bluuebunny/crossref_metadata_2025_split huggingface dataset:
Architecture and regulation of the Ca2+delivery system in muscle cellsThis paper is one of a selection of papers published in this Special Issue, entitled 14th International Biochemistry of Exercise Conference – Muscles as Molecular and Metabolic Machines, and has undergone the Journal’s usual peer review process.
Authors: Franzini-Armstrong Clara 
Published: May 2009

The junctional domain of sarcoplasmic reticulum (jSR) is specialized for receiving signals from the plasmalemma–transverse tubules and for releasing Ca2+during muscle activation. The junctional face of the jSR, facing the transverse tubules, is occupied by a molecular complex composed of the transmembrane Ca2+release channels (ryanodine receptors); the luminal protein calsequestrin (CSQ); the 2 membrane proteins, junctin (Jct), and triadin (Tr), which mediate CSQ-ryanodine receptor interactions; and several other components. Under the conditions prevailing within the sarcoplasmic reticulum lumen (physiological ionic strength, mostly due to K+and Ca2+ions), CSQ forms long linear polymers and the fixed protein gel is clearly visible in the electron microscope. The luminal domains of Jct and Tr are detectable but, overall, the 2 molecules are not clearly delineated. Cardiac muscles either overexpressing or bearing null mutations for 3 proteins of the junctional complex (CSQ, Jct, and Tr) reveal the contribution of these 3 components to the general architecture of the jSR.
Influence of aging and long-term unloading on the structure and function of human skeletal muscleThis paper is one of a selection of papers published in this Special Issue, entitled 14th International Biochemistry of Exercise Conference – Muscles as Molecular and Metabolic Machines, and has undergone the Journal’s usual peer review process.
Authors: Trappe Todd 
Published: May 2009

Understanding the quantitative and qualitative changes in skeletal muscle that control changes in function is crucial in the development of countermeasures to the loss of skeletal muscle function observed with real and simulated microgravity exposure (i.e., unloading) and with aging in humans. Qualitative changes that could influence the force and power producing properties of skeletal muscle are changes in the distribution of the 3 isoforms of the main motor protein myosin heavy chain (MHC), as well as the abundance of MHC, actin (the other main contractile protein), and the force distributing the connective tissue network. Numerous studies have examined quantitative and qualitative changes in skeletal muscle, from the whole muscle to the single myofiber from individuals undergoing real and simulated space flight for a few weeks to several months, as well as from aging men and women. When considering the relative content of the main functional and structural elements (i.e., myosin, actin, collagen), it appears that human muscle appropriately scales changes in size of 10%–40% induced over a relatively short time period (1–3 months) and over the lifespan (in humans 20 to 90+ years old). The main qualitative change with unloading and aging is a redistribution of the 3 MHC isoforms, which have vastly different contractile characteristics. It is now known that the response of skeletal muscle to unloading is muscle and gender specific. In summary, changes in muscle mass (quantity) combined with the alterations in MHC distribution (quality) are the primary determinants of changes in muscle function with unloading and aging. These parameters are the key components of muscle that should be targeted with countermeasures for conditions related to muscle loss, along with considerations for muscle- and gender-specific responses.
HumanGLUD1andGLUD2glutamate dehydrogenase localize to mitochondria and endoplasmic reticulum
Authors: Mastorodemos Vasileios , Kotzamani Dimitra , Zaganas Ioannis , Arianoglou Giovanna , Latsoudis Helen , Plaitakis Andreas 
Published: May 2009

Mammalian glutamate dehydrogenase (GDH), an enzyme central to glutamate metabolism, is thought to localize to the mitochondrial matrix, although there are also suggestions for the extramitochondrial presence of this protein. Whereas GDH in mammals is encoded by the GLUD1 gene, humans and the great apes have, in addition, a GLUD2 gene showing a distinct expression pattern. The encoded hGDH1 and hGDH2 isoenzymes are highly homologous, but their leader sequences are more divergent. To explore their subcellular targeting, we constructed expression vectors in which hGDH1 or hGDH2 was fused with the enhanced green fluorescent protein (EGFP) and used these to transfect COS 7, HeLa, CHO, HEK293, or neuroblastoma SHSY-5Y cells. Confocal microscopy revealed GDH-EGFP fluorescence in the cytoplasm within coarse structures. Cotransfection experiments using organelle-specific markers revealed that hGDH1 or hGDH2 colocalized with the mitochondrial marker DsRed2-Mito and to a lesser extent with the endoplasmic reticulum marker DsRed2-ER. Western blots detected two GDH-EGFP specific bands: a ~90 kDa band and a ~95 kDa band associated with the mitochondria and the endoplasmic reticulum containing cytosol, respectively. Deletion of the signal sequence, while altering drastically the fluoresce distribution within the cell, prevented GDH from entering the mitochondria, with the ~90 kDa band being retained in the cytosol. In addition, the deletion eliminated the ~95 kDa band from cell lysates, thus confirming that it represents the full-length GDH. Hence, while most of the hGDHs translocate into the mitochondria (a process associated with cleavage of the signal sequence), part of the protein localizes to the endoplasmic reticulum, probably serving additional functions.
FRET analysis of actin–myosin interaction in contracting rat aortic smooth muscle
Authors: Black J. , Dykes A. , Thatcher S. , Brown D. , Bryda E.C. , Wright G.L. 
Published: May 2009

We examined the interaction of smooth muscle myosin with α-actin and β-actin isoforms during the contraction of A7r5 smooth muscle cells and rat aortic smooth muscle. The techniques of confocal microscopy and fluorescence resonance energy transfer (FRET) analysis were utilized in examining A7r5 cells and rat aortic rings contracted with phorbol 12,13-dibutyrate. Visual evaluation of confocal images of A7r5 smooth muscle cells contracted by phorbol 12,13-dibutyrate indicated significant disassociation of myosin from α-actin but not β-actin. Whole-cell FRET analysis confirmed these observations (α-actin–myosin –67%, β-actin–myosin –2%). Time course studies further showed that α-actin–myosin complex increased significantly (40%) within 1.5 min after the addition of phorbol 12,13-dibutyrate and then declined as contraction progressed. FRET analysis of rat aortic rings at different intervals of contraction indicated significant increases in α-actin–myosin at the initiation (79%) and plateau (67%) in force development, but not during the intermediate period of slowly developing tension (–4%). By comparison, β-actin–myosin complex was unchanged except during slow force development, in which the association was significantly decreased (–30%). Similar to that of α-actin–myosin, Alexa 488 – phalloidin staining fluorescence indicated increased tissue F-actin content at the initiation (21%) and plateau (62%) in force. FRET images indicated the development of thickened cables and patches of α-actin–myosin in tissue throughout the interval of contraction. The results provide direct evidence of dynamic remodeling of the contractile protein during vascular smooth muscle contraction and suggest that FRET analysis may be a powerful tool for assessment of tissue protein–protein associations.
Effects of omeprazole treatment on nucleoside transporter expression and adenosine uptake in rat gastric mucosa
Authors: Redzic Zoran B. , Hasan Fuad A. , Al-Sarraf Hameed 
Published: May 2009

Increased adenosine concentration inhibits gastric acid secretion in rat via adenosine A1 and A2A receptors, whereas achlorhydria suppresses A1 and A2A receptor gene expression. This study aimed to examine the effects of omeprazole-induced achlorhydria on the expression and functional activity of nucleoside transporters in rat gastric mucosa. Wistar rats were treated for either 1 or 3 days with 0.4 mmol/kg omeprazole via gavage; controls were treated with vehicle. The expression of nucleoside transporters at the transcript level was explored by quantitative real-time polymerase chain reaction assays; the functional activity of nucleoside transporters in gastric mucosa was explored by observing [3H]adenosine uptake in vitro. Gastric mucosa expressed rat equilibrative nucleoside transporter (rENT) 1 and 2, and rat concentrative nucleoside transporter (rCNT) 1, 2, and 3 at the transcript level, and the estimated values for the threshold cycles for target amplification (Ct) were 31.5 ± 2, 28.5 ± 2.1, 32.9 ± 2.2, 29.1 ± 2, and 28.9 ± 2.5, respectively (n = 3 or 4). The Ct value for rat β-actin was 21.9 ± 1.8 (n = 4). In vitro uptake of [3H]adenosine by gastric mucosa samples consisted of Na+-dependent and Na+-independent components. One-day omeprazole treatment caused no change in nucleoside transporter mRNA levels or in [3H]adenosine uptake. Three-day omeprazole treatments, however, led to a 12-fold and 17-fold increase in rENT2 and rCNT1 mRNA levels, respectively. Samples taken after 3 days of treatment also took up significantly more [3H]adenosine than did samples from the corresponding control. In conclusion, the possible modification of nucleoside transport activities by changes in intraluminal acidity may have significance as part of a purinergic regulatory feedback mechanism in the control of gastric acid secretion.
Effect of refuge distance on escape behavior of side-blotched lizards (Uta stansburiana)
Authors: Zani P. A. , Jones T. D. , Neuhaus R. A. , Milgrom J. E. 
Published: May 2009

Side-blotched lizards ( Uta stansburiana Baird and Girard, 1852) use sagebrush desert habitat above cliffs and typically flee over and down the nearest cliff when disturbed. We tested antipredator escape tactics of lizards to a common local snake, the western yellowbelly racer ( Coluber mormon Baird and Girard, 1852). Our goal was to determine if lizards use cliffs as a refuge from snakes, which cannot climb the sheer rock face, and whether distance to refuge affects escape behavior. We located undisturbed lizards above a cliff and approached them from a random direction with a realistic rubber snake model. When the snake model approached, lizards fled nonrandomly toward the nearest cliff refuge, indicating considerable spatial awareness. Lizards fled more directly toward the cliff the farther from the cliff they were found. However, when beyond ~15 m from the cliff the escape behavior of lizards changed to one of flight in circles (nondirectional) without hiding. Performance capacity (endurance) of the lizards is much greater than 15 m, indicating that lizards have the physiological capacity to reach the cliff. We suggest that the costs of potential intraspecific interactions (i.e., escape into unfamiliar or a competitor’s territory) are greater than the immediate risks of predation by snakes.
Visual Object Representations Can Be Formed outside the Focus of Voluntary Attention: Evidence from Event-related Brain Potentials
Authors: Müller Dagmar , Winkler István , Roeber Urte , Schaffer Susann , Czigler István , Schröger Erich 
Published: May 2009

Abstract
There is an ongoing debate whether visual object representations can be formed outside the focus of voluntary attention. Recently, implicit behavioral measures suggested that grouping processes can occur for task-irrelevant visual stimuli, thus supporting theories of preattentive object formation (e.g., Lamy, D., Segal, H., & Ruderman, L. Grouping does not require attention. Perception and Psychophysics, 68, 17–31, 2006; Russell, C., & Driver, J. New indirect measures of “inattentive” visual grouping in a change-detection task. Perception and Psychophysics, 67, 606–623, 2005). We developed an ERP paradigm that allows testing for visual grouping when neither the objects nor its constituents are related to the participant's task. Our paradigm is based on the visual mismatch negativity ERP component, which is elicited by stimuli deviating from a regular stimulus sequence even when the stimuli are ignored. Our stimuli consisted of four pairs of colored discs that served as objects. These objects were presented isochronously while participants were engaged in a task related to the continuously presented fixation cross. Occasionally, two color deviances occurred simultaneously either within the same object or across two different objects. We found significant ERP differences for same- versus different-object deviances, supporting the notion that forming visual object representations by grouping can occur outside the focus of voluntary attention. Also our behavioral experiment, in which participants responded to color deviances—thus, this time the discs but, again, not the objects were task relevant—showed that the object status matters. Our results stress the importance of early grouping processes for structuring the perceptual world.
A Climatology and Case Study of Continental Cold Season Dense Fog Associated with Low Clouds
Authors: Westcott Nancy E. , Kristovich David A. R. 
Published: May 2009

Abstract
This study focuses on dense fog cases that develop in association with low clouds and sometimes precipitation. A climatology of weather conditions associated with dense fog at Peoria, Illinois, for October–March 1970–94 indicated that fog forming in the presence of low clouds is common, in 57% of all events. For events associated with low pressure systems, low clouds precede dense fog in 84% of cases. Therefore, continental fogs often do not form under the clear-sky conditions that have received the most attention in the literature. Surface cooling is usually observed prior to fog on clear nights. With low cloud bases, warming or no change in temperature is frequent. Thus, fog often forms under conditions that are not well understood, increasing the difficulty of forecasting fog. The possible mechanisms for fog development under low cloud-base conditions were explored for an event when dense fog covered much of Illinois on 7 November 2006. Weather Surveillance Radar-1988 Doppler (WSR-88D) and rawinsonde observations indicated that evaporating precipitation aloft was important in moistening the lower atmosphere. Dense fog occurred about 6 h following light precipitation at the surface. The surface was nearly saturated following precipitation, but relative cooling was needed to overcome weak warm air advection and supersaturate the lower atmosphere. Surface (2 m) temperatures were near or slightly cooler than ground temperatures in most of the region, suggesting surface sensible heat fluxes were not important in this relative cooling. Sounding data indicated drying of the atmosphere above 800 hPa. Infrared satellite imagery indicated deep clouds associated with a low pressure system moved east of Illinois by early morning, leaving only low clouds. It is hypothesized that radiational cooling of the low cloud layer was instrumental in promoting the early morning dense fog.
A Sea State–Dependent Spume Generation Function
Authors: Mueller James A. , Veron Fabrice 
Published: May 2009

Abstract
The uncertainty of the sea spray generation function continues to obscure spray-mediated momentum and scalar fluxes, especially for intense wind conditions. Most previous studies assume a constant form (spectral shape) for the droplet distribution, even though a shift to smaller drops with increased wind forcing is expected. In this paper, a new generation function for spume drops is derived, but unlike previous studies, both its form and magnitude change with wind forcing. Fairly good agreement is found between this spume generation function and the limited data available. A potential explanation for the vast size differences among previous spume generation studies is also provided by distinguishing the drops formed at the surface from the drops transported vertically where measurements are routinely made.
The Role of Momentum Transport in the Motion of a Quasi-Idealized Mesoscale Convective System
Authors: Mahoney Kelly M. , Lackmann Gary M. , Parker Matthew D. 
Published: May 2009

Abstract
Momentum transport is examined in a simulated midlatitude mesoscale convective system (MCS) to investigate its contribution to MCS motion. Momentum budgets are computed using model output to quantify the role of specific processes in determining the low-level wind field in the system’s surface-based cold pool. Results show that toward the leading convective line of the MCS and near the leading edge of the cold pool, the momentum field is most strongly determined by the vertical advection of the storm-induced perturbation wind. Across the middle rear of the system, the wind field is largely a product of the pressure gradient acceleration and, to a lesser extent, the vertical advection of the background environmental (i.e., base state) wind. The relative magnitudes of the vertical advection terms in an Eulerian momentum budget suggest that, for gust-front-driven systems, downward momentum transport by the MCS is a significant driver of MCS motion and potentially severe surface winds. Results further illustrate that the contribution of momentum transport to MCS speed occurs mainly via the enhancement of the cold pool propagation speed as higher-momentum air from aloft is transported into the surface-based cold pool.
Clinical and pharmacoeconomic profile of COPD patients with FEV1 50—60% predicted: pilot study on the impact of the extended indication of ICS/LABA
Authors: Dal Negro Roberto Walter , Bonadiman Luca , Turati Claudio , Turco Paola 
Published: May 2009

Background: The use of inhaled corticosteroids (ICS) and long-acting β2 adrenergics (LABA) in fixed combination (ICS/LABA) was recently extended to COPD patients with a baseline FEV1 50—60% predicted, thus broadening the original guideline indications (GOLD 2006) that limited their use only to stages III and IV. Method: The present study was carried out to assess the clinical profile of this new subset of patients, with a view to providing data for future studies on the impact of this novel extension of ICS/LABA use in COPD. Results: Data from the present observational cross-sectional study suggest that COPD patients with FEV1 50—60% predicted depict a dichotomic condition: actually, even though resembling milder patients in terms of frequency and severity of their respiratory symptoms, they are much more similar to severer patients in terms of rate of hospital admissions and resource consumption (p50.01). In other words, this subset of patients seems to represent a peculiar condition in the evolutional phase of COPD during which therapeutic treatment should be intensified in order to slow down the disease progression effectively. Nevertheless, independently of the severity, the general therapeutic approach to COPD was found to be greatly inadequate when compared to GOLD guidelines, particularly in terms of appropriateness. Conclusions: These findings should pave the way for future studies aimed to long-term monitoring of main outcomes and to evaluate the overall impact of earlier ICS/LABA use on disease progression and lung function decline in COPD.
Association between modelled traffic-related air pollution and asthma score in the ECRHS
Authors: Jacquemin B. , Sunyer J. , Forsberg B. , Aguilera I. , Bouso L. , Briggs D. , de Marco R. , García-Esteban R. , Heinrich J. , Jarvis D. , Maldonado J. A. , Payo F. , Rage E. , Vienneau D. , Künzli N. 
Published: May 2009

The aim of our analysis was to study the association between air pollution and asthma among adults. For this goal, a previously developed “asthma score” was used.Persons aged 25–44 yrs were randomly selected (1991–1993) and followed up (2000–2002) within the European Community Respiratory Health Survey (ECRHS I and II, respectively). The asthma score was defined from 0 to 5, based on the positive answers to the following symptoms reported for the last 12 months: wheeze/breathlessness, chest tightness, dyspnoea at rest, dyspnoea after exercise and woken by dyspnoea. Participants' home addresses were linked to outdoor modelled NO2estimates for 2001. Negative binomial regression was used to model the asthma score.The score from ECRHS II was positively associated with NO2(ratio of the mean asthma score (RMS) 1.23, 95% CI 1.09–1.38, for an increase of 10 μg·m−3). After excluding participants with asthma and symptoms at baseline, the association remained (RMS 1.25, 95% CI 1.05–1.51), and was particularly high among those reporting a high score in ECRHS II. The latter probably reflects incident cases of asthma.Our results suggest that traffic-related pollution causes asthma symptoms and possibly asthma incidence in adults. The asthma score offers an alternative with which to investigate the course and aetiology of asthma in adults.
Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments
Authors: Liu Tianqing , Lin Nan , Shi Ningzhong , Zhang Baoxue 
Published: May 2009

Abstract

Background
Time-course microarray experiments produce vector gene expression profiles across a series of time points. Clustering genes based on these profiles is important in discovering functional related and co-regulated genes. Early developed clustering algorithms do not take advantage of the ordering in a time-course study, explicit use of which should allow more sensitive detection of genes that display a consistent pattern over time. Peddada et al. [1] proposed a clustering algorithm that can incorporate the temporal ordering using order-restricted statistical inference. This algorithm is, however, very time-consuming and hence inapplicable to most microarray experiments that contain a large number of genes. Its computational burden also imposes difficulty to assess the clustering reliability, which is a very important measure when clustering noisy microarray data.

Results
We propose a computationally efficient information criterion-based clustering algorithm, called ORICC, that also takes account of the ordering in time-course microarray experiments by embedding the order-restricted inference into a model selection framework. Genes are assigned to the profile which they best match determined by a newly proposed information criterion for order-restricted inference. In addition, we also developed a bootstrap procedure to assess ORICC's clustering reliability for every gene. Simulation studies show that the ORICC method is robust, always gives better clustering accuracy than Peddada's method and saves hundreds of times computational time. Under some scenarios, its accuracy is also better than some other existing clustering methods for short time-course microarray data, such as STEM [2] and Wang et al. [3]. It is also computationally much faster than Wang et al. [3].

Conclusion
Our ORICC algorithm, which takes advantage of the temporal ordering in time-course microarray experiments, provides good clustering accuracy and is meanwhile much faster than Peddada's method. Moreover, the clustering reliability for each gene can also be assessed, which is unavailable in Peddada's method. In a real data example, the ORICC algorithm identifies new and interesting genes that previous analyses failed to reveal.