bluuebunny/crossref_metadata_2025_split huggingface dataset:
Including impacts of particulate emissions on marine ecosystems in life cycle assessment: The case of offshore oil and gas production
Authors: Veltman Karin , Huijbregts Mark AJ , Rye Henrik , Hertwich Edgar G. 
Published: July 2011

Abstract
Life cycle assessment is increasingly used to assess the environmental performance of fossil energy systems. Two of the dominant emissions of offshore oil and gas production to the marine environment are the discharge of produced water and drilling waste. Although environmental impacts of produced water are predominantly due to chemical stressors, a major concern regarding drilling waste discharge is the potential physical impact due to particles. At present, impact indicators for particulate emissions are not yet available in life cycle assessment. Here, we develop characterization factors for 2 distinct impacts of particulate emissions: an increased turbidity zone in the water column and physical burial of benthic communities. The characterization factor for turbidity is developed analogous to characterization factors for toxic impacts, and ranges from 1.4 PAF (potentially affected fraction) ·m3/d/kgp (kilogram particulate) for drilling mud particles discharged from the rig. The characterization factor for burial describes the volume of sediment that is impacted by particle deposition on the seafloor and equals 2.0 × 10−1 PAF· m3/d/kgp for cutting particles. This characterization factor is quantified on the basis of initial deposition layer characteristics, such as height and surface area, the initial benthic response, and the recovery rate. We assessed the relevance of including particulate emissions in an impact assessment of offshore oil and gas production. Accordingly, the total impact on the water column and on the sediment was quantified based on emission data of produced water and drilling waste for all oil and gas fields on the Norwegian continental shelf in 2008. Our results show that cutting particles contribute substantially to the total impact of offshore oil and gas production on marine sediments, with a relative contribution of 55% and 31% on the regional and global scale, respectively. In contrast, the contribution of particulate emissions to the total impact on the marine water column is of minor importance. We conclude that particles are an important stressor in marine ecosystems, particularly for marine sediment, and particulate emissions should therefore be included in a (life cycle) impact assessment of offshore oil and gas production. Integr Environ Assess Manag 2011;7:678–686. © 2011 SETAC
Antitumor activity of HM781‐36B, a highly effective pan‐HER inhibitor in erlotinib‐resistant NSCLC and other EGFR‐dependent cancer models
Authors: Cha Mi Young , Lee Kwang‐Ok , Kim Mira , Song Ji Yeon , Lee Kyu Hang , Park Jongmin , Chae Yun Jung , Kim Young Hoon , Suh Kwee Hyun , Lee Gwan Sun , Park Seung Bum , Kim Maeng Sup 
Published: July 2011

AbstractThe epidermal growth factor receptor (EGFR) family of receptor tyrosine kinases has been implicated in a variety of cancers. In particular, activating mutations such as the L858R point mutation in exon 21 and the small in‐frame deletions in exon 19 of the EGFR tyrosine kinase domain are correlated with sensitivity to EGFR tyrosine kinase inhibitors in non‐small cell lung cancer (NSCLC) patients. Clinical treatment of patients is limited by the development of drug resistance resulting mainly from a gatekeeper mutation (T790M). In this study, we evaluated the therapeutic potential of a novel, irreversible pan‐HER inhibitor, HM781‐36B. The results from this study show that HM781‐36B is a potent inhibitor of EGFR in vitro, including the EGFR‐acquired resistance mutation (T790M), as well as HER‐2 and HER‐4, compared with other EGFR tyrosine kinases inhibitors (erlotinib, lapatinib and BIBW2992). HM781‐36B treatment of EGFR DelE746_A750‐harboring erlotinib‐sensitive HCC827 and EGFR L858R/T790M‐harboring erlotinib‐resistant NCI‐H1975 NSCLC cells results in the inhibition of EGFR phosphorylation and the subsequent deactivation of downstream signaling proteins. Additionally, HM781‐36B shows an excellent efficacy in a variety of EGFR‐ and HER‐2‐dependent tumor xenograft models, including erlotinib‐sensitive HCC827 NSCLC cells, erlotinib‐resistant NCI‐H1975 NSCLC cells, HER‐2 overexpressing Calu‐3 NSCLC cells, NCI‐N87 gastric cancer cells, SK‐Ov3 ovarian cancer cells and EGFR‐overexpressing A431 epidermoid carcinoma cancer cells. On the basis of these preclinical results, HM781‐36B is the most potent pan‐HER inhibitor, which will be advantageous for the treatment of patients with NSCLC including clinical limitation caused by acquired mutation (EGFR T790M), breast cancer and gastric cancer.
Controlled Immobilization of Polysaccharide Derivatives for Efficient Chiral Separation
Authors: Okamoto Yoshio , Ikai Tomoyuki , Shen Jun 
Published: July 2011

AbstractPolysaccharide‐based chiral packing materials (CPMs) for high‐performance liquid chromatography (HPLC) have been widely used to determine the enantiomeric excess of a wide range of chiral compounds and also to resolve them on an industrial scale. These CPMs have conventionally been prepared by physically coating a chromatographic support with the polysaccharide derivatives. However, solvents that swell or dissolve the polysaccharide derivatives cannot be used as an eluent component because the column performance will be drastically decreased. This restriction on eluent selection is sometimes a serious issue for efficient analytical and preparative enantioseparations. In order to enhance the diversity of the eluent selection, immobilized CPMs, in which the polysaccharide derivatives are immobilized onto chromatographic supports, have been developed since 1987. This review summarizes the various immobilization methods of the polysaccharide derivatives mainly onto silica gel as a chromatographic support.
Testing distributional assumptions: A GMM aproach
Authors: Bontemps Christian , Meddahi Nour 
Published: July 2011

SUMMARYWe consider testing distributional assumptions by using moment conditions. A general class of moment conditions satisfied under the null hypothesis is derived and connected to existing moment‐based tests. The approach is simple and easy to implement, yet reasonably powerful. In addition, we provide moment tests that are robust against parameter estimation error uncertainty in the general case which includes the case of serial correlation. In particular, we consider the location‐scale model for which we derive robust moment tests, regardless of the forms of the conditional mean and variance. We study in detail the Student and inverse Gaussian distributions. Simulation experiments are conducted to assess the finite sample properties of the tests. We provide two empirical examples on foreign exchange rates by testing the Student distributional assumption of T‐GARCH daily returns and on daily realized variance by testing the inverse Gaussian distributional assumption. Copyright © 2011 John Wiley & Sons, Ltd.
Induced chronic hypoxia negates the pro‐angiogenic effect of surface immobilized heparin in a polyurethane porous scaffold
Authors: Schmidt Christian , Bezuidenhout Deon , Higham Lawrence , Zilla Peter , Davies Neil H. 
Published: July 2011

AbstractPorous scaffolds are frequently utilized in tissue regeneration. We have developed a polyurethane (PU) scaffold with a freely interconnecting porosity that can be modified with a covalently linked heparinized surface. The ability of this surface functionality to stimulate vessel and cellular growth into the PU scaffold has been evaluated by subcutaneous implantation of discs in the rat under normoxia and chronic hypoxia (hypobaric chamber) for 10 days. The heparinized surface alone was able to significantly increase vascularization and cellularization under normoxia (p < 0.05), but this response was negated by hypoxia. Addition of vascular endothelial growth factor to heparinized discs resulted in increased vascularity and cellularization under both conditions (p < 0.05). This suggests that endogenous growth factor production was limiting under chronic hypoxia but that an angiogenic response could still occur with exogenous delivery of factors. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A:, 2011.
Photochemical cross‐linking of plastically compressed collagen gel produces an optimal scaffold for corneal tissue engineering
Authors: Mi Shengli , Khutoryanskiy Vitaliy V. , Jones Roanne Razalia , Zhu Xiuping , Hamley Ian William , Connon Che John 
Published: July 2011

AbstractThe experiments were designed to use photochemically cross‐linked plastically compressed collagen (PCPCC) gel to support corneal epithelial cells. A plastically compressed collagen (PCC) scaffold was photo cross‐linked by UVA in the presence of riboflavin to form a biomaterial with optimal mechanical properties. The breaking force, rheology, surgical suture strength, transparency, ultrastructure, and cell‐based biocompatibility were compared between PCPCC and PCC gels. The breaking force increased proportionally with an increased concentration of riboflavin. The stress required to reach breaking point of the PCPCC scaffolds was over two times higher compared to the stress necessary to break PCC scaffolds in the presence of 0.1% riboflavin. Rheology results indicated that the structural properties of PCC remain unaltered after UVA cross‐linking. The PCC gels were more easily broken than PCPCC gels when sutured on to bovine corneas. The optical density values of PCPCC and PCC showed no significant differences (p > 0.05). SEM analyses showed that the collagen fibres within the PCPCC gels were similar in morphology to PCC gels. No difference in cell‐based biocompatibility was seen between the PCPCC and PCC scaffolds in terms of their ability to support the ex vivo expansion of corneal epithelial cells or their subsequent differentiation evidenced by similar levels of cytokeratin 14. In conclusion, PCPCC scaffold is an optimal biomaterial for use in therapeutic tissue engineering of the cornea. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 99A: 1–8, 2011.
Hybrid coaxial electrospun nanofibrous scaffolds with limited immunological response created for tissue engineering
Authors: Gluck Jessica M. , Rahgozar Paymon , Ingle Nilesh P. , Rofail Fironia , Petrosian Asdghig , Cline Michael G. , Jordan Maria C. , Roos Kenneth P. , MacLellan William Robb , Shemin Richard J. , Heydarkhan‐Hagvall Sepideh 
Published: July 2011

AbstractElectrospinning using synthetic and natural polymers is a promising technique for the fabrication of scaffolds for tissue engineering. Numerous synthetic polymers are available to maximize durability and mechanical properties (polyurethane) versus degradability and cell adhesion (polycaprolactone). In this study, we explored the feasibility of creating scaffolds made of bicomponent nanofibers from both polymers using a coaxial electrospinning system. We used a core of poly(urethane) and a sheath of a mixture of poly(ε‐caprolactone) and gelatin, all dissolved in 1,1,1,3,3,3‐hexafluror‐2‐propanol. These nanofibrous scaffolds were then evaluated to confirm their core–sheath nature and characterize their morphology and mechanical properties under static and dynamic conditions. Furthermore, the antigenicity of the scaffolds was studied to confirm that there is no significant foreign body response to the scaffold itself that would preclude its use in vivo. The results show the advantages of combining both natural and synethic polymers to create a coaxial scaffold capable of withstanding dynamic culture conditions and encourage cellular migration to the interior of the scaffold for tissue‐engineering applications. Also, the results show that there is no significant immunoreactivity in vivo to the components of the scaffolds. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2011.
The number of the genes in a functional category matters during rat liver regeneration after partial hepatectomy
Authors: Jiang Yun , Zhang Lian‐Xing , Chang Cui‐Fang , Wang Gai‐Ping , Shi Rui‐Jia , Yang Yan‐Jie , Xu Cun‐Shuan 
Published: July 2011

AbstractRat liver regeneration after partial hepatectomy (PH) is a good model to study the regulation of cell proliferation. We isolated hepatocytes from regenerating liver at different time points after PH and used microarray Rat Genome 230 2.0 chip to analyze the functional profiles of all up‐ or down‐regulated genes manually and with automatic gene ontological tools. We found that the transcript expressions of PH and sham operation group were apparently different. For PH group, in the priming phase (2–12 h), signaling, transcription, response to stimulus genes predominated in up‐regulated genes; in the proliferation phase (24–72 h), cell proliferation genes predominated; in the termination phase (120–168 h), differentiation and translation genes predominated; while metabolism genes predominated in the down‐regulated genes at all time points (2–168 h). These functional profiles are consistent with the cellular and molecular phenomenon observed during liver regeneration, and can be closely connected with the biological process. Moreover, the results indicated that not only the quantity of specific genes but also the number of the genes in the specific functional category was regulated during liver regeneration, which means the number of similar genes in a specific functional category matters as well as the regulation of the genes. The changes of the number of the regulated cell proliferation genes and metabolism genes during liver regeneration were similar to the expression patterns of some cell division genes and metabolism genes. J. Cell. Biochem. 112: 3194–3205, 2011. © 2011 Wiley Periodicals, Inc.
Protein kinase CK2 promotes cancer cell viability via up‐regulation of cyclooxygenase‐2 expression and enhanced prostaglandin E2 production
Authors: Yefi Roger , Ponce Daniela P. , Niechi Ignacio , Silva Eduardo , Cabello Pablo , Rodriguez Diego A. , Marcelain Katherine , Armisen Ricardo , Quest Andrew F.G. , Tapia Julio C. 
Published: July 2011

AbstractAugmented expression of protein kinase CK2 is associated with hyperproliferation and resistance to apoptosis in cancer cells. Effects of CK2 are at least partially linked to signaling via the Wnt/β‐catenin pathway, which is dramatically enhanced in colon cancer. Cyclooxygenase‐2 (COX‐2), a Wnt/β‐catenin target gene, has been associated with enhanced cancer progression and metastasis. However, the possibility that a connection may exist between CK2 and COX‐2 has not been explored previously. Here we investigated changes in COX‐2 expression and activity upon CK2 modulation and evaluated how these changes affected cell viability. COX‐2 expression and cell viability decreased upon selective inhibition of COX‐2 with SC‐791 or CK2 with 2‐dimethylamino‐4,5,6,7‐tetrabromo‐1H‐benzimidazole (DMAT), both in human colon (HT29‐ATCC, HT29‐US, DLD‐1) and breast (ZR‐75) cancer cells, as well as in human embryonic kidney (HEK‐293T) cells. On the other hand, ectopic CK2α expression promoted up‐regulation of COX‐2 by activating the Wnt/β‐catenin pathway in HEK‐293T cells. Noteworthy, over‐expression of either CK2α, β‐catenin or COX‐2, as well as supplementation of the medium with prostaglandin E2 (PGE2), all were individually sufficient to overcome limitations in cell viability triggered by CK2 inhibition either upon addition of DMAT or over‐expression of a dominant negative CK2α variant. Altogether, these findings provide new insight to the role of CK2 in cancer by up‐regulating COX‐2 expression and thereby PGE2 production. J. Cell. Biochem. 112: 3167–3175, 2011. © 2011 Wiley Periodicals, Inc.
Two‐level hierarchical parallelization of second‐order Møller–plesset perturbation calculations in divide‐and‐conquer method
Authors: Katouda Michio , Kobayashi Masato , Nakai Hiromi , Nagase Shigeru 
Published: July 2011

AbstractA two‐level hierarchical parallelization scheme including the second‐order Møller–Plesset perturbation (MP2) theory in the divide‐and‐conquer method is presented. The scheme is a combination of coarse‐grain parallelization assigning each subsystem to a group of processors, with fine‐grain parallelization, where the computational tasks for evaluating MP2 correlation energy of the assigned subsystem are distributed among processors in the group. Test calculations demonstrate that the present scheme shows high parallel efficiency and makes MP2 calculations practical for very large molecules. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Optimal scaling factors for CM1 and CM3 atomic charges in RM1‐based aqueous simulations
Authors: Vilseck Jonah Z. , Sambasivarao Somisetti V. , Acevedo Orlando 
Published: July 2011

AbstractScaling factors for atomic charges derived from the RM1 semiempirical quantum mechanical wavefunction in conjunction with CM1 and CM3 charge models have been optimized by minimizing errors in absolute free energies of hydration, ΔGhyd, for a set of 40 molecules. Monte Carlo statistical mechanics simulations and free energy perturbation theory were used to annihilate the solutes in gas and in a box of TIP4P water molecules. Lennard–Jones parameters from the optimized potentials for liquid simulations‐all atom (OPLS–AA) force field were utilized for the organic compounds. Optimal charge scaling factors have been determined as 1.11 and 1.14 for the CM1R and CM3R methods, respectively, and the corresponding unsigned average errors in ΔGhyd relative to experiment were 2.05 and 1.89 kcal/mol. Computed errors in aniline and two derivatives were particularly large for RM1 and their removal from the data set lowered the overall errors to 1.61 and 1.75 kcal/mol for CM1R and CM3R. Comparisons are made to the AM1 method which yielded total errors in ΔGhyd of 1.50 and 1.64 kcal/mol for CM1A*1.14 and CM3A*1.15, respectively. This work is motivated by the need for a highly efficient yet accurate quantum mechanical (QM) method to study condensed‐phase and enzymatic chemical reactions via mixed QM and molecular mechanical (QM/MM) simulations. As an initial test, the Menshutkin reaction between NH3 and CH3Cl in water was computed using a RM1/TIP4P‐Ew/CM3R procedure and the resultant ΔG‡, ΔGrxn, and geometries were in reasonable accord with other computational methods; however, some potentially serious shortcomings in RM1 are discussed. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
A comparison of neighbor search algorithms for large rigid molecules
Authors: Artemova Svetlana , Grudinin Sergei , Redon Stephane 
Published: July 2011

AbstractFast determination of neighboring atoms is an essential step in molecular dynamics simulations or Monte Carlo computations, and there exists a variety of algorithms to efficiently compute neighbor lists. However, most of these algorithms are general, and not specifically designed for a given type of application. As a result, although their average performance is satisfactory, they might be inappropriate in some specific application domains. In this article, we study the case of detecting neighbors between large rigid molecules, which has applications in, e.g., rigid body molecular docking, Monte Carlo simulations of molecular self‐assembly or diffusion, and rigid body molecular dynamics simulations. More precisely, we compare the traditional grid‐based algorithm to a series of hierarchy‐based algorithms that use bounding volumes to rapidly eliminate large groups of irrelevant pairs of atoms during the neighbor search. We compare the performance of these algorithms based on several parameters: the size of the molecules, the average distance between them, the cutoff distance, as well as the type of bounding volume used in the culling hierarchy (AABB, OBB, wrapped, or layered spheres). We demonstrate that for relatively large systems (> 100,000 atoms) the algorithm based on the hierarchy of wrapped spheres shows the best results and the traditional grid‐based algorithm gives the worst timings. For small systems, however, the grid‐based algorithm and the one based on the wrapped sphere hierarchy are beneficial. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
MyMolDB: A micromolecular database solution with open source and free components
Authors: Xia Bing , Tai Zheng‐Fu , Gu Yu‐Cheng , Li Bang‐Jing , Ding Li‐Sheng , Zhou Yan 
Published: July 2011

AbstractBackground:To manage chemical structures in small laboratories is one of the important daily tasks. Few solutions are available on the internet, and most of them are closed source applications. The open‐source applications typically have limited capability and basic cheminformatics functionalities. In this article, we describe an open‐source solution to manage chemicals in research groups based on open source and free components. It has a user‐friendly interface with the functions of chemical handling and intensive searching.Results:MyMolDB is a micromolecular database solution that supports exact, substructure, similarity, and combined searching. This solution is mainly implemented using scripting language Python with a web‐based interface for compound management and searching. Almost all the searches are in essence done with pure SQL on the database by using the high performance of the database engine. Thus, impressive searching speed has been archived in large data sets for no external Central Processing Unit (CPU) consuming languages were involved in the key procedure of the searching.Availability:MyMolDB is an open‐source software and can be modified and/or redistributed under GNU General Public License version 3 published by the Free Software Foundation (Free Software Foundation Inc. The GNU General Public License, Version 3, 2007. Available at: http://www.gnu.org/licenses/gpl.html). The software itself can be found at http://code.google.com/p/mymoldb/. © 2011 Wiley Periodicals, Inc. J Comput Chem 2011
Increasing social capital and personal efficacy through small‐scale community events
Authors: Molitor Fred , Rossi Melissa , Branton Lisa , Field Julie 
Published: July 2011

AbstractCalifornia's voter‐approved Children and Families Act of 1998 calls for money collected from tobacco taxes to support services for families with children up to 5 years of age. Sacramento County uses a portion of its allocation for small community grants with the specific intent of building social capital among neighbors and across communities. The evaluation of the 995 Community Building Initiative (CBI) events funded from July 2007 to June 2010 included randomly selecting parents from a larger population (n=29,607). Structured interviews with 538 parents identified those who had attended community events within the last 6 months and assessed hypothesized outcomes. Attending any community event was related to increased measures of social capital. However, those participating in a CBI event demonstrated the highest levels of familiarity with neighbors, neighborhood cohesion, and efficacy, as revealed through generalized linear mixed model analyses controlling for race/ethnicity, primary language, and education. © 2011 Wiley Periodicals, Inc.