reports and functional limitations. This study examined which of these factors differentiated patients receiving angioplasty from medication; bypass surgery from medication; and bypass surgery from angioplasty.

Methods

Univariate and multivariate logistic regression analyses were conducted on patient data from 214 coronary artery disease patients who at the time of recruitment had been received a clinical assessment and were reviewed by their cardiologist in order to determine the form of treatment they were to undergo: 70 would receive/continue medication, 71 were to undergo angioplasty and 73 were to undergo bypass surgery.

Results

Analyses differentiating patients receiving angioplasty from medication produced 9 significant univariate predictors, of which 5 were also multivariately significant (left anterior descending artery disease, previous coronary interventions, age, hypertension and frequency of angina). The analyses differentiating patients receiving surgery from angioplasty produced 12 significant univariate predictors, of which 4 were multivariately significant (limitations in mobility range, circumflex artery disease, previous coronary interventions and educational level). The analyses differentiating patients receiving surgery from medication produced 14 significant univariate predictors, of which 4 were multivariately significant (left anterior descending artery disease, previous cerebral events, limitations in mobility range and circumflex artery disease).

Conclusion

Variables emphasised in clinical guidelines are clearly involved in coronary artery disease treatment decisions. However, variables beyond these may also be important factors when therapy decisions are undertaken thus their roles require further investigation.
Fungal infection-related mortality versus total mortality as an outcome in trials of antifungal agents
Authors: Due Anne K , Johansen Helle K , Gøtzsche Peter C
Published: August 2006

Background

Disease specific mortality is often used as outcome rather than total mortality in clinical trials. This approach assumes that the classification of cause of death is unbiased. We explored whether use of fungal infection-related mortality as outcome rather than total mortality leads to bias in trials of antifungal agents in cancer patients.

Methods

As an estimate of bias we used relative risk of death in those patients the authors considered had not died from fungal infection. Our sample consisted of 69 trials included in four systematic reviews of prophylactic or empirical antifungal treatment in patients with cancer and neutropenia we have published previously.

Results

Thirty trials met the inclusion criteria. The trials comprised 6130 patients and 869 deaths, 220 (25%) of which were ascribed to fungal infection. The relative risk of death was 0.85 (95% CI 0.75–0.96) for total mortality, 0.57 (95% CI 0.44–0.74) for fungal mortality, and 0.95 (95% CI 0.82–1.09) for mortality among those who did not die from fungal infection.

Conclusion

We could not support the hypothesis that use of disease specific mortality introduces bias in antifungal trials on cancer patients as our estimate of the relative risk for mortality in those who survived the fungal infection was not increased. We conclude that it seems to be reliable to use fungal mortality as the primary outcome in trials of antifungal agents. Data on total mortality should be reported as well, however, to guard against the possible introduction of harmful treatments.
Identification of novel mutant PAX6 alleles in Indian cases of familial aniridia
Authors: Neethirajan Guruswamy , Nallathambi Jeyabalan , Krishnadas Subbaiah Ramasamy , Vijayalakshmi Perumalsamy , Shashikanth Shetty , Collinson Jon Martin , Sundaresan Periasamy
Published: August 2006

Background

Haploinsufficiency at the PAX6 locus causes aniridia, a panocular eye condition characterized by iris hypoplasia and a variety of other anterior and posterior eye defects leading to poor vision. This study was performed to identify novel PAX6 mutations that lead to familial aniridia in Indian patients.

Methods

Genomic DNA was isolated from affected individuals (clinically diagnosed aniridia) from nine unrelated aniridic pedigrees, unaffected family members, and unrelated normal controls. The coding regions of PAX6 were amplified and subjected to single strand conformation polymorphism (SSCP) gel analysis, and direct cloning and sequencing.

Results

SSCP band shifts, indicative of DNA base pair mutations, were observed in five of these unrelated families. Four mutations were shown to be previously unreported insertion or deletions in PAX6, leading to frameshifts. These new mutations were c.1174delTG (in exon 10), c.710delC (exon 6), c.406delTT (exon 5) and c.393insTCAGC (exon 5). The other nonsense mutation, a transition (c.1080C>T) in exon 9, has been reported previously as a mutation hotspot for PAX6 in other ethnic pedigrees. All mutant alleles transmitted through aniridic individuals in each family.

Conclusion

These new deletions and an insertion create frameshifts, which are predicted to introduce premature termination codons into the PAX6 reading frame. The genetic alterations carried by affected individuals are predicted to lead to loss-of-function mutations that would segregate in an autosomal dominant manner to subsequent generations. This is the first report of the 'hotspot' c.1080C>T transition from Indian families.
Knowledge, attitude and practices of pediatricians regarding the prevention of oral diseases in Italy
Authors: Di Giuseppe Gabriella , Nobile Carmelo GA , Marinelli Alessandra , Angelillo Italo F
Published: August 2006

Background

Pediatricians are in an ideal position to advise families about the prevention and management of oral diseases in children. The objective of the study was to determine knowledge, attitude, and practices regarding the prevention of oral diseases among pediatricians in Italy.

Methods

A systematic random sample of 1000 pediatricians received a questionnaire on socio-demographic and practice characteristics; knowledge on risk factors; attitude and practices towards the prevention of oral diseases.

Results

A total of 507 pediatricians participated. More than half knew the main risk factors for oral diseases and this knowledge was higher in primary care pediatricians (p = 0.007), in those with a higher number of hours worked per week (p = 0.012), and who believed that oral diseases may be prevented (p = 0.017). Pediatricians with higher knowledge about the main risk factors (p = 0.006) believe that they have an important role in preventing oral diseases and that they can perform an oral examination. Almost all (89%) prescribed fluoride supplements and those younger (p = 0.016), with a higher number of patients seen in workday (p = 0.001), with longer practice activity (p = 0.004), those who believe that fluoride is effective in preventing caries (p < 0.0001), and who learned about prevention from scientific sources (p = 0.002) were more likely to prescribe fluoride. One-fourth and 40.6% provides and recommends a dental visit once a year and primary care pediatricians (p = 0.014) and those who believed that routine visit is important in preventing oral diseases (p < 0.0001) were more likely to recommend a dental visit once a year.

Conclusion

The results showed a lack of knowledge among pediatricians although almost all believed that they had an important responsibility in preventing oral diseases and provided an oral examination.
Prevalence of self-reported hypertension and its relation to dietary habits, in adults; a nutrition & health survey in Greece
Authors: Pitsavos Christos , Milias George A , Panagiotakos Demosthenes B , Xenaki Dimitra , Panagopoulos George , Stefanadis Christodoulos
Published: August 2006

Background

Hypertension leads to many degenerative diseases, the most common being cardiovascular in origin. This study has been designed to estimate the prevalence of self-reported hypertension in a random nationwide sample of adult Greek population, while focus was set to the assessment of participants' nutritional habits in relation to their hypertension status.

Methods

A random-digit dialed telephone survey. Based on a multistage, stratified sampling, 5003 adults (18 – 74 yr) participated (men: 48.8%, women: 51.2%). All participants were interviewed via telephone by trained personnel who used a standard questionnaire. The questionnaire included demographic and socioeconomic characteristics, medical history, lifestyle habits and nutritional assessment.

Results

The prevalence of self-reported hypertension was 13.3% in men and 17.7% in women (P < 0.001). Furthermore, women reported higher values of systolic blood pressure (180 ± 27 mmHg) than men (169 ± 24 mmHg). Positive relationships were found between hypertension status and the prevalence of the rest investigated health conditions (i.e. hypercholesterolaemia, diabetes mellitus, renal failure and obesity). Nutritional assessment showed that consumption of fish, fruits and juices, cereals, and low fat milk and yogurt was significantly higher among hypertensive subjects while the opposite was observed for food items as red meat, pork, egg, pasta and rice, full fat dairy products and desserts.

Conclusion

Hypertension seems to be a serious public health problem in Greece. It is encouraging that hypertensives may have started adopting some more healthy nutritional behaviour compared to normotensive ones. However, they can gain significant benefits regarding to blood pressure control, if they increase the level of compliance with dietary recommendations.
Emerging advantages and drawbacks of telephone surveying in public health research in Ireland and the U.K
Authors: Boland M , Sweeney MR , Scallan E , Harrington M , Staines A
Published: August 2006

Background

Telephone surveys have been used widely in public health research internationally and are being increasingly used in Ireland and the U.K.

Methods

This study compared three telephone surveys conducted on the island of Ireland from 2000 to 2004, examining study methodology, outcome measures and the per unit cost of each completed survey. We critically examined these population-based surveys which all explored health related attitudes and behaviours.

Results

Over the period from 2000 to 2005 the percentage of calls which succeeded in contacting an eligible member of the public fell, from 52.9% to 31.8%. There was a drop in response rates to the surveys (once contact was established) from 58.6% to 17.7%. Costs per completed interview rose from €4.48 to €15.65.

Respondents were prepared to spend 10–15 minutes being surveyed, but longer surveys yielded poorer completion rates. Respondents were willing to discuss issues of a sensitive nature. Interviews after 9 pm were less successful, with complaints about the lateness of the call. Randomisation from electronic residential telephone directory databases excluded all ex-directory numbers and thus was not as representative of the general population as number generation by the hundred-bank method. However the directory database was more efficient in excluding business and fax numbers.

Conclusion

Researchers should take cognisance of under-representativeness of land-line telephone surveys, of the increasing difficulties in contacting the public and of mounting personnel costs. We conclude that telephone surveying now requires additional strategies such as a multimode approach, or incentivisation, to be a useful, cost-effective means of acquiring data on public health matters in Ireland and the U.K.
Genetic diversity of Plasmodium vivax in Kolkata, India
Authors: Kim Jung-Ryong , Imwong Mallika , Nandy Amitabha , Chotivanich Kesinee , Nontprasert Apichart , Tonomsing Naowarat , Maji Ardhendu , Addy Manjulika , Day Nick PJ , White Nicholas J , Pukrittayakamee Sasithon
Published: August 2006

Background

Plasmodium vivax malaria accounts for approximately 60% of malaria cases in Kolkata, India. There has been limited information on the genotypic polymorphism of P. vivax in this malaria endemic area. Three highly polymorphic and single copy genes were selected for a study of genetic diversity in Kolkata strains.

Methods

Blood from 151 patients with P. vivax infection diagnosed in Kolkata between April 2003 and September 2004 was genotyped at three polymorphic loci: the P. vivax circumsporozoite protein (pvcs), the merozoite surface protein 1 (pvmsp 1) and the merozoite surface protein 3-alpha (pvmsp 3-alpha).

Results

Analysis of these three genetic markers revealed that P. vivax populations in Kolkata are highly diverse. A large number of distinguishable alleles were found from three genetic markers: 11 for pvcs, 35 for pvmsp 1 and 37 for pvmsp 3-alpha. These were, in general, randomly distributed amongst the isolates. Among the 151 isolates, 142 unique genotypes were detected the commonest genotype at a frequency of less than 2% (3/151). The overall rate of mixed genotype infections was 10.6%.

Conclusion

These results indicate that the P. vivax parasite population is highly diverse in Kolkata, despite the low level of transmission. The genotyping protocols used in this study may be useful for differentiating re-infection from relapse and recrudescence in studies assessing of malarial drug efficacy in vivax malaria.