bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temperature‐dependent downhill unfolding of ubiquitin. II. Modeling the free energy surface
Authors: Chung Hoi Sung , Tokmakoff Andrei 
Published: April 2008

AbstractTo provide evidence for the interpretation of temperature‐dependent unfolding kinetics and the downhill unfolding scenario presented in the accompanying experimental article (Part I), the free energy surface of ubiquitin unfolding is calculated using statistical mechanical models of the Muñoz‐Eaton (ME) form. The models allow only two states for each amino acid residue, folded or unfolded, and permutations of these states generate an ensemble of microstates. One‐dimensional free energy curves are calculated using the number of folded residues as a reaction coordinate. The proposed sequential unfolding of ubiquitin's β‐sheet is tested by mapping the free energy onto two reaction coordinates inspired by the experiment as follows: the number of folded residues in ubiquitin's stable β‐strands I and II and those of the less stable strands III–V. Although the original ME model successfully captures folding features of zipper‐like one‐dimensional folders, it misses important tertiary interactions between residues that are far from each other in primary sequence. To take tertiary contacts into account, partially folded microstates based on a spherical growth model are included in the calculation and compared with the original model. By calculating the folding probability of each residue for a given point on the free energy surface, the unfolding pathway of ubiquitin is visualized. At low temperature, thermal unfolding occurs along a sequential unfolding pathway as follows: disruption of the β‐strands III–V followed by unfolding of the strands I and II. At high temperature, multiple unfolding routes are formed. The heterogeneity of the transition state explains the global nonexponential unfolding observed in the T‐jump experiment at high temperature. The calculation also reports a high stability for the α‐helix of ubiquitin. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Temperature‐dependent downhill unfolding of ubiquitin. I. Nanosecond‐to‐millisecond resolved nonlinear infrared spectroscopy
Authors: Chung Hoi Sung , Tokmakoff Andrei 
Published: April 2008

AbstractTransient thermal unfolding of ubiquitin is investigated using nonlinear infrared spectroscopy after a nanosecond laser temperature jump (T‐jump). The abrupt change in the unfolding free energy surface and the ns time resolution allow us to observe a fast response on ns to μs time‐scales, which we attribute to downhill unfolding, before a cross‐over to ms kinetics. The downhill unfolding by a sub‐population of folded proteins is induced through a shift of the barrier toward the native state. By adjusting the T‐jump width, the effect of the initial (Ti) and final (Tf) temperature on the unfolding dynamics can be separated. From the amplitude of the fast downhill unfolding, the fractional population prepared at the unfolding transition state is obtained. This population increases with both Ti and with Tf. A two‐state kinetic analysis of the ms refolding provides thermodynamic information about the barrier height. By a combination of the fast and slow unfolding and folding parameters, a quasi‐two‐state kinetic analysis is performed to calculate the time‐dependent population changes of the folded state. This calculation coincides with the experimentally obtained population changes at low temperature but deviations are found in the T‐jump from 67 to 78°C. Using temperature‐dependent barrier height changes, a temperature Φ value analysis is performed. The result shows a decreasing trend of ΦT with temperature, which indicates an increase of the heterogeneity of the transition state. We conclude that ubiquitin unfolds along a well‐defined pathway at low temperature which expands with increasing temperature to include multiple routes. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Using a strategy based on the concept of convergent evolution to identify residue substitutions responsible for thermal adaptation
Authors: Lin Yeong‐Shin 
Published: April 2008

AbstractFactors that are related to thermostability of proteins have been extensively studied in recent years, especially by comparing thermophiles and mesophiles. However, most of them are global characters. It is still not clear how to identify specific residues or fragments which may be more relevant to protein thermostability. Moreover, some of the differences among the thermophiles and mesophiles may be due to phylogenetic differences instead of thermal adaptation. To resolve these problems, I adopted a strategy to identify residue substitutions evolved convergently in thermophiles or mesophiles. These residues may therefore be responsible for thermal adaptation. Four classes of genomes were utilized in this study, including thermophilic archaea, mesophilic archaea, thermophilic bacteria, and mesophilic bacteria. For most clusters of orthologous groups (COGs) with sequences from all of these four classes of genomes, I can identify specific residues or fragments that may potentially be responsible for thermal adaptation. Functional or structural constraints (represented as sequence conservation) were suggested to have higher impact on thermal adaption than secondary structure or solvent accessibility does. I further compared thermophilic archaea and mesophilic bacteria, and found that the most diverged fragments may not necessarily correspond to the thermostability‐determining ones. The usual approach to compare thermophiles and mesophiles without considering phylogenetic relationships may roughly identify sequence features contributing to thermostability; however, to specifically identify residue substitutions responsible for thermal adaptation, one should take sequence evolution into consideration. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Brucea javanica fruit induces cytotoxicity and apoptosis in pancreatic adenocarcinoma cell lines
Authors: Lau Sin Ting , Lin Zhi‐Xiu , Zhao Ming , Leung Po Sing 
Published: April 2008

AbstractBrucea javanica fruit is thought to have anticancer properties in Chinese medicine and its extract has been shown to possess antiproliferative and pro‐apoptotic activities on human carcinoma cells. In the present study we demonstrated for the first time that Fructus Bruceae extract exhibited cytotoxic effects on the three pancreatic adenocarcinoma cell lines, PANC‐1, SW1990 and CAPAN‐1; the effects were comparable to those exhibited by camptothecin in our culture system. In addition, Fructus Bruceae extract induced fragmentation of genomic DNA, as evidenced by Hoechst staining and the cell death detection ELISAPLUS assay. Western blot analysis further showed down‐regulation of pro‐caspase 3 protein expression, indicating that the observed cytotoxic effects of the extract were associated with induction of apoptosis. These findings are not only significant in the development of traditional Chinese medicine as an alternative treatment for pancreatic cancer, but also in the elucidation of the potential mechanism(s) of Fructus Bruceae extract in cancer therapy. Copyright © 2008 John Wiley & Sons, Ltd.
Antifungal activity of Heterothalamus alienus metabolites
Authors: Pacciaroni Adriana del V. , de los Angeles Gette María , Derita Marcos , Ariza‐Espinar Luis , Gil Roberto R. , Zacchino Susana A. , Silva Gloria L. 
Published: April 2008

AbstractThe chemical study of Heterothalamus alienus gave rutin, spathulenol (1), (1R,7S)‐germacra‐4(15),5,10(14)‐trien‐1β‐ol (2), sakuranetin (3), padmatin 3‐acetate (4), (2R,3R)‐dihydroquercetin‐7,3′,4′‐trimethyl ether (5), (2R,3R)‐dihydroquercetin‐7,4′‐dimethyl ether (6), (2R,3R)‐3‐acetoxy‐5,7,4′‐trihydroxyflavanone (7), as the main components of an antifungal extract of the aerial parts of the plant. Compound 2 showed moderate activity, with Epidermophyton floccosum being the most susceptible species (MIC = 100 µg/mL); compound 3 showed the best antifungal behavior having a broad spectrum of action and the lowest MICs. This flavanone along with flavanolol 5 showed very good activity against standardized (MIC = 31.2 µg/mL) as well as clinical isolates of Trichophyton rubrum and T. mentagrophytes (MIC ranges 31.2–62.5 µg/mL and 31.2–125 µg/mL, respectively) and demonstrated not only fungistatic but also fungicide properties. Flavanolol 6 was active against all the dermatophytes tested with MICs of 62.5–250 µg/mL. Rutin, spathulenol (1) and the 3‐acetylated flavanones 4 and 7 were inactive or marginally active against the fungal panel. Copyright © 2008 John Wiley & Sons, Ltd.
Liquorice‐induced hypokalaemia and water retention in the absence of hypertension
Authors: Francini‐Pesenti F. , Puato M. , Piccoli A. , Brocadello F. 
Published: April 2008

AbstractThis is a case report of a woman who showed headache, weakness, upper‐limb edema and a generalized convulsive seizure after chronic ingestion of liquorice. She was taking oral contraceptives which can predispose to liquorice toxicity. Plasma potassium, aldosterone, renin activity and albumin were below the normal level. The abdominal echography and computerized tomography scan demonstrated a perihepatic and perisplenic thin liquid layer with liquid collection in the pelvis. The bioelectrical impedance suggested a hyperhydration state. After stopping the liquorice, the laboratory and bioelectrical values normalized and clinical upper‐limb edema and the liquid in the abdomen disappeared in a few days. Copyright © 2008 John Wiley & Sons, Ltd.
Keto‐enol tautomerism in linear and cyclic β‐diketones: A DFT study in vacuo and in solution
Authors: Alagona Giuliano , Ghio Caterina 
Published: April 2008

AbstractDFT geometry optimizations have been performed at the B3LYP/6‐31G* level in the gas phase and at the IEF‐PCM/B3LYP/6‐31G* level in tetrahydrofuran (THF) and aqueous solutions using scaled radii for the diketo and ketoenol forms of acetylacetone and cyclohexanedione. To evaluate basis set effects, starting from the aforementioned minima, the 6‐311++G** optimized structures have been obtained. A number of complexes of both systems including one explicit water molecule have been considered up to the B3LYP/6‐311++G** level, for cyclohexanedione taking into account the B3LYP/6‐31G* basis set superposition errors as well. The diketo–ketoenol interconversion mechanisms have been investigated at the B3LYP/6‐31G* level in vacuo. Interestingly, the geometric constraint due to the presence of the ring facilitates the description of the reaction mechanism in cyclohexanedione. Despite the very different flexibility of the two systems that in the case of acetylacetone prevents a straightforward interconversion of the diketo to the most stable of its ketoenol forms, both reactions occur with a very high barrier (about 62–63 kcal/mol), unaffected by continuum solvents, that decreases by 2.5–3.5 kcal/mol after the inclusion of thermal corrections. The barriers are almost halved, becoming ∼31–35 kcal/mol, for the addition of a single water molecule according to various model reaction paths. Thermal corrections are limited (0.8–1.6 kcal/mol) for those adducts. The formation of a 1,1‐diol, explored in the case of acetylacetone, might facilitate the obtainment of the most stable diketo conformation, featuring the carbonyl groups in distinct orientations. Inclusion of dispersion and basis set effects via the G2MP2 protocol does not alter the relative stability of both system tautomers. In contrast, the G2MP2 interconversion barriers for the isolated systems in vacuo are close to the B3LYP ones, whereas they turn out to be somewhat higher than the free energy‐based B3LYP barriers in the presence of a catalytic water molecule. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Quantum‐based models of charge‐dependent potential energy surfaces: Three‐state models
Authors: Valone Steven M. , Li Jiabo , Jindal Saryu 
Published: April 2008

AbstractQuantum‐based models of how potential energies depend on charge are developed from a three‐state model, at the level of neglecting state‐to‐state overlap. The energy as a function of charge is defined as proposed previously (Valone and Atlas, J Chem Phys 2004, 120, 7262). With this definition, addition of a third state smooths the derivatives of the energy model with respect to charge at integer values of charge that are in the interior of the allowed charge range. These derivatives are related to the chemical potential. At the dissociation limit, this model converges to established limits. Another dependence is proposed that uses two different charges simultaneously. The concepts are illustrated, with calculations on an OH molecule. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Revisiting the foundations of quantum theory of atoms in molecules (QTAIM): The variational procedure and the zero‐flux conditions
Authors: Nasertayoob Payam , Shahbazian Shant 
Published: April 2008

AbstractA rigorous mathematical procedure is proposed in order to employ the variational apparatus in “Quantum theory of atoms in molecules.” This mathematical procedure is free from the previously reported mathematical obstacles. Although it is possible to apply the Schrödinger's variational procedure to derive the putative net zero‐flux condition, no claim has been made to derive the equation of motion (Schrödinger equation) from subsystem variational procedure. In this regard, the problem of admissible and general neighborhoods and their relevance to the subsystem variational procedure has been discussed thoroughly in this article. In the end, a brief discussion has been offered to emphasize the difference between the net and local zero‐flux conditions with particular emphasize on its logical consequences. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Koopmans' approximation applied in atoms and diatomic molecules using the diffusion quantum Monte Carlo method
Authors: Delfino Angelotti Wagner Fernando , Streit Lívia , Luiz Da Fonseca André , Custodio Rogério 
Published: April 2008

AbstractKoopmans' theorem was applied to generate trial wave functions for ions from neutral systems and further applied in the determination of vertical ionization energies using the diffusion quantum Monte Carlo (DQMC) method. The results for successive and conventional ionization energies for atoms and diatomic molecules using the Slater minimum basis set with polarization wave functions indicate that DQMC provides a significant quantity of relaxation and electronic correlation effects. The conventional ionizations for core electrons calculated with DQMC for atoms and diatomic molecules yielded an average deviation of around 2–3 eV from the experimental results, which is excellent when compared with a deviation of around 17 eV estimated from Koopmans' theorem. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
The Tyranny of Small Steps: a reoccurring behaviour in management
Authors: Haraldsson Hörður V. , Sverdrup Harald U. , Belyazid Salim , Holmqvist Johan , Gramstad Robin C. J. 
Published: April 2008

AbstractThe Tyranny of Small Steps (TYST) behaviour has been investigated. Explained through a systemic perspective, the behaviour TYST is an unwanted change to a system through a series of small activities that may be independent from one another. These activities are small enough not to be detected by the ‘surveillance’ within the system, but significant enough to encroach upon the ‘tolerance zone’ of the system and compromise integrity of the system. TYST is an unintentional process that is experienced within the system and made possible by the lack of transparency between an overarching level and a local level where the encroachment is taking place. The Örby case study illustrates a real life manifestation of the TYST behaviour in management and planning. The TYST illustrates the necessity for total transparency in any systems in order to avoid unintended consequence. The TYST process may be regarded as a part of wide range of complex systems but depending on the conditions, it can remain dormant, and only become active when the conditions for lack of transparency are fulfilled. Copyright © 2008 John Wiley & Sons, Ltd.
Systems science and complexity: some proposals for future development
Authors: Leleur Steen 
Published: April 2008

AbstractIn this paper some new, conceptual ideas referred to as a complexity orientation are presented on the basis of systemic planning (SP), which has been developed as a proactive, multi‐methodology approach for complex planning tasks. Specifically, the complexity orientation is compared to other systems science research orientations represented by the following labels: functionalist, interpretive, emancipatory and postmodern. After presentation and discussion of the research orientation framework, SP is compared to other current systems and management practice. Finally, the potential of a complexity orientation is treated more generally and also with a focus on its epistemological interpretation, which is carried out with a special emphasis on the work of Luhmann. General findings of the paper are that a complexity orientation ought to complement the other four research orientations to serve as a methodological platform for management practice and that Luhmann's theories ought to be addressed by the systems community as a potential for informing further development of systems science and thinking. Copyright © 2008 John Wiley & Sons, Ltd.
Is management science or art?
Authors: Gao Fei 
Published: April 2008

AbstractIn this paper I have drawn a brief picture to map the nature of management in modern high‐tech organizations from the viewpoint of critical systems thinking. First, I point out the difference between science and art. Then, following Jackson's classification of different systems approaches such as modernism and postmodernism, I connect modernism with objectivism and collective subjectivism, and postmodernism with individual subjectivism. Through clarifying three ways of knowing/understanding the world and introducing a new knowledge systems model of modern high‐tech corporations, I argue that in the knowledge age, management is both a science and an art. Objects under consideration belonging to different parts of reality require different approaches to deal with. The purpose of this article is to give a brief explanation of why management is both a science and an art, and to inspire further debate and discussion on the essence of management among academics and practitioners. Copyright © 2008 John Wiley & Sons, Ltd.
A theoretical framework for a structuration model of social issues in software development in information systems
Authors: Loureiro‐Koechlin Cecilia 
Published: April 2008

AbstractThis study looks at how human and social issues affect software developers' work and the software they produce. It focuses on the development of software to support information systems, and therefore positions software development as an activity within Information Systems Development. Although some research in IS and software development address human and social issues they do so by considering either business organisations or software development environments separately but do not connect both contexts together. This research tries to build this connection through a model of social issues in software development. The model was generated from data collected from an interpretive online ethnography of virtual communities of software developers. The model of social issues complements Orlikowski's structurational model of enactment of technologies‐in‐practice and suggests that human and social issues that affect the production of software emerge from three different contexts: software development environment, software development practices and complex business organisations. Copyright © 2008 John Wiley & Sons, Ltd.
Prenatal ultrasound detection of facial clefts: a prospective study of 49 314 deliveries in a non‐selected population in Norway
Authors: Offerdal K. , Jebens N. , Syvertsen T. , Blaas H.‐G. K. , Johansen O. J. , Eik‐Nes S. H. 
Published: April 2008

AbstractObjectivesTo evaluate prenatal detection of facial clefts by ultrasound examination in a large non‐selected population, and to study trends in detection rates over 18 years, as well as the prevalence of isolated cases and those with associated anomalies.MethodsThis prospective follow‐up study from January 1987 to December 2004 was divided into two 9‐year periods. The study included all registered cases of prenatally or postnatally diagnosed facial clefts in a non‐selected population in Norway.ResultsA total of 101 fetuses or newborns with facial clefts in a population of 49 314 deliveries were registered. The distribution of clefts was: 25 (25%) cleft lip, 52 (51%) cleft lip and palate, and 24 (24%) cleft palate (CP). No CP was detected prenatally. Cleft lip with or without cleft palate (CL(P)) was detected prenatally in 35/77 (45%) cases, with a significant increase in the detection rate from 34% to 58% between the two 9‐year periods (P = 0.03). Over the whole study period CL(P) was detected at a median of 19 + 2 gestational weeks, with no change over time; altogether 24/35 (69%) cases were detected at the routine second‐trimester ultrasound examination. Thirty‐three of 77 (43%) cases of CL(P) and 14/24 (58%) cases of CP had associated anomalies; 12/101 (12%) had chromosomal aberrations. In 18/101 (18%) the clefts were part of a syndrome or sequence.ConclusionsThe detection rate for CL(P) improved significantly over time. Detection of CL(P) is important because nearly half the cases have associated anomalies. Copyright © 2008 ISUOG. Published by John Wiley & Sons, Ltd.
Faith‐based organizing for youth: One organization's district campaign for small schools policy
Authors: Snyder Ron 
Published: April 2008

AbstractOakland Community Organizations (OCO) has worked for over ten years to improve educational opportunities in low‐income neighborhoods in Oakland, California. The work of thousands of parent, teacher, youth, and community leaders has resulted in the formation of nearly fifty new small schools and more than ten charters, creating settings for individualized learning environments and the opportunity for quality choices for many of Oakland's low‐income families. In this article, OCO's executive director, Ron Snyder, outlines a four‐phase organizing process undertaken by OCO, based on a set of organizing principles that have sustained community‐led education reform despite constant changes in the political and school district environment: the centrality of love (self‐interest) as a motivator for advocacy; the importance of quality research and powerful ideas (vision) as alternatives to the status quo; application of a model that creates a common structure, language, and experience to sustain leaders; the need for institutional and network power to apply leverage; the flexibility to seize opportunity when the window is open; and faithfulness to the object of our love: our children.
FDR Explorer
Authors: Freitas Leo , Woodcock Jim 
Published: April 2008

Abstract
We describe: (1) the internal structures of FDR, the refinement model checker for Hoare’s Communicating Sequential Processes (CSP); and (2) an application-programming interface (API) that allows users to interact more closely with FDR and to have finer-grain control over its behaviour and data structures. This API makes it possible to create optimised CSP code to perform refinement checks that are more space or time efficient, enabling the analysis of more complex and data-intensive specifications. The API can be used either by those constructing CSP models or by tools that automatically generate CSP code. We present examples of using our tool, including handling advanced FDR features such as transparent functions, which compress state spaces before checking. We also show how to transform FDR’s graph format into a graph notation such as JGraph, enabling visualisation of labelled transition systems of CSP specifications.