bluuebunny/crossref_metadata_2025 huggingface dataset:
Exact solution of convective mass transfer model for Calciumresponse of endothelium
Authors: Kumar Vineet , Pandey R. N. , Upadhyay S. N.
Published: September 2005

An exact solution for the concentration profile in tubes with surface reaction coupled with permeation have been obtained in terms of fast converging confluent hypergeometric function that gives accurate results. An excellent agreement between the
experimental and theoretical results of the intracellular calcium ion concentration in the
calf aorta endothelial cells and the extracellular ATP concentration provides yet another
example in support of the mass transfer model for intracellular calcium response of the
endothelial cells.
Analysis of a production system with a feedback buffer and ageneral dispatching time
Authors: Lee Ho Woo , Ahn Boo Yong
Published: September 2005

In this paper, we analyze a production system with a finite feedback buffer and dispatching time. Parts enter a “main buffer” before they are processed. Processed parts leave the system with probability 1 − p or are fed back to a “feedback buffer” with probability p. As soon as the feedback buffer becomes full, the parts in the
feedback buffer are dispatched, all at once, to the main buffer by the server for
reprocessing. The dispatching time follows a general distribution. Thus the server is
engaged either in one of the following states: idle, processing, dispatching.

We derive various performance measures such as the mean number of parts in each buffer, the mean system sojourn time and the dispatching rate. We also discuss the effects of the dispatching time on the performance measures. We finally derive the procedure to obtain the optimal buffer size that minimizes the overall operating cost.
Effect of Pulsed Estrogen Therapy on Hemostatic Markers in Comparison with Oral Estrogen Regimen in Postmenopausal Women
Authors: Basurto Lourdes , Saucedo Renata , Zárate Arturo , Martínez Carlos , Gaminio Elizabeth , Reyes Elba , Hernandez Marcelino
Published: September 2005

Background/Aims: Hormone replacement therapy (HRT) is associated with an increased risk of thromboembolism dependent on the type of HRT; therefore, we compared therapy effects of intranasal with oral estrogens on coagulation and fibrinolysis markers in postmenopausal women. Methods: A randomized study in which 29 healthy hysterectomized women received intranasal 17β-estradiol or oral estrogens for 3 months. Results: There were no significant differences in the baseline characteristics between groups. Those women receiving intranasal estradiol showed a mild increment in plasminogen activator inhibitor-1 (PAI-I) (from 6.8 ± 3.5 to 9.6 ± 3.9 U/ml, p < 0.01); however, fibrinogen, factor VII-tissue factor complex (VIIa-rTF), antithrombin III (ATIII), protein C (PC) activity, protein S (PS) activity, plasminogen (PLG), and tissue-type plasminogen activator antigen (t-PA) were unchanged. In contrast, oral unopposed estrogens elevated t-PA (from 4.9 ± 2.9 to 9.6 ± 5.1 ng/ml, p < 0.01) in parallel with a decrement in PAI-I (from 5.2 ± 4.0 to 2.7 ± 1.7 U/ml, p < 0.05) and VIIa-rTF (from 201.2 ± 181.0 to 140.6 ± 108.7 mU/ml, p < 0.05). Fibrinogen, ATIII, PC, PS, and PLG were unchanged. Conclusions: Nasal 17β-estradiol had no effect on the coagulation markers, except a moderate increment in PAI-1. In contrast, oral estrogens elicited a decrement in both VIIa-rTF and PAI-1; however, those changes did not surpass normal limits.
Safety and Potential of Drug Interactions of Caspofungin and Voriconazole in Multimorbid Patients
Authors: Kulemann Vanessa , Bauer Martin , Graninger Wolfgang , Joukhadar Christian
Published: September 2005

Due to their broad antimycotic spectrum and the relatively low rate of side effects, the two antifungals caspofungin and voriconazole are considered as attractive therapeutic alternatives to amphotericin B. However, treatment of severe mycotic infections in patients taking co-medication is associated with the risk of severe adverse drug interactions. The risk of such interactions is increased if voriconazole and, much less pronounced caspofungin, are co-administered with drugs which have an inducing or inhibiting effect on the CYP 450 system, primarily on the isoenzymes CYP2C19, CYP2C9 and CYP3A4. This review provides a comprehensive overview on the potential drug interactions of caspofungin and voriconazole in multimorbid patients.
Budesonide Reduces Superoxide and Peroxynitrite Anion Chemiluminescence during Human Neutrophil Bursts
Authors: Braga Pier Carlo , Dal Sasso Monica , Culici Maria , Bianchi Tiziana , Guffanti Enrico Eugenio
Published: September 2005

Many lung disorders are characterized by airway inflammation involving the recruitment of inflammatory cells, and leading to the release of oxidant and inflammatory mediators. The overproduction of superoxide anion (O2–DELETE) and nitric oxide (NO) during the respiratory bursts of neutrophils leads to production of peroxynitrite, a highly damaging oxidant with an important role in the inflammatory loop causing airway hyper-reactivity in respiratory diseases like asthma. The aim of this study was to investigate in vitro the effects of a 1-hour incubation with budesonide at 2.5 × 10–7, 5 × 10–7, 1 × 10–6, 2 × 10–6 and 4 × 10–6 mol/l on O2–DELETE, NO, and peroxynitrite production during the respiratory burst of human neutrophils stimulated by N-formyl-methionyl-leucyl-phenylalanine (fMLP, 5 × 10–7 mol/l) or phorbol 12-myristate 13-acetate (PMA, 2 × 10–6 mol/l), as documented by luminol-amplified chemiluminescence (LACL). In absence of L-arginine, budesonide (5 × 10–7 to 4 × 10–6 mol/l) dose-dependently reduced both fMLP- and PMA-induced LACL (18.3–50.6%). In the presence of L-arginine (100 µg/ml), a NO donor increasing peroxynitrite production, LACL increased 3–5 times compared with baseline, but budesonide dose-dependently reduced LACL (25.5–59.6%). Mifepristone (4 × 10–6 mol/l), a glucocorticoid receptor antagonist, inhibited the effect of budesonide on LACL, thus confirming that budesonide reacts with glucocorticoid receptors to exert an antioxidant activity. These results suggest that budesonide target rapidly human neutrophils leading to a fast reduction in both NO and peroxynitrite production, and are consistent with decrease in exhaled NO levels after treatment with budesonide in patients with asthma.
Robot-Assisted Endoscopic Surgery: A Four-Year Single-Center Experience
Authors: Ruurda Jelle P. , Draaisma Werner A. , van Hillegersberg Richard , Borel Rinkes Inne H.M. , Gooszen Hein G. , Janssen Lucas W.M. , Simmermacher Rogier K.J. , Broeders Ivo A.M.J.
Published: September 2005

Background: Robotic systems were introduced in the late 1990s with the objective to overcome the technical limitations of endoscopic surgery. In this prospective cohort study the potential safety, feasibility, pitfalls and challenges of robotic systems in gastrointestinal endoscopic surgery are assessed and our vision on future perspectives is presented. Methods:Between August 2000 and December 2004, 208 procedures were performed with support of the Intuitive Surgical da Vinci™ robotic system. We started with cholecystectomies (40) and Nissen fundoplications (41) to gain experience with robot-assisted surgery. In the following years more complex procedures were carried out, i.e. colorectal procedures (7), type III/IV paraesophageal hernia repair (32), redo Nissen fundoplications (9), Heller myotomies (24), esophageal resections (22), rectopexies (16) and aortobifemoral bypasses (3). Results:The median robotic set-up time was 13 min, and 7 min in the last 50 procedures. The median operating time for the total of procedures was 120 min (45–420) and the median blood loss was 30 ml (0–800). Fourteen procedures were converted to open surgery (6.7%). Equipment-related problems, such as start-up failures and positioning difficulties of the robotic arms, were encountered in 11 cases (5.3%). Postoperative complications were seen in 11 patients (11/176, 6.3%) after robot-assisted laparoscopic procedures. Pulmonary complications occurred in 11 patients, cardiac in 3, anastomic leakage in 3, chylous leakage in 3 and vocal cord paralysis in 3 after thoracoscopic esophagolymphadenectomy for esophageal cancer. One patient died 12 days after esophageal resection (0.5%). Conclusion:During the implementation of this robotic system, we experienced an obvious learning curve, particularly with regard to the positioning of the robot cart and communication between the surgeon and operating team. After 4 years, we have experienced that the merits of the current generation of this technology probably is preserved to complex endoscopic procedures with delicate dissection and suturing. In the nearby future we will focus on the treatment of motility disorders and malignancies of the esophagus and stomach. The position of the robot in the endoscopic operating room will have to be clarified by the outcome of prospective research. Furthermore, priorities have to be acclaimed on technical sophistication and cost reduction of these systems.
Progesterone Antagonizes the Vasoprotective Effect of Estrogen on Antioxidant Enzyme Expression and Function
Authors: Wassmann Kerstin , Wassmann Sven , Nickenig Georg
Published: September 2005

Oxidative stress plays an important role in the pathogenesis of atherosclerosis and can be effectively influenced by radical scavenging enzymes. Estrogens exert antioxidative effects in the vasculature; however, cotreatment with progesterone may abrogate the vasoprotective effects of estrogen. Therefore, the effects of progesterone on the production of reactive oxygen species (ROS) and expression and function of antioxidant and oxidant enzymes were investigated in cultured vascular smooth muscle cells (VSMCs) and vascular tissue of mice. Progesterone time- and concentration-dependently downregulated extracellular superoxide dismutase (ecSOD) and manganese superoxide dismutase (MnSOD) expression and enzyme activity and reversed 17β-estradiol–induced overexpression of ecSOD and MnSOD in VSMCs. Nuclear run-on assays revealed that progesterone decreases MnSOD and ecSOD transcription rates. Consequently, progesterone increased ROS release in VSMCs that was prevented by concomitant treatment with 17β-estradiol. Estrogen deficiency in ovariectomized mice was associated with an increase in vascular superoxide release and NADPH oxidase activity. Estrogen replacement prevented this increase, whereas progesterone substitution enhanced ROS production and NADPH oxidase activity. The modulation of superoxide release coincided with decreased expression of ecSOD and MnSOD and upregulation of the p22phox and p67phox subunits of the NADPH oxidase complex in progesterone-treated animals. Furthermore, administration of progesterone to ovariectomized mice treated with 17β-estradiol abrogated the antioxidative effects of estrogen. Progesterone antagonizes the vasoprotective effects of estrogen on ecSOD and MnSOD expression and increases NADPH oxidase activity. These findings may in part explain why hormone replacement therapy with estrogen plus progesterone displayed no beneficial effect on cardiovascular event rates in the prospective clinical trials.
Evaluating Discourse and Dialogue Coding Schemes
Authors: Craggs Richard , Wood Mary McGee
Published: September 2005

Agreement statistics play an important role in the evaluation of coding schemes for discourse and dialogue. Unfortunately there is a lack of understanding regarding appropriate agreement measures and how their results should be interpreted. In this article we describe the role of agreement measures and argue that only chance-corrected measures that assume a common distribution of labels for all coders are suitable for measuring agreement in reliability studies. We then provide recommendations for how reliability should be inferred from the results of agreement statistics.
Oscillatory Synchronization Requires Precise and Balanced Feedback Inhibition in a Model of the Insect Antennal Lobe
Authors: Martinez Dominique
Published: September 2005

In the insect olfactory system, odor-evoked transient synchronization of antennal lobe (AL) projection neurons (PNs) is phase-locked to the oscillations of the local field potential. Sensory information is contained in the spatiotemporal synchronization pattern formed by the identities of the phase-locked PNs. This article investigates the role of feedback inhibition from the local neurons (LNs) in this coding. First, experimental biological results are reproduced with a reduced computational spiking neural network model of the AL. Second, the low complexity of the model leads to a mathematical analysis from which a lower bound on the phase-locking probability is derived. Parameters involved in the bound indicate that PN phase locking depends not only on the number of LN-evoked inhibitory postsynaptic potentials (IPSPs) previously received, but also on their temporal jitter. If the inhibition received by a PN at the current oscillatory cycle is both perfectly balanced (i.e., equal to the mean inhibitory drive) and precise (without any jitter), then the PN will be phase-locked at the next oscillatory cycle with probability one.
A Novel Model-Based Hearing Compensation Design Using a Gradient-Free Optimization Method
Authors: Chen Zhe , Becker Suzanna , Bondy Jeff , Bruce Ian C. , Haykin Simon
Published: September 2005

We propose a novel model-based hearing compensation strategy and gradient-free optimization procedure for a learning-based hearing aid design. Motivated by physiological data and normal and impaired auditory nerve models, a hearing compensation strategy is cast as a neural coding problem, and a Neurocompensator is designed to compensate for the hearing loss and enhance the speech. With the goal of learning the Neurocompensator parameters, we use a gradient-free optimization procedure, an improved version of the ALOPEX that we have developed (Haykin, Chen, & Becker, 2004), to learn the unknown parameters of the Neurocompensator. We present our methodology, learning procedure, and experimental results in detail; discussion is also given regarding the unsupervised learning and optimization methods.
Response Properties of an Integrate-and-Fire Model That Receives Subthreshold Inputs
Authors: Zhang Xuedong , Carney Laurel H.
Published: September 2005

A computational technique is described for calculation of the inter-spike interval and poststimulus time histograms for the responses of an integrate-and-fire model to arbitrary inputs. The effects of the model parameters on the response statistics were studied systematically. Specifically, the probability distribution of the membrane potential was calculated as a function of time, and the mean interspike interval and PST histogram were calculated for arbitrary inputs. For stationary inputs, the regularity of the output was studied in detail for various model parameters. For nonstationary inputs, the effects of the model parameters on the output synchronization index were explored. The results show that enhanced synchronization in response to low-frequency stimuli required a large number (n > 25) of weak inputs. Irregular responses and a linear input-output rate relationship required strong (but subthreshold) inputs with a small time constant. A model cell with mixed-amplitude synaptic inputs can respond to stationary inputs irregularly and have enhanced synchronization to nonstationary inputs that are phase-locked to low-frequency inputs. Both of these response properties have been reported for some cells in the ventral cochlear nucleus in the auditory brainstem.
On the Nonlearnability of a Single Spiking Neuron
Authors: Šíma Jiří , Sgall Jiří
Published: September 2005

We study the computational complexity of training a single spiking neuron N with binary coded inputs and output that, in addition to adaptive weights and a threshold, has adjustable synaptic delays. A synchronization technique is introduced so that the results concerning the nonlearn-ability of spiking neurons with binary delays are generalized to arbitrary real-valued delays. In particular, the consistency problem for N with programmable weights, a threshold, and delays, and its approximation version are proven to be NP-complete. It follows that the spiking neurons with arbitrary synaptic delays are not properly PAC learnable and do not allow robust learning unless RP = NP. In addition, the representation problem for N, a question whether an n-variable Boolean function given in DNF (or as a disjunction of O(n) threshold gates) can be computed by a spiking neuron, is shown to be coNP-hard.
Evaluation of Atmospheric Fields from the ECMWF Seasonal Forecasts over a 15-Year Period
Authors: Jan van Oldenborgh Geert , Balmaseda Magdalena A. , Ferranti Laura , Stockdale Timothy N. , Anderson David L. T.
Published: September 2005

Since 1997, the European Centre for Medium-Range Weather Forecasts (ECMWF) has made seasonal forecasts with ensembles of a coupled ocean–atmosphere model, System-1 (S1). In January 2002, a new version, System-2 (S2), was introduced. For the calibration of these models, hindcasts have been performed starting in 1987, so that 15 yr of hindcasts and forecasts are now available for verification.

The main cause of seasonal predictability is El Niño and La Niña perturbing the average weather in many regions and seasons throughout the world. As a baseline to compare the dynamical models with, a set of simple statistical models (STAT) is constructed. These are based on persistence and a lagged regression with the first few EOFs of SST from 1901 to 1986 wherever the correlations are significant. The first EOF corresponds to ENSO, and the second corresponds to decadal ENSO. The temperature model uses one EOF, the sea level pressure (SLP) model uses five EOFs, and the precipitation model uses two EOFs but excludes persistence.

As the number of verification data points is very low (15), the simplest measure of skill is used: the correlation coefficient of the ensemble mean. To further reduce the sampling uncertainties, we restrict ourselves to areas and seasons of known ENSO teleconnections.

The dynamical ECMWF models show better skill in 2-m temperature forecasts over sea and the tropical land areas than STAT, but the modeled ENSO teleconnection pattern to North America is shifted relative to observations, leading to little pointwise skill. Precipitation forecasts of the ECMWF models are very good, better than those of the statistical model, in southeast Asia, the equatorial Pacific, and the Americas in December–February. In March–May the skill is lower. Overall, S1 (S2) shows better skill than STAT at lead time of 2 months in 29 (32) out of 40 regions and seasons of known ENSO teleconnections.
Atlantic Thermohaline Circulation in a Coupled General Circulation Model: Unforced Variations versus Forced Changes
Authors: Dai Aiguo , Hu A. , Meehl G. A. , Washington W. M. , Strand W. G.
Published: September 2005

A 1200-yr unforced control run and future climate change simulations using the Parallel Climate Model (PCM), a coupled atmosphere–ocean–land–sea ice global model with no flux adjustments and relatively high resolution (∼2.8° for the atmosphere and 2/3° for the oceans) are analyzed for changes in Atlantic Ocean circulations. For the forced simulations, historical greenhouse gas and sulfate forcing of the twentieth century and projected forcing for the next two centuries are used. The Atlantic thermohaline circulation (THC) shows large multidecadal (15–40 yr) variations with mean-peak amplitudes of 1.5–3.0 Sv (1 Sv ≡ 106 m3 s−1) and a sharp peak of power around a 24-yr period in the control run. Associated with the THC oscillations, there are large variations in North Atlantic Ocean heat transport, sea surface temperature (SST) and salinity (SSS), sea ice fraction, and net surface water and energy fluxes, which all lag the variations in THC strength by 2–3 yr. However, the net effect of the SST and SSS variations on upper-ocean density in the midlatitude North Atlantic leads the THC variations by about 6 yr, which results in the 24-yr period. The simulated SST and sea ice spatial patterns associated with the THC oscillations resemble those in observed SST and sea ice concentrations that are associated with the North Atlantic Oscillation (NAO). The results suggest a dominant role of the advective mechanism and strong coupling between the THC and the NAO, whose index also shows a sharp peak around the 24-yr time scale in the control run. In the forced simulations, the THC weakens by ∼12% in the twenty-first century and continues to weaken by an additional ∼10% in the twenty-second century if CO2 keeps rising, but the THC stabilizes if CO2 levels off. The THC weakening results from stabilizing temperature increases that are larger in the upper and northern Atlantic Ocean than in the deep and southern parts of the basin. In both the control and forced simulations, as the THC gains (loses) strength and depth, the separated Gulf Stream (GS) moves southward (northward) while the subpolar gyre centered at the Labrador Sea contracts from (expands to) the east with the North Atlantic Current (NAC) being shifted westward (eastward). These horizontal circulation changes, which are dynamically linked to the THC changes, induce large temperature and salinity variations around the GS and NAC paths.
CD163 is the macrophage scavenger receptor for native and chemically modified hemoglobins in the absence of haptoglobin
Authors: Schaer Dominik J. , Schaer Christian A. , Buehler Paul W. , Boykins Robert A. , Schoedon Gabriele , Alayash Abdu I. , Schaffner Andreas
Published: September 2005

CD163 mediates the internalization of hemoglobin-haptoglobin (Hb-Hp) complexes by macrophages. Because Hp binding capacity is exhausted during severe hemolysis, an Hp-independent Hb-clearance pathway is presumed to exist. We demonstrate that Hb interacts efficiently with CD163 in the absence of Hp. Not only is Hb internalized into an endosomal compartment by CD163 as a result of active receptor-dependent endocytosis; it also inhibits the uptake of Hb-Hp complexes, suggesting a common receptor-binding site. Free Hb further induces heme oxygenase mRNA expression in CD163+ HEK293 cells, but not in CD163- cells. Additional evidence for Hp-independent Hb-CD163 interaction is provided by the demonstration that CD163 mediates the uptake of αα-DBBF crosslinked Hb, a chemically modified Hb that forms minimal Hp complexes. Moreover, certain modifications to Hb, such as polymerization or the attachment of specific functional groups (3 lysyl residues) to the β-Cys93 can reduce or enhance this pathway of uptake. In human macrophages, Hp-complex formation critically enhances Hb uptake at low (1 μg/mL), but not at high (greater than 100 μg/mL), ligand concentrations, lending support for a concentration-dependent biphasic model of macrophage Hb-clearance. These results identify CD163 as a scavenger receptor for native Hb and small-molecular-weight Hb-based blood substitutes after Hp depletion.
Severe secondary deficiency of von Willebrand factor–cleaving protease (ADAMTS13) in patients with sepsis-induced disseminated intravascular coagulation: its correlation with development of renal failure
Authors: Ono Tomoko , Mimuro Jun , Madoiwa Seiji , Soejima Kenji , Kashiwakura Yuji , Ishiwata Akira , Takano Katsuhiro , Ohmori Tsukasa , Sakata Yoichi
Published: September 2005

Deficiency of ADAMTS13 is found in patients with thrombotic thrombocytopenic purpura (TTP), and the genetic defects in the ADAMTS13 gene or the autoantibody against ADAMTS13 is thought to be responsible for the development of TTP. The clinical correlation and mechanisms of secondary ADAMTS13 deficiency in other disease states were investigated. In addition to TTP, ADAMTS13 levels were severely decreased in patients with sepsis-induced disseminated intravascular coagulation (DIC). The incidence of acute renal failure and serum creatinine levels in patients with ADAMTS13 activity levels lower than 20% (incidence, 41.2%; creatinine, 160 ± 150 μM [1.81 ± 1.70 mg/dL]) (P < .05) were significantly higher than they were in patients with ADAMTS13 activity levels higher than 20% (incidence, 15.4%; creatinine, 84 ± 67 μM [0.95 ± 0.76 mg/dL]) (P < .01). Additionally, unusually large von Willebrand factor multimers were detected in 26 (51.0%) of 51 patients with ADAMTS13 activity levels lower than 20%. Lower molecular weight forms of ADAMTS13 were found in the plasma of patients with sepsis-induced DIC, suggesting that the deficiency of ADAMTS13 was partially caused by its cleavage by proteases in addition to decreased synthesis in the liver. These data suggested that severe secondary ADAMTS13 deficiency can be associated with sepsis-induced DIC and may contribute to the development of renal failure.
Ablation of oncogenic ALK is a viable therapeutic approach for anaplastic large-cell lymphomas
Authors: Piva Roberto , Chiarle Roberto , Manazza Andrea D. , Taulli Riccardo , Simmons William , Ambrogio Chiara , D'Escamard Valentina , Pellegrino Elisa , Ponzetto Carola , Palestro Giorgio , Inghirami Giorgio
Published: September 2005

Anaplastic large-cell lymphomas (ALCLs) carry chromosome translocations in which the anaplastic lymphoma kinase (ALK) gene is fused to several partners, most frequently, the NPM1 gene. We have demonstrated that the constitutive activation of ALK fusion proteins results in cellular transformation and lymphoid neoplasia. Herein, we specifically down-regulated ALK protein expression by using small hairpin RNA (shRNA) targeting a sequence coding for the catalytic domain of ALK. The ablation of ALK leads to the down-modulation of known ALK downstream effectors, cell growth arrest, and reversion of the transformed phenotype of ALK+ mouse embryonic fibroblasts in vitro and in vivo. In human ALCL cells lentiviral-mediated ALK knock-down leads to G1 cell-cycle arrest and apoptosis in vitro and tumor growth inhibition and regression in vivo. Using a specific approach we have demonstrated that the survival and growth of ALK+ ALCLs are strictly dependent on ALK activation and signaling. Therefore, ALK is a viable target for therapeutic intervention and its inactivation might represent a pivotal approach for the treatment of ALK lymphomas and other ALK-dependent human tumors.
Stable gene transfer and expression in human primary T cells by the Sleeping Beauty transposon system
Authors: Huang Xin , Wilber Andrew C. , Bao Lei , Tuong Dong , Tolar Jakub , Orchard Paul J. , Levine Bruce L. , June Carl H. , McIvor R. Scott , Blazar Bruce R. , Zhou Xianzheng
Published: September 2005

The Sleeping Beauty (SB) transposon system is a nonviral DNA delivery system in which a transposase directs integration of an SB transposon into TA-dinucleotide sites in the genome. To determine whether the SB transposon system can mediate stable gene expression in human T cells, primary peripheral blood lymphocytes (PBLs) were nucleofected with SB vectors carrying a DsRed reporter gene. Plasmids containing the SB transposase on the same molecule as (cis) or on a molecule separate from (trans) the SB transposon mediated long-term and stable reporter gene expression in human primary T cells. Sequencing of transposon:chromosome junctions confirmed that stable gene expression was due to SB-mediated transposition. In other studies, PBLs were successfully transfected using the SB transposon system and shown to stably express a fusion protein consisting of (1) a surface receptor useful for positive T-cell selection and (2) a “suicide” gene useful for elimination of transfected T cells after chemotherapy. This study is the first report demonstrating that the SB transposon system can mediate stable gene transfer in human primary PBLs, which may be advantageous for T-cell–based gene therapies.
A model of oncogenic rearrangements: differences between chromosomal translocation mechanisms and simple double-strand break repair
Authors: Weinstock David M. , Elliott Beth , Jasin Maria
Published: September 2005

Recurrent reciprocal translocations are present in many hematologic and mesenchymal malignancies. Because significant sequence homology is absent from translocation breakpoint junctions, non-homologous end-joining (NHEJ) pathways of DNA repair are presumed to catalyze their formation. We developed translocation reporters for use in mammalian cells from which NHEJ events can be selected after precise chromosomal breakage. Translocations were efficiently recovered with these reporters using mouse cells, and their breakpoint junctions recapitulated findings from oncogenic translocations. Small deletions and microhomology were present in most junctions; insertions and more complex events also were observed. Thus, our reporters model features of oncogenic rearrangements in human cancer cells. A homologous sequence at a distance from the break site affected the translocation junction without substantially altering translocation frequency. Interestingly, in a direct comparison, the spectrum of translocation breakpoint junctions differed from junctions derived from repair at a single chromosomal break, providing mechanistic insight into translocation formation. (Blood. 2006;107:777-780)
Inhibition of hypoxia-inducible factor activity in endothelial cells disrupts embryonic cardiovascular development
Authors: Licht Alexander H. , Müller-Holtkamp Felix , Flamme Ingo , Breier Georg
Published: September 2005

Hypoxia-inducible factors (HIFs) are transcriptional regulators that mediate the cellular response to low oxygen levels. By stimulating the expression of angiogenic growth factors such as vascular endothelial growth factor (VEGF), they trigger the neovascularization of tissues under physiologic and pathologic conditions. Here, we have investigated the endothelial cell–autonomous HIF function in blood vessel growth and development by expressing a dominant-negative HIF mutant (HIFdn) that inhibits the transcriptional responses mediated by both HIF-1 and HIF-2, specifically in endothelial cells of transgenic mice. HIFdn transgenic embryos were growth retarded and died around E11.5. Primitive vascular networks were established, but vascular remodeling in the yolk sac and in the embryo proper was defective, and vascular sprouts failed to invade the neuroepithelium. In addition, heart looping was incomplete, and the ventricles of the heart were thin-walled and lacked trabeculation. Similar cardiovascular defects have been observed in Tie2–deficient mouse embryos. Consistently, HIFdn transgenic embryos expressed reduced levels of the endothelial angiopoietin receptor, Tie-2, whereas other endothelial markers, such as PECAM-1, Tie-1, and VE-cadherin were not affected. These results show that HIFs in endothelial cells are essential for embryonic heart and blood vessel development and control angiogenesis and vascular remodeling.
Measuring similarities between transcription factor binding sites
Authors: Kielbasa Szymon M , Gonze Didier , Herzel Hanspeter
Published: September 2005

Background

Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of transcription factor binding sites.

Results

We propose to identify and group similar profiles using two independent similarity measures: χ2 distances between position frequency matrices (PFMs) and correlation coefficients between position weight matrices (PWMs) scores.

Conclusion

We show that these measures complement each other and allow to associate Jaspar and Transfac matrices. Clusters of highly similar matrices are identified and can be used to optimise the search for regulatory elements. Moreover, the application of the measures is illustrated by assigning E-box matrices of a SELEX experiment and of experimentally characterised binding sites of circadian clock genes to the Myc-Max cluster.
Reconstructing recent human phylogenies with forensic STR loci: A statistical approach
Authors: Agrawal Suraksha , Khan Faisal
Published: September 2005

Background

Forensic Short Tandem Repeat (STR) loci are effective for the purpose of individual identification, and other forensic applications. Most of these markers have high allelic variability and mutation rate because of which they have limited use in the phylogenetic reconstruction. In the present study, we have carried out a meta-analysis to explore the possibility of using only five STR loci (TPOX, FES, vWA, F13A and Tho1) to carry out phylogenetic assessment based on the allele frequency profile of 20 world population and north Indian Hindus analyzed in the present study.

Results

Phylogenetic analysis based on two different approaches – genetic distance and maximum likelihood along with statistical bootstrapping procedure involving 1000 replicates was carried out. The ensuing tree topologies and PC plots were further compared with those obtained in earlier phylogenetic investigations. The compiled database of 21 populations got segregated and finely resolved into three basal clusters with very high bootstrap values corresponding to three geo-ethnic groups of African, Orientals, and Caucasians.

Conclusion

Based on this study we conclude that if appropriate and logistic statistical approaches are followed then even lesser number of forensic STR loci are powerful enough to reconstruct the recent human phylogenies despite of their relatively high mutation rates.
Epigenetic predisposition to expression of TIMP1 from the human inactive X chromosome
Authors: Anderson Catherine L , Brown Carolyn J
Published: September 2005

Background

X inactivation in mammals results in the transcriptional silencing of an X chromosome in females, and this inactive X acquires many of the epigenetic features of silent chromatin. However, not all genes on the inactive X are silenced, and we have examined the TIMP1 gene, which has variable inactivation amongst females. This has allowed us to examine the features permitting expression from the otherwise silent X by comparing inactive X chromosomes with and without TIMP1 expression.

Results

Expression was generally correlated with euchromatic chromatin features, including DNA hypomethylation, nuclease sensitivity, acetylation of histone H3 and H4 and hypomethylation of H3 at lysines 9 and 27. Demethylation of the TIMP1 gene by 5-azacytidine was able to induce expression from the inactive X chromosome in somatic cell hybrids, and this expression was also accompanied by features of active chromatin. Acetylated histone H3 continued to be observed even when expression was lost in cells that naturally expressed TIMP1; while acetylation was lost upon TIMP1 silencing in cells where expression from the inactive X had been induced by demethylation. Thus ongoing acetylation of inactive X chromosomes does not seem to be simply a 'memory' of expression.

Conclusion

We propose that acetylation of H3 is an epigenetic mark that predisposes to TIMP1 expression from the inactive X chromosome in some females.
Prevalence of human papillomavirus cervical infection in an Italian asymptomatic population
Authors: Centurioni Maria G , Puppo Andrea , Merlo Domenico F , Pasciucco Gennaro , Cusimano Enzo R , Sirito Rodolfo , Gustavino Claudio A
Published: September 2005

Background

In the last decade many studies have definitely shown that human papillomaviruses (HPVs) are the major cause of cervical carcinogenesis and, in the last few years, HPV testing has been proposed as a new and more powerful tool for cervical cancer screening. This issue is now receiving considerable attention in scientific and non scientific press and HPV testing could be considered the most important change in this field since the introduction of cervical cytology. This paper reports our prevalence data of HPV infection collected in the '90s, while a follow up of these patients is ongoing.

Methods

For this study we used polymerase chain reaction (PCR) to search HPV DNA sequences in cervical cell scrapings obtained from 503 asymptomatic women attending regular cervical cancer screening program in the city of Genova, Italy. All patients were also submitted to a self-administered, standardized, questionnaire regarding their life style and sexual activity. On the basis of the presence of HPV DNA sequences women were separated into two groups: "infected" and "non infected" and a statistical analysis of the factors potentially associated with the infection group membership was carried out.

Results

The infection rate was 15.9% and the most frequent viral type was HPV 16.

Conclusion

Our HPV positivity rate (15.9%) was consistent to that reported by other studies on European populations.
Evaluation of the toll-like receptor 6 Ser249Pro polymorphism in patients with asthma, atopic dermatitis and chronic obstructive pulmonary disease
Authors: Hoffjan Sabine , Stemmler Susanne , Parwez Qumar , Petrasch-Parwez Elisabeth , Arinir Umut , Rohde Gernot , Reinitz-Rademacher Karin , Schultze-Werninghaus Gerhard , Bufe Albrecht , Epplen Jörg T
Published: September 2005

Background

For allergic disorders, the increasing prevalence over the past decade has been attributed in part to the lack of microbial burden in developed countries ('hygiene hypothesis'). Variation in genes encoding toll-like receptors (TLRs) as the receptor system for the first innate immune response to microbial stimuli has been implicated in various inflammatory diseases. We evaluated here the role of a coding variation, Ser249Pro, in the TLR6 gene in the pathogenesis of asthma, atopic dermatitis (AD) and chronic obstructive pulmonary disease (COPD).

Methods

Genotyping of the Ser249Pro polymorphism in 68 unrelated adult patients and 132 unrelated children with asthma, 185 unrelated patients with COPD, 295 unrelated individuals with AD and 212 healthy control subjects was performed by restriction enzyme digestion.

Results

We found a weak association of the 249Ser allele with childhood asthma (p = 0.03). Yet, significance was lost after Bonferroni correction. No association was evident for AD or COPD.

Conclusion

Variation in TLR6 might play a role in the pathogenesis of childhood asthma.
Papillary cystic and solid tumour of the pancreas: Report of a case and literature review
Authors: Kasem Abdul , Ali Zainab , Ellul Joseph
Published: September 2005

Background

The papillary cystic and solid tumour of the pancreas (PCSTP) is a rare primary neoplasm of unknown pathogenesis typically found in young women. PCSTP is a low-grade malignant tumour, which is often asymptomatic but it may present with abdominal pain.

Case presentation

A 38 year old female patient who presented with one day history of epigastric pain was diagnosed as PCSTP. The patient was successfully treated with distal pancreatectomy.

Conclusion

It is important to differentiate this tumour from other pancreatic tumours because, unlike malignant pancreatic tumours, this neoplasm does not usually metastasise and is amenable to cure after complete surgical resection. However, the cell origin and the aetiology of this tumour are not clear and further studies are warranted in its pathogenesis.
The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications
Authors:   The Rice Chromosomes 11 and 12 Sequencing Consortia*
Published: September 2005

Background

Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals.

Results

We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes.

Conclusion

Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested.
Hepatitis B Virus: Inactive carriers
Authors: Sharma Sanjeev Kumar , Saini Nitin , Chwla Yogesh
Published: September 2005

Inactive carriers forms the largest group in chronic HBV infected patients. Around 300 million people are inactive carriers The inactive HBsAg carrier state is diagnosed by absence of HBeAg and presence of anti-HBe, undetectable or low levels of HBV DNA in PCR-based assays, repeatedly normal ALT levels, and minimal or no necroinflammation, slight fibrosis, or even normal histology on biopsy. Inactive cirrhosis may be present in patients who had active liver disease during the replicative phase of infection. The prognosis of the inactive HBsAg carrier state is usually benign. Long-term follow- up (up to 18 years) of these carriers has indicated that the vast majority show sustained biochemical remission and very low risk of cirrhosis or hepatocellular carcinoma (HCC). Rarely, patients, even noncirrhotics, may develop liver cancer during the inactive HBsAg carrier state. In addition, approximately 20 to 30% of persons in the inactive HBsAg carrier state may undergo spontaneous reactivation of hepatitis B during follow-up. Multiple episodes of reactivation or sustained reactivation can cause progressive hepatic damage and even hepatic decompensation. Introduction
Protocol: Precision engineering of plant gene loci by homologous recombination cloning in Escherichia coli
Authors: Roden Laura C , Göttgens Berthold , Mutasa-Göttgens Effie S
Published: September 2005

Plant genome sequence data now provide opportunities to conduct molecular genetic studies at the level of the whole gene locus and above. Such studies will be greatly facilitated by adopting and developing further the new generation of genetic engineering tools, based on homologous recombination cloning in Escherichia coli, which are free from the constraints imposed by the availability of suitably positioned restriction sites. Here we describe the basis for homologous recombination cloning in E. coli, the available tools and resources, together with a protocol for long range cloning and manipulation of an Arabidopsis thaliana gene locus, to create constructs co-ordinately driven by locus-specific regulatory elements.
Selection of ovine housekeeping genes for normalisation by real-time RT-PCR; analysis of PrPgene expression and genetic susceptibility to scrapie
Authors: Garcia-Crespo David , Juste Ramón A , Hurtado Ana
Published: September 2005

Background

Cellular prion protein expression is essential for the development of transmissible spongiform encephalopathies (TSEs), and in sheep, genetic susceptibility to scrapie has been associated to PrP gene polymorphisms. To test the hypothetical linkage between PrP gene expression and genetic susceptibility, PrP mRNA levels were measured by real-time RT-PCR in six ovine tissues of animals with different genotypes.

Results

Previous to the PrP gene expression analysis the stability of several housekeeping (HK) genes was assessed in order to select the best ones for relative quantification. The normalisation of gene expression was carried out using a minimum of three HK genes in order to detect small expression differences more accurately than using a single control gene. The expression stability analysis of six HK genes showed a large tissue-associated variation reflecting the existence of tissue-specific factors. Thereby, a specific set of HK genes was required for an accurate normalisation of the PrP gene expression within each tissue. Statistical differences in the normalised PrP mRNA levels were found among the tissues, obtaining the highest expression level in obex, followed by ileum, lymph node, spleen, cerebellum and cerebrum. A tendency towards increased PrP mRNA levels and genetic susceptibility was observed in central nervous system. However, the results did not support the hypothesis that PrP mRNA levels vary between genotypes.

Conclusion

The results on PrP gene expression presented here provide valuable baseline data for future studies on scrapie pathogenesis. On the other hand, the results on stability data of several HK genes reported in this study could prove very useful in other gene expression studies carried out in these relevant ovine tissues.
The dog and rat olfactory receptor repertoires
Authors: Quignon Pascale , Giraud Mathieu , Rimbault Maud , Lavigne Patricia , Tacher Sandrine , Morin Emmanuelle , Retout Elodie , Valin Anne-Sophie , Lindblad-Toh Kerstin , Nicolas Jacques , Galibert Francis
Published: September 2005

Background

Dogs and rats have a highly developed capability to detect and identify odorant molecules, even at minute concentrations. Previous analyses have shown that the olfactory receptors (ORs) that specifically bind odorant molecules are encoded by the largest gene family sequenced in mammals so far.

Results

We identified five amino acid patterns characteristic of ORs in the recently sequenced boxer dog and brown Norway rat genomes. Using these patterns, we retrieved 1,094 dog genes and 1,493 rat genes from these shotgun sequences. The retrieved sequences constitute the olfactory receptor repertoires of these two animals. Subsets of 20.3% (for the dog) and 19.5% (for the rat) of these genes were annotated as pseudogenes as they had one or several mutations interrupting their open reading frames. We performed phylogenetic studies and organized these two repertoires into classes, families and subfamilies.

Conclusion

We have established a complete or almost complete list of OR genes in the dog and the rat and have compared the sequences of these genes within and between the two species. Our results provide insight into the evolutionary development of these genes and the local amplifications that have led to the specific amplification of many subfamilies. We have also compared the human and rat ORs with the human and mouse OR repertoires.