bluuebunny/crossref_metadata_2025 huggingface dataset:
Agreement between Theory and Measurement in Quantification of Ammonia-Oxidizing Bacteria
Authors: Coskuner Gulnur , Ballinger Stuart J. , Davenport Russell J. , Pickering Rheanne L. , Solera Rosario , Head Ian M. , Curtis Thomas P.
Published: October 2005

Autotrophic ammonia-oxidizing bacteria (AOB) are of vital importance to wastewater treatment plants (WWTP), as well as being an intriguing group of microorganisms in their own right. To date, corroboration of quantitative measurements of AOB by fluorescence in situ hybridization (FISH) has relied on assessment of the ammonia oxidation rate per cell, relative to published values for cultured AOB. Validation of cell counts on the basis of substrate transformation rates is problematic, however, because published cell-specific ammonia oxidation rates vary by over two orders of magnitude. We present a method that uses FISH in conjunction with confocal scanning laser microscopy to quantify AOB in WWTP, where AOB are typically observed as microcolonies. The method is comparatively simple, requiring neither detailed cell counts or image analysis, and yet it can give estimates of either cell numbers or biomass. Microcolony volume and diameter were found to have a log-normal distribution. We were able to show that virtually all (>96%) of the AOB biomass occurred as microcolonies. Counts of microcolony abundance and measurement of their diameter coupled with a calibration of microcolony dimensions against cell numbers or AOB biomass were used to determine AOB cell numbers and biomass in WWTP. Cell-specific ammonia oxidation rates varied between plants by over three orders of magnitude, suggesting that cell-specific ammonia oxidation is an important process variable. Moreover, when measured AOB biomass was compared with process-based estimates of AOB biomass, the two values were in agreement.
Differentiation of
Campylobacter
Populations as Demonstrated by Flagellin Short Variable Region Sequences
Authors: Meinersmann Richard J. , Phillips Robert W. , Hiett Kelli L. , Fedorka-Cray Paula
Published: October 2005

The DNA sequence of the
flaA
short variable region (SVR) was used to analyze a random population of
Campylobacter
isolates to investigate the weakly clonal population structure of members of the genus. The SVR sequence from 197 strains of
C. jejuni
and
C. coli
isolated from humans, bovine, swine, and chickens identified a group of 43 strains containing disparate short variable region sequences compared to the rest of the population. This group contains both
C. jejuni
and
C. coli
strains but disproportionately consisted of bovine isolates. Relative synonymous codon usage analysis of the sequences identified two groups: one group typified
C. jejuni
, and the second group was characteristic for
C. coli
and the disparate alleles were not clustered. The data show that there is significant differentiation of
Campylobacter
populations according to the source of the isolate even without considering the disparate isolates. Even though there is significant differentiation of chicken and bovine isolates, the bovine isolates did not show any difference in ability to colonize chickens. It is possible that disparate sequences were obtained through the lateral transfer of DNA from
Campylobacter
species other than
C. jejuni
and
C. coli
. It is evident that recombination within the
flaA
SVR occurs rapidly. However, the rate of migration between populations appears to limit the distribution of sequences and results in a weakly clonal population structure.
Effects of Dissolved Sulfide, pH, and Temperature on Growth and Survival of Marine Hyperthermophilic Archaea
Authors: Lloyd Karen G. , Edgcomb Virginia P. , Molyneaux Stephen J. , Böer Simone , Wirsen Carl O. , Atkins Michael S. , Teske Andreas
Published: October 2005

The ability of metabolically diverse hyperthermophilic archaea to withstand high temperatures, low pHs, high sulfide concentrations, and the absence of carbon and energy sources was investigated. Close relatives of our study organisms,
Methanocaldococcus jannaschii
,
Archaeoglobus profundus
,
Thermococcus fumicolans
, and
Pyrococcus
sp. strain GB-D, are commonly found in hydrothermal vent chimney walls and hot sediments and possibly deeper in the subsurface, where highly dynamic hydrothermal flow patterns and steep chemical and temperature gradients provide an ever-changing mosaic of microhabitats. These organisms (with the possible exception of
Pyrococcus
strain GB-D) tolerated greater extremes of low pH, high sulfide concentration, and high temperature when actively growing and metabolizing than when starved of carbon sources and electron donors/acceptors. Therefore these organisms must be actively metabolizing in the hydrothermal vent chimneys, sediments, and subsurface in order to withstand at least 24 h of exposure to extremes of pH, sulfide, and temperature that occur in these environments.
Engineering
Candida tenuis
Xylose Reductase for Improved Utilization of NADH: Antagonistic Effects of Multiple Side Chain Replacements and Performance of Site-Directed Mutants under Simulated In Vivo Conditions
Authors: Petschacher Barbara , Nidetzky Bernd
Published: October 2005

Six single- and multiple-site variants of
Candida tenuis
xylose reductase that were engineered to have side chain replacements in the coenzyme 2′-phosphate binding pocket were tested for NADPH versus NADH selectivity (
R
sel
) in the presence of physiological reactant concentrations. The experimental
R
sel
values agreed well with predictions from a kinetic mechanism describing mixed alternative coenzyme utilization. The Lys-274→Arg and Arg-280→His substitutions, which individually improved wild-type
R
sel
50- and 20-fold, respectively, had opposing structural effects when they were combined in a double mutant.
Effect of Bovine Manure onCryptosporidium parvumOocyst Attachment to Soil
Authors: Kuczynska Ewa , Shelton Daniel R. , Pachepsky Yakov
Published: October 2005

The objective of this work was to assess the effect of dilute bovine manure (1.0% and 0.1%) versus that of no manure on attachment and subsequent detachment ofCryptosporidium parvumoocysts to soil. Manure enhanced the attachment of oocysts to soil particles; the maximum attachment was observed with 0.1% manure. Oocyst attachment was partially reversible; maximum detachment was observed with dilute manure. These results indicate that oocyst attachment to soil is substantially affected by bovine manure in a complex manner and should have implications for how oocysts may be transported through or over soils.
Sau-PCR, a Novel Amplification Technique for Genetic Fingerprinting of Microorganisms
Authors: Corich Viviana , Mattiazzi Alessandro , Soldati Elisa , Carraro Angela , Giacomini Alessio
Published: October 2005

The proposed technique is based on the digestion of genomic DNA with the restriction endonuclease Sau3AI and subsequent amplification with primers whose core sequence is based on the Sau3AI recognition site. The method was tested on strains of lactic acid bacteria but could be proposed for virtually any culturable organism from which DNA can be extracted.
Reduction of Uranium(VI) Phosphate during Growth of the Thermophilic Bacterium
Thermoterrabacterium ferrireducens
Authors: Khijniak T. V. , Slobodkin A. I. , Coker V. , Renshaw J. C. , Livens F. R. , Bonch-Osmolovskaya E. A. , Birkeland N.-K. , Medvedeva-Lyalikova N. N. , Lloyd J. R.
Published: October 2005

The thermophilic, gram-positive bacterium
Thermoterrabacterium ferrireducens
coupled organotrophic growth to the reduction of sparingly soluble U(VI) phosphate. X-ray powder diffraction and X-ray absorption spectroscopy analysis identified the electron acceptor in a defined medium as U(VI) phosphate [uramphite; (NH
4
)(UO
2
)(PO
4
) · 3H
2
O], while the U(IV)-containing precipitate formed during bacterial growth was identified as ningyoite [CaU(PO
4
)
2
· H
2
O]. This is the first report of microbial reduction of a largely insoluble U(VI) compound.
Fecal Microbiota Composition and Frailty
Authors: van Tongeren Sandra P. , Slaets Joris P. J. , Harmsen H. J. M. , Welling Gjalt W.
Published: October 2005

The relationship between fecal microbiota composition and frailty in the elderly was studied. Fecal samples from volunteers with high frailty scores showed a significant reduction in the number of lactobacilli (26-fold). At much higher population levels, both theBacteroides/Prevotella(threefold) and theFaecalibacterium prausnitzii(fourfold) groups showed a significant reduction in percentage of total number of hybridizable bacteria in the elderly with high frailty scores. In contrast to this, the number ofEnterobacteriaceaewas significantly higher (sevenfold) in samples from very frail volunteers.
Humoral and Cellular Immunity in Children withMycoplasma pneumoniaeInfection: a 1-Year Prospective Study
Authors: Stelmach Iwona , Podsiadłowicz-Borzęcka Malgorzata , Grzelewski Tomasz , Majak Pawel , Stelmach Wlodzimierz , Jerzyńska Joanna , Popławska Marta , Dziadek Jaroslaw
Published: October 2005

To determine whether children have persistent abnormalities in cellular and humoral immunity development after acuteMycoplasma pneumoniaeinfection, serum immunoglobulin G (IgG), IgA, IgM, and IgE levels and lymphocyte phenotypes were determined. There were no changes in the levels of IgG, IgM, IgA, or CD4+or CD19+lymphocytes that were measured inM. pneumoniae-positive patients after 3 months or after 12 months, but there were increases in these inM. pneumoniae-negative patients. Serum IgE increased inM. pneumoniae-positive patients. We have shown alterations in immunity development afterM. pneumoniaeinfection.
ANALYSIS OF MULTI-ELEMENT POWDERS AND SOLUTIONS OF METALS WITH A PYROELECTRIC X-RAY GENERATOR
Authors: KOYAMA TETSUYA , KAWAI JUN
Published: October 2005

Applications of X-ray fluorescence (XRF) analysis to solid and liquid samples with a pyroelectric X-ray generator are described. The X-ray generator is driven by a 9 V dry electric battery and small dimensions. It enables compact and portable XRF spectrometer. It has disadvantages in low power and periodically changing X-ray flux. Measured solid samples are briquettes from powdery oxides of Ti , V , Cr , Mn , Fe , Co , Ni and Cu , and sulfide of Zn . Each sample is prepared to contain equal molar metal elements. Liquid samples are solutions of Fe , Cr , Zn , Pb , Bi , Cd . K α and K β lines of all metals in solid samples are detected. Although background level was relatively high for liquids, all metals in the measured samples were detected within 70 seconds, except for Cd . The capability of XRF with the pyroelectric X-ray generator is discussed.
EXAMINATION OF QUANTITATIVE ACCURACY OF PIXE ANALYSIS FOR ATMOSPHERIC AEROSOL PARTICLE SAMPLES: PIXE ANALYSIS OF NIST AIR PARTICULATE ON FILTER MEDIA
Authors: SAITOH KATSUMI , SERA KOICHIRO
Published: October 2005

In order to confirm accuracy of the direct analysis of filter samples containing atmospheric aerosol particles collected on a polycarbonate membrane filter by PIXE, we carried out PIXE analysis on a National Institute of Standards and Technology (NIST, USA) air particulate on filter media (SRM 2783). For 16 elements with NIST certified values determined by PIXE analysis — Na , Mg , Al , Si , S , K , Ca , Ti , V , Cr , Mn , Fe , Ni , Cu , Zn and Pb — quantitative values were 80–110% relative to NIST certified values except for Na , Al , Si and Ni . Quantitative values of Na , Al and Si were 140–170% relative to NIST certified values, which were all high, and Ni was 64%. One possible reason why the quantitative values of Na , Al and Si were higher than the NIST certified values could be the difference in the X-ray spectrum analysis method used.
NEW PROTON AND NEUTRON MAGIC NUMBERS IN NEUTRON-RICH NUCLEI
Authors: ABBAS AFSAR
Published: October 2005

It is now known that in neutron-rich nuclei, old magic numbers disappear and new ones appear. Single nucleon and double nucleon separation energies are plotted here in all possible manner. Using this data it is shown here that nuclei with pair of proton number Z and neutron number N(Z,N): (6, 12), (8, 16), (10, 20), (11, 22) and (12, 24) exhibit exceptional stability or magicity. As such these magic numbers appear in pairs. This correlation is shown here to be indicative of predominance of tritons in the ground state of these neutron-rich nuclei. Thus [Formula: see text] has the structure of 10 [Formula: see text] in the ground state. It is shown here that this is due to fundamental symmetry arguments based on a new symmetry group [Formula: see text] nusospin.
CALCULATION OF THE GROUND STATE HYPERFINE STRUCTURE FOR MUONIC HELIUM ATOMS WITH THE USE OF SOME LOCAL PROPERTIES OF THE WAVE FUNCTIONS
Authors: ESKANDARI M. R. , REZAIE B. , MOHAMMADI S.
Published: October 2005

The ground-state hyperfine structure and other properties are calculated for muonic helium atoms (3 He +2μ-e- and 4 He +2μ-e-), with the use of some local properties of the wave functions in the domains where two particles are close to each other or far away. Simple wave functions incorporating these properties with one variational parameter is developed. Also, the electron-muon correlation function is considered in proposed wave functions. It has a correct behavior for r12 tending to zero and infinity. The calculated values for hyperfine structure, energy and expectation values of r2n in ground-state, are compared with the multibox variational approach and the correlation function hyperspherical harmonic method. Our obtained results are very close to the values calculated by mentioned methods and giving strong indications that the proposed wave functions in addition to being very simple, provide relatively accurate values for hyperfine structure, energy and expectation values of r2n, emphasizing on the importance of the local properties of the wave functions.
LIEB'S SIMPLE PROOF OF CONCAVITY OF (A, B) ↦ Tr Ap K† B1-p K AND REMARKS ON RELATED INEQUALITIES
Authors: RUSKAI MARY BETH
Published: October 2005

A simple, self-contained proof is presented for the concavity of the map (A, B) ↦ Tr Ap K† B1-p K. The author makes no claim to originality; this paper gives Lieb's original argument in its simplest, rather than its most general, form. A sketch of the chain of implications from this result to concavity of A ↦ Tr eK+ log A is then presented. An independent elementary proof is given for the joint convexity of the map [Formula: see text], which plays a key role in entropy inequalities.
Eplerenone Inhibits Atherosclerosis in Nonhuman Primates
Authors: Takai Shinji , Jin Denan , Muramatsu Michiko , Kirimura Kazuyoshi , Sakonjo Hiroshi , Miyazaki Mizuo
Published: October 2005

Aldosterone may be involved in the pathogenesis of atherosclerosis. We investigated the effect of eplerenone, a selective mineralocorticoid receptor blocker, on atherosclerosis in monkeys fed a high-cholesterol diet. Monkeys fed a high-cholesterol diet for 9 months were divided into 3 groups: those treated with a low dose of eplerenone (30 mg/kg per day); those treated with a high dose of eplerenone (60 mg/kg per day); and the placebo-treated group. The normal group consisted of monkeys fed a normal diet. There were no significant differences in blood pressure and cholesterol levels between the placebo- and eplerenone-treated groups. On the other hand, monocyte chemoattractant protein-1 and malondialdehyde-modified LDL were significantly higher in the placebo-treated group than in the normal group, whereas they were suppressed in the eplerenone-treated groups. The ratio of intimal volume to total volume by intravascular ultrasound analysis imaging of the aortas was dose-dependently lower in the eplerenone-treated groups than in the placebo-treated group. Acetylcholine-induced vasorelaxation was significantly weaker in the placebo-treated group than in the normal group, but the vasorelaxation was strengthened in the eplerenone-treated groups. A significant upregulation of angiotensin-converting enzyme activity was observed in the placebo-treated group, but the activity was suppressed in the eplerenone-treated groups. In conclusion, eplerenone may strengthen the endothelium-dependent relaxation and suppress angiotensin-converting enzyme activity in the vasculature, thus preventing the development of atherosclerosis in nonhuman primates.
Lipid Accumulation and Transforming Growth Factor-β Upregulation in the Kidneys of Rats Administered Angiotensin II
Authors: Saito Kan , Ishizaka Nobukazu , Hara Masumi , Matsuzaki Gen , Sata Masataka , Mori Ichiro , Ohno Minoru , Nagai Ryozo
Published: October 2005

Abnormal lipid metabolism may play a role in progressive renal failure. We studied whether lipid accumulation occurs and whether lipid deposits are colocalized with transforming growth factor-β1 (TGF-β1) in the kidney of angiotensin II–infused animals. Oil red O staining showed marked lipid deposition in the tubular epithelial and vascular wall cells of angiotensin II–treated but not in norepinephrine-treated rats. Histological analyses showed that increased amounts of superoxide and intense TGF-β1 mRNA expression were present in lipid-positive tubular epithelial cells in angiotensin II–infused animals. Protein expression of sterol regulatory element-binding protein 1 (SREBP-1) and mRNA expression of fatty acid synthase in the kidney were &3 times and 1.5 times, respectively, higher in angiotensin II–treated rats than in controls. Treatment of angiotensin II–infused animals with an iron chelator, deferoxamine, attenuated the angiotensin II–induced increases in renal expression of SREBP-1 and fatty acid synthase and normalized the lipid content in the renal cortical tissues. Abnormal lipid metabolism may be associated with upregulation of TGF-β1 expression and aberrant iron homeostasis in the kidneys of angiotensin II–infused animals.
Impact of Chronic Psychosocial Stress on Autonomic Cardiovascular Regulation in Otherwise Healthy Subjects
Authors: Lucini Daniela , Di Fede Gaetana , Parati Gianfranco , Pagani Massimo
Published: October 2005

Elevated psychosocial stress might favor the occurrence of cardiovascular disease; however, mechanisms are incompletely understood. We hypothesized that patients (n=126; 44±1 years of age) referred to an internal medicine clinic because of symptoms related to chronic psychosocial stress would demonstrate signs of autonomic dysregulation compared with controls (n=132; 42±1 years of age). We used autoregressive spectral analysis of RR interval variability to obtain indirect markers of sympathetic and of vagal (respectively, low-frequency and high-frequency components, both expressed in normalized units) oscillatory modulation of sinoatrial node, as well as of sympathetic vasomotor regulation (low-frequency component of systolic arterial pressure variability) and of cardiac baroreflex sensitivity (α-index). Higher values of systolic and diastolic arterial pressure (respectively, 124±1 versus 117±1 mm Hg and 80±1 versus 75±1 mm Hg; both
P
<0.001), altered markers of autonomic regulation (increased normalized low-frequency and reduced high-frequency component of RR variability,
P
<0.005; increased-low frequency component of systolic arterial pressure variability,
P
<0.002), and reduced baroreflex sensitivity (19.3±1.4 versus 23.0±2.0 ms/mm Hg;
P
<0.05) were observed in patients compared with controls. Autonomic responses to active standing were also blunted in stressed patients. Autonomic markers were significantly correlated to stress perception score and were capable of discriminating between controls and patients with a high degree of accuracy. Chronic real-life stress in humans appears associated to increased arterial pressure and to impaired autonomic regulation of cardiovascular functions. The combination of sympathetic predominance, vagal withdrawal, and blunted baroreflex sensitivity might represent a treatable mechanistic link between psychosocial factors and future incidence of hypertension.
Body Fat Distribution, Liver Enzymes, and Risk of Hypertension
Authors: Stranges Saverio , Trevisan Maurizio , Dorn Joan M. , Dmochowski Jacek , Donahue Richard P.
Published: October 2005

γ-Glutamyltransferase (GGT) has been associated with hypertension (HTN); however, the nature of this association remains unclear. GGT is a marker of alcohol consumption, but it is also related to the infiltration of fat in the liver (fatty liver). The association between GGT and HTN was examined in a 6-year longitudinal investigation among 1455 men and women who returned for the follow-up visit. Baseline variables included serum GGT, blood pressure, and anthropometric measures. Incident HTN was defined as blood pressure ≥140/90 or on antihypertensive medication at the follow-up visit. To eliminate individuals with potential liver pathology, analyses focused only on individuals with GGT within its normal range (n=897). Participants were divided in quintiles (Q) based on their baseline GGT levels. Multiple logistic regression analyses [odds ratio (95% confidence intervals)] revealed a significant association of GGT with incident hypertension [2.1 (1.1 to 4.0) Q5 versus Q1]. In subgroup analyses, GGT and HTN were significantly associated among both noncurrent and current drinkers, but only for participants above the median of anthropometric measures [eg, body mass index >26.4, 2.3 (0.9 to 5.7), waist circumference >86.1 cm, 3.7 (1.4 to 9.9), and abdominal height >19.8 cm, 3.1 (1.2 to 8.5), for Q5 versus Q1, in fully adjusted models]. These findings suggest that the association between GGT and hypertension is not caused solely by alcohol consumption and indicate that serum GGT, within its normal range, may predict hypertension among individuals with increased central fat distribution, suggesting that fatty liver may represent an important underlying mechanism for this association.
Altered Right Atrial Excitation and Propagation in Connexin40 Knockout Mice
Authors: Bagwe Suveer , Berenfeld Omer , Vaidya Dhananjay , Morley Gregory E. , Jalife José
Published: October 2005

Background—

Intercellular coupling via connexin40 (Cx40) gap junction channels is an important determinant of impulse propagation in the atria.

Methods and Results—

We studied the role of Cx40 in intra-atrial excitation and propagation in wild-type (Cx40
+/+
) and knockout (Cx40
−/−
) mice using high-resolution, dual-wavelength optical mapping. On ECG, the P wave was significantly prolonged in Cx40
−/−
mice (13.4±0.5 versus 11.4±0.3 ms in Cx40
+/+
). In Cx40
+/+
hearts, spontaneous right atrial (RA) activation showed a focal breakthrough at the junction of the right superior vena cava, sulcus terminalis, and RA free wall, corresponding to the location of the sinoatrial node. In contrast, Cx40
−/−
hearts displayed ectopic breakthrough sites at the base of the sulcus terminalis, RA free wall, and right superior vena cava. Progressive ablation of such sites in 4 Cx40
−/−
mice resulted in ectopic focus migration and cycle length prolongation. In all Cx40
−/−
hearts the focus ultimately shifted to the sinoatrial node at a very prolonged cycle length (initial ectopic cycle length, 182±20 ms; postablation sinus cycle length, 387±44 ms). In a second group of experiments, epicardial pacing at 10 Hz revealed slower conduction in the RA free wall of 5 Cx40
−/−
hearts than in 5 Cx40
+/+
hearts (0.61±0.07 versus 0.94±0.07 m/s;
P
<0.05). Dominant frequency analysis in Cx40
−/−
RA demonstrated significant reduction in the area of 1:1 conduction at 16 Hz (40±10% versus 69±5% in Cx40
+/+
) and 25 Hz (36±11% versus 65±9% in Cx40
+/+
).

Conclusions—

This is the first demonstration of intra-atrial block, ectopic rhythms, and altered atrial propagation in the RA of Cx40
−/−
mice.
Treatment Variation in Older Black and White Patients Undergoing Aortic Valve Replacement
Authors: Schelbert Erik B. , Rosenthal Gary E. , Welke Karl F. , Vaughan-Sarrazin Mary S.
Published: October 2005

Background—

Most prior studies of racial differences in the delivery of cardiac care have focused on potential differences in treatment by individual physicians and hospitals. However, differential use of hospitals with variable practice patterns might also contribute to variations in care.

Methods and Results—

We compared the use of bioprosthetic valves (BPVs) in 78 154 black and white Medicare beneficiaries ≥65 years of age undergoing aortic valve replacement in 904 US hospitals during 1999 through 2001. Generalized linear mixed models were used to account first for differences in patient characteristics and then for differences in hospitals used by black and white patients. BPV use was lower in black patients relative to white patients after adjustment for patient characteristics (relative risk, 0.93; 95% CI, 0.91 to 0.95;
P
<0.001). However, black patients were more likely to undergo surgery in hospitals in the lowest quintile of BPV use overall (29% versus 20% of white patients;
P
<0.001). After hospital-level variability in BPV use was accounted for, the use of BPVs was actually somewhat higher in black patients (relative risk, 1.06; 95% CI, 1.04 to 1.09;
P
<0.001). Model discrimination as measured by the
c
statistic was markedly higher after the addition of hospital effects (0.80 versus 0.59 for patient characteristics alone;
P
<0.001).

Conclusions—

Accounting for differences in hospitals preferentially used by black and white patients had a major impact on estimating racial differences in the use of BPVs in patients undergoing aortic valve replacement. Hospital-level effects explained a larger proportion of the variation in BPV use than race and other patient characteristics alone.
Discontinuous Conduction in Mouse Bundle Branches Is Caused by Bundle-Branch Architecture
Authors: van Veen Toon A.B. , van Rijen Harold V.M. , van Kempen Marjan J.A. , Miquerol Lucile , Opthof Tobias , Gros Daniel , Vos Marc A. , Jongsma Habo J. , de Bakker Jacques M.T.
Published: October 2005

Background—

Recordings of the electrical activity of mouse bundle branches (BBs) suggest reduced conduction velocity (CV) in the midseptal compared with the proximal part of the BB. The present study was performed to elucidate the mechanism responsible for this slowing of conduction.

Methods and Results—

Hearts of 16 mice were isolated and Langendorff perfused. After the right and left ventricular free walls were removed, the extracellular activity of the BB was mapped with a 247-point electrode. Premature stimulation was used to estimate CV restitution in the BBs. Expression/distribution of connexin40 (Cx40), Cx43, and Cx45 was determined. Morphology of the conduction system was assessed by whole-mount acetylcholine esterase staining and in Cx40
+/KI-GFP
hearts. Effective CV in the midseptal part of the left and right BBs was reduced by 50% compared with the proximal BB. CV restitution in the proximal and midseptal parts of the BBs was similar. Myocytes labeled positive for Cx40 and Cx45 in the entire BB. Cx43 colocalized with Cx40 and Cx45 only in the very distal BB. Subcellular distribution of gap junctions differed between proximal and distal BBs. Geometry of the midseptal and distal BBs revealed on both sides a profuse network of interlacing fibers, whereas the proximal BB consisted of a single (right BB) or multiple (left BB) parallel fibers.

Conclusions—

Comparison of connexin expression/distribution, geometry of the BBs, and CV characteristics suggests that increased path length for activation resulting from BB geometry is responsible for the apparently reduced CV in the midseptal BB of the mouse heart.
Diagnosis of Unexplained Cardiac Arrest
Authors: Krahn Andrew D. , Gollob Michael , Yee Raymond , Gula Lorne J. , Skanes Allan C. , Walker Bruce D. , Klein George J.
Published: October 2005

Background—

Cardiac arrest with preserved left ventricular function may be caused by uncommon genetic conditions. Although these may be evident on the ECG, long-term monitoring or provocative testing is often necessary to unmask latent primary electrical disease.

Methods and Results—

Patients with unexplained cardiac arrest and no evident cardiac disease (normal left ventricular function, coronary arteries, and resting corrected QT) underwent pharmacological challenge with adrenaline and procainamide infusions to unmask subclinical primary electrical disease. Family members underwent noninvasive screening and directed provocative testing on the basis of findings in the proband. Eighteen patients (mean±SD age, 41±17 years; 11 female) with unexplained cardiac arrest were assessed. The final diagnosis was catecholaminergic ventricular tachycardia (CPVT) in 10 patients (56%), Brugada syndrome in 2 patients (11%), and unexplained (idiopathic ventricular fibrillation) in 6 patients (33%). Of 55 family members (mean±SD age, 27±17 years; 33 female), 9 additional affected family members were detected from 2 families, with a single Brugada syndrome patient and 8 CPVT patients.

Conclusions—

Provocative testing with adrenaline and procainamide infusions is useful in unmasking the etiology of apparent unexplained cardiac arrest. This approach helps to diagnose primary electrical disease, such as CPVT and Brugada syndrome, and provides the opportunity for therapeutic intervention in identified, asymptomatic family members who harbor the same disease.
Headstarting in European pond turtles (Emys orbicularis): Does it work?
Authors: Mitrus Sławomir
Published: October 2005

The European pond turtle (Emys orbicularis) is an endangered species in Poland. From 1998 to 2000, as part of an active protection program for the species in central Poland, 123 one-year-old headstarted individuals were released into their original population. Survival rate in artificial rearing was 0.85. Annual recapture rate of the released turtles during the first year in the wild was 0.24, and during next year 0.43 or higher. For comparable groups of one-year-old turtles the annual recapture rates of wild vs. headstarted were not statistically different, but they were based on small samples. Analysis of the data based on a life table for Emydoidea blandingii and data on survival rate of E. orbicularis to age one suggests that headstarting programs can increase population size only if a large percentage of hatchlings is taken to artificial rearing. However, as we know nothing about behaviour and survivorship of older headstarted turtles, such programs still should be considered as experiments.
Optimizing Parameters in an Atmospheric General Circulation Model
Authors: Severijns C. A. , Hazeleger W.
Published: October 2005

An efficient method to optimize the parameter values of the subgrid parameterizations of an atmospheric general circulation model is described. The method is based on the downhill simplex minimization of a cost function computed from the difference between simulated and observed fields. It is used to find optimal values of the radiation and cloud-related parameters. The model error is reduced significantly within a limited number of iterations (about 250) of short integrations (5 yr). The method appears to be robust and finds the global minimum of the cost function. The radiation budget of the model improves considerably without violating the already well simulated general circulation. Different aspects of the general circulation, such as the Hadley and Walker cells improve, although they are not incorporated into the cost function. It is concluded that the method can be used to efficiently determine optimal parameters for general circulation models even when the model behavior has a strong nonlinear dependence on these parameters.
Surface Albedo of the Antarctic Sea Ice Zone
Authors: Brandt Richard E. , Warren Stephen G. , Worby Anthony P. , Grenfell Thomas C.
Published: October 2005

In three ship-based field experiments, spectral albedos were measured at ultraviolet, visible, and near-infrared wavelengths for open water, grease ice, nilas, young “grey” ice, young grey-white ice, and first-year ice, both with and without snow cover. From the spectral measurements, broadband albedos are computed for clear and cloudy sky, for the total solar spectrum as well as for visible and near-infrared bands used in climate models, and for Advanced Very High Resolution Radiometer (AVHRR) solar channels. The all-wave albedos vary from 0.07 for open water to 0.87 for thick snow-covered ice under cloud. The frequency distribution of ice types and snow coverage in all seasons is available from the project on Antarctic Sea Ice Processes and Climate (ASPeCt). The ASPeCt dataset contains routine hourly visual observations of sea ice from research and supply ships of several nations using a standard protocol. Ten thousand of these observations, separated by a minimum of 6 nautical miles along voyage tracks, are used together with the measured albedos for each ice type to assign an albedo to each visual observation, resulting in “ice-only” albedos as a function of latitude for each of five longitudinal sectors around Antarctica, for each of the four seasons. These ice albedos are combined with 13 yr of ice concentration estimates from satellite passive microwave measurements to obtain the geographical and seasonal variation of average surface albedo. Most of the Antarctic sea ice is snow covered, even in summer, so the main determinant of area-averaged albedo is the fraction of open water within the pack.
Modeling Bottom Mixed Layer Variability on the Mid-Oregon Shelf during Summer Upwelling
Authors: Kurapov A. L. , Allen J. S. , Egbert G. D. , Miller R. N.
Published: October 2005

Results from a model of wind-driven circulation are analyzed to study spatial and temporal variability in the bottom mixed layer (BML) on the mid-Oregon shelf in summer 2001. The model assimilates acoustic Doppler profiler velocities from two cross-shore lines of moorings 90 km apart to provide improved accuracy of near-bottom velocities and turbulence variables in the area between the mooring lines. Model results suggest that the response of the BML thickness to upwelling- and downwelling-favorable winds differs qualitatively between an area of “simple” bathymetric slope at 45°N and a wider shelf area east of Stonewall Bank (44.5°N). At 45°N, the BML grows in response to downwelling-favorable conditions, in agreement with known theories. East of Stonewall Bank, the BML thickness is increased following upwelling events. In this area, the southward upwelling jet detaches from the coast and flows over a wider part of the Oregon shelf, creating conditions for Ekman pumping near the bottom. Based on computations of bottom stress curl, the vertical pumping velocity in this area may reach 15 m day−1 following periods of intensified upwelling-favorable winds. A column of denser, near-bottom water upwelled over the Ekman flow convergence area is tilted as a result of vertical shear in horizontal velocities, causing unstable stratification and convective overturning. As a result of this process, BML thickness values east of Stonewall Bank can be in excess of 20 m following upwelling, comparable to maximum values at 45°N following downwelling.
Relating River Plume Structure to Vertical Mixing
Authors: Hetland Robert D.
Published: October 2005

The structure of a river plume is related to the vertical mixing using an isohaline-based coordinate system. Salinity coordinates offer the advantage of translating with the plume as it moves or expanding as the plume grows. This coordinate system is used to compare the relative importance of different dynamical processes acting within the plume and to describe the effect each process has on the structure of the plume. Vertical mixing due to inertial shear in the outflow of a narrow estuary and wind mixing are examined using a numerical model of a wind-forced river plume. Vertical mixing, and the corresponding entrainment of background waters, is greatest near the estuary mouth where inertial shear mixing is large. This region is defined as the near field, with the more saline, far-field plume beyond. Wind mixing increases the mixing throughout the plume but has the greatest effect on plume structure at salinity ranges just beyond the near field. Wind mixing is weaker at high salinity classes that have already been mixed to a critical thickness, a point where turbulent mixing of the upper layer by the wind is reduced, protecting these portions of the plume from further wind mixing. The work done by mixing on the plume is of similar magnitude in both the near and far fields.
Boundary Layer Forcing of a Semidiurnal, Cross-Channel Seiche
Authors: Martin Wayne , MacCready Parker , Dewey Richard
Published: October 2005

The outer Strait of Juan de Fuca is a stratified, tidal channel about 100 km long, 20 km wide, and 200 m deep. Tidal currents of O(0.5 m s−1) occur at both diurnal and semidiurnal periods and there is a pronounced spring–neap variation in the stratification due to changes in tidal mixing. Vertical isotherm excursions of O(50 m) have previously been observed along the northern side of the channel that appear to be phase locked to the tidal currents. Analyses of recent ADCP and thermistor chain data confirm the isotherm excursions and find that they are accompanied by distinctive baroclinic structures in the horizontal currents that persist across spring–neap cycles, and from year to year. The authors find that the phase of the semidiurnal signal does not vary along the channel, as would be expected of an along-channel internal tide. Instead, comparison of the semidiurnal measurements with two-dimensional analytical and numerical models indicate that much of the baroclinic structure can be explained as a cross-channel, internal seiche that is locally driven by reversing Ekman forcing in the bottom boundary layer. Near the bottom, the vertical motions are kinematic, resulting primarily from cross-channel flow on the side slopes. In the middepths, the seiche appears to explain part but not all of the vertical motions. The seiche appears to persist and to maintain a similar mode shape across large, O(2), changes in stratification. In Juan de Fuca, it is expected that these motions affect the overall salt balance of the system by enhancing mixing between the upper and lower layers of the estuary.
Globalization, Democracy, and Effective Welfare Spending in the Developing World
Authors: Rudra Nita , Haggard Stephan
Published: October 2005

The literature on the effects of globalization on social policy and welfare, and the parallel literature on the effects of democracy, operate in mutual isolation to a surprising degree. This article extends the debate on the welfare state in the developing world by examining the social policy reactions of democratic and authoritarian governments to globalization. Using unbalanced panel data on 57 developing nations, and considering social security and health and education spending, the authors examine whether democratic and authoritarian regimes exhibit similar or different social spending priorities in the context of increasing economic openness. The results show that social spending in “hard” authoritarian regimes is more sensitive to the pressures of globalization than in democratic or intermediate regimes.
Habit Reversal Training for Tic Disorders in Children and Adolescents
Authors: Piacentini John , Chang Susanna
Published: October 2005

Chronic tic disorders, including Tourette’s syndrome (TS), affect approximately .5% of children and adolescents. Although strong evidence exists supporting a neurobiological etiology, operant factors may play a role in the maintenance of tic behaviors. Pharmacological approaches remain the most commonly used intervention for chronic tic disorder in children and adults. Nevertheless, the unpredictable efficacy and serious side effects associated with medication along with parental concerns about long-term medication use in children underlie the need for nonpharmacological interventions for tics in this age group. This article reviews the rationale and evidence base for the use of habit reversal training (HRT), a multicomponent behavioral treatment package, as a treatment for childhood tics. Each of the primary treatment components of HRT is described and implementation is illustrated in case report format. Agrowing body of data suggests that HRT is a well-tolerated and efficacious intervention for tic disorders in this age group.
Three Approaches to Qualitative Content Analysis
Authors: Hsieh Hsiu-Fang , Shannon Sarah E.
Published: October 2005

Content analysis is a widely used qualitative research technique. Rather than being a single method, current applications of content analysis show three distinct approaches: conventional, directed, or summative. All three approaches are used to interpret meaning from the content of text data and, hence, adhere to the naturalistic paradigm. The major differences among the approaches are coding schemes, origins of codes, and threats to trustworthiness. In conventional content analysis, coding categories are derived directly from the text data. With a directed approach, analysis starts with a theory or relevant research findings as guidance for initial codes. A summative content analysis involves counting and comparisons, usually of keywords or content, followed by the interpretation of the underlying context. The authors delineate analytic procedures specific to each approach and techniques addressing trustworthiness with hypothetical examples drawn from the area of end-of-life care.
Limitations and transformations of habitus in Child-Directed Communication
Authors: Ochs Elinor , Solomon Olga , Sterponi Laura
Published: October 2005

This article offers an alternative approach to paradigms that cast culture solely as a nurturing influence on children's language development. It proposes a dimensional model of Child-Directed Communication (CDC) to delineate ways in which a community's habitus may impede the communicative potential of children with neuro-developmental conditions such as severe autism. It argues that certain features of Euro-American CDC are illadapted for autistic children. Due to inertia, caregivers often find themselves unable to transcend the limitations of CDC habitus. Yet, occasionally, a transformation in CDC emerges that more effectively engages children with impairments. The article analyzes one such transformation forged in the niche of a unique mother–son relationship in India and then introduced in the USA.
‘Everybody knows him’
Authors: Clawson Laura
Published: October 2005

The importance of social networks and social capital has been well established, but our understanding of exactly how people maintain useful ties, and how those ties operate day to day, is less advanced. In this article, I examine the networks of a self-employed construction contractor in the Sand Mountain area of Alabama who relies entirely on networks for job referrals. Though the core of his business comes from people in his own and related occupations, I argue that his use of purely social ties, maintained by extensive socializing, are also crucial, and that forms of conversation with no obvious utility, such as gossip, are actually central to his ability to maintain extremely large and occupationally valuable networks.
Electoral Verdicts
Authors: Bonneau Chris W.
Published: October 2005

The election of judges has been an enduring, though controversial, institution. Although there have been many popular accounts of howthese elections are decided by factors irrelevant to a fair and impartial judiciary, recent scholarship has shown that electoral competition in races for the state high court bench can be understood in systematic ways. Yet, although we know the factors that can make races more or less competitive, we lack understanding of the factors that contribute to the electoral defeat of sitting justices. In this article, I examine the determinants of electoral defeat for all incumbent state supreme court justices who ran for reelection between 1990 and 2000. Contrary to the arguments of those who claim that judicial elections are decided in a random, nonsystematic manner, I find that the probability of an incumbent’s being defeated is based on characteristics of the candidates, the state and electoral context, and institutional arrangements.
Phylogenetic detection of conserved gene clusters in microbial genomes
Authors: Zheng Yu , Anton Brian P , Roberts Richard J , Kasif Simon
Published: October 2005

Background

Microbial genomes contain an abundance of genes with conserved proximity forming clusters on the chromosome. However, the conservation can be a result of many factors such as vertical inheritance, or functional selection. Thus, identification of conserved gene clusters that are under functional selection provides an effective channel for gene annotation, microarray screening, and pathway reconstruction. The problem of devising a robust method to identify these conserved gene clusters and to evaluate the significance of the conservation in multiple genomes has a number of implications for comparative, evolutionary and functional genomics as well as synthetic biology.

Results

In this paper we describe a new method for detecting conserved gene clusters that incorporates the information captured by a genome phylogenetic tree. We show that our method can overcome the common problem of overestimation of significance due to the bias in the genome database and thereby achieve better accuracy when detecting functionally connected gene clusters. Our results can be accessed at database GeneChords http://genomics10.bu.edu/GeneChords.

Conclusion

The methodology described in this paper gives a scalable framework for discovering conserved gene clusters in microbial genomes. It serves as a platform for many other functional genomic analyses in microorganisms, such as operon prediction, regulatory site prediction, functional annotation of genes, evolutionary origin and development of gene clusters.
High-throughput metal susceptibility testing of microbial biofilms
Authors: Harrison Joe J , Turner Raymond J , Ceri Howard
Published: October 2005

Background

Microbial biofilms exist all over the natural world, a distribution that is paralleled by metal cations and oxyanions. Despite this reality, very few studies have examined how biofilms withstand exposure to these toxic compounds. This article describes a batch culture technique for biofilm and planktonic cell metal susceptibility testing using the MBEC assay. This device is compatible with standard 96-well microtiter plate technology. As part of this method, a two part, metal specific neutralization protocol is summarized. This procedure minimizes residual biological toxicity arising from the carry-over of metals from challenge to recovery media. Neutralization consists of treating cultures with a chemical compound known to react with or to chelate the metal. Treated cultures are plated onto rich agar to allow metal complexes to diffuse into the recovery medium while bacteria remain on top to recover. Two difficulties associated with metal susceptibility testing were the focus of two applications of this technique. First, assays were calibrated to allow comparisons of the susceptibility of different organisms to metals. Second, the effects of exposure time and growth medium composition on the susceptibility of E. coli JM109 biofilms to metals were investigated.

Results

This high-throughput method generated 96-statistically equivalent biofilms in a single device and thus allowed for comparative and combinatorial experiments of media, microbial strains, exposure times and metals. By adjusting growth conditions, it was possible to examine biofilms of different microorganisms that had similar cell densities. In one example, Pseudomonas aeruginosa ATCC 27853 was up to 80 times more resistant to heavy metalloid oxyanions than Escherichia coli TG1. Further, biofilms were up to 133 times more tolerant to tellurite (TeO3
2-) than corresponding planktonic cultures. Regardless of the growth medium, the tolerance of biofilm and planktonic cell E. coli JM109 to metals was time-dependent.

Conclusion

This method results in accurate, easily reproducible comparisons between the susceptibility of planktonic cells and biofilms to metals. Further, it was possible to make direct comparisons of the ability of different microbial strains to withstand metal toxicity. The data presented here also indicate that exposure time is an important variable in metal susceptibility testing of bacteria.