bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional regulation of the myosin heavy chain IIB gene in inactive rat soleus
Authors: McCall Gary E. , Haddad Fadia , Roy Roland R. , Zhong Hui , Edgerton V. Reggie , Baldwin Kenneth M. 
Published: July 2009

AbstractThe myosin heavy chain (MHC) isoform composition of skeletal muscle is dependent, in part, on the functional demands of the muscle. The rat soleus muscle primarily expresses the slow‐contracting type I MHC; however, chronic inactivity increases expression of the faster‐contracting type II MHC isoforms. The purpose of this study was to identify the type IIb MHC promoter region(s) that regulate de novo transcription during chronic inactivity of the soleus induced by spinal cord isolation (SI; complete mid‐thoracic and high sacral spinal cord transections plus deafferentation). Seven days after SI, transcription of IIb MHC was evidenced by increases in IIb pre‐mRNA and mRNA. The activity of an ≈2.2‐kb IIb promoter‐firefly luciferase reporter plasmid increased in SI soleus over control as compared to that of a promoterless plasmid. Deletion analyses indicated that the regions encompassing −2237 to −1431, −1048 to −461, and −192 to −161 basepairs (bp) each contributed to the increase in transcriptional activity. Moreover, deletions or mutations of AT‐rich regions in the proximal −192 bp region abolished the increased promoter activity. These results provide important insights related to how proximal IIb MHC promoter elements regulate the increased expression of the IIb MHC gene in response to inactivity of a predominantly slow postural muscle as it undergoes a remodeling of its phenotype and functional characteristics. Muscle Nerve, 2009
Isolated posterior femoral cutaneous neuropathy following intragluteal injection
Authors: Kim Jee‐Eun , Kang Ji‐Hoon , Chol Choi Jay , Seok Lee Jung , Kang Sa‐Yoon 
Published: July 2009

AbstractIsolated posterior femoral cutaneous nerve lesions are rarely encountered. Electrophysiological documentation has only been made in a few cases. In this study we evaluated a 22‐year‐old woman with sensory loss and pain in the lower buttock and posterior thigh after left gluteal intramuscular injection. We assessed the posterior femoral cutaneous nerve using an accepted conduction technique. The results showed a normal response on the asymptomatic side, but no response on the symptomatic side. Muscle Nerve, 2009
Utility of cystatin C to monitor renal function in duchenne muscular dystrophy
Authors: Viollet Laurence , Gailey Susan , Thornton David J. , Friedman Neil R. , Flanigan Kevin M. , Mahan John D. , Mendell Jerry R. 
Published: July 2009

AbstractCreatinine as a marker of renal function has limited value in Duchenne muscular dystrophy (DMD) because of reduced muscle mass. Alternative methods of assessing renal function are sorely needed. Cystatin C, a nonglycosylated protein unaffected by muscle mass, is potentially an ideal biomarker of nephrotoxicity for this population but requires validation. In all, 75 subjects were recruited: 35 DMD (mean age 10.8 ± 5.4 years, corticosteroids n = 19, ambulatory n = 26), 29 healthy controls, 10 with renal disease, and one DMD with renal failure. Cystatin C levels in DMD were normal irrespective of age, ambulation, or corticosteroid treatment. Serum cystatin C was 0.67 ± 0.11 mg/l compared to normal controls 0.69 ± 0.09. mg/l. In these same individuals serum creatinine was severely reduced (0.27 ± 0.12 mg/dl) versus normals (0.75 ± 0.15 mg/dl, P < 0.01). In one DMD subject in renal failure, cystatin C was elevated. This study demonstrates the potential value of cystatin C as a biomarker for monitoring renal function in DMD. Its applicability extends to other neuromuscular diseases. Muscle Nerve, 2009
Antidepressant use and colorectal cancer risk
Authors: Coogan Patricia F. , Strom Brian L. , Rosenberg Lynn 
Published: July 2009

AbstractPurposeA previous epidemiologic study reported a 30% reduced risk of colorectal cancer among users of high doses of selective serotonin reuptake inhibitors (SSRIs). We assessed the association of colorectal cancer risk with SSRI and tricyclic antidepressant use in our hospital‐based Case Control Surveillance Study.MethodsFor the SSRI analyses, we used data collected on 529 colorectal cancer cases and 1955 hospitalized controls collected from 1995 to 2008. For the tricyclic antidepressant analyses, we used data on 2889 cases and 7122 controls collected from 1976 to 2008. We used multivariable logistic regression analysis to evaluate the association of regular SSRI use and regular tricyclic antidepressant use (daily use for at least 3 continuous months) with colorectal cancer risk.ResultsThe odds ratio for regular SSRI use was 0.55 (95% CI 0.35–0.88) and it did not differ by duration of use. The odds ratio was 0.47 (95% CI 0.26–0.85) for colon cancer and 0.72 (95% CI 0.37–1.41) for rectal cancer. The odds ratio for regular use of tricyclic antidepressants was 0.77 (95% CI 0.52–1.16)ConclusionsWe found an association of reduced risk of colorectal cancer with regular use of SSRIs. In light of laboratory data indicating that SSRIs may inhibit colon cancer and one previous epidemiologic study that also observed a decreased risk, further investigation of the effect of SSRIs on the risk of colorectal cancer is warranted. Copyright © 2009 John Wiley & Sons, Ltd.
Local anaesthetic drugs: adverse effects as reported through the ADROIT system in the UK
Authors: Nazir Muhummad Sohaib , Holdcroft Anita 
Published: July 2009

AbstractPurposeAdverse drug reactions (ADRs) to local anaesthetic drugs are reported voluntarily through the Adverse Drug Reporting On Line Tracking system (ADROIT). We aimed to determine hazards associated with drugs commonly used in anaesthesia including ropivacaine and levobupivacaine.MethodsThe ADROIT database was queried for all ADRs to local anaesthetics used in anaesthesia and surgery between 1967 and 2005. Details of age, sex, suspect drug, date and reaction details were analysed.ResultsThere were 985 reports analysed, 797 for lidocaine, 160 for bupivacaine, 16 for ropivacaine and 12 for levobupivacaine. The female to male ratio was 1.6:1 and age was not a factor determining the frequency of reactions. A vasoconstrictor was included in the lidocaine formulation in 27% of reports. When methylprednisolone (Depo‐Medrone®) or prilocaine (as EMLA™ cream) were used in combination with lidocaine, the frequency of allergic reports increased significantly (p < 0.0001). Levobupivacaine demonstrated a hazard signal for cardiovascular symptoms. Fatality rate within the reports was higher for bupivacaine (11%) than for lidocaine (3%).ConclusionsThe patient's age and sex were not found to influence the type of reactions reported. Lidocaine with methylprednisolone or prilocaine (as EMLATM cream) generated the largest number of reports of allergic phenomena. Fatalities were most frequently reported in association with bupivacaine. Copyright © 2009 John Wiley & Sons, Ltd.
Synthesis and characterization of conductive polypyrrole with improved conductivity and processability
Authors: Wu Tzong‐Ming , Chang Hsiang‐Ling , Lin Yen‐Wen 
Published: July 2009

AbstractBACKGROUND: The solubility and conductivity of chemically synthesized polypyrrole (PPy) are dependent on the synthesis procedure and composition. Enhanced processability of PPy with high conductivity can be achieved using the anionic polyelectrolyte poly(styrene sulfonate) (PSS).RESULTS: High‐conductivity PPy with better processability was successfully synthesized by in situ chemical oxidation polymerization using various concentrations of PSS. Elemental analysis results show that the C/S and N/S molar ratios of the PPy fabricated in the presence of PSS are in good agreement with theoretical values for PPy–SO4. The S/N ratio increases with increasing PSS content, indicating the high doping level for PPy as the PSS content increases. Scanning electron microscopy and high‐resolution transmission electron microscopy images show that the fabricated PPy has spherical structures with the average particle size for the pure PPy being about 250 nm and markedly decreasing to 20–40 nm with the addition of PSS.CONCLUSION: The conductivities of PPy synthesized with a PSS/pyrrole monomer weight ratio of 0.25 are about five times higher than that of PPy matrix. These results are perhaps due to the part played by PSS serving as a dopant to be incorporated into the PPy structure to improve the conductivity of the fabricated PPy. Copyright © 2009 Society of Chemical Industry
Wear Mechanism, Wear Rate and Contact Pressure in PIII Nitrided CoCr Alloys
Authors: Lutz Johanna , Mändl Stephan 
Published: July 2009

AbstractNitrogen plasma immersion ion implantation (PIII) into CoCr alloys in the temperature range from 300 to 600 °C leads to the formation of thick diffusion layers of up to 5 µm, consisting of an expanded austenitic phase at lower temperatures and CrN precipitates, dissolved in a matrix, at higher temperatures. In addition, a large increase of the wear resistance by up to a factor of 10 is observed, with the wear rate nearly independent of the alloy's composition and process temperature. No significant difference in the wear behaviour was observed for a 10 µm diameter diamond ball and a 4.8 mm diameter alumina employed as counterbody in the oscillating wear tests.
Epigenetic regulation of Myc on retinoic acid receptor beta and PDLIM4 in RWPE1 cells
Authors: He Meilan , Vanaja Donkena Krishna , Karnes R. Jeffrey , Young Charles Y.F. 
Published: July 2009

AbstractBACKGROUNDHypermethylation of CpG islands is a common epigenetic alteration associated with cancer. Tumor suppressor genes retinoic acid receptor beta (RARβ) and PDLIM4 are hypermethylated and silenced in prostate cancer (PCa) tissues and PCa cell lines compared to normal prostate cells.METHODSIn this study, a benign prostate epithelial cell line RWPE1 was used as a model to study the epigenetic regulation of Myc on the RARβ and PDLIM4 promoters. Forced Myc overexpression inhibited the RARβ and PDLIM4 expression.RESULTSPyrosequencing study showed that Myc overexpression increased methylation in several CpG sites of both promoters. A DNA methylation inhibitor 5‐aza‐2′‐deoxycytidine reversed the epigenetic alteration effect of Myc on both RARβ and PDLIM4.CONCLUSIONThe epigenetic regulation of Myc may be related to its up‐regulation of the DNA methyltransferase DNMT3a and DNMT3b. Prostate 69: 1643–1650, 2009. © 2009 Wiley‐Liss, Inc.
Modeling the possible conformations of the extracellular loops in G‐protein‐coupled receptors
Authors: Nikiforovich Gregory V. , Taylor Christina M. , Marshall Garland R. , Baranski Thomas J. 
Published: July 2009

AbstractThis study presents the results of a de novo approach modeling possible conformational dynamics of the extracellular (EC) loops in G‐protein‐coupled receptors (GPCRs), specifically in bovine rhodopsin (bRh), squid rhodopsin (sRh), human β‐2 adrenergic receptor (β2AR), turkey β‐1 adrenergic receptor (β1AR), and human A2 adenosine receptor (A2AR). The approach deliberately sacrificed a detailed description of any particular 3D structure of the loops in GPCRs in favor of a less precise description of many possible structures. Despite this, the approach found ensembles of the low‐energy conformers of the EC loops that contained structures close to the available X‐ray snapshots. For the smaller EC1 and EC3 loops (6–11 residues), our results were comparable with the best recent results obtained by other authors using much more sophisticated techniques. For the larger EC2 loops (25–34 residues), our results consistently yielded structures significantly closer to the X‐ray snapshots than the results of the other authors for loops of similar size. The results suggested possible large‐scale movements of the EC loops in GPCRs that might determine their conformational dynamics. The approach was also validated by accurately reproducing the docking poses for low‐molecular‐weight ligands in β2AR, β1AR, and A2AR, demonstrating the possible influence of the conformations of the EC loops on the binding sites of ligands. The approach correctly predicted the system of disulfide bridges between the EC loops in A2AR and elucidated the probable pathways for forming this system. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Assessment of the protein‐structure refinement category in CASP8
Authors: MacCallum Justin L. , Hua Lan , Schnieders Michael J. , Pande Vijay S. , Jacobson Matthew P. , Dill Ken A. 
Published: July 2009

AbstractHere, we summarize the assessment of protein structure refinement in CASP8. Twenty‐four groups refined a total of 12 target proteins. Averaging over all groups and all proteins, there was no net improvement over the original starting models. However, there are now some individual research groups who consistently do improve protein structures relative to a starting starting model. We compare various measures of quality assessment, including (i) standard backbone‐based methods, (ii) new methods from the Richardson group, and (iii) ensemble‐based methods for comparing experimental structures, such as NMR NOE violations and the suitability of the predicted models to serve as templates for molecular replacement. On the whole, there is a general correlation among various measures. However, there are interesting differences. Sometimes a structure that is in better agreement with the experimental data is judged to be slightly worse by GDT‐TS. This suggests that for comparing protein structures that are already quite close to the native, it may be preferable to use ensemble‐based experimentally derived measures of quality, in addition to single‐structure‐based methods such as GDT‐TS. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Structure of the heme/hemoglobin outer membrane receptor ShuA from Shigella dysenteriae: Heme binding by an induced fit mechanism
Authors: Cobessi David , Meksem Ahmed , Brillet Karl 
Published: July 2009

AbstractShigella dysentriae and other Gram‐negative human pathogens are able to use iron from heme bound to hemoglobin for growing. We solved at 2.6 Å resolution the 3D structure of the TonB‐dependent heme/hemoglobin outer membrane receptor ShuA from S. dysenteriae. ShuA binds to hemoglobin and transports heme across the outer membrane. The structure consists of a C‐terminal domain that folds into a 22‐stranded transmembrane β‐barrel, which is filled by the N‐terminal plug domain. One distal histidine ligand of heme is located at the apex of the plug, exposed to the solvent. His86 is situated 9.86 Å apart from His420, the second histidine involved in the heme binding. His420 is in the extracellular loop L7. The heme coordination by His86 and His420 involves conformational changes. The comparisons with the hemophore receptor HasR of Serratia marcescens bound to HasA‐Heme suggest an extracellular induced fit mechanism for the heme binding. The loop L7 contains hydrophobic residues which could interact with the hydrophobic porphyring ring of heme. The energy required for the transport by ShuA is derived from the proton motive force after interactions between the periplasmic N‐terminal TonB‐box of ShuA and the inner membrane protein, TonB. In ShuA, the TonB‐box is buried and cannot interact with TonB. The structural comparisons with HasR suggest its conformational change upon the heme binding for interacting with TonB. The signaling of the heme binding could involve a hydrogen bond network going from His86 to the TonB‐box. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Crystal structure of a trimeric archaeal adenylate kinase from the mesophile Methanococcus maripaludis with an unusually broad functional range and thermal stability
Authors: Davlieva Milya , Shamoo Yousif 
Published: July 2009

AbstractThe structure of the trimeric adenylate kinase from the Archaebacteria Methanococcus mariplaludis (AKMAR) has been solved to 2.5‐Å resolution and the temperature dependent stability and kinetics of the enzyme measured. The KM and Vmax of AKMAR exhibit only modest temperature dependence from 30°–60°C. Although M. mariplaludis is a mesophile with a maximum growth temperature of 43°C, AKMAR has a very broad functional range and stability (Tm = 74.0°C) that are more consistent with a thermophilic enzyme with high thermostability and exceptional activity over a wide range of temperatures, suggesting that this microbe may have only recently invaded a mesophilic niche and has yet to fully adapt. A comparison of the Local Structural Entropy (LSE) for AKMAR to the related adenylate kinases from the mesophile Methanococcus voltae and thermophile Methanococcus thermolithotrophicus show that changes in LSE are able to fully account for the intermediate stability of AKMAR and highlights a general mechanism for protein adaptation in this class of enzymes. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Reproductive success of rose‐ringed parakeets Psittacula krameri in a captive UK population
Authors: Lambert Mark S , Massei Giovanna , Bell Jennifer , Berry Leslie , Haigh Carol , Cowan David P 
Published: July 2009

AbstractBACKGROUND: Rose‐ringed parakeets Psittacula krameri (Scop.) have recently become established in several European countries, with potential for significant negative economic and ecological impacts. However, in northern Europe the potential for reproductive output is largely unknown. In 2005 the authors established a captive outdoor colony in north‐east England and examined breeding success over 2 years.RESULTS: In 2006 (19 pairs, 15 clutches) the average first clutch size was 3.6 (±0.3) eggs. Six clutches were infertile, and overall the colony produced 1.4 (±0.5) fertile eggs per pair. Eleven pairs produced a second clutch following removal of the first; seven were infertile, and overall productivity was 0.7 (±0.4) fertile eggs per pair. Unsuccessful pairs were rearranged or replaced. In 2007, overall productivity was 2.5 (±0.4) and 1.8 (±0.4) fertile eggs per pair for the first and second attempts respectively. For pairs that remained unchanged through 2006–2007, productivity was consistent between years and breeding attempts.CONCLUSION: Where food and nest sites were not limiting, clutch sizes in north‐east England were similar to those in the native range, and consistent between first and second attempts. This has implications for the future expansion and management of the species. © Crown Copyright 2009. Reproduced with permission of Her Majesty's Stationery Office. Published by John Wiley & Sons, Ltd.
Gene expression analysis on anterior temporal neocortex of patients with intractable epilepsy
Authors: Xi Zhi‐Qin , Xiao Fei , Yuan Jie , Wang Xue‐Feng , Wang Liang , Quan Feng‐Yin , Liu Guang‐Wei 
Published: July 2009

AbstractTo elucidate the molecular basis of intractable epilepsy (IE), we used a whole‐genome transcriptomic approach to identify genes involved in the pathogenesis of this disease. Using a complementary DNAs microarray representing 4096 human genes, we analyzed differential gene expression in the anterior temporal neocortex (ATN) of IE patients relative to control patients who had an operation to relieve head trauma‐related intracranial pressure. The results were validated by real‐time fluorescence‐quantitative polymerase chain reaction (FQ‐PCR) and reverse transcription‐PCR (RT‐PCR). The expression of 143 genes (3.5%) was significantly altered in IE patients. Thirty‐seven genes (26%) were reduced relative to controls, and 106 (74%) were elevated (more than twofold change vs. controls), including genes involved in immunity, signal transduction, apoptosis, stress, synaptic plasticity, structural, and cellular reorganization, among other processes. Results for 13 of the 14 differentially expressed genes tested by FQ‐PCR were consistent with the microarray. Twelve abnormally expressed cytoskeletal genes were confirmed by RT‐PCR. Expression of 11 was significantly higher in the ATN of IE patients than in controls. Gene productsalteredin IE, namely HSPBAP1, TRAP220, glycogen synthase kinase‐3β (GSK‐3β), and cyclin‐dependent kinase 5 (CDK5), were tested by immunohistochemistry and immunoblotting. GSK‐3β and CDK5 levels were significantly higher in the ATN of IE patients. Our gene chip data are generally in agreement with the published findings on epilepsy. Thus, gene chips may serve as a screening tool to elucidate the pathophysiology of IE. Investigation of some of these newly identified genes should enhance our understanding of the molecular mechanisms of epileptogenesis. Synapse 63:1017–1028, 2009. © 2009 Wiley‐Liss, Inc.
Zinc: The brain's dark horse
Authors: Bitanihirwe Byron K.Y. , Cunningham Miles G. 
Published: July 2009

AbstractZinc is a life‐sustaining trace element, serving structural, catalytic, and regulatory roles in cellular biology. It is required for normal mammalian brain development and physiology, such that deficiency or excess of zinc has been shown to contribute to alterations in behavior, abnormal central nervous system development, and neurological disease. In this light, it is not surprising that zinc ions have now been shown to play a role in the neuromodulation of synaptic transmission as well as in cortical plasticity. Zinc is stored in specific synaptic vesicles by a class of glutamatergic or “gluzinergic” neurons and is released in an activity‐dependent manner. Because gluzinergic neurons are found almost exclusively in the cerebral cortex and limbic structures, zinc may be critical for normal cognitive and emotional functioning. Conversely, direct evidence shows that zinc might be a relatively potent neurotoxin. Neuronal injury secondary to in vivo zinc mobilization and release occurs in several neurological disorders such as Alzheimer's disease and amyotrophic lateral sclerosis, in addition to epilepsy and ischemia. Thus, zinc homeostasis is integral to normal central nervous system functioning, and in fact its role may be underappreciated. This article provides an overview of zinc neurobiology and reviews the experimental evidence that implicates zinc signals in the pathophysiology of neuropsychiatric diseases. A greater understanding of zinc's role in the central nervous system may therefore allow for the development of therapeutic approaches where aberrant metal homeostasis is implicated in disease pathogenesis. Synapse 63:1029–1049, 2009. © 2009 Wiley‐Liss, Inc.
Improved gap‐repair cloning method that uses oligonucleotides to target cognate sequences
Authors: Kitazono Ana A. 
Published: July 2009

AbstractIn vivo or gap‐repair cloning in yeast has been widely recognized as one of the most efficient means for error‐free construction of plasmids. A protocol is described here that allows easy and efficient gap‐repair cloning that is based on two major modifications. Instead of subcloning, the targeting plasmids are constructed using oligonucleotides from sequences derived from the upstream and downstream sequences of the fragment to be cloned. These sequences are selected so that they can lead to the generation of recognition sites for restriction enzymes that produce blunt ends. Accordingly, this procedure can be applied to any DNA fragment, regardless of whether these include unique restriction sites to generate the targeting ends. With the strategy described, ∼50 bp upstream and downstream targeting ends are generated that allow efficient cloning. Further, to allow easy identification of the positive clones, the annealed oligonucleotides are cloned in frame with the lacZ fragment present in the plasmid. Accordingly, these plasmids produce blue Escherichia coli colonies on media containing X‐Gal. On the other hand, plasmids rescued from yeast that have acquired the respective cognate sequences produce white colonies. To demonstrate the efficiency of the method, this report includes the cloning of fragments harbouring the CDC28, CAK1, CIN5 and CLB2 genes. We found that 30–100% of the analysed plasmids carried the expected inserts. Copyright © 2009 John Wiley & Sons, Ltd.