bluuebunny/crossref_metadata_2025 huggingface dataset:
Biosynthesis of γ-butyrolactone autoregulators that switch on secondary metabolism and morphological development in
Streptomyces
Authors: Kato Jun-ya , Funa Nobutaka , Watanabe Hidenori , Ohnishi Yasuo , Horinouchi Sueharu
Published: February 2007

A factor (2-isocapryloyl-3
R
-hydroxymethyl-γ-butyrolactone) is a representative of the γ-butyrolactone autoregulators that trigger secondary metabolism and morphogenesis in the Gram-positive, filamentous bacterial genus
Streptomyces
. Here, we report the A factor biosynthesis pathway in
Streptomyces griseus
. The monomeric AfsA, containing a tandem repeat domain of ≈80 aa, catalyzed β-ketoacyl transfer from 8-methyl-3-oxononanoyl-acyl carrier protein to the hydroxyl group of dihydroxyacetone phosphate (DHAP), thus producing an 8-methyl-3-oxononanoyl-DHAP ester. The fatty acid ester was nonenzymatically converted to a butenolide phosphate by intramolecular aldol condensation. The butenolide phosphate was then reduced by BprA that was encoded just downstream of
afsA
. The phosphate group on the resultant butanolide was finally removed by a phosphatase, resulting in formation of A factor. The 8-methyl-3-oxononanoyl-DHAP ester produced by the action of AfsA was also converted to A factor in an alternative way; the phosphate group on the ester was first removed by a phosphatase and the dephosphorylated ester was converted nonenzymatically to a butenolide, which was then reduced by a reductase different from BprA, resulting in A factor. Because introduction of
afsA
alone into
Escherichia coli
caused the host to produce a substance having A factor activity, the reductase(s) and phosphatase(s) were not specific to the A factor biosynthesis but commonly present in bacteria. AfsA is thus the key enzyme for the biosynthesis of γ-butyrolactones.
Indirect activation of a plant nucleotide binding site–leucine-rich repeat protein by a bacterial protease
Authors: Ade Jules , DeYoung Brody J. , Golstein Catherine , Innes Roger W.
Published: February 2007

Nucleotide binding site–leucine-rich repeat (NBS–LRR) proteins mediate pathogen recognition in both mammals and plants. The molecular mechanisms by which pathogen molecules activate NBS–LRR proteins are poorly understood. Here we show that RPS5, a NBS–LRR protein from
Arabidopsis
, is activated by AvrPphB, a bacterial protease, via an indirect mechanism. When transiently expressed in
Nicotiana benthamiana
leaves, full-length RPS5 protein triggered programmed cell death, but only when coexpressed with AvrPphB and a second
Arabidopsis
protein, PBS1, which is a specific substrate of AvrPphB. Using coimmunoprecipitation analysis, we found that PBS1 is in a complex with the N-terminal coiled coil (CC) domain of RPS5 before exposure to AvrPphB. Deletion of the RPS5 LRR domain caused RPS5 to constitutively activate programmed cell death, even in the absence of AvrPphB and PBS1, and this activation depended on both the CC and NBS domains. The LRR and CC domains both coimmunoprecipitate with the NBS domain but not with each other. Thus, the LRR domain appears to function in part to inhibit RPS5 signaling, and cleavage of PBS1 by AvrPphB appears to release RPS5 from this inhibition. An amino acid substitution in the NBS site of RPS5 that is known to inhibit ATP binding in other NBS–LRR proteins blocked activation of RPS5, whereas a substitution thought to inhibit ATP hydrolysis constitutively activated RPS5. Combined, these data suggest that ATP versus ADP binding functions as a molecular switch that is flipped by cleavage of PBS1.
Transcriptomic analysis of growth heterosis in larval Pacific oysters (
Crassostrea gigas
)
Authors: Hedgecock Dennis , Lin Jing-Zhong , DeCola Shannon , Haudenschild Christian D. , Meyer Eli , Manahan Donal T. , Bowen Ben
Published: February 2007

Compared with understanding of biological shape and form, knowledge is sparse regarding what regulates growth and body size of a species. For example, the genetic and physiological causes of heterosis (hybrid vigor) have remained elusive for nearly a century. Here, we investigate gene-expression patterns underlying growth heterosis in the Pacific oyster (
Crassostrea gigas
) in two partially inbred (
f
= 0.375) and two hybrid larval populations produced by a reciprocal cross between the two inbred families. We cloned cDNA and generated 4.5 M sequence tags with massively parallel signature sequencing. The sequences contain 23,274 distinct signatures that are expressed at statistically nonzero levels and show a highly positively skewed distribution with median and modal counts of 9.25 million and 3 transcripts per million, respectively. For nearly half of these signatures, expression level depends on genotype and is predominantly nonadditive (hybrids deviate from the inbred average). Statistical contrasts suggest ≈350 candidate genes for growth heterosis that exhibit concordant nonadditive expression in reciprocal hybrids; this represents only ≈1.5% of the >20,000 transcripts. Patterns of gene expression, which include dominance for low expression and even underdominance of expression, are more complex than predicted from classical dominant or overdominant explanations of heterosis. Preliminary identification of ribosomal proteins among candidate genes supports the suggestion from previous studies that efficiency of protein metabolism plays a role in growth heterosis.
Role of the C terminus of the ribonucleotide reductase large subunit in enzyme regeneration and its inhibition by Sml1
Authors: Zhang Zhen , Yang Kui , Chen Chin-Chuan , Feser Jason , Huang Mingxia
Published: February 2007

Ribonucleotide reductase maintains cellular deoxyribonucleotide pools and is thus tightly regulated during the cell cycle to ensure high fidelity in DNA replication. The Sml1 protein inhibits ribonucleotide reductase activity by binding to the R1 subunit. At the completion of each turnover cycle, the active site of R1 becomes oxidized and subsequently regenerated by a cysteine pair (CX
2
C) at its C-terminal domain (R1-CTD). Here we show that R1-CTD acts in trans to reduce the active site of its neighboring monomer. Both Sml1 and R1-CTD interact with the N-terminal domain of R1 (R1-NTD), which involves a conserved two-residue sequence motif in the R1-NTD. Mutations at these two positions enhancing the Sml1–R1 interaction cause
SML1
-dependent lethality. These results point to a model whereby Sml1 competes with R1-CTD for association with R1-NTD to hinder the accessibility of the CX
2
C motif to the active site for R1 regeneration.
Electronic gJFactors, Natural Lifetimes, and Electric Quadrupole Interaction for Rb87in the np2P3/2Series of the Rb I Spectrum
Authors: G Belin  , S Svanberg
Published: February 2007

For Rb87the level crossing method was applied to the first four levels (n= 5, 6, 7, and 8) of thenp2P3/2series in the Rb I spectrum. By using magnetic dipole interaction constants from corresponding zero field optical double resonance experiments, the electronicgJfactors of 5, 6, and 7p2P3/2were calculated from the level crossing data. For these levels the natural radiative lifetimes were determined from the half-widths of the level crossing signals. For 8p2P3/2theafactor was obtained assuminggJ= -1.336 (2). From the measured electric quadrupole interaction constantsb, decreasing values of the nuclear quadrupole momentQwere obtained in 5, 6, 7, and 8p2P3/2. When core polarization effects are taken into account, the different2P3/2levels yield consistent values for the quadrupole moment. We find

gJ(5p2P3/2) = -1.3362 (6)gJ(6p2P3/2) = -1.3347 (10)τ (5p2P3/2) = 25.8 (8) nsτ (6p2P3/2) = 111 (3) nsb(5p2P3/2) = 12.510 (57) MHzb(6p2P3/2) = 3.947 (13) MHzQ(5p2P3/2) = 0.131 barnQ(6p2P3/2) = 0.133 barngJ(7p2P3/2) = -1.3359 (11)a(8p2P3/2) = 6.747 (14) MHzτ (7p2P3/2) = 233 (10) nsb(8p2P3/2) = 0.933 (20) MHzb(7p2P3/2) = 1.768 (8) MHzQ(8p2P3/2) = 0.131 barnQ(7p2P3/2) = 0.133 barn

Considering possible sources of error in the evaluation of the quadrupole moment we obtainQ(Rb87) = +0.132 (9) barn.
Hardware acceleration of processing of mass spectrometric data for proteomics
Authors: Bogdan Istvan , Coca Daniel , Rivers Jenny , Beynon Robert J
Published: February 2007

Motivation: High-resolution mass spectrometers generate large data files that are complex, noisy and require extensive processing to extract the optimal data from raw spectra. This processing is readily achieved in software and is often embedded in manufacturers’ instrument control and data processing environments. However, the speed of this data processing is such that it is usually performed off-line, post data acquisition. We have been exploring strategies that would allow real-time advanced processing of mass spectrometric data, making use of the reconfigurable computing paradigm, which exploits the flexibility and versatility of Field Programmable Gate Arrays (FPGAs). This approach has emerged as a powerful solution for speeding up time-critical algorithms. We describe here a reconfigurable computing solution for processing raw mass spectrometric data generated by MALDI-ToF instruments. The hardware-implemented algorithms for de-noising, baseline correction, peak identification and deisotoping, running on a Xilinx Virtex 2 FPGA at 180 MHz, generate a mass fingerprint over 100 times faster than an equivalent algorithm written in C, running on a Dual 3 GHz Xeon workstation.

Contact:  D.Coca@sheffield.ac.uk
SCOOP: a simple method for identification of novel protein superfamily relationships
Authors: Bateman Alex , Finn Robert D.
Published: February 2007

Motivation: Profile searches of sequence databases are a sensitive way to detect sequence relationships. Sophisticated profile–profile comparison algorithms that have been recently introduced increase search sensitivity even further.

Results: In this article, a simpler approach than profile–profile comparison is presented that has a comparable performance to state-of-the-art tools such as COMPASS, HHsearch and PRC. This approach is called SCOOP (Simple Comparison Of Outputs Program), and is shown to find known relationships between families in the Pfam database as well as detect novel distant relationships between families. Several novel discoveries are presented including the discovery that a domain of unknown function (DUF283) found in Dicer proteins is related to double-stranded RNA-binding domains.

Availability: SCOOP is freely available under a GNU GPL license from http://www.sanger.ac.uk/Users/agb/SCOOP/

Contact:  agb@sanger.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
Diverse Subcellular Locations of Cryptogein-Induced Reactive Oxygen Species Production in Tobacco Bright Yellow-2 Cells
Authors: Ashtamker Cher , Kiss Vladimir , Sagi Moshe , Davydov Olga , Fluhr Robert
Published: February 2007

Reactive oxygen species (ROS) play a crucial role in many cellular responses and signaling pathways, including the oxidative burst defense response to pathogens. We have examined very early events in cryptogein-induced ROS production in tobacco (Nicotiana tabacum) Bright Yellow-2 suspension cells. Using Amplex Red and Amplex Ultra Red reagents, which report real-time H2O2 accumulation in cell populations, we show that the internal signal for H2O2 develops more rapidly than the external apoplastic signal. Subcellular accumulation of H2O2 was also followed in individual cells using the 2′,7′-dichlorofluorescein diacetate fluorescent probe. Major accumulation was detected in endomembrane, cytoplasmic, and nuclear compartments. When cryptogein was added, the signal developed first in the nuclear region and, after a short delay, in the cell periphery. Interestingly, isolated nuclei were capable of producing H2O2 in a calcium-dependent manner, implying that nuclei can serve as a potential active source of ROS production. These results show complex spatial compartmentalization for ROS accumulation and an unexpected temporal sequence of events that occurs after cryptogein application, suggesting novel intricacy in ROS-signaling cascades.
S-Nitrosoglutathione Reductase Affords Protection against Pathogens in Arabidopsis, Both Locally and Systemically
Authors: Rustérucci Christine , Espunya M. Carme , Díaz Maykelis , Chabannes Matthieu , Martínez M. Carmen
Published: February 2007

Nitric oxide and S-nitrosothiols (SNOs) are widespread signaling molecules that regulate immunity in animals and plants. Levels of SNOs in vivo are controlled by nitric oxide synthesis (which in plants is achieved by different routes) and by S-nitrosoglutathione turnover, which is mainly performed by the S-nitrosoglutathione reductase (GSNOR). GSNOR is encoded by a single-copy gene in Arabidopsis (Arabidopsis thaliana; Martínez et al., 1996; Sakamoto et al., 2002). We report here that transgenic plants with decreased amounts of GSNOR (using antisense strategy) show enhanced basal resistance against Peronospora parasitica Noco2 (oomycete), which correlates with higher levels of intracellular SNOs and constitutive activation of the pathogenesis-related gene, PR-1. Moreover, systemic acquired resistance is impaired in plants overexpressing GSNOR and enhanced in the antisense plants, and this correlates with changes in the SNO content both in local and systemic leaves. We also show that GSNOR is localized in the phloem and, thus, could regulate systemic acquired resistance signal transport through the vascular system. Our data corroborate the data from other authors that GSNOR controls SNO in vivo levels, and shows that SNO content positively influences plant basal resistance and resistance-gene-mediated resistance as well. These data highlight GSNOR as an important and widely utilized component of resistance protein signaling networks conserved in animals and plants.
Twelve Design Patterns for Integrating and Normalizing Product Model Schemas
Authors: Lee Ghang , Eastman Charles M. , Sacks Rafael
Published: February 2007

Abstract:  This article reviews a method for generating a product model from user data and introduces 12 design patterns for resolving conflicts that may occur in the integration and normalization process. The generating method and design patterns were evaluated during a project to integrate the product models collected from three different precast concrete companies in the United States, testing the new method of product model generation. The application results indicate that the 12 design patterns are effective and sufficient for resolving most known schema conflicts and for integrating and normalizing multiple product models into a single well‐formed product model.
A Probabilistic Framework for Bayesian Adaptive Forecasting of Project Progress
Authors: Gardoni Paolo , Reinschmidt Kenneth F. , Kumar Ramesh
Published: February 2007

Abstract: A methodology to forecast project progress and final time‐to‐completion is developed. An adaptive Bayesian updating method is used to assess the unknown model parameters based on recorded data and pertinent prior information. Recorded data can include equality, upper bound, and lower bound data. The proposed approach properly accounts for all the prevailing uncertainties, including model errors arising from an inaccurate model form or missing variables, measurement errors, statistical uncertainty, and volitional uncertainty.

As an illustration of the proposed approach, the project progress and final time‐to‐completion of an example project are forecasted. For this illustration construction of civilian nuclear power plants in the United States is considered. This application considers two cases (1) no information is available prior to observing the actual progress data of a specified plant and (2) the construction progress of eight other nuclear power plants is available. The example shows that an informative prior is important to make accurate predictions when only a few records are available. This is also the time when forecasts are most valuable to the project manager. Having or not having prior information does not have any practical effect on the forecast when progress on a significant portion of the project has been recorded.
Hippocampal Sclerosis: MR Prediction of Seizure Intractability
Authors: Briellmann Regula S. , Mark Wellard R. , Masterton Richard A. J. , Abbott David F. , Berkovic Samuel F. , Jackson Graeme D.
Published: February 2007

Summary: Purpose:Patients with refractory temporal lobe epilepsy (refractory TLE) often have hippocampal sclerosis (HS). However, some HS patients have less‐severe, drug‐responsive epilepsy (mild TLE). We investigated the pattern of MR changes in these two HS groups.

Methods:We acquired a 3D volumetric sequence, T2relaxation times (T2) and proton MR spectroscopy (MRS) in 41 HS patients (24 refractory TLE, 17 mild TLE) and 60 controls. Hippocampal volumes were measured bilaterally. T2 was measured in the hippocampus, amygdala, thalamus, in the white matter of the anterior temporal lobe (ATL), and in the frontal lobe. The temporal lobe MRS established concentrations ofN‐acetylaspartate (NAA), choline, creatine, myoinositol and glutamine/glutamate.

Results:The degree of hippocampal volume loss and hippocampal T2 increase was not different between the two HS groups. However, in refractory TLE, the T2 signal in the ipsilateral ATL was increased, and the ipsilateral NAA concentration was reduced (p ≤ 0.05).

Conclusions:In this group of HS patients, the degree of HS was not related to the clinical course, possibly reflecting the common cause of epilepsy. In contrast, refractory TLE patients had pronounced white matter changes and metabolite disturbance in the ipsilateral temporal lobe. These abnormalities may indicate the refractory nature of the epilepsy.
PET Imaging in the Photosensitive Baboon: Case‐controlled Study
Authors: Szabó C. Ákos , Narayana Shalini , Kochunov Peter V. , Franklin Crystal , Knape Koyle , Davis M. Duff , Fox Peter T. , Leland M. Michelle , Williams Jeff T.
Published: February 2007

Summary:  Purpose: The baboon (Papio hamadryas spp) offers a natural primate animal model of photosensitive generalized epilepsy. This study compared changes in cerebral blood flow (CBF) during intermittent light stimulation (ILS) between photosensitive and asymptomatic baboons.

Methods: Six photosensitive, epileptic (PS) and four nonphotosensitive, asymptomatic (CTL) baboons, matched for age, gender, and weight, were selected based on previous scalp EEG evaluation. Continuous intravenous ketamine (5–13 mg/kg) was used for sedation. Subjects underwent five sequential blood‐flow PET studies within 60 min with 20 mCi 15O‐labeled water. Images were acquired in 3D mode (CTI/Siemens HR+ scanner, 63 contiguous slices, 2.4‐mm thickness). Three resting scans were alternated with two activation scans during ILS. ILS was performed at 25 Hz for 60 s before to 60 s after the start of an activation scan. PET images were coregistered with MRI (3T Siemens Trio, T1‐weighted 3D Turboflash sequence; TE/TR/TI, 3.04/2,100/785 ms; flip angle, 13 degrees). PET scans were reviewed and corrected for motion artifact. Resting scans were contrasted with activation scans and averaged independently for both groups. Quantitative CBF analyses were performed for the occipital and motor cortices.

Results: The CTL baboons showed greatest ILS‐induced activation in the left middle frontal and inferior temporal gyri, left brainstem structures and right postcentral gyrus, bilateral occipital lobes, and in the posterior cingulate gyrus and cerebellum. In contrast, the PS animals showed strongest ILS activation in the right anterior cingulate and medial orbital gyri, amygdala, globus pallidum, and left inferior and superior temporal gyri. A striking finding was the absence of occipital and variable motor cortex activation in the PS animals. Deactivations were noted in the right orbitofrontal and anterior cingulate cortices in the CTL baboons and in the posterior cingulate gyrus, brainstem and cerebellum of the PS animals.

Conclusions: The patterns of ILS‐induced CBF changes differed between CTL and PS groups. These differences of activations and inhibitions suggest involvement of specific cortical–subcortical or networks in photosensitivity.
Intrinsic Ictal Dynamics at the Seizure Focus: Effects of Secondary Generalization Revealed by Complexity Measures
Authors: Jouny Christophe C. , Adamolekun Bola , Franaszczuk Piotr J. , Bergey Gregory K.
Published: February 2007

Summary:  Purpose: Partial seizures (PSs) may be self‐limited regional events or propagate further and secondarily generalize. The mechanisms and dynamics of secondarily generalized tonic–clonic seizures (GTCSs) are not well understood. Methods with which to assess the dynamic of those events are also limited.

Methods: Seizures were analyzed from patients with intractable partial seizures undergoing monitoring with intracranial electrodes. Inclusion in this study required patients to have at least one PS and one GTCS. From >120 patients, seven patients fulfilled these criteria, three with mesial temporal (MTLE) onset seizures and four with neocortical lesional (NCLE) onset seizures. In total, 50 seizures were analyzed by using the matching pursuit (MP) method and the Gabor atom density (GAD), a measure of signal complexity derived from the MP method.

Results: The GAD complexity pattern at the seizure focus for the initial ictal period is remarkably consistent in a given patient, regardless of whether secondary generalization occurs. Secondary generalization produces greater modification of seizure activity at the focus in patients with NCLE than in patients with MTLE. In seizures from four patients with NCLE, secondary generalization resulted in an average increase of 115% in complexity at the focus compared to PSs.

Conclusions: GAD shows that seizure dynamics of PSs are often very stereotyped from seizure to seizure in a given patient, particularly during early ictal evolution. Secondary generalization is more likely to produce changes in the duration and dynamics at the seizure focus in NCLE patients compared with MTLE patients. These observations suggest distinct mechanisms (e.g., feedback) that are operational during secondary generalization.
Correlation between Provoked Ictal SPECT and Depth Recordings in Adult Drug‐Resistant Epilepsy Patients
Authors: Barba Carmen , Di Giuda Daniela , Policicchio Domenico , Bruno Isabella , Papacci Fabio , Colicchio Gabriella
Published: February 2007

Summary:  Purpose: To correlate ictal hyperperfusion single‐photon emission computed tomography (SPECT) area during provoked seizures to the epileptogenic zone (EZ), as defined by depth recordings in adult drug‐resistant patients.

Methods: We included in the study eight drug‐resistant epilepsy patients, subjected to both noninvasive and invasive (stereo‐electroencephalography, SEEG) presurgical evaluation in the Epilepsy Surgery Center of the Catholic University in Rome, from 2001 to 2003. All patients were subjected to interictal and provoked ictal SPECT scans during scalp video‐EEG monitoring. The ictal hyperperfusion area assessed by visual image analysis and, when possible, by statistical parametric mapping (SPM), was compared with the EZ, as assessed by SEEG, to define whether they colocalized.

Results: For each provoked seizure, we obtained a SPECT hyperperfusion area. In five patients, the SPECT hyperperfusion area was included in the EZ as assessed by SEEG. The effectiveness of provoked SPECT was confirmed by comparison with SEEG data, SPM analysis (four patients), and spontaneous ictal SPECT (two patients). Our data were obtained in adult drug‐resistant epilepsy patients whose EZ was either located in or extended to extratemporal regions in all but two patients.

Conclusions: Provoked ictal SPECT confirmed its efficacy and accuracy in the presurgical evaluation because of the colocalization to the EZ. Although the low number of patients precluded any statistical correlation with the surgical outcome, it is worth pointing out that the five patients in whom the hyperperfusion area was included in the EZ showed very satisfactory results.
Evaluation of Effects of Intra aortic Balloon Counterpulsation on Autonomic Nervous System Functions by Heart Rate Variability Analysis
Authors: Ozdemir Ozcan , Alyan Omer , Kacmaz Fehmi , Kaptan Zekeriya , Ozbakir Cemal , Geyik Bilal , Cagirci Goksel , Soylu Mustafa , Demir Ahmet Duran
Published: February 2007

Background: In patients with acute myocardial infarction (AMI), intraaortic balloon counterpulsation (IABC) may improve cardiac performance, decrease the incidence of recurrent ischemia, and improve survival. Although there have been several reports concerning circulatory maintenance with the IABC, response of the autonomic nervous system to these hemodynamic changes is not clear. Heart rate variability (HRV) analysis has been extensively used to evaluate autonomic modulation of sinus node and to identify patients at risk for an increased cardiac mortality. In this study, we evaluated effects of the IABC on autonomic nervous system functions by HRV analysis.

Methods: The study group was composed of 32 consecutive patients (13 female, 19 male aged 61.8 ± 8.8 years) undergoing IABC. Transthoracic echocardiography and 1‐hour Holter recordings for HRV analysis in each IAB pumping mode were obtained.

Results: The IABC improved left ventricular diastolic and systolic functions as well as caused an increase in SDNN1, PNN50(1), RMSSD1, and HF1 and a decrease in LF1, LF/HF1, mean heart rate, and the number of ventricular extrasystoles. The improvements in HRV parameters were correlated with some hemodynamic changes such as the increase in MAP and CO during counterpulsation. The only independent factors affecting in‐hospital mortality were the change in LF/HF1 ratio (ΔLF/HF1) and the change in the number of ventricular extrasystole (ΔVES). The decrease in LF/HF1 ≥4.9 decreased the mortality by 1.7‐folds (RR = 0.6, P = 0.04, 95% CI: 0.1–2.3). The decrease in VES ≥27/15 minutes resulted in mortality reduction by 16‐folds (RR = 0.06, P = 0.02, 95% CI: 0.01–0.4).

Conclusions: As a result, the IABC, especially in 1:1 support, causes an increase in HRV, decrease in sympathetic overactivity, and improvement in sympathovagal balance besides the favorable hemodynamic changes, and these electrophysiologic changes may explain the role of the IABC in the treatment of ventricular arrhythmias.
QT Dispersion Significantly Increases after Implantable Cardioverter‐Defibrillator Shocks
Authors: Topaloglu Serkan , Aras Dursun , Sahin Onur , Ergun Kumral , Deveci Bulent , Ozdemir Ozcan , Ozeke Ozcan , Yildiz Ali , Alyan Omer , Demir Ahmet Duran , Soylu Mustafa , Kisacik Halil Lutfi , Korkmaz Sule
Published: February 2007

Objective: To determine whether QT dispersion (QTd), a noninvasive electrocardiographic parameter of ventricular tachyarrhythmia risk assessment, is changed by implantable cardioverter‐defibrillator (ICD) shocks delivered during implantation process, to analyze the duration of these changes, and to further evaluate the effect of amiodarone on these parameters.

Methods: Twenty‐six consecutive patients who are scheduled to undergo ICD implantation for aborted sudden cardiac death or documented symptomatic sustained ventricular tachycardia were enrolled into the study. A simultaneous 12‐lead electrocardiogram (ECG) was recorded after the ICD implantation just before starting the testing shock when the patients were under general anesthesia (baseline record) and at 1st, 5th, 10th, 15th, 20th, 25th, and 30th minutes after the successful shocks. RR interval, QT interval, corrected QT interval (QTc), QTd, and corrected QTd (QTcd) were all measured and calculated on ECG.

Results: At 1st minute after the successful shock, an abrupt increase (from 67.0 ± 13.8 ms to 94.8±21 ms, P < 0.0001) was observed in QTcd, which was followed by a gradual return to the preshock values at 20th minute. Analysis of patients with and without long‐term oral amiodarone treatment showed that in amiodarone‐pretreated patients QTcd returned to the baseline value earlier than in patients without amiodarone treatment (15 minutes vs 20 minutes, respectively).

Conclusions: ICD shocks cause an increase in QTcd lasting for up to 20th minute, which may predominate in some important clinical problems like electrical storm. Amiodarone, with the desirable effect on QTcd, may reduce the proarrhythmic effects of ICD shocks.
The Relationship between Heart Rate Variability and Heart Rate Turbulence Dynamics after Primary Coronary Angioplasty
Authors: Kurpesa Małgorzata , Trzos Ewa , Rechciński Tomasz , Krzemińska‐Pakuła Maria
Published: February 2007

Background: The application of heart rate turbulence (HRT) analysis for risk assessment after pharmacologically treated myocardial infarction (MI) was described in 1999. The aim of the present study was to evaluate the dynamics of HRT changes in long‐term observation after MI treated with primary coronary angioplasty (PTCA). Moreover, the usefulness was assessed of early postinfarction heart rate variability (HRV) analysis for predicting HRT dynamics.

Methods: The study group consisted of 96 patients with MI treated with primary PTCA. Holter monitoring with HRV and HRT analysis was performed 3 days after the procedure and 1 year later.

Results: Twelve months after primary PTCA, an improvement (Type I HRT dynamics) was noted in 51 patients, and the worsening of both the HRT parameters (Type II HRT dynamics) in 34 patients. Fourteen patients showed the worsening of only one HRT parameter (Type III HRT dynamics). The following HRV parameters recorded in early postinfarction Holter monitoring had a significant influence on the risk of Type II HRT dynamics: SDNN, RMSSD, Triangle Index and Δ LF/HF (mean day‐time LF/HF – mean night‐time LF/HF). Only the latter was found in the multivariate analysis as significantly connected with worsened HRT. During the follow‐up, SDNN and Triangular Index improved in all the patients.

Conclusions: HRT after myocardial infarction treated with primary PTCA presents a significant dynamics, which is different than dynamics of HRV. An abnormal circadian pattern of autonomic activity is a finding that helps identify patients who need to have HRT analysis repeated during a long‐term follow‐up, due to the tendency for HRT to change with time toward the prognostically unfavorable values.
Slow Delayed Rectifier Potassium Current (IKs) and the Repolarization Reserve
Authors: Jost Norbert , Papp Julius Gy , Varró András
Published: February 2007

The aim of this review is to present the properties of the slow component of the delayed rectifier potassium current (IKs) in the human ventricle. The review gives a detailed description of the physiology, molecular biology and pharmacology of the IKs current, including kinetic properties, genetic structures, agonists and antagonists. The authors also present the role of the IKs current in the human cardiac repolarization focusing on several pathophysiological situations, such as the LQT syndrome and the Torsade de Pointes arrhythmia.
The ECG Pattern of Isolated Right Ventricular Infarction during Percutaneous Coronary Intervention
Authors: Eskola Markku J. , Kosonen Petteri , Sclarovsky Samuel , Vikman Saila , Nikus Kjell C.
Published: February 2007

Isolated right ventricular infarction (RVI) is a rare event. The electrocardiographic (ECG) pattern of RVI, ST‐elevation in lead V4R and in anterior chest leads V1‐3 is similar to that of a proximal occlusion of a small, nondominant right coronary artery (RCA). The ECG changes may be misinterpreted as signs of infarction of the anterior wall. This paper describes a case of isolated temporary occlusion of the major side branches of the RCA during percutaneous coronary intervention, recognized by angiography findings and typical ECG changes. This case demonstrates how one might avoid wrong decisions even in the catheterization laboratory by putting attention to the anatomical interpretation of the ECG.
Experimental Study and Numerical Simulation of the FLINDT Draft Tube Rotating Vortex
Authors: Ciocan Gabriel Dan , Iliescu Monica Sanda , Vu Thi Cong , Nennemann Bernd , Avellan François
Published: February 2007

The dynamics of the rotating vortex taking place in the discharge ring of a Francis turbine for partial flow rate operating conditions and cavitation free conditions is studied by carrying out both experimental flow survey and numerical simulations. 2D laser Doppler velocimetry, 3D particle image velocimetry, and unsteady wall pressure measurements are performs to investigate thoroughly the velocity and pressure fields in the discharge ring and to give access to the vortex dynamics. Unsteady RANS simulation are performed and compared to the experimental results. The computing flow domain includes the rotating runner and the elbow draft tube. The mesh size of 500,000 nodes for the 17 flow passages of the runner and 420,000 nodes for the draft tube is optimized to achieve reasonable CPU time for a good representation of the studied phenomena. The comparisons between the detailed experimental flow field and the CFD solution yield to a very good validation of the modeling of the draft tube rotating vortex and, then, validate the presented approach for industrial purpose applications.
Mean and Fluctuating Velocity Characteristics of a Separated Shear Layer Past a Surface Mounted Block
Authors: Özkol Ü. , Wark C. , Fabris D.
Published: February 2007

The mean velocity, Reynolds stress, and mean vorticity regions of a separated shear layer over a surface mounted block are investigated by 2D Digital Particle Image Velocimetry (DPIV) for three Reynolds numbers (Rea=500, 1000, and 2500) and two channel-to-block height ratios (H∕a=1.825 and 4.6). The recirculation region’s height and length are determined for the separated shear layer by means of U¯=0 contours. It is observed that the high Reynolds stress regions lay just outside of the U¯=0 contours. The flow visualization and DPIV measurement of vorticity indicate that the differing normalized Reynolds stresses between Rea=500 and 1000 are most probably due to the initiation of the vortex shedding between these two Reynolds numbers while, differences are minimal between Rea=1000 and 2500. A sign change in the Reynolds shear stress distribution of the separated shear layer near the leading edge of the block was recognized for every Reynolds number and channel width.
Assessment of Some Integrated Cooling Mechanisms for an Active Integrated Power Electronics Module
Authors: Pang Y. , Scott E. , van Wyk J. D. , Liang Z.
Published: February 2007

The increased heat generation in power electronic components can greatly reduce the reliability of the components and increase the chances of malfunction to the components. A good understanding of the thermal behavior of these components can help in deciding an effective thermal management scheme. Recognizing the inherent need for the thermal design of the active integrated power electronics modules, this paper assesses various possibilities of integrated thermal management for integrated power electronics modules. These integrated thermal management strategies include employing high thermal conductivity materials as well as structural modifications to the current module structure while not adding complexity to the fabrication process to reduce the cost.
Design Optimization and Reliability of PWB Level Electronic
Package
Authors: Hossain Mohammad Masum , Jagarkal Sudhakar G. , Agonafer Dereje , Lulu Menberu , Reh Stefan
Published: February 2007

As the electronic packaging industry develops technologies for fabrication of smaller, faster, economical and reliable products, thermal management and design play an important role. Temperature fluctuations caused by either power consumption or environmental changes, along with the resulting thermal expansion mismatch between the various packages materials result in deformation stresses in packages/assemblies especially in solder interconnects. Increased power dissipation and density in modern electronics system requires efficient and intelligent design and thermal management strategies to ensure the reliability of electronic products. In the past reliability issues related to optimization of electronic packages were dealt with by coupling analysis tools with optimization solvers. In this paper, ANSYS APDL code is used with a built-in optimization tool for optimization of electronic packages, and for improving the solder joint life and arriving at optimal design. It has been shown that, design optimization would enormously decrease the lead time. The finite element tool ANSYS is used to estimate the cycles to fatigue failure of solder joint of the package coupled with optimization module present in the solver for providing the details on determining optimal design parameters that affect the product reliability. Four model characteristics: printed wiring board (PWB) core in-plane Young’s modulus, PWB core in-plane coefficient of thermal expansion, PWB core thickness, and the standoff solder joint height are chosen as the optimization inputs (design variables) that ensure higher reliability and improved performance of the assembled product. The objective junction of the paper is to minimize average plastic work to improve the fatigue life of solder joints of the package. Subapproximation, design of experiment and central composite design based response surface modeling methodologies are used to study the effects of each design variables on the fatigue life.
Constitutive Modeling on Time-Dependent Deformation Behavior of 96.5Sn-3.5Ag Solder Alloy Under Cyclic Multiaxial Straining
Authors: Yang Xianjie , Luo Yan , Gao Qing
Published: February 2007

Based on the time dependent multiaxial deformation behavior of 96.5Sn-3.5Ag solder alloy, a constitutive model is proposed which considers the nonproportional multiaxial cyclic deformation properties. In the back stress evolution equations of this model, the nonproportionality which affects the back stress evolution rate is introduced. The approach for the determination of model parameters is proposed. The model is used to describe the time-dependent cyclic deformation behavior of 96.5Sn-3.5Ag solder alloy under cross, rectangular, rhombic, and double-triangular tensile–torsion multiaxial strain paths at different strain rates with different dwell time. The comparison between the predicted and experimental results demonstrates that the model can satisfactorily describe the time-dependent multiaxial cyclic deformation behavior under complicated nonproportional cyclic straining.
Effect of Test Conditions on Electromigration Reliability of Sn-Ag-Cu Flip-Chip Solder Interconnects
Authors: Lai Yi-Shao , Lee Chiu-Wen , Kao Chin-Li
Published: February 2007

The high-temperature operation life test (HTOL) was conducted in this paper to study electromigration phenomena of solder interconnects in a flip-chip package assembly. We examined the fatigue reliability and morphological patterns of three solder compositions: Sn-4Ag-0.5Cu, Sn-3.5Ag-1Cu, and Sn-3Ag-1.5Cu, subjected to two test conditions consisting of different average current densities and ambient temperatures (5kA∕cm2 at 150°C and 20kA∕cm2 at 30°C). It is interesting to realize that as the Cu weight content of the solder composition increases, the fatigue life increases under 5kA∕cm2 at 150°C but decreases under 20kA∕cm2 at 30°C. Observed electromigration morphologies along with computed current density and temperature distributions on solder interconnects from the electrothermal coupling analysis were examined, correlated, and discussed.
Design Guideline for Ball Impact Test Apparatus
Authors: Yeh Chang-Lin , Lai Yi-Shao
Published: February 2007

The ball impact test is developed as a package-level measure of the board-level reliability of solder joints in the sense that it leads to brittle intermetallic fracturing, similar to that from a board-level drop test. Following classical structural dynamics principles, the ball impact test process is analyzed to provide insights into transient characteristics of this particular test methodology. A design guideline for the ball impact test apparatus based on characteristics of the measured impact force profile is proposed.
Erosion from
Staphylococcus aureus
Biofilms Grown under Physiologically Relevant Fluid Shear Forces Yields Bacterial Cells with Reduced Avidity to Collagen
Authors: Ymele-Leki Patrick , Ross Julia M.
Published: February 2007

An estimated 65% of infective diseases are associated with the presence of bacterial biofilms. Biofilm-issued planktonic cells promote blood-borne, secondary sites of infection by the inoculation of the infected sites with bacteria from the intravascular space. To investigate the potential role of early detachment events in initiating secondary infections, we studied the phenotypic attributes of
Staphylococcus aureus
planktonic cells eroding from biofilms with respect to expression of the collagen adhesin, CNA. The collagen-binding abilities of
S. aureus
have been correlated to the development of osteomyelitis and septic arthritis. In this study, we focused on the impact of CNA expression on
S. aureus
adhesion to immobilized collagen in vitro under physiologically relevant shear forces. In contrast to the growth phase-dependent adhesion properties characteristic of
S. aureus
cells grown in suspension, eroding planktonic cells expressed invariant and lower effective adhesion rates regardless of the age of the biofilm from which they originated. These results correlated directly with the surface expression level of CNA. However, subsequent analysis revealed no qualitative differences between biofilms initiated with suspension cells and secondary biofilms initiated with biofilm-shed planktonic cells. Taken together, our findings suggest that, despite their low levels of CNA expression,
S. aureus
planktonic cells shed from biofilms retain the capacity for metastatic spread and the initiation of secondary infection. These findings demonstrate the need for a better understanding of the phenotypic properties of eroding planktonic cells, which could lead to new therapeutic strategies to target secondary infections.
Comparison of a Reporter Assay and Immunomagnetic Separation Real-Time Reverse Transcription-PCR for the Detection of Enteroviruses in Seeded Environmental Water Samples
Authors: Hwang Yu-Chen , Leong Oymon M. , Chen Wilfred , Yates Marylynn V.
Published: February 2007

Two newly developed protocols for infective virus detection were compared to the plaque assay. An immunomagnetic separation procedure coupled with real-time reverse transcription-PCR of viral nucleic acids was developed to identify intact enteroviral particles, and a reporter cell system responding to viral replication based on fluorescent resonance energy transfer for detection of infectious enteroviruses was tested. Both new procedures detected infective viruses in environmental samples at the same level as the plaque assay.
Rapid Screening Method for Analyzing the Conjugated Linoleic Acid Production Capabilities of Bacterial Cultures
Authors: Barrett E. , Ross R. P. , Fitzgerald G. F. , Stanton C.
Published: February 2007

In this paper we describe a rapid method for identifying bacteria which convert free linoleic acid to conjugated linoleic acid (CLA). This method is based on spectrophotometric detection of CLA and compares well with the standard gas-liquid chromatography method. This method should facilitate high-throughput screening of bacterial isolates for the ability to produce conjugated fatty acids.
Vertical Transmission of a Phylogenetically Complex Microbial Consortium in the Viviparous SpongeIrcinia felix
Authors: Schmitt Susanne , Weisz Jeremy B. , Lindquist Niels , Hentschel Ute
Published: February 2007

Many marine demosponges contain large amounts of phylogenetically complex yet highly sponge-specific microbial consortia within the mesohyl matrix, but little is known about how these microorganisms are acquired by their hosts. Settlement experiments were performed with the viviparous Caribbean demospongeIrcinia felixto investigate the role of larvae in the vertical transmission of the sponge-associated microbial community. Inspections by electron microscopy revealed large amounts of morphologically diverse microorganisms in the center ofI. felixlarvae, while the outer rim appeared to be devoid of microorganisms. In juveniles, microorganisms were found between densely packed sponge cells. Denaturing gradient gel electrophoresis (DGGE) was performed to compare the bacterial community profiles of adults, larvae, and juvenile sponges. Adults and larvae were highly similar in DGGE band numbers and banding patterns. Larvae released by the same adult individual contained highly similar DGGE banding patterns, whereas larvae released by different adult individuals showed slightly different DGGE banding patterns. Over 200 bands were excised, sequenced, and phylogenetically analyzed. The bacterial diversity of adultI. felixand its larvae was comparably high, while juveniles showed reduced diversity. In total, 13 vertically transmitted sequence clusters, hereafter termed “IF clusters,” that contained sequences from both the adult sponge and offspring (larvae and/or juveniles) were found. The IF clusters belonged to at least four different eubacterial phyla and one possibly novel eubacterial lineage. In summary, it could be shown that inI. felix, vertical transmission of microorganisms through the larvae is an important mechanism for the establishment of the sponge-microbe association.
Novel Method for Rapid Assessment of Antibiotic Resistance in
Escherichia coli
Isolates from Environmental Waters by Use of a Modified Chromogenic Agar
Authors: Watkinson A. J. , Micalizzi G. R. , Bates J. R. , Costanzo S. D.
Published: February 2007

We validated a novel method for screening
Escherichia coli
resistance to antibiotics in environmental samples using modified Difco MI agar (Becton Dickinson) impregnated with selected antibiotics (tetracycline, ampicillin, cephalexin, and sulfamethoxazole), termed MI-R. This method combines an existing rapid assessment technique for
E. coli
enumeration with clinical reference data for breakpoint analysis of antibiotic resistance and was developed to address issues encountered when clinical methods are used with environmental samples. Initial trials conducted using strains of
E. coli
with resistance to the selected antibiotics showed that this method was reproducible and accurate with respect to antibiotic resistance. Trials using wastewater effluent demonstrated the precision of the method, and the levels of resistance found in effluent were directly comparable to the levels of antibiotic resistance determined using the more traditional CLSI (formerly NCCLS) disk susceptibility test. All wastewater isolates growing on MI-R plates were confirmed to be resistant using the CLSI disk susceptibility test. Bacterial resistance to ampicillin (38% ± 4% overall), sulfamethoxazole, tetracycline (21% ± 3% overall), and ciprofloxacin (6% ± 1%) were found in wastewater effluent. A successful trial was also conducted with water collected from the Brisbane River, Australia. The levels of antibiotic resistance in
E. coli
ranged from 0 to 47% for ampicillin, from 0 to 24% for tetracycline, from 0 to 63% for sulfamethoxazole, and from 0 to 1% for ciprofloxacin, with the highest incidence of resistance associated with wastewater treatment plant discharges. This method has great potential for rapid and representative assessment of antibiotic resistance in
E. coli
and could allow increased sample analysis, resulting in greater confidence in spatial analysis in environmental studies.