bluuebunny/crossref_metadata_2025_split huggingface dataset:
PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data
Authors: Hawkins Troy , Chitale Meghana , Luban Stanislav , Kihara Daisuke 
Published: July 2008

AbstractProtein function prediction is a central problem in bioinformatics, increasing in importance recently due to the rapid accumulation of biological data awaiting interpretation. Sequence data represents the bulk of this new stock and is the obvious target for consideration as input, as newly sequenced organisms often lack any other type of biological characterization. We have previously introduced PFP (Protein Function Prediction) as our sequence‐based predictor of Gene Ontology (GO) functional terms. PFP interprets the results of a PSI‐BLAST search by extracting and scoring individual functional attributes, searching a wide range of E‐value sequence matches, and utilizing conventional data mining techniques to fill in missing information. We have shown it to be effective in predicting both specific and low‐resolution functional attributes when sufficient data is unavailable. Here we describe (1) significant improvements to the PFP infrastructure, including the addition of prediction significance and confidence scores, (2) a thorough benchmark of performance and comparisons to other related prediction methods, and (3) applications of PFP predictions to genome‐scale data. We applied PFP predictions to uncharacterized protein sequences from 15 organisms. Among these sequences, 60–90% could be annotated with a GO molecular function term at high confidence (≥80%). We also applied our predictions to the protein–protein interaction network of the Malaria plasmodium (Plasmodium falciparum). High confidence GO biological process predictions (≥90%) from PFP increased the number of fully enriched interactions in this dataset from 23% of interactions to 94%. Our benchmark comparison shows significant performance improvement of PFP relative to GOtcha, InterProScan, and PSI‐BLAST predictions. This is consistent with the performance of PFP as the overall best predictor in both the AFP‐SIG ′05 and CASP7 function (FN) assessments. PFP is available as a web service athttp://dragon.bio.purdue.edu/pfp/. Proteins 2009. © 2008 Wiley‐Liss, Inc.
The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium‐loaded state
Authors: Almog Orna , González Ana , Godin Noa , de Leeuw Marina , Mekel Marlene J. , Klein Daniela , Braun Sergei , Shoham Gil , Walter Richard L. 
Published: July 2008

AbstractWe determine and compare the crystal structure of two proteases belonging to the subtilisin superfamily: S41, a cold‐adapted serine protease produced by Antarctic bacilli, at 1.4 Å resolution and Sph, a mesophilic serine protease produced by Bacillus sphaericus, at 0.8 Å resolution. The purpose of this comparison was to find out whether multiple calcium ion binding is a molecular factor responsible for the adaptation of S41 to extreme low temperatures. We find that these two subtilisins have the same subtilisin fold with a root mean square between the two structures of 0.54 Å. The final models for S41 and Sph include a calcium‐loaded state of five ions bound to each of these two subtilisin molecules. None of these calcium‐binding sites correlate with the high affinity known binding site (site A) found for other subtilisins. Structural analysis of the five calcium‐binding sites found in these two crystal structures indicate that three of the binding sites have two side chains of an acidic residue coordinating the calcium ion, whereas the other two binding sites have either a main‐chain carbonyl, or only one acidic residue side chain coordinating the calcium ion. Thus, we conclude that three of the sites are of high affinity toward calcium ions, whereas the other two are of low affinity. Because Sph is a mesophilic subtilisin and S41 is a psychrophilic subtilisin, but both crystal structures were found to bind five calcium ions, we suggest that multiple calcium ion binding is not responsible for the adaptation of S41 to low temperatures. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Epitaxial electrodeposition of ZnO thin film on GaN(0001) bulk single crystal
Authors: Ichinose Keigo , Yoshida Tsukasa 
Published: July 2008

AbstractGa terminated surface of heavily doped conductive GaN(0001) bulk single crystal was used as a rotating disk electrode (RDE) to electrodeposit ZnO thin film employing reduction of O2. Although the native surface was rather inactive for the reduction of O2, it was activated by dipping in HCl and further by prolonged electrolysis to reduce O2 in a Zn2+ free solution. Koutecky–Levich analysis revealed important kinetic constants, such as the standard charge transfer rate constant (k0) of 2.4 × 10–14 cm s–1 and the transfer coefficient (α) of 0.11 at 70 °C for the reduction of O2 at the most activated GaN(0001). Electrodeposition of ZnO from the bath containing ZnCl2 lead to an epitaxial growth of ZnO in a ZnO[100] ‖ GaN[100] alignment as confirmed from the XRD ω scan with θ adjusted to ZnO(10$ \bar 1 $2). The higher level of epitaxy was achieved for the more active surfaces of GaN as estimated from narrowing of the full width at half maximum (fwhm) of the peaks in the XRD ω ‐scan. Such films were also fully covering the surface of GaN as found in the SEM observation. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrodeposition and impedance spectroscopy characterization of ZnO nanowire arrays
Authors: Tena‐Zaera R. , Elias J. , Lévy‐Clément C. , Mora‐Seró I. , Luo Y. , Bisquert J. 
Published: July 2008

AbstractAn overview of the electrodeposition of ZnO nanowire arrays from the reduction of dissolved molecular oxygen in zinc chloride solutions was reported. In spite of the internal structure of ZnO which favours the anisotropic growth along the [0001] direction, the change in the local composition of the electrolyte around the nanowire during the electrodeposition was proposed as a major parameter to affect the nanowire growth mechanism. The influence of the ratio between the O2 reduction rate and the diffusion of Zn2+ to the cathode was emphasized. Due to the particular morphology of the nanowire arrays, no lateral growth was observed when the reduction of O2 was relatively fast, while the corresponding deposition efficiency was very low. The decrease of the O2 reduction rate resulted in an enhancement of the deposition efficiency. The highest efficiencies (40–55%) were attained by using high chloride concentrations ([KCl] = 3.4 M) resulting not only in an enhancement of the longitudinal growth, but also in a considerable lateral growth. The influence of the electrodeposition conditions on the donor density of ZnO nanowires was investigated by using electrochemical impedance spectroscopy. Donor densities from 5 × 1019 cm–3 to 3 × 1020 cm–3 were obtained for as deposited samples. They decreased to values in the range of 1017–1018 cm–3 after annealing in air (1 hour at 450 °C). (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Synthesis of ZnO nanorod/nanotube arrays formed by hydrothermal growth at a constant zinc ion concentration
Authors: Ndifor‐Angwafor N. George , Riley D. Jason 
Published: July 2008

AbstractIn the hydrothermal growth of macroscopic arrays of 1‐dimensional zinc oxide on seeded substrates the morphology of the individual nanoparticles changes during the reaction, typically nanorods taper to nanotubes for reaction times in excess of 3 hours. In this paper it is demonstrated that by keeping the zinc ion concentration in the reaction solution constant, using potentiostatically controlled dissolution of a sacrificial zinc working electrode, during the precipitation of zinc oxide, it is possible to synthesise arrays of 1‐dimensional zinc oxide particles which have a constant diameter along their entire length, even after 10 hours of growth. These finding indicate the importance of the concentration of zinc ions in determining the morphology of the deposited nanorods. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Analysis of ethylenethiourea as a biomarker in human urine using liquid chromatography/triple quadrupole mass spectrometry
Authors: Lindh Christian H. , Littorin Margareta , Johannesson Gunvor , Jönsson Bo A. G. 
Published: July 2008

AbstractEthylenebisdithiocarbamates (EBDCs) are widely used fungicides. Ethylenethiourea (ETU), the main metabolite and also a contaminant in the commercially available products, is of major toxicological concern. In this study, a method using liquid chromatography/triple quadrupole mass spectrometry (LC/MS/MS) is described for the analysis of ETU in human urine after a single‐step extractive derivatization using pentafluorobenzyl bromide (PFBBr). Analysis was carried out using selected reaction monitoring (SRM) in the positive ion mode. Quantification of ETU was performed using [2H4]‐labeled ETU as internal standard (IS). The limit of detection (LOD) was determined to 0.05 ng/mL. The method was linear in the range 0.1–54 ng/mL urine and had a within‐run precision of 3–5%. The between‐run precision was determined at an average urine level of 2 and 10 ng/mL urine and found to be 9%. The inter‐batch precision was 6%. To validate ETU as a biomarker of exposure, the method was applied in a human experimental oral exposure to the commercial fungicide Ridomil Gold, containing 64% mancozeb and 4.5% ETU. Two healthy volunteers received 8.9 µg/kg body weight (b.w.) Ridomil Gold in a single oral dose followed by urine sampling for 104 h post‐exposure. The elimination half‐life of ETU was estimated to 17–23 h. Copyright © 2008 John Wiley & Sons, Ltd.
Malathion‐induced oxidative stress in human erythrocytes and the protective effect of vitamins C and E in vitro
Authors: Durak Dilek , Uzun Fatma Gökce , Kalender Suna , Ogutcu Ayse , Uzunhisarcikli Meltem , Kalender Yusuf 
Published: July 2008

AbstractMalathion is an organophosphate (OP) pesticide that has been shown to induce oxidative stress in erythrocytes through the generation of free radicals and alteration of the cellular antioxidant defense system. We examined the effect of several different doses of malathion (25, 75, 200 μM), or malathion in combination with vitamin C (VC; 10 μM) or vitamin E (VE; 30 μM), on the levels of malondialdehyde (MDA), and superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) activities in human erythrocytes in vitro. Erythrocytes were incubated under various treatment conditions (malathion alone, vitamins alone, or malathion plus vitamin) at 37°C for 60 min, and the levels of MDA, and SOD, CAT and GPx activities, were determined. Treatment with malathion alone increased the levels of MDA and decreased SOD, CAT, and GPx activities in erythrocytes (P < 0.05). There were no statistical differences among VC‐treated, VE‐treated, or VC + VE‐treated erythrocyes, as compared with nontreated control cells. Treatment of cells with malathion + VC, malathion + VE, or a combination of all three agents prevented malathion‐induced changes in antioxidant enzyme activity and lipid peroxidation. However, this effect was seen only at low concentrations of malathion (25 and 75 μM), and the combination of VC + VE had a more protective effect than VC or VE alone. These results indicated that the presence of vitamins at concentrations that are similar to the levels found in plasma have no effect on malathion‐induced toxicity in erythrocytes at a concentration of malathion (200 μM) that is typically used in pesticides. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
Adrenomedullin reduces antioxidant defense system and enhances kidney tissue damage in cadmium and lead exposed rats
Authors: Yurekli Muhittin , Esrefoglu M. , Ilker Doğru M. , Doğru Arzu , Gul M. , Whidden M. 
Published: July 2008

AbstractAdrenomedullin (AdM) is synthesized and secreted by a number of cells and tissue. AdM is a potent vasodilator but it is also considered a neuromodulator, an angiogenic factor, and a hormone regulator. AdM possess antiapoptotic, antioxidant, and antimicrobial properties. Heavy metals such as cadmium and lead are found widely in the environment and they have important biological functions. Lead (Pb) and cadmium (Cd) can accumulate in the lungs, liver, bone, and kidneys and cause serious organ damage. In the present study, we investigated the effect of AdM, Pb + AdM, and Cd + AdM treatments on superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH‐Px) activities as well as the level of malondialdehyde (MDA) in the kidney. Heavy metal accumulation was determined in kidney with and without AdM infusion and kidney damage was evaluated by light and electron microscopy. Increased heavy metal accumulation was observed in the heavy metal and AdM treated groups. SOD, CAT, GSH‐Px activities, and MDA levels were significantly different in the treatment groups when compared with the control group. Tubular degeneration, necrosis, cell swelling, mononuclear cell infiltration, and degenerated organelles were observed in the kidney following treatment. Therefore, AdM infusion has no beneficial and/or compensatory role in cadmium and lead toxicity in the kidney. We conclude that heavy metal accumulation in the kidney in conjunction with AdM infusion is cytotoxic despite the known beneficial effects of adrenomedullin. © 2008 Wiley Periodicals, Inc. Environ Toxicol, 2009.
Performance analysis of a P2P‐enabled TDD‐CDMA network with intra‐cell spatial resource reuse
Authors: Zhang Yan , Du Lin , Shang Dan , Yang Yuhang 
Published: July 2008

AbstractIn this paper a scheme of intra‐cell spatial resource reuse is proposed for a peer‐to‐peer (P2P) enabled TDD‐CDMA system to increase the system capacity via only software update. On account of the new interference scenario in our scheme, a more accurate model of signal to interference and noise ratio (SINR) is deduced and analyzed instead of using the conventional equation. As demonstrated by our system‐level simulations, the capacity is significantly improved by reusing the same radio resource among different P2P transmitters within a single cellular cell in the spatial domain. Furthermore, we employ critical values of SINR target observed from simulation results to indicate whether the P2P‐enabled system is resource‐restricted or interference‐restricted for a certain application scenario. By means of a hexagon‐padding plan, the relation between co‐channel reuse distance and single‐hop distance is also pointed out to help to apply our scheme to a real implementation. Copyright © 2008 John Wiley & Sons, Ltd.
A Versatile Route for the Synthesis of Nickel Oxide Nanostructures Without Organics at Low Temperature
Authors: Shah MA 
Published: July 2008

Abstract
Nickel oxide nanoparticles and nanoflowers have been synthesized by a soft reaction of nickel powder and water without organics at 100 °C. The mechanism for the formation of nanostructures is briefly described in accordance with decomposition of metal with water giving out hydrogen. The structure, morphology, and the crystalline phase of resulting nanostructures have been characterized by various techniques. Compared with other methods, the present method is simple, fast, economical, template-free, and without organics. In addition, the approach is nontoxic without producing hazardous waste and could be expanded to provide a general and convenient strategy for the synthesis of nanostructures to other functional nanomaterials.
Growth of Y-shaped Carbon Nanofibers from Ethanol Flames
Authors: Cheng Jin , Zou Xiaoping , Zhang Hongdan , Li Fei , Ren Pengfei , Zhu Guang , Su Yi , Wang Maofa 
Published: July 2008

Abstract
Y-shaped carbon nanofibers as a multi-branched carbon nanostructure have potential applications in electronic devices. In this article, we report that several types of Y-shaped carbon nanofibers are obtained from ethanol flames. These Y-shaped carbon nanofibers have different morphologies. According to our experimental results, the growth mechanism of Y-shaped carbon nanofibers has been discussed and a possible growth model of Y-shaped carbon nanofibers has been proposed.
Paracrine action of HO‐1‐modified mesenchymal stem cells mediates cardiac protection and functional improvement
Authors: Zeng Bin , Ren Xiaofeng , Lin Guosheng , Zhu Chengang , Chen Honglei , Yin Jiechao , Jiang Hong , Yang Bo , Ding Danhua 
Published: July 2008

AbstractThe aim has been to determine whether the supernatants of mesenchymal stem cells (MSCs) transfected with adenovirus carrying human heme oxygenase‐1 (hHO‐1) gene protect cardiomyocytes from ischemic injury. We have found that hHO‐1 infected MSCs (hHO‐1‐MSCs) increased expression of hHO‐1 protein. Apoptosis of cultured hHO‐1‐MSCs exposed to hypoxia was suppressed. Several cytokines, including HGF, bFGF, TGF‐β, VEGF and IL‐1β, were produced by hHO‐1‐MSCs, some being significantly enhanced under hypoxia stimulation. Meanwhile, those cytokines reduced caspase‐3 level and activity in cultured adult rat ventricular cardiomyocytes (ARVCs) exposed to hypoxia. Supernatants obtained from hHO‐1‐MSCs improved left ventricular function, limited myocardial infarct size, increased microvessel density, and inhibited apoptosis of cardiomyocytes in rat myocardial infarction. It can be concluded hHO‐1‐modified MSCs prevent myocardial cell injury via secretion of paracrine‐acting mediators.
Effects of thymic polypeptides on the thymopoiesis of mouse embryonic stem cells
Authors: Peng Yanwen , Chen Zhenguang , Yu Weihua , Zhou Qifeng , Xu Lin , Mao Frank Fuxiang , Huang Gang , Zhang Xiuming , Li Shunong , Lahn Bruce T. , Xiang Andy Peng 
Published: July 2008

AbstractThe thymus provides a unique cellular and hormonic microenvironment for the development of immunocompetent T cells. Thymic polypeptides have been widely used clinically for the treatment of tumors, infectious diseases and immune deficiency diseases. They have already shown the ability to stimulate the maturation of hematopoietic stem cells towards the CD3+CD4+ T cell lineage. However, their effects on the thymopoiesis of embryonic stem cells are still unexplored.In this paper, we compared the effects of three thymic polypeptides, thymopentin (TP5), thymosin alpha‐1 (Tα‐1) and thymopeptides on the in vitro thymopoiesis of mouse embryonic stem (ES) cells. Using the embryoid body induction system, we found that both Tα‐1 and thymopeptides effectively induced ES cells to differentiate sequentially into the CD3+ and CD4+/CD8+ T cells. These T cells had T cell receptor (TCR) Vβ gene rearrangement and most were TCRαβ T cells. We also found that the expression of the Notch receptor and its ligands Delta‐like‐1 and Delta‐like‐4 gradually increased during the induction. However, TP5 failed to induce the T cell differentiation of the ES cells.In summary, this is the first report to demonstrate that Tα‐1 can stimulate the T cell early stage differentiation from ES cells using the embryoid body protocol. These findings provide a powerful model for studying T cell development and may open new venues for the clinical application of Tα‐1.
Lysine induces lipid and protein damage and decreases reduced glutathione concentrations in brain of young rats
Authors: Seminotti Bianca , Leipnitz Guilhian , Amaral Alexandre U. , Fernandes Carolina G. , Silva Lucila de Bortoli da , Tonin Anelise Miotti , Vargas Carmen R. , Wajner Moacir 
Published: July 2008

AbstractThe present work investigated the in vitro effects of lysine on important parameters of oxidative stress in cerebral cortex of young rats. Our results show that lysine significantly induced lipid peroxidation, as determined by increase of thiobarbituric acid‐reactive substances and chemiluminescence levels, as well as protein oxidative damage since carbonyl formation and sulfhydryl oxidation were enhanced by this amino acid. Furthermore, the addition of free radical scavengers significantly prevented lysine‐induced lipid oxidative damage, suggesting that free radicals were involved in this effect. Lysine also significantly diminished glutathione levels in cortical supernatants, decreasing, therefore, the major brain antioxidant defense. Finally, lysine markedly oxidized a glutathione commercial solution in a medium devoid of brain supernatants, indicating that it behaved as a direct acting oxidant. The present data indicate that lysine induces oxidative stress in cerebral cortex of young rats. Therefore, it is presumed that this pathomechanism may be involved at least in part in the neurological damage found in patients affected by disorders with hyperlysinemia.
Lingual tonsillectomy: A review of 5 years experience and evolution of surgical technique
Authors: Barakate Michael , Havas Thomas 
Published: July 2008

OBJECTIVESTo assess the indications for lingual tonsillectomy; to report our experience with lingual tonsillectomy, and to present the evolution of our surgical technique.METHODSA review of 5‐years experience from a prospectively maintained database of 28 patients was performed together with a focused review of the international literature. Therapeutic procedures included lingual tonsillectomy with access via the Boyle‐Davis gag or suspended video laryngoscope and with the resection via diathermy, CO2 laser, or microdebrider.RESULTSThe indication for lingual tonsillectomy was upper airways obstruction in 22 patients and recurrent infection in six. The operative time for lingual tonsillectomy ranged from 35 to 80 minutes (mean time, 43 minutes). The perioperative in‐hospital stay ranged from one to three days for 27 patients. All did very well postoperatively.CONCLUSIONLingual tonsillar pathology may cause significant morbidity and is frequently the cause of persisting peripheral obstructive sleep apnea syndrome after adenotonsillectomy. Lingual tonsillectomy performed with video laryngoscopy and microdebrider resection is feasible and safe and provides good results.
Evaluation of meta‐analyses in the otolaryngological literature
Authors: Rudmik Luke R. , Walen Scott G. , Dixon Elijah , Dort Joseph 
Published: July 2008

OBJECTIVETo evaluate the quality of meta‐analyses written on otolaryngological topics and define areas that can be improved upon in future studies.DATA SOURCESMEDLINE (PubMed) and EMBASE databases were searched. The Cochrane database of systematic reviews was excluded, because these meta‐analyses have already been critically evaluated and found to be of high quality.REVIEW METHODSA systematic review of otolaryngological meta‐analyses published between 1997 and 2006 (10 years) was performed in duplicate and independently by two authors. The search included 16 common otolaryngological terms. Inclusion criteria were meta‐analytic methodology, otolaryngological topic, and at least one author from a department of otolaryngology. Fifty‐one articles fulfilled eligibility criteria. In duplicate and independently, two reviewers assessed the quality of eligible metaanalyses using a validated 10‐item index called the Overview Quality Assessment Questionnaire. Using the methods of Spearman, correlation coefficients are reported for associations examined between covariates and the Overall Score Quality.RESULTSThe majority of studies had methodologic flaws (mean score 3.9, scale of 1‐7). Variables predicting higher‐quality meta‐analyses were publication in journals with higher impact factors (P = 0.0007) and authors who previously published metaanalyses (P = 0.0001). Using and reporting about a validity assessment tool needs to be improved upon in future studies.CONCLUSIONThe quality of meta‐analyses on otolaryngological topics is moderate. Future meta‐analyses can be improved upon by following evidence‐based guidelines for the reporting of metaanalyses, which include the use of a validity assessment tool, and consulting with an author familiar with meta‐analysis methodology.