bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ribosome: The Structure–Function Relation and a New Paradigm to the Protein Folding Problem
Authors: Das Debasis , Samanta Dibyendu , Das Anindita , Ghosh Jaydip , Bhattacharya Arpita , Basu Arunima , Chakrabarti Abhijit , Das Gupta Chanchal 
Published: May 2010

AbstractThe rate of protein synthesis is about seven and fifteen amino acids per second, in the eukaryotic and the bacterial ribosome, respectively. Hence, a few minutes is required to synthesize a polypeptide of an average length. This is much longer than the time needed for the hydrophobic collapse (folding) to take place. So a polypeptide gets enough time to form its local secondary to tertiary structures cotranslationally and put such segments in proper order while in association with the ribosome, unless something prevents its entire length from folding. As reported earlier, ribosomes from prokaryotes, eukaryotes, and mitochondria act as molds for protein folding, and each mold has a set of recognition sites for all proteins. More specifically, the mold is the peptidyl transferase center (PTC), a part of the large RNA of the large ribosomal subunit. Specific amino acids from different random coil regions in a protein interact with specific nucleotides in the PTC, which brings the entire length of the protein into the small space of the PTC mold. The mold thus helps to stabilize the entropy‐driven collapsed state of the polypeptide. The process also divides the protein into small segments; each segment is connected at two ends with two nucleotides and can fold in the ribosomal environment. The segments dissociate in such a sequence that the organization proceeds hierarchically from the core of the globular protein radially towards the outer surface. Then the protein dissociates from the ribosome in a “folding competent state” which does the final fine tuning in folding outside the ribosome. While the ribosomal contact and release are over in 1–2 minutes in vitro, the fine tuning takes about 5–10 minutes. Release from the ribosome needs no added energy factor from outside, like ATP.
Nitric oxide in paraquat‐mediated toxicity: A review
Authors: Morán José M. , Ortiz‐Ortiz Miguel A. , Ruiz‐Mesa Luz M. , Fuentes José M. 
Published: May 2010

AbstractParaquat, a cationic herbicide, produces degenerative lesions in the lung and in the nervous system after systemic administration to man and animals. Many cases of acute poisoning and death have been reported over the past few decades. Although a definitive mechanism of toxicity of paraquat has not been delineated, a cyclic single electron reduction/oxidation is a critical mechanistic event. The redox cycling of paraquat has two potentially important consequences relevant to the development of toxicity: the generation of the superoxide anion, which can lead to the formation of more toxic reactive oxygen species which are highly reactive to cellular macromolecules; and the oxidation of reducing equivalents (e.g., NADPH, reduced glutathione), which results in the disruption of important NADPH‐requiring biochemical processes necessary for normal cell function. Nitric oxide is an important signaling molecule that reacts with superoxide derived from the paraquat redox cycle, to form the potent oxidant peroxynitrite, which causes serious cell damage. Although nitric oxide has been involved in the mechanism of paraquat‐mediated toxicity, the role of nitric oxide has been controversial as both protective and harmful effects have been described. The present review summarizes recent findings in the field and describes new knowledge on the role of nitric oxide in the paraquat‐mediated toxicity. © 2010 Wiley Periodicals, Inc. J Biochem Mol Toxicol 24:402–409, 2010; View this article online atwileyonlinelibrary.com. DOI 10.1002/jbt.20348
RETRACTED: Protective effects of caffeic acid on lactate dehydrogenase isoenzymes, electrocardiogram, adenosine triphosphatases, and hematology on isoproterenol‐induced myocardial infarcted rats
Authors: Senthil Kumaran K. , Stanely Mainzen Prince P. 
Published: May 2010

AbstractThe present study aims to evaluate the protective effects of caffeic acid on isoproterenol‐treated myocardial infarction. Male albino Wistar rats were pretreated with caffeic acid (15 mg/kg) daily for 10 days. After the pretreatment, rats were injected with isoproterenol (100 mg/kg) at an interval of 24 h for 2 days to induce myocardial infarction. Isoproterenol‐treated rats showed increased intensity of lactate dehydrogenase‐1 and 2 isoenzyme bands and elevated ST segments. The activity of the heart sodium potassium adenosine triphosphatase was decreased, and the activities of the heart magnesium adenosine triphosphatase and calcium adenosine triphosphatase were increased in isoproterenol‐treated rats. Isoproterenol‐treated rats also showed a significant increase in the concentration of heart calcium. Furthermore, it significantly increased the counts of red blood cells, hemoglobin, white blood cells, and neutrophils and decreased significantly the concentration of erythrocyte sedimentation rate and the counts of lymphocytes and eosinophils. Pretreatment with caffeic acid showed protective effects on all the biochemical parameters, hematology and minimized alterations in lactate dehydrogenase isoenzymes and electrocardiogram. In vitro study confirmed the free radical scavenging potential of caffeic acid. The observed effects might be due to the free radical scavenging and membrane‐stabilizing property of caffeic acid. © 2010 Wiley Periodicals, Inc. J Biochem Mol Toxicol 25:60–67, 2011; View this article online atwileyonlinelibrary.com. DOI 10.1002/jbt.20359
SDOVS: A solvent dipole ordering‐based method for virtual screening
Authors: Murata Katsumi , Nagata Naoya , Nakanishi Isao , Kitaura Kazuo 
Published: May 2010

AbstractWe previously reported that solvent dipole ordering (SDO) at the ligand binding site of a protein indicates an outline of the preferred shape and binding pose of the ligands. We suggested that SDO‐mimetic pseudo‐molecules that mimic the 3D shape of the SDO region could be used as molecular queries with a shape similarity matching method in virtual screening. In this work, a virtual screening method based on SDO, named SDOVS, was proposed. This method was applied to virtual screening of ligands for four typical drug target proteins and the performance compared with that of FRED (well‐known rigid docking method); the efficiency of SDOVS was demonstrated to be better than FRED. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Effect of substrate stiffness and PDGF on the behavior of vascular smooth muscle cells: Implications for atherosclerosis
Authors: Brown Xin Q. , Bartolak‐Suki Erzsebet , Williams Corin , Walker Mathew L. , Weaver Valerie M. , Wong Joyce Y. 
Published: May 2010

AbstractVascular disease, such as atherosclerosis, is accompanied by changes in the mechanical properties of the vessel wall. Although altered mechanics is thought to contribute to disease progression, the molecular mechanisms whereby vessel wall stiffening could promote vascular occlusive disease remain unclear. It is well known that platelet‐derived growth factor (PDGF) is a major stimulus for the abnormal migration and proliferation of vascular smooth muscle cells (VSMCs) and contributes critically to vascular disease. Here we used engineered substrates with tunable mechanical properties to explore the effect of tissue stiffness on PDGF signaling in VSMCs as a potential mechanism whereby vessel wall stiffening could promote vascular disease. We found that substrate stiffness significantly enhanced PDGFR activity and VSMC proliferation. After ligand binding, PDGFR followed distinct routes of activation in cells cultured on stiff versus soft substrates, as demonstrated by differences in its intensity and duration of activation, sensitivity to cholesterol extracting agent, and plasma membrane localization. Our results suggest that stiffening of the vessel wall could actively promote pathogenesis of vascular disease by enhancing PDGFR signaling to drive VSMC growth and survival. J. Cell. Physiol. 225: 115–122, 2010. © 2010 Wiley‐Liss, Inc.
Adsorption of Reactive Red 120 from aqueous solutions by cetylpyridinium‐bentonite
Authors: Tabak Ahmet , Baltas Nimet , Afsin Beytullah , Emirik Mustafa , Caglar Bulent , Eren Erdal 
Published: May 2010

AbstractBACKGROUND: The removal of Reactive Red 120 (RR 120) from aqueous solutions using cetylpyridinium modified Resadiye bentonite (CP‐bentonite) prepared by ion exchange was investigated with particular reference to the effects of temperature, pH and ionic strength on adsorption.RESULTS: Fourier transform infrared (FTIR) and thermal analysis (TG‐DTG/DTA) techniques revealed that the anionic dye (RR 120) molecules replaced partly cationic surfactant species on interacting with CP‐bentonite. The positive surface charge originating from the cationic surfactant species located on the external surface of the modified bentonite sample increased at low pH values. The significant amount of dye removal by CP‐bentonite at high pH values proved the importance of π and van der Waals interactions other than the electrostatic attraction in the duration of the adsorption process. The adsorption isotherms and the kinetic data were well described by the Langmuir and pseudo‐second‐order kinetic model, respectively. The Gibbs energy (ΔG), enthalpy (ΔH) and entropy (ΔS) changes in the temperature range 25–65 °C pointed out that the RR 120 uptake increased in parallel with the temperature.CONCLUSION: This study showed that the structural arrangement of cetylpyridinium ions in the CP‐bentonite sample as well as the pH, temperature and ionic strength of the bulk solution influenced the adsorption of RR 120 dye from aqueous solutions by CP‐bentonite. Copyright © 2010 Society of Chemical Industry
Depth‐dependent anisotropies of amides and sugar in perpendicular and parallel sections of articular cartilage by Fourier transform infrared imaging
Authors: Xia Yang , Mittelstaedt Daniel , Ramakrishnan Nagarajan , Szarko Matthew , Bidthanapally Aruna 
Published: May 2010

AbstractFull thickness blocks of canine humeral cartilage were microtomed into both perpendicular sections and a series of 100 parallel sections, each 6 μm thick. Fourier transform infrared (IR) imaging was used to image each tissue section eleven times under different IR polarizations (from 0° to 180° polarization states in 20° increments and with an additional 90° polarization), at a spatial resolution of 6.25 μm and a wavenumber step of 8 cm−1. With increasing depth from the articular surface, amide anisotropies increased in the perpendicular sections and decreased in the parallel sections. Both types of tissue sectioning identified a 90° difference between amide I and amide II in the superficial zone (SZ) of cartilage. The fibrillar distribution in the parallel sections from the SZ was shown to not be random. Sugar had a weak but recognizable anisotropy in the upper part of the radial zone (RZ) in the perpendicular sections. The depth‐dependent anisotropic data were fitted with a theoretical equation that contained three signature parameters, which illustrate the arcade structure of collagens with the aid of a fibril model. Fourier‐transform IR imaging of both perpendicular and parallel sections provides the possibility of determining the three‐dimensional macromolecular structures in articular cartilage. Being sensitive to the orientation of the macromolecular structure in healthy articular cartilage aids the prospect of detecting the early onset of the tissue degradation that may lead to pathological conditions such as osteoarthritis. Microsc. Res. Tech. 74:122–132, 2011. © 2010 Wiley‐Liss, Inc.
The effects of acute carbon dioxide on behavior and physiology inProcambarus clarkii
Authors: Bierbower S.M. , Cooper R.L. 
Published: May 2010

AbstractVertebrates and invertebrates show a similar response of rapid anesthesia with high levels of carbon dioxide. In this study, we use crayfish to examine both behavioral and physiological responses to increasing [CO2] to explain the rapid unresponsiveness and cessation of an autonomic response. Hypoxic and low pH environments that are induced by CO2exposure were also examined, although neither produced the identified CO2effects. In insects, low concentrations play a vital role in providing information for task performance such as food location through attraction cues, whereas high concentrations produce avoidance responses. We found behavioral responses in crayfish that demonstrate a strong repellent effect to high [CO2] and that the avoidance behavior decreases with lower [CO2]. There was not a preference and/or repellent behavioral response with 5% CO2, hypoxic or low pH environments. Mechanosensory stimulation showed that only at high [CO2] there is an unresponsiveness to stimuli within a 30 min time period. Additionally, the autonomic bioindex of heart and ventilatory rates showed a complete cessation with high acute exposure within in the same time period for unresponsiveness to mechanosensory stimulation.J. Exp. Zool. 313A:484–497, 2010. © 2010 Wiley‐Liss, Inc.
Site‐adjusted organic matter–balance method for use in arable farming systems
Authors: Kolbe Hartmut 
Published: May 2010

AbstractOrganic‐matter (OM) balancing can provide useful information for sustainable arable farm management. However, the balance methods commonly used are rather inaccurate and fail to meet current requirements. Therefore, an improved, site‐adjusted, semiquantitative technique based on the VDLUFA method developed by Körschens et al. (2004) in Germany was worked out for terrestrial soils for manual (i.e., not computer‐based) use in agricultural practice and consulting. It was optimized using results from 39 long‐term field trials to take into account site‐specific effects in Central Europe. The climatic, geogenic, and soil‐chemical influences on the process of OM decay were taken into consideration by adapting organic‐carbon (OC) coefficients of the organic material and the cultivation effects of crop species divided into six site‐specific groups. The balances calculated were adjusted to the soil organic‐carbon (SOC) concentrations, and the evaluation system was developed for use in conventional and organic agriculture on sites in Central Europe. The statistical deviation between calculated and field data is ± 3.7 g kg–1 for the VDLUFA method and ± (2.1–2.3) g kg–1 SOC for the site‐adjusted method, and the variance is reduced by 62%–68%. For use in farming, little information about soil and climatic characteristics, crop species, or organic material supply is needed, and the results can be used for in‐depth farm analyses and regulative reasons.
Holocene flooding history of the Lower Tagus Valley (Portugal)
Authors: Vis Geert‐Jan , Bohncke Sjoerd J. P. , Schneider Heike , Kasse Cornelis , Coenraads‐Nederveen Sander , Zuurbier Koen , Rozema Jouke 
Published: May 2010

AbstractThe present paper aims to reconstruct the Lower Tagus Valley flooding history for the last ca. 6500 a, to explore the suitability of pollen‐based local vegetation development in supporting the reconstruction of flooding history, and to explain fluvial activity changes in terms of allogenic (climate, human impact) and autogenic (system intrinsic) processes. The flooding history has been determined by cored sedimentary records located ∼18 km apart in distal, low‐energy backswamps on both sides of the Tagus channel. In these low‐energy backswamps, fine‐grained sediment layers deposited from suspended load of overbank flood water reflect periods with multiple overbank floods. By means of a multi‐proxy approach (sedimentology, magnetic susceptibility, grain size, loss‐on‐ignition, carbonate content and pollen), sedimentary and environmental changes were identified. At both sites, synchronous lithological intervals accumulated, suggesting a common origin for the changes in fluvial activity since ca. 6500 cal. a BP. Based on lithological changes, three phases of high fluvial activity (6500–5500, 4900–3500 and 1000–0 cal. a BP) and two phases of low fluvial activity (5500–4900 and 3500–1000 cal. a BP) were identified. Two periods with dominant allogenic controls on fluvial activity in the Lower Tagus Valley were identified: relative sea level (6500–5500 cal. a BP) and human impact (1000–0 cal. a BP). During the intermediate period, changes in fluvial activity may have been caused by climate (5500–1000 cal. BP), but unambiguous correlations are difficult to make. This is due to the way allogenic controls are translated through the fluvial system, the geomorphological differences between upstream and downstream studies and autogenic processes. The comparison of local vegetation development and flooding phases as reconstructed using sedimentology shows a limited added value of using local palynology as a proxy for fluvial activity. Copyright © 2010 John Wiley & Sons, Ltd.
Gaucher disease ascertained through a Parkinson's center: Imaging and clinical characterization
Authors: Saunders‐Pullman Rachel , Hagenah Johann , Dhawan Vijay , Stanley Kaili , Pastores Gregory , Sathe Swati , Tagliati Michele , Condefer Kelly , Palmese Christina , Brüggemann Norbert , Klein Christine , Roe AM , Kornreich Ruth , Ozelius Laurie , Bressman Susan 
Published: May 2010

AbstractAmong the genes implicated for parkinsonism is glucocerebrosidase (GBA), which causes Gaucher disease (GD). Despite a growing literature that GD may present as parkinsonism, neuroimaging, olfaction, and neuropsychological testing have not been extensively reported. We describe transcranial sonography (TCS), 18F‐fluorodopa (F‐dopa) and fluorodeoxyglucose (FDG) Positron emission tomography, olfaction testing, neuropsychological testing, and clinical features in homozygous and compound heterozygous GBA mutation carriers identified through screening of 250 Ashkenazi Jewish parkinsonian individuals treated at a tertiary care center. We identified two individuals with N370S/R496H compound heterozygous mutations and two with N370S homozygous mutations; one individual died before completing detailed evaluation. TCS (n = 3) demonstrated nigral hyperechogenicity that was greater than controls [median area maximal substantia nigra echogenicity (aSNmax) = 0.28 cm2 vs. 0.14 cm2, P = 0.005], but similar to idiopathic PD (aSNmax = 0.31 cm2). FDG PET (n = 2) demonstrated hypermetabolism of the lentiform nuclei, and F‐fluorodopa PET (n = 2), bilateral reduction in striatal F‐dopa uptake. Olfaction was markedly impaired in the two tested cases, including onset of smell disturbance in adolescence in one. Neuropsychological features (n = 3) were consistent with Parkinson's disease (PD) or diffuse Lewy body disease (DLB). The imaging, neuropsychological and olfactory markers suggest the GD phenotype includes PD with and without features of DLB, marked olfactory loss, nigral hyperechogenicity on TCS, and F‐dopa and FDG PET abnormalities. © 2010 Movement Disorder Society
Early versus delayed bilateral subthalamic deep brain stimulation for parkinson's disease: A decision analysis
Authors: Espay Alberto J. , Vaughan Jennifer E. , Marras Connie , Fowler Rob , Eckman Mark H. 
Published: May 2010

AbstractThe long‐term benefits of subthalamic nucleus deep brain stimulation (STN DBS) applied earlier in the disease course, before significant disability accumulates, remain to be determined. We developed a Markov state transition decision analytic model to compare effectiveness in quality‐adjusted life years (QALYs) of STN DBS applied to patients with PD at an “early” (“off time” 10–20%) versus “delayed” stage (“off time” >40%). A lifelong time horizon and societal perspective were assumed. Probabilities and rates were obtained from literature review; utilities were derived using the time trade‐off technique and a computer‐assisted utility assessment software tool applied to a cohort of 22 STN‐DBS and 21 non‐STN‐DBS PD patients. Uncertainty was assessed through one‐ and two‐way sensitivity analyses and probabilistic sensitivity analysis using second‐order Monte Carlo simulations. Early STN DBS was preferred with a quality‐adjusted life expectancy of 22.3 QALYs, a gain of 2.5 QALYs over those with delayed surgery (19.8 QALYs). Early STN DBS was preferred in 69% of 5,000 Monte Carlo simulations. Early surgery was robustly favored through most sensitivity analyses. Delayed STN DBS afforded greater QALYs when using utility estimates exclusively from non‐STN‐DBS patients and, for the entire group, if the rate of motor progression were to exceed 25% per year. Although decision modeling requires assumptions and simplifications, our exploratory analysis suggests that STN DBS performed in early PD may convey greater quality‐adjusted life expectancy when compared to a delayed procedure. These findings support further evaluation of early STN DBS in a controlled clinical trial. © 2010 Movement Disorder Society
Identification of testis‐specific ubiquitin‐conjugating enzyme in the ascidian Ciona intestinalis
Authors: Yokota Naoto , Harada Yoshito , Sawada Hitoshi 
Published: May 2010

AbstractThe ubiquitin–proteasome system is known to play a key role in fertilization in ascidians, sea urchins, and mammals. To obtain insights into the ubiquitin‐conjugating enzymes (Ube2) involved in reproductive systems, we systematically explored Ube2 enzymes expressed in the testis of the ascidian Ciona intestinalis. Here, we report cDNA cloning and characterization of a novel type of Ube2r (Ci0100152677) that is capable of making a thiolester bond with ubiquitin. Northern analysis, whole‐mount in situ hybridization and immunocytochemistry indicate that this enzyme is exclusively expressed in the testis, mainly in the germ cells during the late stage of spermatogenesis, and is localized in the sperm head and tail, suggesting possible participation in fertilization or spermatogenesis/spermiogenesis. Mol. Reprod. Dev. 77: 640–647, 2010. © 2010 Wiley‐Liss, Inc.
Echo‐planar spectroscopic imaging (EPSI) of the water resonance structure in human breast using sensitivity encoding (SENSE)
Authors: Medved Milica , Ivancevic Marko K. , Olopade Olufunmilayo I. , Newstead Gillian M. , Karczmar Gregory S. 
Published: May 2010

AbstractHigh spectral and spatial resolution MRI, based on echo‐planar spectroscopic imaging, has been applied successfully in diagnostic breast imaging, but acquisition times are long. One way of increasing acquisition speed is to apply the sensitivity encoding algorithm for complex high spectral and spatial resolution data. We demonstrate application of a complex sensitivity encoding algorithm to high spectral and spatial resolution MRI data, in a phantom and human breast, with 7‐ and 16‐channel dedicated breast phased‐array coils. Very low g factors are obtained using the breast coils, and the signal‐to‐noise ratio (SNR) penalty for water resonance peak height and water resonance asymmetry images is small at acceleration factors of up to 6 and 4, respectively, as evidenced by high Pearson correlation factors between fully sampled and accelerated data. This is the first application of the sensitivity encoding algorithm to characterize the structure of the water resonance at high spatial resolution. Magn Reson Med 63:1557–1563, 2010. © 2010 Wiley‐Liss, Inc.