bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting structurally conserved contacts for homologous proteins using sequence conservation filters
Authors: Michino Mayako , Brooks Charles L. 
Published: April 2009

AbstractThe prediction of intramolecular contacts has a useful application in predicting the three‐dimensional structures of proteins. The accuracy of the template‐based contact prediction methods depends on the quality of the template structures. To reduce the false positive predictions associated with using the entire set of template‐derived contacts, we develop selection filters that use sequence conservation information to predict subsets of contacts more likely to be structurally conserved between the template and the target. The method is developed specifically for protein families with few available templates such as the G protein‐coupled receptor (GPCR) family. It is validated on a test set of 342 template‐target pairs from three protein families, and applied to one template‐target pair from the GPCR family. We find that the filter selection method increases the accuracy of contact prediction with sufficient coverage for structure prediction. Proteins 2009. © 2009 Wiley‐Liss, Inc.
A distance‐dependent atomic knowledge‐based potential and force for discrimination of native structures from decoys
Authors: Mirzaie Mehdi , Eslahchi Changiz , Pezeshk Hamid , Sadeghi Mehdi 
Published: April 2009

AbstractThe purpose of this article is to introduce a novel model for discriminating correctly folded proteins from well designed decoy structures using mechanical interatomic forces. In our model, we consider a protein as a collection of springs and the force imposed to each atom is calculated. A potential function is obtained from statistical contact preferences within known protein structures. Combining this function with the spring equation, the interatomic forces are calculated. Finally, we consider a structure and define a score function on the 3D structure of a protein. We compare the force imposed to each atom of a protein with the corresponding atom in the other structures. We then assign larger scores to those atoms with lower forces. The total score is the sum of partial scores of atoms. The optimal structure is assumed to be the one with the highest score in the data set. To evaluate the performance of our model, we apply it on several decoy sets. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Optimizing the test power for a radiation retention model in the human body
Authors: Amo‐Salas M. , López‐Fidalgo J. , Rodríguez‐Díaz J. M. 
Published: April 2009

AbstractThe model that describes the retention in lungs of radioisotope particles is studied in this paper, considering the situation of an accident in facilities that handle radioactive materials. Optimal times to make the bioassays are computed for D‐ and c‐optimality, and efficiencies for the computed designs are provided and compared. Moreover, the test power is checked by means of simulations and replications. After that the inverse of the Fisher information matrix is compared to an estimation of the covariance matrix of the parameters. Finally, a study taking into consideration the randomness of the designs space is performed. Copyright © 2009 John Wiley & Sons, Ltd.
Dependence of the wittig reaction mechanism on the environment and on the substituents at the aldehyde group and at the phosphonium ylide
Authors: Alagona Giuliano , Ghio Caterina 
Published: April 2009

AbstractThe B3P86/6‐31G* mechanistic results for the Wittig reaction of acetaldehyde, CH3CHO, in vacuo and in tetrahydrofuran (THF) solution in the IEF‐PCM framework, with an unsubstituted trimethylphosphonium or triphenylphosphonium ylide, that is Me3PCH2 or Ph3PCH2, have been compared to those recently obtained at the same levels for the reaction of Ph3PCH2 with a bulky chiral aldehyde, (2S,3R)‐2,4‐dimethyl‐3‐pyrrol‐1‐yl‐pentanal [TCA (DOI: 10.1007/s00214‐009‐0521‐4)], here named sys for short. The two model systems show distinct, but similar, behaviors that however differ from the large system one. In particular, betaine‐type intermediates are not located in vacuo when Me3PCH2 is used, while only a gauche betaine is obtained using Ph3PCH2; the relevant barriers are anyway smaller than those found for sys. Conversely, in THF, the concerted and stepwise mechanisms are both represented and show TS1/TSb barriers, which are negligibly small for sys. Thus, in contrast to assessed literature, models with methyl groups in place of phenyl rings and branched aldehyde chains show a different behavior from realistic systems and prevent inferring general rules from their use, suggesting to resort to Ph3PCH2 whose results in vacuo and in THF are closer to sys. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Sample size for two‐stage studies with maintenance therapy
Authors: Feng Wentao , Wahed Abdus S. 
Published: April 2009

AbstractAn adaptive treatment strategy (ATS) is defined as a sequence of treatments and intermediate responses. ATS' arise when chronic diseases such as cancer and depression are treated over time with various treatment alternatives depending on intermediate responses to earlier treatments. Clinical trials are often designed to compare ATSs based on appropriate designs such as sequential randomization designs. Although recent literature provides statistical methods for analyzing data from such trials, very few articles have focused on statistical power and sample size issues. This paper presents a sample size formula for comparing the survival probabilities under two treatment strategies sharing same initial, but different maintenance treatment. The formula is based on the large sample properties of inverse‐probability‐weighted estimator. Simulation study shows strong evidence that the proposed sample size formula guarantees desired power, regardless of the true distributions of survival times. Copyright © 2009 John Wiley & Sons, Ltd.
Quantitative defects management in iterative development with BiDefect
Authors: Gou Lang , Wang Qing , Yuan Jun , Yang Ye , Li Mingshu , Jiang Nan 
Published: April 2009

AbstractIterative development methodology has been widely adopted in recent years since it is flexible and capable of dealing with requirement volatility. However, how to quantitatively manage iterative projects, and in particular, how to quantitatively manage defects across multiple iterations, remains a challenging issue. In this article, we identify three main challenges of quantitative defects management in iterative development in a leading Chinese telecommunications company (named ZZNode). The three challenges are: identifying appropriate ‘control points’ in each iteration, selecting appropriate measures and corresponding measurement methods, and determining the ‘sweet spot’ amount of effort for performing testing and defect‐fixing activities. We propose a process performanceBaselines basediterationDefects management (BiDefect) method to address the three challenges. We also report an industrial experience where several iterative development projects of ZZNode successfully applied the BiDefect method in initial estimating, analyzing, re‐estimating, and controlling number of defects and defect detecting/fixing effort. In addition, we provide the evaluation of using BiDefect method, and discuss the benefits and lessons learned from BiDefect and its application. Copyright © 2009 John Wiley & Sons, Ltd.
Polycyclic aromatic hydrocarbons from diesel emissions exert proallergic effects in birch pollen allergic individuals through enhanced mediator release from basophils
Authors: Lubitz Stefanie , Schober Wolfgang , Pusch Gudrun , Effner Renate , Klopp Norman , Behrendt Heidrun , Buters Jeroen T. M. 
Published: April 2009

AbstractBackground:Diesel exhaust particles (DEPs) act as adjuvants in the immune system and contribute to the increased prevalence and morbidity of asthma and allergic rhinitis. Polycyclic aromatic hydrocarbons (PAHs) are major components of DEPs, which may be involved in the induction and enhancement of proallergic processes. In this study we explored adjuvant effects of DEP‐PAHs on activation parameters of human basophils, fostering allergic inflammation through the release of preformed or granule‐derived mediators.Methods:Heparinized blood samples from birch pollen allergic and control donors were stimulated with Bet v 1, the major allergen of birch pollen grains, alone or together with a mixture of 16 environmental prominent PAHs (EPA‐PAH standard). Flow cytometric analysis was performed for quantitative determination of PAH‐enhanced basophil activation. To assess direct PAH effects on basophils, enriched cultures from both donor groups were exposed to benzo[a]pyrene (B[a]P) or phenanthrene (Phe), two major DEP‐PAHs, with and without allergen. Supernatants were assayed for IL‐4 and IL‐8 secretion and histamine release by means of ELISA.Results:At environmental relevant exposure levels EPA‐PAH standard synergized with antigen and significantly enhanced basophil activation of all birch pollen allergic individuals up to 95%. Single PAHs significantly drove IL‐8 secretion from sensitized basophils of all patients tested, and there was no further enhancement by addition of rBet v 1. B[a]P and Phe also significantly induced IL‐4 secretion, a key factor for Th2 development, from purified sensitized basophils in the absence of antigen suggesting an adjuvant role of DEP‐PAHs in allergic sensitization. None of the basophil samples from healthy controls showed any PAH effect on mediator release.Conclusion:DEP‐PAHs exert proallergic effects on sensitized basophils in an allergen independent fashion, suggesting a potential role of these pollutants for the allergic breakthrough in atopic individuals, who have not developed an allergic disease yet. © 2009 Wiley Periodicals, Inc. Environ Toxicol, 2010.
[Gd(OH)(H2O)(b18c6)]I(I3)(CH3CN), a New Cationic In‐cavity Complex with Iodide and Triiodide as Anions
Authors: Walbaum Christine , Pantenburg Ingo , Meyer Gerd 
Published: April 2009

AbstractSingle crystals of [Gd(OH)(H2O)(b18c6)]I(I3)(CH3CN) were obtained from an acetonitrile solution of GdI3, I2 and benzo‐18‐crown‐6. The crystal structure (monoclinic, P21/a (no. 14), Z = 4, a = 1233.8(1) pm, b = 1925.0(2) pm, c = 1252.3(1) pm, β = 104.375(7)°) contains hydroxide bridged cationic dimers and iodide as well as triiodide as anions.
Ag9I(GeO4)2 – Containing Two‐dimensionally Linked [IAg12] Metallo Complexes
Authors: Pitzschke Dragan , Curda Jan , Jansen Martin 
Published: April 2009

AbstractAg9I(GeO4)2 was obtained for the first time by reacting a stoichiometric mixture of Ag2O, AgI, and GeO2, at elevated oxygen pressures, adding a small portion of distilled water. The synthesis was done at 480 °C and 110 MPa of oxygen pressure. It crystallizes in space group C2/m, with the unit cell dimensions a = 17.3736(9) Å, b = 6.9177(4) Å, c = 5.7176(3) Å, β = 105.501(3)°, V = 662.18(6) Å3, and Z = 2. The structure refinement was based on 638 independent reflections and resulted in R1 = 6.26 %. The crystal structure consists of isolated (GeO4)4– ions and [IAg12] metallo complexes, the latter are interconnected through each two common edges and corners corresponding to [IAg6/1Ag6/2], thus forming infinite layers within the (100) plane. The Ag/I slabs are stacked perpendicular to the a‐axis with an interlayer distance of about 3.4 Å. The (GeO4)4– anions are located in the gaps between the silver iodide layers. According to the results of impedance measurements, Ag9I(GeO4)2 is a good silver ion conductor. The compound shows an increase in the ionic conductivity in the temperature range of 30 to 310 °C, and has a silver ion conductivity of 1.1 × 10–3 Ω–1 cm–1 at room temp. The activation energy for silver ion conduction is 0.35 eV, in the temperature range from 25 to 190 °C.
Development of a field‐friendly technique for fecal steroid extraction and storage using the African wild dog (Lycaon pictus)
Authors: Santymire R. M. , Armstrong D. M. 
Published: April 2009

AbstractHormonal analysis provides information about wildlife populations, but is difficult to conduct in the field. Our goal was to develop a rapid and effective field method for fecal steroid analysis by comparing: (1) three extraction methods (laboratory (LAB), homogenize (HO) and handshake (HS)) and (2) two storage methods (solid‐phase extraction (SPE) tubes vs. plastic tubes (PT)). Samples (n=23) from captive African wild dogs (Lycaon pictus) were thoroughly mixed, three aliquots of each were weighed (∼0.5 g) and 5 ml of 90% ethanol was added. For LAB, samples were agitated (mixer setting 60; 30 min), centrifuged (1,500 rpm; 20 min) and poured into glass tubes. Or aliquots were HO (1 min) or HS (1 min) and poured through filter paper into glass tubes. Samples were split, analyzed for corticosterone (C) and testosterone (T) metabolites using enzyme immunoassays or stored in SPE or PT. Samples were stored (room temperature) for 30, 60 or 180 days, reconstituted in buffer and analyzed. Mean C and T recoveries of HO were greater (P=0.03) than HS compared with LAB, which was similar to HO (P>0.05). After 30 days <21% of C and T was recovered from SPE, but ∼100% of each was recovered from HO‐PT and HS‐PT. Similarly, after 60 and 180 days, ∼100% of C and T was recovered from HO‐PT and HS‐PT. Results demonstrated that, for C and T, HO was more comparable (P<0.001) to LAB than HS and PT storage was more efficient than SPE (P<0.001). Zoo Biol 29:289–302, 2010. © 2009 Wiley‐Liss, Inc.
Value of Multidetector Row CT in the Assessment of Longitudinal Extension of Cholangiocarcinoma—Correlation Between MDCT and Microscopic Findings
Authors: Senda Yoshiki , Nishio Hideki , Oda Koji , Yokoyama Yukihiro , Ebata Tomoki , Igami Tsuyoshi , Sugiura Teiichi , Shimoyama Yoshie , Nimura Yuji , Nagino Masato 
Published: April 2009

AbstractBackgroundA few authors have reported the value of multidetector row CT (MDCT) for evaluating the longitudinal extent of cholangiocarcinoma. They have not focused on CT attenuation of a tumor and actual tumor extent along the bile ducts. We designed the present study to analyze attenuation.MethodsBetween January 2003 and July 2005, 113 consecutive patients with cholangiocarcinoma underwent a surgical resection following MDCT. Of these MDCT studies, 73 (perihilar cholangiocarcinoma, n = 62; middle and distal cholangiocarcinoma, n = 11) were suitable for analysis, and the patients were enrolled in the study. Patients were divided according to tumor hypoattenuation and hyperattenuation on MDCT. Histologic differentiation, desmoplastic reaction, and vascular density were microscopically compared with the tumor attenuation to differentiate the characteristics of the attenuation. The extent of cancer along the bile duct diagnosed by MDCT was compared with the actual extent determined by the microscopic findings.ResultsHyperattenuated tumor was observed in 40 patients. There was no difference in histologic differentiation, desmoplastic reaction, or vascular density between the hyperattenuated and hypoattenuated cholangiocarcinomas. Neither the proximal nor the distal borders between the normal and thickened bile duct wall could be determined in the 33 patients with hypoattenuated tumor; in contrast, an accurate assessment of extent of tumor was obtained in 76% of the proximal borders and 82% of the distal borders in the 40 patients with hyperattenuated tumor.ConclusionsAlthough the cause of the difference between the hyperattenuated and hypoattenuated cholangiocarcinoma still is unclear, MDCT can be an alternative to direct cholangiography in selected patients with hyperattenuated cholangiocarcinoma.
Early‐onset hyperargininaemia: A severe disorder?
Authors: Schiff M. , Benoist J.‐F. , Cardoso M. L. , Elmaleh‐Bergès M. , Forey P. , Santiago J. , Ogier de Baulny H. 
Published: April 2009

SummaryHyperargininaemia is a rare inborn error of metabolism due to a defect in the final step of the urea cycle. Infantile onset is the most common presentation with recurrent vomiting and psychomotor delay associated with spastic paraparesis; chronic hyperammonaemia is often overlooked. Neonatal and early‐onset presentations are very uncommon and their clinical course not well‐described. We report on a 3‐week‐old hyperargininaemic girl who presented with neurological deterioration associated with liver failure and 47‐day ammonia intoxication before diagnosis could be made and treatment started. Despite appropriate but delayed treatment, our patient exhibited severe psychomotor delay at age 1 year. Conclusion Early identification and management of this rare but potentially treatable affection is crucial as delayed management may result in poor neurological outcome.
New Method to Prepare Mitomycin C Loaded PLA-Nanoparticles with High Drug Entrapment Efficiency
Authors: Hou Zhenqing , Wei Heng , Wang Qian , Sun Qian , Zhou Chunxiao , Zhan Chuanming , Tang Xiaolong , Zhang Qiqing 
Published: April 2009

Abstract
The classical utilized double emulsion solvent diffusion technique for encapsulating water soluble Mitomycin C (MMC) in PLA nanoparticles suffers from low encapsulation efficiency because of the drug rapid partitioning to the external aqueous phase. In this paper, MMC loaded PLA nanoparticles were prepared by a new single emulsion solvent evaporation method, in which soybean phosphatidylcholine (SPC) was employed to improve the liposolubility of MMC by formation of MMC–SPC complex. Four main influential factors based on the results of a single-factor test, namely, PLA molecular weight, ratio of PLA to SPC (wt/wt) and MMC to SPC (wt/wt), volume ratio of oil phase to water phase, were evaluated using an orthogonal design with respect to drug entrapment efficiency. The drug release study was performed in pH 7.2 PBS at 37 °C with drug analysis using UV/vis spectrometer at 365 nm. MMC–PLA particles prepared by classical method were used as comparison. The formulated MMC–SPC–PLA nanoparticles under optimized condition are found to be relatively uniform in size (594 nm) with up to 94.8% of drug entrapment efficiency compared to 6.44 μm of PLA–MMC microparticles with 34.5% of drug entrapment efficiency. The release of MMC shows biphasic with an initial burst effect, followed by a cumulated drug release over 30 days is 50.17% for PLA–MMC–SPC nanoparticles, and 74.1% for PLA–MMC particles. The IR analysis of MMC–SPC complex shows that their high liposolubility may be attributed to some weak physical interaction between MMC and SPC during the formation of the complex. It is concluded that the new method is advantageous in terms of smaller size, lower size distribution, higher encapsulation yield, and longer sustained drug release in comparison to classical method.
On the Enhanced Antibacterial Activity of Antibiotics Mixed with Gold Nanoparticles
Authors: Burygin GL , Khlebtsov BN , Shantrokha AN , Dykman LA , Bogatyrev VA , Khlebtsov NG 
Published: April 2009

Abstract
The bacterial action of gentamicin and that of a mixture of gentamicin and 15-nm colloidal-gold particles onEscherichia coli K12 was examined by the agar-well-diffusion method, enumeration of colony-forming units, and turbidimetry. Addition of gentamicin to colloidal gold changed the gold color and extinction spectrum. Within the experimental errors, there were no significant differences in antibacterial activity between pure gentamicin and its mixture with gold nanoparticles (NPs). Atomic absorption spectroscopy showed that upon application of the gentamicin-particle mixture, there were no gold NPs in the zone of bacterial-growth suppression in agar. Yet, free NPs diffused into the agar. These facts are in conflict with the earlier findings indicating an enhancement of the bacterial activity of similar gentamicin–gold nanoparticle mixtures. The possible causes for these discrepancies are discussed, and the suggestion is made that a necessary condition for enhancement of antibacterial activity is the preparation of stable conjugates of NPs coated with the antibiotic molecules.
What’s in an intron? CCN1 mRNA splicing in cancer
Authors: Leask Andrew 
Published: April 2009

AbstractThe CCN family of matricellular signaling regulators shares a common domain structure. Variants of individual CCN proteins exist, which contain different combinations of these domains. Although mRNA splicing is likely to play a key role on CCN biology, this hypothesis has not been thoroughly tested. In a recent report, Hirschfeld and colleagues (Cancer Res 69:2082‐90, 2009), show that CCN1 (cyr61) mRNA is normally present in a form in which intron 3 is retained. In cancers, or upon hypoxia, intron 3 is removed resulting in the appearance of CCN1 protein. The significance of this paper is discussed.
Induction of genomic instability in cultured human colon epithelial cells following exposure to isocyanates
Authors: Mishra Pradyumna Kumar , Bhargava Arpit , Raghuram Gorantla Venkata , Jatawa Suresh Kumar , Akhtar Nabila , Khan Saba , Tiwari Archana , Maudar Kewal Krishan 
Published: April 2009

AbstractThe toxic response of cultured human colon epithelial‐FHC cells to methyl isocyanate was investigated with regard to genomic instability. Qualitative and quantitative assessments of the extent of phosphorylation of DNA damage signaling factors such as ATM, γH2AX and p53, was increased in treated cells compared to controls. At the same time, many treated cells were arrested at the G2/M phase of the cell cycle, and had an elevated apoptotic index and increased inflammatory cytokine levels. Cytogenetic analyses revealed varied chromosomal anomalies, with abnormal expression of pericentrin protein. Analysis through ISSR PCR demonstrated increased microsatellite instability. The results imply that isocyanates can cause genomic instability in colonocytes.
Estradiol promotes proliferation of dopaminergic precursors resulting in a higher proportion of dopamine neurons derived from mouse embryonic stem cells
Authors: Díaz Néstor F. , Díaz‐Martínez Néstor E. , Camacho‐Arroyo Ignacio , Velasco Iván 
Published: April 2009

AbstractEstradiol protects dopamine neurons of the substantia nigra from toxic insults. Such neurons succumb in Parkinson's disease; one strategy for restoring dopamine deficiency is cell therapy with neurons differentiated from embryonic stem cells. We investigated the effects of 17β‐estradiol on dopaminergic induction of embryonic stem cells using the 5‐stage protocol. Cells were incubated with different steroid concentrations during the proliferation (stage 4) or differentiation (stage 5) phases. Estradiol added at nM concentrations only during stage 4 increases the proliferation of dopaminergic precursors expressing Lmx1a, inducing a higher proportion of dopamine neurons at stage 5. These actions were mediated by activation of estrogen receptors, because co‐incubation of cells with estradiol and ICI 182,780 completely abolished the positive effect on both proliferation of committed precursors, and subsequent differentiation to dopaminergic neurons. Our results suggest that estradiol should be useful in producing higher proportions of dopamine neurons from embryonic stem cells aimed for treating Parkinson's disease.