bluuebunny/crossref_metadata_2025 huggingface dataset:
Developing a Promotional Strategy: Important Questions for Social Marketing
Authors: Thackeray Rosemary , Neiger Brad L. , Hanson Carl L.
Published: November 2007

Health practitioners often use the terms marketing and promotion interchangeably. Yet, promotion is just one element of an overall marketing strategy. To realize the greatest impact there must be a combination of all the marketing components, including product, price, place, and promotion. The purpose of this article is to clarify the role of promotion and describe key elements of developing a promotional strategy within the broader context of a social marketing initiative.
Homegrown Institutional Legitimacy
Authors: Cann Damon M. , Yates Jeff
Published: November 2007

Since the United States Supreme Court's decision in Bush v. Gore, the public's support for the judicial system looms as an especially important concern. Although studies have confirmed that the Supreme Court's reservoir of public goodwill has remained largely intact following the politically divisive decision, the status of public support for other American courts has received little attention. This reflects a broader trend in judicial politics scholarship toward placing inordinate attention on explaining public support for the U.S. Supreme Court while largely ignoring the courts where most of the policymaking in the nation occurs—state courts. We use a national survey to assess the factors influencing diffuse support for state courts. We find that although many considerations affecting diffuse support for state courts parallel the determinants of such support for the nation's high Court, important differences exist between explanations of citizen support for state courts and the Supreme Court. Most notably, judicial elections and concerns over judicial campaign contributions work to undermine citizens' support for their state courts.
p53 signaling in response to increased DNA damage sensitizes AML1-ETO cells to stress-induced death
Authors: Krejci Ondrej , Wunderlich Mark , Geiger Hartmut , Chou Fu-Sheng , Schleimer David , Jansen Michael , Andreassen Paul R. , Mulloy James C.
Published: November 2007

Chromosomal translocation (8;21) is present in 10% to 15% of patients with acute myeloid leukemia. Expression of the AML1-ETO (AE) fusion protein alone is not sufficient to induce leukemia, but the nature of the additional genetic alterations is unknown. It is unclear whether AE facilitates acquisition of these cooperating events. We show that AE down-regulates genes involved in multiple DNA repair pathways, potentially through a mechanism involving direct binding at promoter elements, and increases the mutation frequency in vivo. AE cells display increased DNA damage in vitro and have an activated p53 pathway. This results in increased basal apoptosis and enhanced sensitivity to DNA damaging agents. Intriguingly, microarray data indicate that t(8;21) patient samples exhibit decreased expression of DNA repair genes and increased expression of p53 response genes compared with other acute myeloid leukemia (AML) patient samples. Inhibition of the p53 pathway by RNAi increases the resistance of AE cells to DNA damage. We thus speculate that AML1-ETO may facilitate accumulation of genetic alterations by suppressing endogenous DNA repair. It is possible that the superior outcome of t(8;21) patients is partly due to an activated p53 pathway, and that loss of the p53 response pathway is associated with disease progression.
In vivo kinetics of kinase domain mutations in CML patients treated with dasatinib after failing imatinib
Authors: Khorashad Jamshid S. , Milojkovic Dragana , Mehta Puja , Anand Mona , Ghorashian Sara , Reid Alistair G. , De Melo Valeria , Babb Anna , de Lavallade Hugues , Olavarria Eduardo , Marin David , Goldman John M. , Apperley Jane F. , Kaeda Jaspal S.
Published: November 2007

We sought kinase domain (KD) mutations at the start of treatment with dasatinib in 46 chronic myeloid leukemia (CML) patients resistant to or intolerant of imatinib. We identified BCR-ABL mutant subclones in 12 (26%) cases and used pyrosequencing to estimate subsequent changes in their relative size after starting dasatinib. Four patients lost their mutations, which remained undetectable, 3 patients retained the original mutation or lost it only transiently, 3 lost their original mutations but acquired a new mutation (F317L), and 2 developed another mutation (T315I) in addition to the original mutation within the same subclone. This study shows that expansion of a mutant Ph-positive clone that responds initially to a second generation tyrosine kinase inhibitor may be due either to late acquisition of a second mutation in the originally mutated clone, such as the T315I, or to acquisition of a completely new mutant clone, such as F317L.
RHAMM-R3 peptide vaccination in patients with acute myeloid leukemia, myelodysplastic syndrome, and multiple myeloma elicits immunologic and clinical responses
Authors: Schmitt Michael , Schmitt Anita , Rojewski Markus T. , Chen Jinfei , Giannopoulos Krzysztof , Fei Fei , Yu Yingzhe , Götz Marlies , Heyduk Marta , Ritter Gerd , Speiser Daniel E. , Gnjatic Sacha , Guillaume Philippe , Ringhoffer Mark , Schlenk Richard F. , Liebisch Peter , Bunjes Donald , Shiku Hiroshi , Dohner Hartmut , Greiner Jochen
Published: November 2007

The receptor for hyaluronic acid–mediated motility (RHAMM) is an antigen eliciting both humoral and cellular immune responses in patients with acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and multiple myeloma (MM). We initiated a phase 1 clinical trial vaccinating 10 patients with R3 (ILSLELMKL), a highly immunogenic CD8+ T-cell epitope peptide derived from RHAMM. In 7 of 10 patients, we detected an increase of CD8+/HLA-A2/RHAMM R3 tetramer+/CD45RA+/CCR7−/CD27−/CD28− effector T cells in accordance with an increase of R3-specific CD8+ T cells in enzyme linked immunospot (ELISpot) assays. In chromium release assays, a specific lysis of RHAMM-positive leukemic blasts was shown. Three of 6 patients with myeloid disorders (1/3 AML, 2/3 MDS) achieved clinical responses: one patient with AML and one with MDS showed a significant reduction of blasts in the bone marrow after the last vaccination. One patient with MDS no longer needed erythrocyte transfusions after 4 vaccinations. Two of 4 patients with MM showed a reduction of free light chain serum levels. Taken together, RHAMM-R3 peptide vaccination induced both immunologic and clinical responses, and therefore RHAMM constitutes a promising target for further immunotherapeutic approaches. This study is registered at http://ISRCTN.org as ISRCTN32763606 and is registered with EudraCT as 2005-001706-37.
Treatment of newly diagnosed acute promyelocytic leukemia (APL): a comparison of French-Belgian-Swiss and PETHEMA results
Authors: Adès Lionel , Sanz Miguel A. , Chevret Sylvie , Montesinos Pau , Chevallier Patrice , Raffoux Emmanuel , Vellenga Edo , Guerci Agnès , Pigneux Arnaud , Huguet Francoise , Rayon Consuelo , Stoppa Anne Marie , de la Serna Javier , Cahn Jean-Yves , Meyer-Monard Sandrine , Pabst Thomas , Thomas Xavier , de Botton Stéphane , Parody Ricardo , Bergua Juan , Lamy Thierry , Vekhoff Anne , Negri Silvia , Ifrah Norbert , Dombret Hervé , Ferrant Augustin , Bron Dominique , Degos Laurent , Fenaux Pierre
Published: November 2007

All-trans retinoic acid (ATRA) plus anthracycline chemotherapy is the reference treatment of newly diagnosed acute promyelocytic leukemia (APL), whereas the role of cytosine arabinoside (AraC) remains disputed. We performed a joint analysis of patients younger than 65 years included in Programa para el Estudio de la Terapéutica en Hemopatía Maligna (PETHEMA) LPA 99 trial, where patients received no AraC in addition to ATRA, high cumulative dose idarubicin, and mitoxantrone, and APL 2000 trial, where patients received AraC in addition to ATRA and lower cumulative dose daunorubicin. In patients with white blood cell (WBC) count less than 10 × 109/L, complete remission (CR) rates were similar, but 3-year cumulative incidence of relapse (CIR) was significantly lower in LPA 99 trial: 4.2% versus 14.3% (P = .03), although 3-year survival was similar in both trials. This suggested that AraC is not required in APL with WBC count less than 10 × 109/L, at least in trials with high-dose anthracycline and maintenance treatment. In patients with WBC of 10 × 109/L or more, however, the CR rate (95.1% vs 83.6% P = .018) and 3-year survival (91.5% vs 80.8%, P = .026) were significantly higher in APL 2000 trial, and there was a trend for lower 3-year CIR (9.9% vs 18.5%, P = .12), suggesting a beneficial role for AraC in those patients.
Application of high-throughput screening to identify a novel αIIb-specific small- molecule inhibitor of αIIbβ3-mediated platelet interaction with fibrinogen
Authors: Blue Robert , Murcia Marta , Karan Charles , Jiroušková Markéta , Coller Barry S.
Published: November 2007

Small-molecule αIIbβ3 antagonists competitively block ligand binding by spanning between the D224 in αIIb and the MIDAS metal ion in β3. They variably induce conformational changes in the receptor, which may have undesirable consequences. To identify αIIbβ3 antagonists with novel structures, we tested 33 264 small molecules for their ability to inhibit the adhesion of washed platelets to immobilized fibrinogen at 16 μM. A total of 102 compounds demonstrated 50% or more inhibition, and one of these (compound 1, 265 g/mol) inhibited ADP-induced platelet aggregation (IC50: 13± 5 μM), the binding of soluble fibrinogen to platelets induced by mAb AP5, and the binding of soluble fibrinogen and a cyclic RGD peptide to purified αIIbβ3. Compound 1 did not affect the function of GPIb, α2β1, or the other β3 family receptor αVβ3. Molecular docking simulations suggest that compound 1 interacts with αIIb but not β3. Compound 1 induced partial exposure of an αIIb ligand-induced binding site (LIBS), but did not induce exposure of 2 β3 LIBS. Transient exposure of purified αIIbβ3 to eptifibatide, but not compound 1, enhanced fibrinogen binding (“priming”). Compound 1 provides a prototype for small molecule selective inhibition of αIIbβ3, without receptor priming, via targeting αIIb.
Endogenous lipid mediators in the resolution of airway inflammation
Authors: Haworth O. , Levy B. D.
Published: November 2007

Acute inflammation in the lung is fundamentally important to host defence, but chronic or excessive inflammation leads to several common respiratory diseases, including asthma and acute respiratory distress syndrome.

The resolution of inflammation is an active process. In health, events at the onset of acute inflammation establish biosynthetic circuits for specific chemical mediators that later serve as agonists to orchestrate a return to tissue homeostasis. In addition to an overabundance of pro-inflammatory stimuli, pathological inflammation can also result from defects in resolution signalling.

The understanding of anti-inflammatory, pro-resolution molecules and their counter-regulatory signalling pathways is providing new insights into the molecular pathophysiology of lung disease and opportunities for the design of therapeutic strategies.

In the present review, the growing family of lipid mediators of resolution is examined, including lipoxins, resolvins, protectins, cyclopentenones and presqualene diphosphate. Roles are uncovered for these compounds, or their structural analogues, in regulating airway inflammation.
Tracheal aspirate pH is alkaline in pre-term human infants
Authors: Paget-Brown A. O. , Hunt J. F. , Gaston B.
Published: November 2007

The pH of sputum and exhaled breath condensate is abnormal in several pulmonary disorders. Though airway pH regulatory proteins may be abnormally expressed in human development, the tracheal aspirate pH of infants born prematurely has not been studied.

Undiluted mid-tracheal aspirate samples were obtained on the first day of life from pre-term (23–30 weeks’ gestation) and term (≥37 weeks’ gestation) infants for pH measurement; subsequently, pH was measured on days 7, 14 and 21 from the pre-term infants who remained intubated.

Thirty-five pre-term infants and eight term infants had samples collected on the first day of life. The mean pH of the pre-term infant samples (8.31±0.35) was significantly higher than that of the term infants (7.83±0.39). The pH in pre-term infants' airways fell with prolonged endotracheal intubation; the maximal decrease was of -1.37±0.96 pH units to 6.89±0.77.

Pre-term infants have a higher tracheal aspirate pH than full-term infants, and their airways tend to become more acidic with prolonged mechanical ventilation. The present data demonstrate for the first time that premature infants may have abnormal tracheal aspirate pH.
Azathioprine and diffuse alveolar haemorrhage: the pharmacogenetics of thiopurine methyltransferase
Authors: Perri D. , Cole D. E. C. , Friedman O. , Piliotis E. , Mintz S. , Adhikari N. K. J.
Published: November 2007

Current guidelines support the use of corticosteroids and azathioprine as one possible treatment strategy for idiopathic pulmonary fibrosis (IPF). However, some patients with genetic polymorphisms of thiopurine methyltransferase (TPMT) are at risk of severe azathioprine myelotoxicity.

The current authors present the case of an 85-yr-old Caucasian male with IPF who developed diffuse alveolar haemorrhage as a complication of azathioprine-induced myelosuppression.

Leukocyte genetic TPMT testing revealed that the patient had homozygous polymorphisms associated with the absence of TPMT activity and severe azathioprine-induced myelotoxicity.

Thiopurine methyltransferase deficiency should be considered in patients who develop leukopenia early in treatment with azathiopurine, or who present with severe marrow suppression at usual doses. For centres with equipped laboratories, a dosing suggestion is provided based on thiopurine methyltransferase testing. Even with screening strategies, frequent monitoring of complete blood count and liver biochemistry should remain the mainstay of surveillance for azathioprine toxicity.
Definition, epidemiology and natural history of COPD
Authors: Viegi G. , Pistelli F. , Sherrill D. L. , Maio S. , Baldacci S. , Carrozzi L.
Published: November 2007

Chronic obstructive pulmonary disease (COPD) is the fifth cause of morbidity and mortality in the developed world and represents a substantial economic and social burden. Patients experience a progressive deterioration up to end-stage COPD, characterised by very severe airflow limitation, severely limited and declining performance status with chronic respiratory failure, advanced age, multiple comorbidities and severe systemic manifestations/complications.

COPD is frequently underdiagnosed and under-treated. Today, COPD develops earlier in life and is less gender specific. Tobacco smoking is the major risk factor for COPD, followed by occupation and air pollution. Severe deficiency for α1-antitrypsin is rare; several phenotypes are being associated with elevated risk for COPD in the presence of risk factor exposure. Any patient presenting with cough, sputum production or dyspnoea should be assessed by standardised spirometry. Continued exposure to noxious agents promotes a more rapid decline in lung function and increases the risk for repeated exacerbations, eventually leading to end-stage disease.

Without major efforts in prevention, there will be an increasing proportion of end-stage patients who can live longer through long-term oxygen therapy and assisted ventilation, but with elevated suffering and huge costs. Smoking prevention and smoking cessation are the most important epidemiological measurements to counteract chronic obstructive pulmonary disease epidemics.
Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks
Authors: Li Peng , Zhang Chaoyang , Perkins Edward J , Gong Ping , Deng Youping
Published: November 2007

Background

The regulation of gene expression is achieved through gene regulatory networks (GRNs) in which collections of genes interact with one another and other substances in a cell. In order to understand the underlying function of organisms, it is necessary to study the behavior of genes in a gene regulatory network context. Several computational approaches are available for modeling gene regulatory networks with different datasets. In order to optimize modeling of GRN, these approaches must be compared and evaluated in terms of accuracy and efficiency.

Results

In this paper, two important computational approaches for modeling gene regulatory networks, probabilistic Boolean network methods and dynamic Bayesian network methods, are compared using a biological time-series dataset from the Drosophila Interaction Database to construct a Drosophila gene network. A subset of time points and gene samples from the whole dataset is used to evaluate the performance of these two approaches.

Conclusion

The comparison indicates that both approaches had good performance in modeling the gene regulatory networks. The accuracy in terms of recall and precision can be improved if a smaller subset of genes is selected for inferring GRNs. The accuracy of both approaches is dependent upon the number of selected genes and time points of gene samples. In all tested cases, DBN identified more gene interactions and gave better recall than PBN.
Automatic delineation of malignancy in histopathological head and neck slides
Authors: Mete Mutlu , Xu Xiaowei , Fan Chun-Yang , Shafirstein Gal
Published: November 2007

Background

Histopathology, which is one of the most important routines of all laboratory procedures used in pathology, is decisive for the diagnosis of cancer. Experienced histopathologists review the histological slides acquired from biopsy specimen in order to outline malignant areas. Recently, improvements in imaging technologies in terms of histological image analysis led to the discovery of virtual histological slides. In this technique, a computerized microscope scans a glass slide and generates virtual slides at a resolution of 0.25 μm/pixel. As the recognition of intrinsic cancer areas is time consuming and error prone, in this study we develop a novel method to tackle automatic squamous cell carcinoma of the head and neck detection problem in high-resolution, wholly-scanned histopathological slides.

Results

A density-based clustering algorithm improved for this study plays a key role in the determination of the corrupted cell nuclei. Using the Support Vector Machines (SVMs) Classifier, experimental results on seven head and neck slides show that the proposed algorithm performs well, obtaining an average of 96% classification accuracy.

Conclusion

Recent advances in imaging technology enable us to investigate cancer tissue at cellular level. In this study we focus on wholly-scanned histopathological slides of head and neck tissues. In the context of computer-aided diagnosis, delineation of malignant regions is achieved using a powerful classification algorithm, which heavily depends on the features extracted by aid of a newly proposed cell nuclei clustering technique. The preliminary experimental results demonstrate a high accuracy of the proposed method.
Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis
Authors: Dozmorov Mikhail G , Kyker Kimberly D , Saban Ricardo , Shankar Nathan , Baghdayan Arto S , Centola Michael B , Hurst Robert E
Published: November 2007

Background

To better understand the response of urinary epithelial (urothelial) cells to Enterococcus faecalis, a uropathogen that exhibits resistance to multiple antibiotics, a genome-wide scan of gene expression was obtained as a time series from urothelial cells growing as a layered 3-dimensional culture similar to normal urothelium. We herein describe a novel means of analysis that is based on deconvolution of gene variability into technical and biological components.

Results

Analysis of the expression of 21,521 genes from 30 minutes to 10 hours post infection, showed 9553 genes were expressed 3 standard deviations (SD) above the system zero-point noise in at least 1 time point. The asymmetric distribution of relative variances of the expressed genes was deconvoluted into technical variation (with a 6.5% relative SD) and biological variation components (>3 SD above the mode technical variability). These 1409 hypervariable (HV) genes encapsulated the effect of infection on gene expression. Pathway analysis of the HV genes revealed an orchestrated response to infection in which early events included initiation of immune response, cytoskeletal rearrangement and cell signaling followed at the end by apoptosis and shutting down cell metabolism. The number of poorly annotated genes in the earliest time points suggests heretofore unknown processes likely also are involved.

Conclusion

Enterococcus infection produced an orchestrated response by the host cells involving several pathways and transcription factors that potentially drive these pathways. The early time points potentially identify novel targets for enhancing the host response. These approaches combine rigorous statistical principles with a biological context and are readily applied by biologists.
Metabonomics evaluations of age-related changes in the urinary compositions of male Sprague Dawley rats and effects of data normalization methods on statistical and quantitative analysis
Authors: Schnackenberg Laura K , Sun Jinchun , Espandiari Parvaneh , Holland Ricky D , Hanig Joseph , Beger Richard D
Published: November 2007

Background

Urine from male Sprague-Dawley rats 25, 40, and 80 days old was analyzed by NMR and UPLC/MS. The effects of data normalization procedures on principal component analysis (PCA) and quantitative analysis of NMR-based metabonomics data were investigated. Additionally, the effects of age on the metabolic profiles were examined by both NMR and UPLC/MS analyses.

Results

The data normalization factor was shown to have a great impact on the statistical and quantitative results indicating the need to carefully consider how to best normalize the data within a particular study and when comparing different studies. PCA applied to the data obtained from both NMR and UPLC/MS platforms reveals similar age-related differences. NMR indicated many metabolites associated with the Krebs cycle decrease while citrate and 2-oxoglutarate, also associated with the Krebs cycle, increase in older rats.

Conclusion

This study compared four different normalization methods for the NMR-based metabonomics spectra from an age-related study. It was shown that each method of normalization has a great effect on both the statistical and quantitative analyses. Each normalization method resulted in altered relative positions of significant PCA loadings for each sample spectra but it did not alter which chemical shifts had the highest loadings. The greater the normalization factor was related to age, the greater the separation between age groups was observed in subsequent PCA analyses. The normalization factor that showed the least age dependence was total NMR intensity, which was consistent with UPLC/MS data. Normalization by total intensity attempts to make corrections due to dietary and water intake of the individual animal, which is especially useful in metabonomics evaluations of urine. Additionally, metabonomics evaluations of age-related effects showed decreased concentrations of many Krebs cycle intermediates along with increased levels of oxidized antioxidants in urine of older rats, which is consistent with current theories on aging and its association with diminishing mitochondrial function and increasing levels of reactive oxygen species. Analysis of urine by both NMR and UPLC/MS provides a comprehensive and complementary means of examining metabolic events in aging rats.
Statistical tools for transgene copy number estimation based on real-time PCR
Authors: Yuan Joshua S , Burris Jason , Stewart Nathan R , Mentewab Ayalew , Stewart C Neal
Published: November 2007

Background

As compared with traditional transgene copy number detection technologies such as Southern blot analysis, real-time PCR provides a fast, inexpensive and high-throughput alternative. However, the real-time PCR based transgene copy number estimation tends to be ambiguous and subjective stemming from the lack of proper statistical analysis and data quality control to render a reliable estimation of copy number with a prediction value. Despite the recent progresses in statistical analysis of real-time PCR, few publications have integrated these advancements in real-time PCR based transgene copy number determination.

Results

Three experimental designs and four data quality control integrated statistical models are presented. For the first method, external calibration curves are established for the transgene based on serially-diluted templates. The Ct number from a control transgenic event and putative transgenic event are compared to derive the transgene copy number or zygosity estimation. Simple linear regression and two group T-test procedures were combined to model the data from this design. For the second experimental design, standard curves were generated for both an internal reference gene and the transgene, and the copy number of transgene was compared with that of internal reference gene. Multiple regression models and ANOVA models can be employed to analyze the data and perform quality control for this approach. In the third experimental design, transgene copy number is compared with reference gene without a standard curve, but rather, is based directly on fluorescence data. Two different multiple regression models were proposed to analyze the data based on two different approaches of amplification efficiency integration. Our results highlight the importance of proper statistical treatment and quality control integration in real-time PCR-based transgene copy number determination.

Conclusion

These statistical methods allow the real-time PCR-based transgene copy number estimation to be more reliable and precise with a proper statistical estimation. Proper confidence intervals are necessary for unambiguous prediction of trangene copy number. The four different statistical methods are compared for their advantages and disadvantages. Moreover, the statistical methods can also be applied for other real-time PCR-based quantification assays including transfection efficiency analysis and pathogen quantification.
Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida
Authors: Pirooznia Mehdi , Gong Ping , Guan Xin , Inouye Laura S , Yang Kuan , Perkins Edward J , Deng Youping
Published: November 2007

Background

Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR.

Results

A total of 3144 good quality ESTs (GenBank dbEST accession number EH669363–EH672369 and EL515444–EL515580) were obtained from the raw clone sequences after cleaning. Clustering analysis yielded 2231 unique sequences including 448 contigs (from 1361 ESTs) and 1783 singletons. Comparative genomic analysis showed that 743 or 33% of the unique sequences shared high similarity with existing genes in the GenBank nr database. Provisional function annotation assigned 830 Gene Ontology terms to 517 unique sequences based on their homology with the annotated genomes of four model organisms Drosophila melanogaster, Mus musculus, Saccharomyces cerevisiae, and Caenorhabditis elegans. Seven percent of the unique sequences were further mapped to 99 Kyoto Encyclopedia of Genes and Genomes pathways based on their matching Enzyme Commission numbers. All the information is stored and retrievable at a highly performed, web-based and user-friendly relational database called EST model database or ESTMD version 2.

Conclusion

The ESTMD containing the sequence and annotation information of 4032 E. fetida ESTs is publicly accessible at http://mcbc.usm.edu/estmd/.
Churchill regulates cell movement and mesoderm specification by repressing Nodal signaling
Authors: Londin Eric R , Mentzer Laura , Sirotkin Howard I
Published: November 2007

Background

Cell movements are essential to the determination of cell fates during development. The zinc-finger transcription factor, Churchill (ChCh) has been proposed to regulate cell fate by regulating cell movements during gastrulation in the chick. However, the mechanism of action of ChCh is not understood.

Results

We demonstrate that ChCh acts to repress the response to Nodal-related signals in zebrafish. When ChCh function is abrogated the expression of mesodermal markers is enhanced while ectodermal markers are expressed at decreased levels. In cell transplant assays, we observed that ChCh-deficient cells are more motile than wild-type cells. When placed in wild-type hosts, ChCh-deficient cells often leave the epiblast, migrate to the germ ring and are later found in mesodermal structures. We demonstrate that both movement of ChCh-compromised cells to the germ ring and acquisition of mesodermal character depend on the ability of the donor cells to respond to Nodal signals. Blocking Nodal signaling in the donor cells at the levels of Oep, Alk receptors or Fast1 inhibited migration to the germ ring and mesodermal fate change in the donor cells. We also detect additional unusual movements of transplanted ChCh-deficient cells which suggests that movement and acquisition of mesodermal character can be uncoupled. Finally, we demonstrate that ChCh is required to limit the transcriptional response to Nodal.

Conclusion

These data establish a broad role for ChCh in regulating both cell movement and Nodal signaling during early zebrafish development. We show that chch is required to limit mesodermal gene expression, inhibit Nodal-dependant movement of presumptive ectodermal cells and repress the transcriptional response to Nodal signaling. These findings reveal a dynamic role for chch in regulating cell movement and fate during early development.
The Drosophila Perlecan gene trol regulates multiple signaling pathways in different developmental contexts
Authors: Lindner Jonathan R , Hillman Paul R , Barrett Andrea L , Jackson Megan C , Perry Trinity L , Park Youngji , Datta Sumana
Published: November 2007

Background

Heparan sulfate proteoglycans modulate signaling by a variety of growth factors. The mammalian proteoglycan Perlecan binds and regulates signaling by Sonic Hedgehog, Fibroblast Growth Factors (FGFs), Vascular Endothelial Growth Factor (VEGF) and Platelet Derived Growth Factor (PDGF), among others, in contexts ranging from angiogenesis and cardiovascular development to cancer progression. The Drosophila Perlecan homolog trol has been shown to regulate the activity of Hedgehog and Branchless (an FGF homolog) to control the onset of stem cell proliferation in the developing brain during first instar. Here we extend analysis of trol mutant phenotypes to show that trol is required for a variety of developmental events and modulates signaling by multiple growth factors in different situations.

Results

Different mutations in trol allow developmental progression to varying extents, suggesting that trol is involved in multiple cell-fate and patterning decisions. Analysis of the initiation of neuroblast proliferation at second instar demonstrated that trol regulates this event by modulating signaling by Hedgehog and Branchless, as it does during first instar. Trol protein is distributed over the surface of the larval brain, near the regulated neuroblasts that reside on the cortical surface. Mutations in trol also decrease the number of circulating plasmatocytes. This is likely to be due to decreased expression of pointed, the response gene for VEGF/PDGF signaling that is required for plasmatocyte proliferation. Trol is found on plasmatocytes, where it could regulate VEGF/PDGF signaling. Finally, we show that in second instar brains but not third instar brain lobes and eye discs, mutations in trol affect signaling by Decapentaplegic (a Transforming Growth Factor family member), Wingless (a Wnt growth factor) and Hedgehog.

Conclusion

These studies extend the known functions of the Drosophila Perlecan homolog trol in both developmental and signaling contexts. These studies also highlight the fact that Trol function is not dedicated to a single molecular mechanism, but is capable of regulating different growth factor pathways depending on the cell-type and event underway.
A new GFP-tagged line reveals unexpected Otx2 protein localization in retinal photoreceptors
Authors: Fossat Nicolas , Le Greneur Coralie , Béby Francis , Vincent Stéphane , Godement Pierre , Chatelain Gilles , Lamonerie Thomas
Published: November 2007

Background

Dynamic monitoring of protein expression and localization is fundamental to the understanding of biological processes. The paired-class homeodomain-containing transcription factor Otx2 is essential for normal head and brain development in vertebrates. Recent conditional knockout studies have pointed to multiple roles of this protein during late development and post-natal life. Yet, later expression and functions remain poorly characterized as specific reagents to detect the protein at any stage of development are still missing.

Results

We generated a new mouse line harbouring an insertion of the GFP gene within the Otx2 coding sequence to monitor the gene activity while preserving most of its functions. Our results demonstrate that this line represents a convenient tool to capture the dynamics of Otx2 gene expression from early embryonic stages to adulthood. In addition, we could visualize the intracellular location of Otx2 protein. In the retina, we reinterpret the former view of protein distribution and show a further level of regulation of intranuclear protein localization, which depends on the cell type.

Conclusion

The GFP-tagged Otx2 mouse line fully recapitulates previously known expression patterns and brings additional accuracy and easiness of detection of Otx2 gene activity. This opens up the way to live imaging of a highly dynamic actor of brain development and can be adapted to any mutant background to probe for genetic interaction between Otx2 and the mutated gene.
Investigation of MYST4 histone acetyltransferase and its involvement in mammalian gametogenesis
Authors: McGraw Serge , Morin Guillaume , Vigneault Christian , Leclerc Pierre , Sirard Marc-André
Published: November 2007

Background

Various histone acetylases (HATs) play a critical role in the regulation of gene expression, but the precise functions of many of those HATs are still unknown. Here we provide evidence that MYST4, a known HAT, may be involved in early mammalian gametogenesis.

Results

Although MYST4 mRNA transcripts are ubiquitous, protein expression was restricted to select extracts (including ovary and testis). Immunohistochemistry experiments performed on ovary sections revealed that the MYST4 protein is confined to oocytes, granulosa and theca cells, as well as to cells composing the blood vessels. The transcripts for MYST4 and all-MYST4-isoforms were present in oocytes and in in vitro produced embryos. In oocytes and embryos the MYST4 protein was localized in both the cytoplasm and nucleus. Within testis sections, the MYST4 protein was specific to only one cell type, the elongating spermatids, where it was exclusively nuclear.

Conclusion

We established that MYST4 is localized into specialized cells of the ovary and testis. Because the majority of these cells are involved in male and female gametogenesis, MYST4 may contribute to important and specific acetylation events occurring during gametes and embryo development.
Evaluation of the models handling heterotachy in phylogenetic inference
Authors: Zhou Yan , Rodrigue Nicolas , Lartillot Nicolas , Philippe Hervé
Published: November 2007

Background

The evolutionary rate at a given homologous position varies across time. When sufficiently pronounced, this phenomenon – called heterotachy – may produce artefactual phylogenetic reconstructions under the commonly used models of sequence evolution. These observations have motivated the development of models that explicitly recognize heterotachy, with research directions proposed along two main axes: 1) thecovarionapproach, where sites switch from variable to invariable states; and 2) themixture of branch lengths(MBL) approach, where alignment patterns are assumed to arise from one of several sets of branch lengths, under a given phylogeny.

Results

Here, we report the first statistical comparisons contrasting the performance of covarion and MBL modeling strategies. Using simulations under heterotachous conditions, we explore the properties of three model comparison methods: the Akaike information criterion, the Bayesian information criterion, and cross validation. Although more time consuming, cross validation appears more reliable than AIC and BIC as it directly measures the predictive power of a model on 'future' data. We also analyze three large datasets (nuclear proteins of animals, mitochondrial proteins of mammals, and plastid proteins of plants), and find the optimal number of components of the MBL model to be two for all datasets, indicating that this model is preferred over the standard homogeneous model. However, the covarion model is always favored over the optimal MBL model.

Conclusion

We demonstrated, using three large datasets, that the covarion model is more efficient at handling heterotachy than the MBL model. This is probably due to the fact that the MBL model requires a serious increase in the number of parameters, as compared to two supplementary parameters of the covarion approach. Further improvements of the both the mixture and the covarion approaches might be obtained by modeling heterogeneous behavior both along time and across sites.
Patterns of selective constraints in noncoding DNA of rice
Authors: Guo Xingyi , Wang Yu , Keightley Peter D , Fan Longjiang
Published: November 2007

Background

Several studies have investigated the relationships between selective constraints in introns and their length, GC content and location within genes. To date, however, no such investigation has been done in plants. Studies of selective constraints in noncoding DNA have generally involved interspecific comparisons, under the assumption of the same selective pressures acting in each lineage. Such comparisons are limited to cases in which the noncoding sequences are not too strongly diverged so that reliable sequence alignments can be obtained. Here, we investigate selective constraints in a recent segmental duplication that includes 605 paralogous intron pairs that occurred about 7 million years ago in rice (O. sativa).

Results

Our principal findings are: (1) intronic divergence is negatively correlated with intron length, a pattern that has previously been described in Drosophila and mammals; (2) there is a signature of strong purifying selection at splice control sites; (3) first introns are significantly longer and have a higher GC content than other introns; (4) the divergences of first and non-first introns are not significantly different from one another, a pattern that differs from Drosophila and mammals; and (5) short introns are more diverged than four-fold degenerate sites suggesting that selection reduces divergence at four-fold sites.

Conclusion

Our observation of stronger selective constraints in long introns suggests that functional elements subject to purifying selection may be concentrated within long introns. Our results are consistent with the presence of strong purifying selection at splicing control sites. Selective constraints are not significantly stronger in first introns of rice, as they are in other species.
Role of NOD2/CARD15 in coronary heart disease
Authors: El Mokhtari Nour Eddine , Ott Stephan J , Nebel Almut , Schäfer Arne , Rosenstiel Philip , Förster Matti , Nothnagel Michael , Simon Rüdiger , Schreiber Stefan
Published: November 2007

Background:

Bacterial DNA has been repeatedly detected in atheromatous lesions of coronary heart disease (CHD) patients. Phylogenetic signatures in the atheroma lesions that are similar to those of bacterial biofilms on human barrier organs, including the respiratory or gastrointestinal tract, raise the question of a defective barrier function in CHD. NOD2 plays a major role in defense against bacterial invasion. Genetic variation in the CARD15 gene, which encodes NOD2, was previously shown to result in a barrier defect that causes chronic inflammatory disorders (e.g. Crohn disease). In the present study, we investigated the possible involvement of NOD2/CARD15 in the pathology of CHD by i) analyzing the local expression of NOD2 in atherectomy versus healthy tissue (n = 5 each) using histochemical immunofluorescence and ii) by testing the three major functional CARD15 variants (R702W, G908R and 1007fs) for association with early-onset CHD in 900 German patients and 632 healthy controls.

Results:

In atherectomy tissue of CHD patients, NOD2 was detected in inflammatory cells at the luminal sides of the lesions. However, the allele and genotype frequencies of the three major CARD15 polymorphisms did not differ between CHD patients and controls.

Conclusion:

The NOD2 up-regulation in atheroma lesions indicates an involvement of this protein in the pathology of CHD. Although NOD2 could be important in local immune response mechanisms, none of the analyzed CARD15 variants seem to play a significant role in the etiology of CHD.
Cigarette smoking and tooth loss experience among young adults: a national record linkage study
Authors: Ojima Miki , Hanioka Takashi , Tanaka Keiko , Aoyama Hitoshi
Published: November 2007

Background

Various factors affect tooth loss in older age including cigarette smoking; however, evidence regarding the association between smoking and tooth loss during young adulthood is limited. The present study examined the association between cigarette smoking and tooth loss experience among adults aged 20–39 years using linked data from two national databases in Japan.

Methods

Two databases of the National Nutrition Survey (NNS) and the Survey of Dental Diseases (SDD), which were conducted in 1999, were obtained from the Ministry of Health, Labor and Welfare with permission for analytical use. In the NNS, participants received physical examinations and were interviewed regarding dietary intake and health practices including cigarette smoking, whereas in the SDD, participants were asked about their frequency of daily brushing, and received oral examinations by certified dentists. Among 6,805 records electronically linked via household identification code, 1314 records of individuals aged 20 to 39 years were analyzed. The prevalence of 1+ tooth loss was compared among non-, former, and current smokers. Multiple logistic regression models were constructed including confounders: frequency of tooth brushing, body mass index, alcohol consumption, and intake of vitamins C and E.

Results

Smoking rates differed greatly in men (53.3%) and women (15.5%). The overall prevalence of tooth loss was 31.4% (31.8% men and 31.1% women). Tooth loss occurred more frequently among current smokers (40.6%) than former (23.1%) and non-smokers (27.9%). Current smoking showed a significant association with 1+ tooth loss in men (adjusted OR = 2.21 [1.40–3.50], P = 0.0007) and women (1.70 [1.13–2.55], P = 0.0111). A significant positive exposure-related relationship between cigarette smoking status and tooth loss was observed (P for trend < 0.0001 and 0.0004 in men and women, respectively). Current smoking was also associated with the prevalence of decayed teeth (1.67 [1.28–2.20], P = 0.0002).

Conclusion

An association between cigarette smoking and tooth loss was evident among young adults throughout Japan. Due to limitations of the available variables in the present databases, further studies including caries experience and its confounders should be conducted to examine whether smoking is a true risk of premature tooth loss in young adults.
Training pediatric health care providers in prevention of dental decay: results from a randomized controlled trial
Authors: Slade Gary D , Rozier R Gary , Zeldin Leslie P , Margolis Peter A
Published: November 2007

Background

Physicians report willingness to provide preventive dental care, but optimal methods for their training and support in such procedures are not known. This study aimed to evaluate the effect of three forms of continuing medical education (CME) on provision of preventive dental services to Medicaid-enrolled children by medical personnel in primary care physician offices.

Methods

Practice-based, randomized controlled trial. Setting: 1,400 pediatric and family physician practices in North Carolina providing care to an estimated 240,000 Medicaid-eligible children aged 0–3 years. Interventions: Group A practices (n = 39) received didactic training and course materials in oral health screening, referral, counseling and application of fluoride varnish. Group B practices (n = 41) received the same as Group A and were offered weekly conference calls providing advice and support. Group C practices (n = 41) received the same as Group B and were offered in-office visit providing hands-on advice and support. In all groups, physicians were reimbursed $38–$43 per preventive dental visit. Outcome measures were computed from reimbursement claims submitted to NC Division of Medical Assistance. Primary outcome measure: rate of preventive dental services provision per 100 well-child visits. Secondary outcome measure: % of practices providing 20 or more preventive dental visits.

Results

121 practices were randomized, and 107 provided data for analysis. Only one half of Group B and C practices took part in conference calls or in-office visits. Using intention-to-treat analysis, rates of preventive dental visits did not differ significantly among CME groups: GroupA = 9.4, GroupB = 12.9 and GroupC = 8.5 (P = 0.32). Twenty or more preventive dental visits were provided by 38–49% of practices in the three study groups (P = 0.64).

Conclusion

A relatively high proportion of medical practices appear capable of adopting these preventive dental services within a one year period regardless of the methods used to train primary health care providers.

Trial Registration

ClinicalTrials.gov NCT00464009