bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptively biased molecular dynamics: An umbrella sampling method with a time‐dependent potential
Authors: Babin Volodymyr , Karpusenka Vadzim , Moradi Mahmoud , Roland Christopher , Sagui Celeste 
Published: August 2009

AbstractWe discuss an adaptively biased molecular dynamics (ABMD) method for the computation of a free energy surface for a set of reaction coordinates. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential. It is characterized by a small number of control parameters and an O(t) numerical cost with simulation time t. The method naturally allows for extensions based on multiple walkers and replica exchange mechanism. The workings of the method are illustrated with a number of examples, including sugar puckering, and free energy landscapes for polymethionine and polyproline peptides, and for a short β‐turn peptide. ABMD has been implemented into the latest version (Case et al., AMBER 10; University of California: San Francisco, 2008) of the AMBER software package and is freely available to the simulation community. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Electronic structure of the Li2 [X 1Σ] Li [2p] excited 2A″ surface
Authors: Byrd Jason N. , Montgomery John A. , Michels H. Harvey , Côté Robin 
Published: August 2009

AbstractPotential energy surface calculations are reported for the lowest 2A″ surface arising from the Li2 [X 1Σ] + Li* [2P] interaction. The 2A″ surface with Cs symmetry, which correlates to the 2B1 surface in C2v symmetry and to the 2Pi surface in C∞v, has been calculated using second order restricted open‐shell Møller–Plesset theory. Our calculated surface has a minimum in C2v symmetry that resembles the ground state surface but does not exhibit the Jahn–Teller splitting found for the ground state potential energy surface. Dipole transition moments are calculated in C2v geometry near the 2A″ minima using the internally contracted multireference singles and doubles configuration interaction theory. We have also analyzed the long range behavior of this 2A″ surface by fitting the ab initio calculations at long range with a functional series of the form ±Cn/Rn. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Computing vibrational properties in hydrogen‐bonded systems using quantum wavepacket ab initio molecular dynamics
Authors: Iyengar Srinivasan S. 
Published: August 2009

AbstractThe recently developed quantum wavepacket ab initio molecular dynamics method is discussed. The approach combines quantum wavepacket dynamics with ab initio molecular dynamics and is useful in studying problems where nuclear quantum effects play an important role. Computational bottlenecks and associated solutions are outlined. Chemical applications dealing with vibrational properties in hydrogen‐bonded clusters are discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Few‐parameter exponentially correlated wavefunctions for the ground state of lithium
Authors: Albert Victor V. , Guevara Nicolais L. , Sabin John R. , Harris Frank E. 
Published: August 2009

AbstractCompact, but relatively accurate wavefunctions for the ground state of the Li atom were obtained through the use of a limited basis of exponentially correlated functions with optimized nonlinear parameters. In contrast to our earlier work, the basis contains pre‐exponential factors that improve the rate of convergence of the basis‐set expansion. The matrix elements needed in the present work were evaluated analytically using recursive methods reported recently by one of us; a check on the programming was provided by comparison with numerical evaluations carried out by Turbiner and Guevara. The rate of convergence of the expansion is compared with those of Hylleraas‐basis computations, and a comparison is also made with exponentially correlated studies of He‐like systems. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Distinguishing a phosphate ester prodrug from its isobaric sulfate metabolite by mass spectrometry without the metabolite standard
Authors: Wu Steven T. , Cao Kai , Bonacorsi Samuel J. , Zhang Hongwei , Jemal Mohammed 
Published: August 2009

AbstractA phosphate prodrug of a phenolic or alcoholic drug is isobaric with the putative sulfate metabolite of the drug. During liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis of biological samples obtained after the administration of a phosphate prodrug, a product ion arising from the parent drug portion of the prodrug molecule is commonly used in selected reaction monitoring (SRM) utilized for the simultaneous quantitation of the prodrug and the in vivo generated parent drug. While the advantage of using a drug moiety‐specific LC‐SRM method is obvious, one drawback is that the sulfate metabolite will also respond to such an SRM transition since the metabolite will invariably yield the same product ion as the prodrug. Thus, the sulfate metabolite could be mistaken for the prodrug unless chromatographic separation between the two is achieved. In the absence of a reference standard for the sulfate metabolite to demonstrate chromatographic separation, it is important to establish a procedure that can ascertain the absence of the sulfate metabolite in the study samples to ensure the specificity of the method for the prodrug. To this end, we studied the MS/MS behavior of model phosphate and sulfate ester compounds and developed a procedure based on phosphate‐specific and sulfate‐specific product ions for distinguishing the phosphate prodrug from the sulfate metabolite. Copyright © 2009 John Wiley & Sons, Ltd.
Online high‐precision δ2H and δ18O analysis in water by pyrolysis
Authors: Lu Feng H. 
Published: August 2009

AbstractA method for online simultaneous δ2H and δ18O analysis in water by high‐temperature conversion is presented. Water is injected by using a syringe into a high‐temperature carbon reactor and converted into H2 and CO, which are separated by gas chromatography (GC) and carried by helium to the isotope ratio mass spectrometer for hydrogen and oxygen isotope analysis. A series of experiments was conducted to evaluate several issues such as sample size, temperature and memory effects. The δ2H and δ18O values in multiple water standards changed consistently as the reactor temperature increased from 1150 to 1480°C. The δ18O in water can be measured at a lower temperature (e.g. 1150°C) although the precision was relatively poor at temperatures <1300°C. Memory effects exist for δ2H and δ18O between two waters, and can be reduced (to <1%) with proper measures. The injection of different amounts of water may affect the isotope ratio results. For example, in contrast to small injections (100 nL or less) from small syringes (e.g. 1.2 µL), large injections (1 µL or more) from larger syringes (e.g. 10 µL) with dilution produced asymmetric peaks and shifts of isotope ratios, e.g. 4‰ for δ2H and 0.4‰ for δ18O, probably resulting from isotope fractionation during dilution via the ConFlo interface. This method can be used to analyze nanoliter samples of water (e.g. 30 nL) with good precision of 0.5‰ for δ2H and 0.1‰ for δ18O. This is important for geosciences; for instance, fluid inclusions in ancient minerals may be analyzed for δ2H and δ18O to help understand the formation environments. Copyright © 2009 John Wiley & Sons, Ltd.
Comparison of collision‐ versus electron‐induced dissociation of Pt(II) ternary complexes of histidine‐ and methionine‐containing peptides
Authors: Feketeová Linda , Ryzhov Victor , O'Hair Richard A. J. 
Published: August 2009

AbstractIncubation of the histidine‐containing peptides (GH, HG, GGH, GHG, HGG) and methionine‐containing peptides (GM, MG, GGM, GMG, MGG) with the platinum complexes [Pt(terpy)Cl]+ (A) and [Pt(dien)Cl]+ (B) followed by electrospray ionisation (ESI) led to a number of singly and doubly charged ternary platinum peptide complexes, including [Pt(L)M]2+ and [Pt(L)M–H]+ (where L = the ligand terpy or dien; M is a peptide). Each of the [Pt(L)M]2+ complexes was subjected to electron capture dissociation (ECD), collision‐induced dissociation (CID) and electron‐induced dissociation (EID), while each of the [Pt(L)M–H]+ complexes was subjected to CID and EID. Results from ECD suggest that the free electron is captured by the metal ion thus weakening the bonds to its ligands. In the case of the ligand terpy, which binds more strongly than dien, this weakening leads to the loss of the peptide. The minor products in the ECD spectra of [Pt(terpy)M]2+ complexes do show fragmentation along the peptide backbone, but the ions observed are of the a‐, b‐, and y‐type. For the complexes with methionine‐containing peptides, a marker ion, [Pt(L)SCH3]+, was found which is indicative of binding of Pt to the methionine side chain. For the histidine‐containing peptides, an ion containing platinum, the auxiliary ligand, and the histidine imine was observed in many instances, thus indicating the binding of the histidine side chain to the metal, but other modes of Pt coordination (N‐terminus) were also found to be competitive. These findings are consistent with a recent finding (Sze et al. J. Biol. Inorg. Chem. 2009; 14: 163) that Pt occupies the methionine‐rich copper(I)‐binding site rather than histidine‐rich copper(II)‐binding site in the CopC protein. Copyright © 2009 John Wiley & Sons, Ltd.
Molecular mechanisms mediated by human endogenous retroviruses (HERVs) in autoimmunity
Authors: Balada Eva , Ordi‐Ros Josep , Vilardell‐Tarrés Miquel 
Published: August 2009

AbstractEight per cent of the human genome is derived from the integration of retroviral sequences that were incorporated in our DNA more than 25 million years ago. Although some of these elements show mutations and deletions, some HERVs are transcriptionally active and produce functional proteins. Different mechanisms have been described which link HERVs to some chronic diseases such as several cancers, nervous system diseases and autoimmune rheumatic and connective tissue diseases. They could cause disease because of their capacity for being moved and inserted next to certain genes whose expression would be consequentially altered. Another way in which disease could potentially arise is when HERV‐encoded proteins are expressed. These proteins would be considered as [foreign] and they could trigger B‐cells to produce antibodies against them, which, in turn, might cross‐react with other proteins of our bodies. This mechanism could give rise to autoimmune diseases such as rheumatoid arthritis (RA), lupus erythematosus, Sjögren's syndrome (SJS), mixed connective tissue diseases and inflammatory neurological disease. Furthermore, it should be pointed out that HERV‐proteins may act as superantigens. Interestingly, some environmental agents seem to induce the expression of HERVs. Thus, ultraviolet light and several chemical agents could reactivate such sequences by altering their structure without modifying their nucleotide composition when the methylation pattern is changed. Therefore, the epigenetic changes observed in pathological conditions such as systemic lupus erythematosus (SLE) or cancer could be translated into an effect on the activation of some of the retroelements present in our genome which ultimately could have a direct or indirect role on the initiation and clinical evolution of certain chronic diseases. Copyright © 2009 John Wiley & Sons, Ltd.
The history of antiretrovirals: key discoveries over the past 25 years
Authors: De Clercq Erik 
Published: August 2009

AbstractWithin 25 years after zidovudine (3′‐azido‐2′,3′‐dideoxythymidine, AZT) was first described as an inhibitor of HIV replication, 25 anti‐HIV drugs have been formally approved for clinical use in the treatment of HIV infections: seven nucleoside reverse transcriptase inhibitors (NRTIs): zidovudine, didanosine, zalcitabine, stavudine, lamivudine, abacavir and emtricitabine; one nucleotide reverse transcriptase inhibitor (NtRTI): tenofovir [in its oral prodrug form: tenofovir disoproxil fumarate (TDF)]; four non‐nucleoside reverse transcriptase inhibitors (NNRTIs): nevirapine, delavirdine, efavirenz and etravirine; ten protease inhibitors (PIs): saquinavir, ritonavir, indinavir, nelfinavir, amprenavir, lopinavir, atazanavir, fosamprenavir, tipranavir and darunavir; one fusion inhibitor (FI): enfuvirtide; one co‐receptor inhibitor (CRI): maraviroc and one integrase inhibitor (INI): raltegravir. These compounds are used in various drug combination (some at fixed dose) regimens so as to achieve the highest possible benefit and tolerability, and to diminish the risk of virus‐drug resistance development. Copyright © 2009 John Wiley & Sons, Ltd.
Scientific discourse in three urban classrooms: The role of the teacher in engaging high school students in argumentation
Authors: McNeill Katherine L. , Pimentel Diane Silva 
Published: August 2009

AbstractArgumentation is a core practice of science and has recently been advocated as an essential goal of science education. Our research focuses on the discourse in urban high school science classrooms in which the teachers used the same global climate change curriculum. We analyzed transcripts from three teachers' classrooms examining both the argument structure as well the dialogic interactions between students. Between 19% and 35% of the discourse focused on scientific argumentation in that students were using evidence and reasoning to justify their claims. Yet in terms of dialogic interactions, only one teacher's classroom was characterized by student‐to‐student interactions and students explicitly supporting or refuting the ideas presented by their peers. This teacher's use of open questions appeared to encourage students to construct and justify their claims using both their scientific and everyday knowledge. Furthermore, her explicit connections to previous students' comments appeared to encourage students to consider multiple views, reflect on their thinking and reflect on the thinking of their classmates. This study suggests that a teacher's use of open‐ended questions may play a key role in supporting students in argumentation in terms of both providing evidence and reasoning for students' claims and encouraging dialogic interactions between students. © 2009 Wiley Periodicals, Inc. Sci Ed 94:203–229, 2010
Stem Cell Activity in the Developing Human Cornea
Authors: Davies Sarah B. , Chui Jeanie , Madigan Michelle C. , Provis Jan M. , Wakefield Denis , Di Girolamo Nick 
Published: August 2009

Abstract
The adult cornea harbors stem cells (SCs) in its periphery, in a niche known as the limbus. Over the past 2 decades there has been substantial research into these adult corneal SCs, their limbal niche, and their therapeutic applications. However, few studies have investigated how this niche and its SCs develop in humans. To better characterize this development, human fetal corneas from 8.5- to 22-weeks'-gestation (n = 173), neonatal (n = 2), and adult (n = 10) specimens were obtained. Histological and immunohistochemical assessments were conducted to determine embryological changes and expression of developmental and SC-related genes. Fresh fetal corneas were explanted to propagate corneal progenitors and cells characterized using reverse transcription-polymerase chain reaction, immunohistochemistry, flow cytometry, and colony-forming assays. A novel “ridge-like” structure was identified, circumscribing the fetal cornea, which we hypothesize represents the rudimentary SC niche. Immunohistochemistry disclosed “stem-like” cells across the cornea, becoming confined to this ridge with increasing gestational age. In addition, for the first time, pure long-term cultures of fetal corneal epithelium, which displayed phenotypical and functional properties similar to those of adult limbal SCs, were established. Optimization of culture techniques and purification of this SC population will allow for further investigation of their proliferative ability, with potential research and clinical applications. This study expands our understanding of limbal niche development and opens new avenues for investigation.
Disclosure of potential conflicts of interest is found at the end of this article.
Testing with model checkers: a survey
Authors: Fraser Gordon , Wotawa Franz , Ammann Paul E. 
Published: August 2009

AbstractAbout a decade after the initial proposal to use model checkers for the generation of test cases we take a look at the results in this field of research. Model checkers are formal verification tools, capable of providing counterexamples to violated properties. Normally, these counterexamples are meant to guide an analyst when searching for the root cause of a property violation. They are, however, also very useful as test cases. Many different approaches have been presented, many problems have been solved, yet many issues remain. This survey paper reviews the state of the art in testing with model checkers. Copyright © 2008 John Wiley & Sons, Ltd.
A systems integration framework for process analysis and improvement
Authors: Jain Rashmi , Chandrasekaran Anithashree , Erol Ozgur 
Published: August 2009

AbstractSystems Integration (SI) is an important element of Systems Engineering. It involves the integration of hardware, software, products, services, processes, and humans. The ever‐increasing scale of complexity of systems and its impact on the business requires that we revisit the processes involved in the development and integration of a system. This paper proposes a Systems Integration Process Model (SIPM) based on a comprehensive lifecycle view of systems integration. As part of the ongoing SI research at Stevens Institute of Technology, the authors have developed a Systems Integration Framework (SIF) which incorporates the relevant aspects of integration from a lifecycle perspective and sets a foundation to an end‐to‐end approach to SI. Our end‐to‐end approach focuses on how integration issues can be addressed up‐front to minimize integration related complexities and challenges later on in the system engineering process. This paper discusses the merits and benefits of applying the SIPM to evaluate and improve current SI processes in organizations. The paper provides, in addition to an overview of the SI framework, the activities included in the model. The model was pilot tested to evaluate the SI processes at a government agency. The results were used to provide recommendations for SI process reengineering. © 2009 Wiley Periodicals, Inc. Syst Eng
Unintended consequences of performance specifications for the reliability of military weapon systems
Authors: Kujawski Edouard 
Published: August 2009

AbstractThe use of performance specifications became a key US Department of Defense (DoD) acquisition reform in the 1990s. Gone were the detailed military specifications for parts and materials selection, workmanship, derating, and fault tolerance. Maximum use was to be made of commercial specs. Reliability would be specified only in quantitative terms such as Mean‐Time‐To‐Failure (MTTF) and/or the reliability R(t). However, there are significant differences between commercial and military weapon systems whereby performance specifications might bring in significantly greater mission risk. Reliability data from 1996 to 2000 might be an indicator of negative unintended consequences of the cancellation of military specifications. The acquisition of successful military systems requires a mix of performance and prescriptive reliability requirements that depend on the application, technology maturity, and complexity. © 2009 Wiley Periodicals, Inc. Syst Eng
Persistent Photoconductivity Studies in Nanostructured ZnO UV Sensors
Authors: Hullavarad Shiva , Hullavarad Nilima , Look David , Claflin Bruce 
Published: August 2009

Abstract
The phenomenon of persistent photoconductivity is elusive and has not been addressed to an extent to attract attention both in micro and nanoscale devices due to unavailability of clear material systems and device configurations capable of providing comprehensive information. In this work, we have employed a nanostructured (nanowire diameter 30–65 nm and 5 μm in length) ZnO-based metal–semiconductor–metal photoconductor device in order to study the origin of persistent photoconductivity. The current–voltage measurements were carried with and without UV illumination under different oxygen levels. The photoresponse measurements indicated a persistent conductivity trend for depleted oxygen conditions. The persistent conductivity phenomenon is explained on the theoretical model that proposes the change of a neutral anion vacancy to a charged state.
A simple approach for mouse embryonic stem cells isolation and differentiation inducing embryoid body formation
Authors: Fagundez Carol B. , Loresi Mónica A. , Quintana Ojea Marcos E. , Delcourt Stella M. , Testa Roberto , Gogorza Sebastián J. , Argibay Pablo F. 
Published: August 2009

AbstractStem cells were derived from hatched blastocyst‐stage mouse embryos of the C57BL/6 strain employing a knockout serum replacement instead of the traditional fetal calf serum, thereby avoiding the use of immunosurgery. Although fetal calf serum was not good for isolation of stem cells, a combination of this serum plus knockout serum increased the expansion rate of the cell culture. The derived cells were capable of maintaining an undifferentiated state during several passages, as demonstrated by the presence of alkaline phosphatase activity, stage‐specific embryonic antigen 1 (SSEA‐1), and octamer binding protein 4 (Oct‐4). Suspension culture in bacteriological dishes gave better results than the hanging drop method for differentiation by means of embryoid body formation. Mouse embryonic stem cells showed spontaneous differentiation into derivatives of the 3 germ layers in culture media supplemented with fetal calf serum but not with knockout serum.
Effects of an endothelial cell‐conditioned medium on the hematopoietic and endothelial differentiation of embryonic stem cells
Authors: Sun Xuan , Cheng Lamei , Duan Huaxin , Lu Guangxiu 
Published: August 2009

AbstractWe have examined the effect of mouse bone marrow endothelial cell‐conditioned medium (mEC‐CM) on hematopoietic and endothelial differentiation of mouse embryonic stem cells (mESCs). mEC‐CM can efficiently promote the differentiation of mESCs into Flk+ cells and hematopoietic colony‐forming cells. mEC‐CM proved to be as potent as a cytokine cocktail comprised of VEGF, bFGF, IGF and EGF. After inducing mESCs with mEC‐CM, cobblestone‐like cells were mechanically selected and identified which had the ability to incorporate DiI‐Ac‐LDL. DiI‐Ac‐LDL‐positive cells were endothelial‐like cells due to their expression of CD31 and Flk1, ability to bind to UEA1 and capacity to form capillary‐like tube structures on matrigel. In conclusion, mEC‐CM can efficiently promote the differentiation of mESCs into endothelial cells and hematopoietic colony‐forming cells. The differentiated endothelial‐like cells can be isolated by using DiI‐Ac‐LDL labeling and mechanical selection.