bluuebunny/crossref_metadata_2025_split huggingface dataset:
Connectivity and binding‐site recognition: Applications relevant to drug design
Authors: Illingworth Christopher J. R. , Scott Paul D. , Parkes Kevin E. B. , Snell Christopher R. , Campbell Matthew P. , Reynolds Christopher A. 
Published: May 2010

AbstractHere, we describe a family of methods based on residue–residue connectivity for characterizing binding sites and apply variants of the method to various types of protein–ligand complexes including proteases, allosteric‐binding sites, correctly and incorrectly docked poses, and inhibitors of protein–protein interactions. Residues within ligand‐binding sites have about 25% more contact neighbors than surface residues in general; high‐connectivity residues are found in contact with the ligand in 84% of all complexes studied. In addition, a k‐means algorithm was developed that may be useful for identifying potential binding sites with no obvious geometric or connectivity features. The analysis was primarily carried out on 61 protein–ligand structures from the MEROPS protease database, 250 protein–ligand structures from the PDBSelect (25%), and 30 protein–protein complexes. Analysis of four proteases with crystal structures for multiple bound ligands has shown that residues with high connectivity tend to have less variable side‐chain conformation. The relevance to drug design is discussed in terms of identifying allosteric‐binding sites, distinguishing between alternative docked poses and designing protein interface inhibitors. Taken together, this data indicate that residue–residue connectivity is highly relevant to medicinal chemistry. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
Closed loop folding units from structural alignments: Experimental foldons revisited
Authors: Chintapalli Sree V. , Yew Boon K. , Illingworth Christopher J. R. , Upton Graham J. G. , Reeves Philip J. , Parkes Kevin E. B. , Snell Christopher R. , Reynolds Christopher A. 
Published: May 2010

AbstractNonoverlapping closed loops of around 25–35 amino acids formed via nonlocal interactions at the loop ends have been proposed as an important unit of protein structure. This hypothesis is significant as such short loops can fold quickly and so would not be bound by the Leventhal paradox, giving insight into the possible nature of the funnel in protein folding. Previously, these closed loops have been identified either by sequence analysis (conservation and autocorrelation) or studies of the geometry of individual proteins. Given the potential significance of the closed loop hypothesis, we have explored a new strategy for determining closed loops from the insertions identified by the structural alignment of proteins sharing the same overall fold. We determined the locations of the closed loops in 37 pairs of proteins and obtained excellent agreement with previously published closed loops. The relevance of NMR structures to closed loop determination is briefly discussed. For cytochrome c, cytochrome b562 and triosephophate isomerase, independent folding units have been determined on the basis of hydrogen exchange experiments and misincorporation proton‐alkyl exchange experiments. The correspondence between these experimentally derived foldons and the theoretically derived closed loops indicates that the closed loop hypothesis may provide a useful framework for analyzing such experimental data. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
The youth coping responses inventory: development and initial validation
Authors: Hernandez Brittany C. , Vigna Julia F. , Kelley Mary L. 
Published: May 2010

AbstractThis study aimed to develop a comprehensive and representative measure of youths' dispositional coping. A sample of 450 youth, aged 10 to 16 years old, were recruited from public and private schools. The majority of the sample consisted of African American and Caucasian youth. After initial item generation, pilot testing, and item elimination, exploratory factor analyses resulted in a 44‐item coping measure with a 3‐factor solution (Diversion, Ameliorative Coping, and Destructive Coping). Internal consistency analyses indicated strong reliabilities (all coefficient alphas above .85) for the three scales and the composite score across races. Preliminary validity data confirmed that Diversion is the most adaptive coping factor and Destructive Coping the most maladaptive. These preliminary results indicate that the Youth Coping Responses Inventory presents a promising new measure of youths' coping. © 2010 Wiley Periodicals, Inc. J Clin Psychol: 66:1–18, 2010.
MicroRNA as a new player in the cell cycle
Authors: Chen Dongliang , Farwell Mary A. , Zhang Baohong 
Published: May 2010

AbstractMicroRNAs (miRNAs) are a newly identified class of small regulatory non‐coding endogenous RNAs that are ubiquitous from animals to plants and have pivotal functions in nearly all biological and metabolic processes. Increasing evidence shows that miRNAs are also new players regulating many protein‐coding genes and specific pathways during the cell cycle. This review focuses on the functions of miRNAs in the cell cycle of differentiated cells and embryonic stem (ES) cells. Aberrant expression of these cell‐cycle‐related miRNAs may result in carcinogenesis, revealing the potential of miRNAs as therapeutic targets for clinical purposes. J. Cell. Physiol. 225: 296–301, 2010. © 2010 Wiley‐Liss, Inc.
Transcription factors and ovarian functions
Authors: Sirotkin Alexander V. 
Published: May 2010

AbstractThis study represents a first review of contemporarily knowledge concerning involvement of transcription factors in control of different ovarian functions. After introduction of basic functions and classification of transcription factors, the available data concerning involvement of transcription factors in control of the following ovarian events are present: follicular development and selection, ovarian cell proliferation and cancerogenesis, ovarian cell apoptosis, ovarian secretory activity, oocyte/cumulus maturation, ovulation and luteogenesis, mediation effect of hormones, growth factors, and cytokines. The importance of transcription factors of Smad family, of forkhead transcription factor (Fox) family, of breast cancer‐associated genes/transcription factor, hypoxia‐induced transcription factors and of other transcription factors in control of these processes has been demonstrated. J. Cell. Physiol. 225: 20–26, 2010. © 2010 Wiley‐Liss, Inc.
Thrombin down‐regulates the TGF‐β‐mediated synthesis of collagen and fibronectin by human proximal tubule epithelial cells through the EPCR‐dependent activation of PAR‐1
Authors: Bae Jong‐Sup , Kim In‐San , Rezaie Alireza R. 
Published: May 2010

AbstractHuman proximal tubule (HK‐2) cells are commonly used as cellular models to understand the mechanism by which inflammatory mediators cause renal injury. It has been observed that thrombin stimulates the expression of TGF‐β, extracellular matrix (ECM) proteins and proinflammatory cytokines by HK‐2 cells. These in vitro responses correlate well with the pathology of glomerular and tubular diseases observed in acute renal injury. HK‐2 cells express PAR‐1 and the thrombin activation of this receptor has been reported to up‐regulate the TGF‐β‐mediated expression of ECM proteins, suggesting a possible pathogenic role for PAR‐1 signaling by thrombin in acute renal injury. On the other hand, several recent studies have indicated that activated protein C plays a renoprotective role, thus inhibiting the inflammatory responses and attenuating renal injury, presumably by activating the same cell surface receptor. In this study, we show that HK‐2 cells express endothelial protein C receptor (EPCR) and that the occupancy of this receptor by protein C switches the signaling specificity of thrombin so that the activation of PAR‐1 by thrombin inhibits the TNF‐α‐mediated synthesis of IL‐6 and IL‐8 and down‐regulates the TGF‐β‐mediated expression of ECM proteins. These results suggest a possible protective role for EPCR in acute kidney injury. J. Cell. Physiol. 225: 233–239, 2010. © 2010 Wiley‐Liss, Inc.
C2 and C2C12 murine skeletal myoblast models of atrophic and hypertrophic potential: Relevance to disease and ageing?
Authors: Sharples Adam P. , Al‐Shanti Nasser , Stewart Claire E. 
Published: May 2010

AbstractReduced muscle mass and increased susceptibility to TNF‐induced degradation accompany inflamed ageing and chronic diseases. Furthermore, C2 myoblasts display diminished differentiation and increased susceptibility to TNF‐α‐induced cell death versus subcloned C2C12 cells, providing relevant models to assess: differentiation (creatine kinase), growth (protein), death (trypan‐blue) and anabolic/catabolic parameters (RT‐PCR) over 72 h ± TNF‐α (20 ng ml−1). At 48 and 72 h, respectively, larger myotubes and significantly higher CK activity (320.26 ± 6.82 vs. 30.71 ± 2.5, P < 0.05; 544.94 ± 27.7 vs. 39.4 ± 3.37 mU mg ml−1, P < 0.05), fold increases in myoD (21.45 ± 3.12 vs. 3.97 ± 1.76, P < 0.05; 31.07 ± 3.1 vs. 6.82 ± 1.93, P < 0.05) and myogenin mRNA (241.8 ± 40 vs. 36.80 ± 19.3, P < 0.05; 440 ± 100.5 vs. 201.1 ± 86, P < 0.05) were detected in C2C12 versus C2. C2C12 showed significant increases in IGF‐I mRNA (243.05 ± 3.87 vs. 105.75 ± 21.95, P < 0.05), reduced proliferation and significantly lower protein expression (1.21 ± 0.28 vs. 1.79 ± 0.29 mg ml−1, P < 0.05) at 72 h versus C2 cells. Significant temporal reductions in C2C12 IGFBP2 mRNA (28.02 ± 15.44, 13.82 ± 8.07, 6.92 ± 4.37, P < 0.05) contrasted increases in C2s (4.31 ± 3.31, 13.02 ± 9.92, 82.9 ± 58.9, P < 0.05) at 0, 48 and 72 h, respectively. TNF‐α increased cell death in C2s (2.67 ± 1.54%, 34.42 ± 5.39%, 29.71 ± 5.79% (0, 48, 72 h), P < 0.05), yet was without effect in C2C12s at 48 h but caused a small significant increase at 72 h (9.88 ± 4.02% (TNF‐α) vs. 6.17 ± 0.749% (DM), 72 h). TNF‐α and TNFRI mRNA were unchanged; however, larger reductions in IGF‐I (8.2‐ and 7.5‐fold vs. 4.5‐ and 4.1‐fold (48, 72 h)), IGF‐IR (2‐fold vs. no‐significant reduction (72 h)) and IGFBP5 (3.24 vs. 1.38 (48 h) and 2.21 vs. 1.71 (72 h), P < 0.05) mRNA were observed in C2 versus C2C12 with TNF‐α. This investigation provides insight into regulators of altered basal hypertrophy and TNF‐induced atrophy, providing a model for future investigation into therapeutic initiatives for ageing/wasting disorders. J. Cell. Physiol. 225: 240–250, 2010. © 2010 Wiley‐Liss, Inc.
Measuring number‐concentrations of nanoparticles and viruses in liquids on‐line
Authors: Du Shangfeng , Kendall Kevin , Morris Susan , Sweet Clive 
Published: May 2010

AbstractBACKGROUND: The surge of studies on artificial and natural nanoparticles has revealed a new world for engineering and life sciences, but in most instances, the small scale has made their number‐concentration determination in liquids a challenging problem. Former success has mostly been limited to special particles measured by indirect techniques. A new approach is required for this determination to facilitate the production and application of nanoparticles in different systems.RESULT: Here, an approach is described using a nanoparticle tracking system based on Brownian motion, which can be used to determine the number‐concentration of nanoparticles, including viruses, in liquids on‐line. Extensive analysis showed the influence of suspension concentration and particle size on the accuracy of measurements. Natural nanoparticles of Adenovirus and several types of artificial nanoparticles, including precision nanobeads, uniform inorganic silica microspheres, monodisperse gold metal colloids and aggregated Aerosil nanoparticles, were measured and compared by counting the monitored particle number obtained using light scattered from individual particles, from which the particle number‐concentration, the product yield and the aggregation could be evaluated.CONCLUSION: This approach was compared with the mathematical calculation method and the emission spectrophotometry technique used for practical applications. The results showed this new approach had improved accuracy for determination of the particle number‐concentration. Copyright © 2010 Society of Chemical Industry
On the difference of equilibrium constants of DNA hybridization in bulk solution and at the solid‐solution interface
Authors: Oliviero Giulio , Federici Stefania , Colombi Paolo , Bergese Paolo 
Published: May 2010

AbstractThe origin of the difference between the equilibrium (affinity) constants of ligand–receptor binding in bulk solution and at a solid‐solution interface is discussed in terms of Gibbsian interfacial thermodynamics. It results that the difference is determined by the surface work that the ligand–receptor interaction spends to accommodate surface binding, and in turn that the value of the surface equilibrium constant (strongly) depends on the surface that confines the event. This framework consistently describes a wide set of experimental observations of DNA surface hybridization, correctly predicting that within the surface work window for DNA hybridization, that ranges from −90 to 75 kJmol−1, the ratio between surface and bulk equilibrium constants ranges from 10−16 to 1013, spanning 29 orders of magnitude. Copyright © 2010 John Wiley & Sons, Ltd.
Pathological prognostic score as a simple criterion to predict outcome in gastric carcinoma
Authors: Nozoe Tadahiro , Iguchi Tomohiro , Egashira Akinori , Adachi Eisuke , Matsukuma Akito , Ezaki Takahiro 
Published: May 2010

AbstractPurposeThe aim of this study was to establish a simple criterion to predict prognosis of patients with gastric carcinoma.MethodsTwo hundred four patients with gastric carcinoma, who had been treated with curative resection, were enrolled.One point was added for each category among four pathological factors of depth of tumor, lymph node metastasis, venous invasion, and lymphatic invasion. Pathological Prognostic Score (PPS) was determined by an aggregate of these points for each category.ResultsThere existed a significant difference between survivals of patients with PPS 0 or 1 and 2 or 3 (P = 0.0002). Similarly, there also existed a significant difference between survivals of patients with PPS 2 or 3 and 4 (P = 0.010).ConclusionsPPS can be quite simple criteria to predict prognosis of gastric carcinoma with a strict stratification. J. Surg. Oncol. 2010;102:11–17. J. Surg. Oncol. 2010;102:73–76. © 2010 Wiley‐Liss, Inc.
Multidimensional chromatography coupled to mass spectrometry in analysing complex proteomics samples
Authors: Horvatovich Péter , Hoekman Berend , Govorukhina Natalia , Bischoff Rainer 
Published: May 2010

AbstractMultidimensional chromatography coupled to mass spectrometry (LCn‐MS) provides more separation power and an extended measured dynamic concentration range to analyse complex proteomics samples than one dimensional liquid chromatography coupled to mass spectrometry (1D‐LC‐MS). This review gives an overview of the most important aspects of LCn‐MS with respect to optimizing peak capacity and evaluate orthogonality. We review recent developments in LCn‐MS to analyse proteomics samples from the analyst point of view and give an overview over methods and future developments to process LCn‐MS data for comprehensive differential protein expression profiling. Examples from our research, such as combining protein fractionation using high temperature reverse phase (RP) columns followed by analysis of the trypsin‐digested fractions by RP LC‐MS, serve to highlight possibilities and shortcomings of present‐day approaches. Other LCn‐MS systems that have been used to analyse highly complex shotgun proteomic samples, such as the combination of RP columns using low and high pH eluents or the combination of hydrophilic interaction liquid chromatography (HILIC) with RP‐MS is discussed in detail.
The Ultrafilter Closure in ZF
Authors: Gutierres Gonçalo 
Published: May 2010

AbstractIt is well known that, in a topological space, the open sets can be characterized using ?lter convergence. In ZF (Zermelo‐Fraenkel set theory without the Axiom of Choice), we cannot replace filters by ultrafilters. It is proven that the ultra?lter convergence determines the open sets for every topological space if and only if the Ultrafilter Theorem holds. More, we can also prove that the Ultra?lter Theorem is equivalent to the fact that uX = kX for every topological space X, where k is the usual Kuratowski closure operator and u is the Ultra?lter Closure with uX (A):= {x ∈ X: (∃ U ultrafilter in X)[U converges to x and A ∈ U ]}. However, it is possible to built a topological space X for which uX ≠ kX, but the open sets are characterized by the ultra?lter convergence. To do so, it is proved that if every set has a free ultra?lter, then the Axiom of Countable Choice holds for families of non‐empty finite sets. It is also investigated under which set theoretic conditions the equality u = k is true in some subclasses of topological spaces, such as metric spaces, second countable T0‐spaces or {ℝ} (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Prion protein expression and the M129V polymorphism of the PRNP gene in patients with colorectal cancer
Authors: Antonacopoulou Anna G. , Palli Maria , Marousi Stella , Dimitrakopoulos Fotinos‐Ioannis , Kyriakopoulou Urania , Tsamandas Athanasios C. , Scopa Chrisoula D. , Papavassiliou Athanasios G. , Kalofonos Haralabos P. 
Published: May 2010

AbstractThe prion protein, PrPC, is known mostly for its involvement in neurodegenerative spongiform encephalopathies. However, a role for this molecule in cancer is becoming increasingly recognized partly because it promotes cell proliferation and inhibits apoptosis. Moreover, the codon 129 polymorphism (M129V) of the PRNP gene (the PrPC‐encoding gene) has been associated with neurodegenerative disease development and severity, while no information is available regarding its role in colorectal cancer (CRC) incidence and disease progression. We have previously reported that expression levels of PRNP may have a prognostic value in CRC, suggesting a role for the prion protein in CRC. The aim of this study was to investigate retrospectively the possible role of M129V and PrPC expression in patients with CRC. The M129V single nucleotide polymorphism was genotyped by real time polymerase chain reactions in 110 patients with CRC and 124 healthy donors. Moreover, protein expression was assessed by immunohistochemistry in 68 patients with CRC. Allele frequencies were similar in patients and healthy controls indicating that the M129V polymorphism is not a risk factor for CRC. Furthermore, it did not correlate with any clinicopathological parameters. By contrast, PrPC expression was highly elevated in neoplastic compared to normal tissue and differed depending on the primary site. Interestingly, protein levels were correlated with disease recurrence (P = 0.007). Conclusively, PrPC overexpression may constitute a prognostic marker for disease recurrence and potentially a new target for anticancer therapy. However, further studies are needed to evaluate prospectively the role of PrPC expression in patients with CRC. © 2010 Wiley‐Liss, Inc.
Effect of dietary selenium on the progression of heart failure in the ageing spontaneously hypertensive rat
Authors: Lymbury Robyn S. , Marino Matthew J. , Perkins Anthony V. 
Published: May 2010

AbstractOxidative stress has been directly implicated in hypertension and myocardial remodelling, two pathologies fundamental to the development of chronic heart failure. Selenium (Se) can act directly and indirectly as an antioxidant and a lowered Se status leads to a higher risk of cardiovascular disease. This study examined the role of Se on the development of hypertension and subsequent progression to chronic heart failure in spontaneously hypertensive rats (SHR). Three dietary groups were studied: (i) Se‐free; (ii) normal Se (50 μg Se/kg food); and (iii) high Se (1000 μg Se/kg food). Systolic blood pressure and echocardiography were used to detect cardiac changes in vivo. At study end, cardiac tissues were assayed for glutathione peroxidase activity, thioredoxin reductase activity, and protein carbonyls. The major finding of this study was the high heart failure‐related mortality rate in SHRs fed an Se‐free diet (70%). Normal and high levels of dietary Se resulted in higher survival rates of 78 and 100%, respectively. Furthermore, high dietary Se was clearly associated with lower levels of cardiac oxidative damage and increased antioxidant expression, as well as a reduction in disease severity and mortality in the SHR.
Influence of initial mixing methods on melt‐extruded single‐walled carbon nanotube–polypropylene nanocomposites
Authors: Radhakrishnan Vinod K. , Davis Edward W. , Davis Virginia A. 
Published: May 2010

AbstractWe report the first direct comparison of melt‐extruded polypropylene–single‐walled carbon nanotube (PP/SWNT) nanocomposites prepared by three different initial mixing methods. The standard deviation of the G‐band intensity obtained using Raman mapping was found to be the best measure of dispersion uniformity in the extruded composites, and dispersion uniformity was found to generally correlate with rheological and thermal properties. For all three initial mixing methods, both unmodified and sidewall‐functionalized purified SWNTs were evaluated. Surprisingly, in all cases, dodecylated SWNTs prepared using the reductive alkylation method were less uniformly dispersed in the final composite than the unmodified SWNTs. The simplest process, dry blending, resulted in poor nanotube dispersion and only polymer crystallization was significantly affected by the presence of the nanotubes. A slightly more complex rotary evaporation process resulted in significantly more uniform dispersion and significant changes in rheological properties, polymer crystallization, and thermal stability. The most elaborate process tested, hot coagulation, enabled the most uniform dispersion and the greatest change in properties but also resulted in some polymer degradation. POLYM. ENG. SCI., 50:1831–1842, 2010. © 2010 Society of Plastics Engineers
Rheological properties of fiber suspensions flowing through a curved expansion duct
Authors: Lin Jianzhong , Zhang Qihua , Zhang Kai 
Published: May 2010

AbstractA numerical method based on finite volume method for solving Fokker‐Planck equation on a unit sphere was first developed to simulate numerically the fiber orientation distribution of fiber suspensions flowing through a curved expansion duct. The momentum equation with fiber extra stress was used to explore the rheological properties of the fiber suspensions. The second‐order fiber orientation tensors in present simulation are compared with the previous numerical results for validating the model and computational code. The results showed that the pressure increases from inlet to outlet, and changes along the lateral direction nonmonotonically except at outlet. The extra shear stress and normal stress difference decrease from inlet to outlet, and changes along the lateral direction nonmonotonically. The effect of fiber aspect ratio on the extra shear stress and normal stress difference is negligible near the wall region. The extra shear stress and normal stress difference increase with the fiber aspect ratio near the centerline. The lateral distribution curves of extra shear stress and normal stress difference become flat with increasing the distance from the inlet. POLYM. ENG. SCI., 50:1994–2003, 2010. © 2010 Society of Plastics Engineers