bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative symmetry and chirality—A fast computational algorithm for large structures: Proteins, macromolecules, nanotubes, and unit cells
Authors: Dryzun Chaim , Zait Amir , Avnir David 
Published: May 2011

AbstractSymmetry is one of the most fundamental properties of nature and is used to understand and investigate physical properties. Classically, symmetry is treated as a binary qualitative property, although other physical properties are quantitative. Using the continuous symmetry measure (CSM) methodology one can quantify symmetry and correlate it quantitatively to physical, chemical, and biological properties. The exact analytical procedures for calculating the CSM are computationally expensive and the calculation time grows rapidly as the structure contains more atoms. In this article, we present a new method for calculating the CSM and the related continuous chirality measure (CCM) for large systems. The new method is much faster than the full analytical procedures and it reduces the calculation time dependency fromN! toN2, whereNis the number of atoms in the structure. We evaluate the cost of the applied approximations, estimate the error of the method, and show that deviations from the analytical solutions are within an error of 2%, and in many cases even less. The method is applicable at the moment for the cyclic symmetry point groups—Ci,Cs,Cn, andSn, and therefore it can be used also for chirality measures, which are the minimal of theSnmeasures. We demonstrate the application of the method for large structures across chemistry: proteins, macromolecules, nanotubes, and large unit cells of crystals. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
SDOCK: A global protein‐protein docking program using stepwise force‐field potentials
Authors: Zhang Changsheng , Lai Luhua 
Published: May 2011

AbstractFast Fourier transform (FFT) method limits the forms of scoring functions in global protein‐protein docking. On the other hand, force field potentials can effectively describe the energy hyper surface of biological macromolecules. In this study, we developed a new protein‐protein docking program, SDOCK, that incorporates van der Waals attractive potential, geometric collision, screened electrostatic potential, and Lazaridis‐Karplus desolvation energy into the scoring function in the global searching process. Stepwise potentials were generated from the corresponding continuous forms to treat the structure flexibility. After optimization of the atom solvation parameters and the weights of different potential terms based on a new docking test set that contains 142 cases with small or moderate conformational changes upon binding, SDOCK slightly outperformed the well‐known FFT based global docking program ZDOCK3.0. Among the 142 cases tested, 52.8% gave at least one near‐native solutions in the top 100 solutions. SDOCK was also tested on six blind testing cases in Critical Assessment of Predicted Interactions rounds 13 to 18. In all six cases, the near‐native solutions could be found within the top 350 solutions. Because the SDOCK approach performs global docking based on force‐field potentials, one of its advantages is that it provides global binding free energy surface profiles for further analysis. The efficiency of the program is also comparable with that of other FFT based protein‐protein docking programs. SDOCK is available for noncommercial applications at http://mdl.ipc.pku.edu.cn/cgi‐bin/down.cgi. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Induction of torpor: Mimicking natural metabolic suppression for biomedical applications
Authors: Bouma Hjalmar R. , Verhaag Esther M. , Otis Jessica P. , Heldmaier Gerhard , Swoap Steven J. , Strijkstra Arjen M. , Henning Robert H. , Carey Hannah V. 
Published: May 2011

AbstractMammalian hibernation consists of periods of depressed metabolism and reduced body temperature called “torpor” that are interspersed by normothermic arousal periods. Numerous cellular processes are halted during torpor, including transcription, translation, and ion homeostasis. Hibernators are able to survive long periods of low blood flow and body temperature followed by rewarming and reperfusion without overt signs of organ injury, which makes these animals excellent models for application of natural protective mechanisms to human medicine. This review examines efforts to induce torpor‐like states in non‐hibernating species using pharmacological compounds. Elucidating the underlying mechanisms of natural and pharmacologically induced torpor will speed the development of new clinical approaches to treat a variety of trauma and stress states in humans. J. Cell. Physiol. 227: 1285–1290, 2012. © 2011 Wiley Periodicals, Inc.
The nuclear form of glutathione peroxidase 4 is associated with sperm nuclear matrix and is required for proper paternal chromatin decondensation at fertilization
Authors: Puglisi Rossella , Maccari Irene , Pipolo Simona , Conrad Marcus , Mangia Franco , Boitani Carla 
Published: May 2011

AbstractThe nuclear isoform of the selenoprotein Phospholipid Hydroperoxide Glutathione Peroxidase (nGPx4) is expressed in haploid male germ cells, contains several cysteines and is able to oxidize protein thiols, besides glutathione. In this study we have investigated the subnuclear localization of this isoform in isolated mouse male germ cells at different steps of maturation. Immunoblotting and confocal microscopy analyses of subnuclear fractions showed that nGPx4 is localized to the nuclear matrix together with well known markers of this subnuclear compartment like lamin B and topoisomerase IIβ at all stages of germ cell differentiation. The peculiar nGPx4 distribution was confirmed by both biochemical and morphological analyses of COS‐1 cells overexpressing Flag‐tagged nGPx4. To test the functional role of nGPx4 in the process of chromatin assembly, sperm isolated from the caput and the cauda epididymides of wild‐type (WT) and genetically deficient in nGPx4 (nGPx4‐KO) mice were analyzed in an in vitro chromatin decondensation assay. Results showed that sperm from nGPx4‐KO mice were more prone to decondense than those from WT mice at all stages of epididymal maturation, providing conclusive evidence that nGPx4 is required for a correct sperm chromatin compaction. We next addressed the issue of whether the lack of nGPx4 impacts on early events occurring at fertilization. Indeed, in vitro fertilization experiments showed an acceleration of sperm chromatin dispersion in oocytes fertilized by nGpx4‐KO sperm compared with control. Overall these data indicate that the absence of nGPx4 leads to sperm nuclear matrix/chromatin instability that may negatively affect the embryo development. J. Cell. Physiol. 227: 1420–1427, 2012. © 2011 Wiley Periodicals, Inc.
Anthrax lethal toxin disrupts the endothelial permeability barrier through blocking p38 signaling
Authors: Liu Tiegang , Milia Erica , Warburton Rod R. , Hill Nicholas S. , Gaestel Matthias , Kayyali Usamah S. 
Published: May 2011

AbstractExposure to anthrax causes life‐threatening disease through the action of the toxin produced by the Bacillus anthracis bacteria. Lethal factor (LF), an anthrax toxin component which causes severe vascular leak and edema, is a protease which specifically degrades MAP kinase kinases (MKK). We have recently shown that p38 MAP kinase activation leading to HSP27 phosphorylation augments the endothelial permeability barrier. We now show that treatment of rat pulmonary microvascular endothelial cells with anthrax lethal toxin (LeTx), which is composed of LF and the protective antigen, increases endothelial barrier permeability and gap formation between endothelial cells through disrupting p38 signaling. LeTx treatment increases MKK3b degradation and in turn decreases p38 activity at baseline as well as after activation of p38 signaling. Consequently, LeTx treatment decreases activation of the p38 substrate kinase, MK2, and the phosphorylation of the latter's substrate, HSP27. LeTx treatment disrupts other signaling pathways leading to suppression of Erk‐mediated signaling, but these effects do not correlate with LeTx‐induced barrier compromise. Overexpressing phosphomimicking (pm)HSP27, which protects the endothelial permeability barrier against LeTx, blocks LeTx inactivation of p38 and MK2, but it does not block MKK3b degradation or Erk inactivation. Our results suggest that LeTx might cause vascular leak through inactivating p38‐MK2‐HSP27 signaling and that activating HSP27 phosphorylation specifically restores p38 signaling and blocks anthrax LeTx toxicity. The fact that barrier integrity could be restored by pmHSP27 overexpression without affecting degradation of MKK3b, or inactivation of Erk, suggests a specific and central role for p38‐MK2‐HSP27 in endothelial barrier permeability regulation. J. Cell. Physiol. 227: 1438–1445, 2012. © 2011 Wiley Periodicals, Inc.
Dual‐color fluorescence lifetime correlation spectroscopy to quantify protein–protein interactions in live cell
Authors: Padilla‐Parra Sergi , Audugé Nicolas , Coppey‐Moisan Maïté , Tramier Marc 
Published: May 2011

AbstractDual‐color fluorescence correlation spectroscopy is an interesting method to quantify protein interaction in living cells. But, when performing these experiments, one must compensate for a known spectral bleed through artifact that corrupts cross‐correlation data. In this article, problems with crosstalk were overcome with an approach based on fluorescence lifetime correlation spectroscopy (FLCS). We show that FLCS applied to dual‐color EGFP and mCherry cross‐correlation allows the determination of protein–protein interactions in living cells without the need of spectral bleed through calibration. The methodology was validated by using EGFP‐mCherry tandem in comparison with coexpressed EGFP and mCherry in live cell. The dual‐color FLCS experimental procedure where the different laser intensities do not have to be controlled during experiment is really very helpful to study quantitatively protein interactions in live sample. Microsc. Res. Tech. 2011. © 2011 Wiley‐Liss, Inc.
Effect of alveolex on the bone defects repair stimulated by rhBMP‐2: Histomorphometric study
Authors: Pereira Nathalia Terra , Issa João Paulo Mardegan , Nascimento Cássio Do , Pitol Dimitrius Leonardo , Ervolino Edilson , Cunha Marcelo Rodrigues Da , Pedrazzi Vinícius 
Published: May 2011

AbstractOBJECTIVE:The aim of this study was to evaluate histomorphometrically the effect of alveolex (Propolis 10%) on the repair of bone cavities in the calvaria of rats.MATERIALS AND METHODS:A 5 mm diameter bone defect was made in the calvaria of male Wistar rats using the drill‐type trephine. The defects were filled with rhBMP‐2+Alveolex, rhBMP‐2, Alveolex, or coagulum. Twenty‐eight animals with seven subjects on each were sacrificed 30 days after surgery and samples were fixed and embedded in paraffin. Histological sections stained by HE (hematoxylin and eosin) were obtained from the calvaria bone defect and analyzed by a differential point‐counting method.RESULTS:Group I and II, rhBMP‐2+Alveolex and rhBMP‐2, respectively, presented higher levels of newly formed bone than other groups (P < 0.001). There were not significant differences between groups I and II (P > 0.05). In addition, there was not significant difference between groups III and IV, Control‐Coagulum and Alveolex, respectively (P > 0.05).CONCLUSION:Alveolex has increased the bone repair in calvaria defects of rats when associated to rhBMP‐2, however without significant differences for rhBMP‐2 isolated group; Alveolex isolated group showed the lowest levels of newly formed bone with no significant differences to coagulum group (control). Microsc. Res. Tech. 2012. © 2011 Wiley Periodicals, Inc.
In vitro evaluation of the microbial contamination on new toothbrushes: A preliminary study
Authors: Do Nascimento Cássio , Scarabel Thayla Tessa , Miani Paola Kirsten , Watanabe Evandro , Pedrazzi Vinícius 
Published: May 2011

AbstractObjective: The presence and survival of microorganisms on toothbrush bristles might play a role on the etiology of oral infections. The aim of this in vitro study was to evaluate the presence of bacterial contamination on new toothbrushes before oral contact. Materials and methods: Forty toothbrushes from five different manufacturers were used in this experimental study. Each manufacturer was divided according to conventional local of obtaining: industry, drugstore, market, and perfumery. The toothbrush heads were completely immersed into tubes containing 5.0 mL of sterile peptonated water (dilution 1:10). A group of eight tubes containing the sterile solution was used as control. After 21 days of anaerobic incubation, occurrence of contamination was visually evaluated and confirmed by light microscopy. Results: Bacterial growth in the medium, indicative of bristles contamination, was found in a total of 19 out of 40 samples (47.5%) evaluated: 6 out of 14 samples (42.85%) from industry group, 4 out of 8 samples (50.0%) from drugstore, 5 out of 10 samples (50.0%) from market, and 4 out of 8 samples (50.0%) from perfumery. Only the toothbrushes with bristles coated with chlorhexidine did not show contamination. The Gram‐negative sporulating bacilli were the most prevalent form recovered. Conclusions: Except for chlorhexidine group, bacterial growth was observed in all groups evaluated irrespective local of obtaining. Microsc. Res. Tech., 2012. © 2011 Wiley Periodicals, Inc.
Application of microscopy in authentication of valuable Chinese medicine i—Cordyceps sinensis, its counterfeits, and related products
Authors: Au Dawn , Wang Lijing , Yang Dajian , Mok Daniel K.W. , Chan Albert S.C. , Xu Hongxi 
Published: May 2011

AbstractLight and polarized microscope was applied to authenticate 32 Cordyceps and 6 artificial counterfeits and 8 fermented Cordyceps as well as 7 Cordyceps capsules available in Hong Kong markets. Results showed that transverse sections of stroma and powder of larvae can be used to differentiate C. sinensis from its counterfeits. The fermented Cordyceps are in powder form. Among the eight fermented Cordyceps collected, half of them were pure; three were a mixture of fermented Cordyceps and soya beans; one was a mixture of unknown plant tissues and soya beans. For the seven Cordyceps capsules, the powders of five samples were a mixture of fermented Cordyceps and soya beans; the powders of other two were a mixture of C. sinensis stroma powder and fermented Cordyceps. The study indicated that the microscopy is an unambiguous method that requests fewer sample for the authentication of valuable Chinese medicine—C. sinensis and its related products. Microsc. Res. Tech. 2012. © 2011 Wiley Periodicals, Inc.
An imaging technique using rotational polarization microscopy for the microstructure analysis of carbon/carbon composites
Authors: Miaoling Li , Lehua Qi , Hejun Li 
Published: May 2011

AbstractA novel image analysis technique was proposed for microstructure investigation of carbon/carbon (C/C) composites. The rotational polarization microscopy was developed to meet the special imaging requirements. The samples of C/C composites were observed in reflection polarized light microscope, where the analyzer was rotated instead of the stage, and the polarizer was taken out. The bireflectance of like‐graphite negative uniaxial crystal was analyzed. It was the theoretic foundation of image collection and data processing. The analyzer was rotated through 36 × 10° intervals without any movement of the specimen. The polished cross‐section of C/C composites took micrographs at each analyzer orientation. All image data collected from the same field of view were processed by image registration and image fusion. The synthesized images were obtained by calculating the maximum and minimum gray values and their differences at each point of the million pixels at 18 orientations of the analyzer. They are unique and quite reliable to be applied to analyze the microstructure of C/C composites. Subsequently, image segmentation was performed, and the feature parameters of each component were calculated. Good agreement was found between the results from image analysis and experimental data. Microsc. Res. Tech., 2012. © 2011 Wiley Periodicals, Inc.
New insights into the synthesis and characterization of 2‐methoxy‐3‐alkylpyrazines and their deuterated isotopologues
Authors: Schmarr H.‐G. , Sang W. , Ganß S. , Koschinski S. , Meusinger R. 
Published: May 2011

AbstractA previously described synthetic route for preparation of 2‐methoxy‐3‐alkylprazines (MPs) based on condensation of glyoxal with an α‐amino acid amide, followed by methylation with iodomethane yields 3‐alkyl‐1‐methyl‐1H‐pyrazin‐2‐ones (N‐methyl derivatives), rather than the designated 2‐methoxy‐3‐alkylpyrazines (O‐methyl derivatives). Despite similar nuclear magnetic resonance and mass spectral properties, gas chromatographic (GC) retention indices differ significantly, indicating chemical difference. With the example of 3‐sec‐butyl‐1‐methyl‐1H‐pyrazin‐2‐one and its 3‐sec‐butyl‐1‐[2H3]methyl‐1H‐pyrazin‐2‐one isotopologue, the position of the methyl group introduced could be assigned unambiguously, using heteronuclear multiple bond correlation (HMBC) NMR experiments. For future characterization, the spectroscopic (NMR, EI+MS) as well as GC retention index data on two stationary phases of the most aroma relevant MPs and their deuterated isotopologues are summarized. Copyright © 2011 John Wiley & Sons, Ltd.
A new interpretation of stomatogenesis in a peritrich ciliate: Using Campanella umbellaria as a model system
Authors: Wang Hongliang , Shi Xinlu , Clamp John C. , Liu Guijie , Wu Shu , Ma Limin 
Published: May 2011

AbstractThe process of stomatogenesis in peritrich ciliates is still incompletely understood. Previous studies on the stomatogenesis of four species of peritrichs, Telotrochidium sp., Carchesium polypinum, Opercularia coarctata, and Astylozoon pyriforme conflict with one another in some cases and omit details of events in others. We described the entire process of stomatogenesis in the peritrich ciliate Campanella umbellaria (C. umbellaria) using an improved method of staining with protargol. Our results disagree with some previous studies with regard to the formation of some rudimentary structures, reorganization of the parental haplokinety, formation of new germinal rows, and separation of daughter oral complexes. The pattern of stomatogenesis characteristic of peritrichs is compared to the stomatogenetic patterns of three other oligohymenophorean subclasses and a hypothesis about the evolution of stomatogenesis in the class Oligohymenophorea is offered. Details of stomatogenesis need to be described and verified in a greater variety of peritrichs to clarify possible differences between taxa and make it possible to relate stomatogenesis to evolution within the subclass Peritrichia. Ultrastructural studies are the next step in description of morphogenetic processes in peritrichs, and characteristics of C. umbellaria make it a useful model for this work. J. Morphol., 2011. © 2011 Wiley‐Liss, Inc.
Prediction and identification‐based prediction of Chinese hepatitis C viral‐specific cytotoxic T lymphocyte epitopes
Authors: Duan Li , Lei Pan , Yumei Xie , Xiaoping Xue , Futao Zhao , Li Ma , Xin Wei , Jiuping Wang , Xuefan Bai , Zhansheng Jia 
Published: May 2011

AbstractCytotoxic T lymphocytes (CTLs) play a critical role in the host immune response to infection by the Hepatitis C Virus (HCV). In the current study, a number of HCV CTL epitopes that represent the HLA polymorphisms found in the majority of Chinese people were predicted based on genomic and bioinformatic approaches. The predicted epitopes were evaluated for validity by examining the peptide‐binding affinity for MHC class I molecules, the stability of peptide–MHC complexes, and frequencies of IFN γ‐positive T cells. Among the predicted epitope peptides, HLA‐A2 restricted epitopes [NS4B (1793–1801) SMMAFSAAL] and HLA‐B7 restricted epitopes [P7 (774–782) AAWYIKGRL] were able to induce high frequencies of IFN γ‐producing T cells, and the specific CTLs for other epitopes were not detected in peripheral blood lymphocytes from patients with HCV. Moreover, NS4B (1793–1801) exhibited high binding affinity for HLA‐A2 molecules, and its stability of peptide–MHC class I complexes was sufficient, indicating that the high binding affinity for MHC class I molecules is an important factor for immunogenicity. Primary analyses of the immunogenicity of predicted epitopes, such as in the current study, will contribute to the future design of an efficient vaccine that will be able to induce vigorous, sustainable, and broad HCV‐specific CTL responses for the Chinese population. J. Med. Virol. 83:1315–1320, 2011. © 2011 Wiley‐Liss, Inc.
Human papillomavirus type distribution in vulval intraepithelial neoplasia determined using PapilloCheck DNA Microarray
Authors: Bryant Dean , Rai Nirmala , Rowlands Gareth , Hibbitts Sam , Jones Joanne , Tristram Amanda , Fiander Alison , Powell Ned 
Published: May 2011

AbstractVulval intraepithelial neoplasia is a precursor of vulval carcinoma, and is frequently associated with human papillomavirus (HPV) infection. Estimates of HPV prevalence in vulval intraepithelial neoplasia vary widely in the UK. The objective of this study was to assess HPV infection in a sample of women with vulval intraepithelial neoplasia, confirmed histologically, and determine the proportion of disease associated with HPV types targeted by prophylactic HPV vaccines. HPV infection was assessed in biopsies from 59 patients using the Greiner Bio‐One PapilloCheck® DNA chip assay. Valid results were obtained for 54 cases. HPV infection was present in 43 of the 54 cases (79.6%: 95% CI 67.1–88.2%). The most common HPV types were HPV 16 (33/54: 61.1%), HPV 33 (8/54: 14.8%), HPV 6 (5/54: 9.3%), and HPV 42 (3/54: 5.6%). The mean age of HPV positive women was significantly less than the mean age of HPV negative women. This is the largest UK series of vulval intraepithelial neoplasia in which HPV type has been investigated, and 34/54 (63.0%, 95% CI: 49.6–78.6%) cases were associated with HPV 16/18, which are targeted by current prophylactic HPV vaccines. J. Med. Virol. 83:1358–1361, 2011. © 2011 Wiley‐Liss, Inc.