bluuebunny/crossref_metadata_2025 huggingface dataset:
Cationic ring‐opening polymerization behavior of a five‐membered cyclic thiocarbonate having a spiro‐linked adamantane moiety
Authors: Nemoto Nobukatsu , Ito Yoshinori , Endo Takeshi
Published: November 2004

This work deals with the synthesis and cationic ring‐opening polymerization behavior of a novel five‐membered cyclic thiocarbonate bearing a spiro‐linked adamantane moiety, tricyclo[3.3.1.13,7]decane‐2‐spiro‐4′‐(1′,3′‐dioxolane‐2′‐thione) (TC2). The cationic ring‐opening polymerization of TC2 did not proceed with trifluoromethanesulfonic acid, methyl trifluoromethanesulfonate, triethyloxonium tetrafluoroborate (Et3OBF4), boron trifluoride etherate (BF3OEt2), titanium tetrachloride, or methyl iodide as the initiator, presumably because of the steric hindrance of the adamantane moiety. However, the cationic ring‐opening copolymerization of TC2 with five‐ or six‐membered cyclic thiocarbonates, that is, 1,3‐dioxolane‐2‐thione, 1,3‐dioxane‐2‐thione, 5‐methyl‐1,3‐dioxane‐2‐thione, or 5,5‐dimethyl‐1,3‐dioxane‐2‐thione, initiated by BF3OEt2 or Et3OBF4, proceeded to afford the corresponding copolymer via a selective ring‐opening direction. The increase in the feed ratio of TC2 in the copolymerization increased the unit ratio derived from TC2 in the copolymer; however, the molecular weight of the copolymer decreased. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 699–707, 2003
Bicyclobutanes and cyclobutenes: Unusual carbocyclic monomers
Authors: Hall H. K. , Padias Anne Buyle
Published: November 2004

Bicyclobutanes and cyclobutenes substituted with electron‐attracting groups represent novel classes of reactive monomers. They readily undergo free‐radical and anionic polymerizations to give high polymers consisting of 1,3‐ and 1,2‐enchained cyclobutane rings, respectively. They also copolymerize readily with conventional vinyl monomers. These polymers display numerous attractive properties in comparison with their vinyl counterparts, including enhanced thermal stability, superior optical properties, and higher glass‐transition temperatures. The syntheses of these monomers are reviewed, and suggestions toward future larger scale production are made. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 625–635, 2003
Grafting of poly(styrene‐co‐p‐chloromethyl styrene) with ethyl methacrylate via atom transfer radical polymerization catalyzed by CuCl/1,2‐dipiperidinoethane
Authors: Coşkun Mehmet , Mürşi̇t Temüz Mehmet
Published: November 2004

Poly(styrene‐graft‐ethyl methacrylate) graft copolymer was prepared by atom transfer radical polymerization (ATRP) with poly(styrene‐co‐p‐chloromethyl styrene)s in various compositions as macroinitiator in the presence of CuCl/1,2‐dipiperidinoethane at 130 °C in N,N‐dimethylformamide. Both macroinitiators and graft copolymers were characterized by elemental analysis, IR, 1H and 13C NMR, and differential scanning calorimetry. 1,2‐Dipiperidinoethane was an effective ligand of CuCl for ATRP in the graft copolymerization. The controlled growth of the side chain provided the graft copolymers with polydispersities of 1.60–2.05 in the case of poly(styrene‐co‐p‐chloromethyl styrene) (62:38) macroinitiator. Thermal stabilities of poly(styrene‐graft‐ethyl methacrylate) graft copolymers were investigated by thermogravimetric analysis as compared with those of the macroinitiators. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 668–673, 2003
Molecular deformation mechanisms of isotactic polypropylene in α‐ and β‐crystal forms by FTIR spectroscopy
Authors: Huy Trinh An , Adhikari Rameshwar , Lüpke Thomas , Henning Sven , Michler Goerg H.
Published: November 2004

The orientation behavior of isotactic polypropylene (iPP) in α‐ and β‐crystal form was investigated by rheo‐optical Fourier transformed infrared (FTIR) spectroscopy. This method enabled quantification of the degree of orientation as a feature of structural changes during uniaxial elongation in not only the crystalline phase but also the amorphous one. Molecular orientation mechanisms can be successfully derived from experimental results. Generally, three mechanisms were detected for iPP: (1) interlamellar separation in the amorphous phase, (2) interlamellar slip and lamellar twisting at small elongations, and (3) intralamellar slip at high elongations. The third mechanism was favored by α‐PP, whereas β‐PP favored the second mechanism, which, in fact, was responsible for the different mechanical properties of both materials at the macroscopic level. On the other hand, crystallization conditions may have significantly affected the amorphous orientation. Nevertheless, for both iPP types the chains in the amorphous phase always oriented less than did those in the crystalline phase. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 4478–4488, 2004
Comparing stress levels of parents of children with cancer and parents of children with physical disabilities
Authors: Hung Jen Wen , Wu Yee‐Hwa , Yeh Chao‐Hsing
Published: November 2004

Aim: To evaluate whether parental stress differs between parents of children with physical disabilities and parents of children with cancer.

Methods: Parents (92 with disabled children and 89 with children with cancer) were recruited to complete the measures of the Parenting Stress Index/Short Form.

Results: Diagnostic group differences were found across the parenting stress measures used in this study. The parents of children with cancer experienced significantly higher levels of stress compared with the parents of disabled children. The mean scores of each subscale (PD, PCDI, and DC) and total score scales in both groups approached were above the 90th percentile of Abidin's normative sample (PD=36, PCDI=27, DC=36, Total=91), except for the PD and DC subscales in the disabled children group, which approached the 90th percentile.

Conclusion: The results of the study suggest that most of the parents in our sample should be referred for more in‐depth diagnostic study and professional counseling in stress management. Therefore, a normative score on the PSI/SF for Taiwanese parents with healthy children should be established to identify whether differences exist between parents whose children are healthy and those whose children have been diagnosed with a chronic illness. Copyright © 2004 John Wiley & Sons, Ltd.
Molego‐based definition of the architecture and specificity of metal‐binding sites
Authors: Schein Catherine H. , Zhou Bin , Oezguen Numan , Mathura Venkatarajan S. , Braun Werner
Published: November 2004

Decomposing proteins into “molegos,” building blocks that are conserved in sequence and 3D‐structure, can identify functional elements. To demonstrate the specificity of the decomposition method, the PCPMer program suite was used to numerically define physical chemical property motifs corresponding to the molegos that make up the metal‐containing active sites of three distinct enzyme families, from the dimetallic phosphatases, DNase 1 related nucleases/phosphatases, and dioxygenases. All three superfamilies bind metal ions in a β‐strand core region but differ in the number and type of ions needed for activity. The motifs were then used to automatically identify proteins in the ASTRAL40 database that contained similar motifs. The proteins with the highest PCPMer score in the database were primarily metal‐binding enzymes that were related in function to those in the alignment used to generate the PCPMer motif lists. The proteins that contained motifs similar to the dioxygenases differed from those found with PCP‐motifs for phosphatases and nucleases. Relatively few metal‐binding enzymes were detected when the search was done with PCP‐motifs defined for interleukin‐1 related proteins, which have a β‐strand core but do not bind metal ions. While the box architecture was constant in each superfamily, the specificity for the metal ion preferred for enzymatic activity is determined by the pattern of carbonyl, hydroxyl or imadazole groups in key positions in the molegos. These results have implications for the design of metal‐binding enzymes, and illustrate the ability of the PCPMer approach to distinguish, at the sequence level, structural and functional elements. Proteins 2005. © 2004 Wiley‐Liss, Inc.
Applications of extensive survey techniques to describe freshwater pearl mussel distribution and macrohabitat in the River Spey, Scotland
Authors: Hastie L. C. , Cooksley S. L. , Scougall F. , Young M. R. , Boon P. J. , Gaywood M. J.
Published: November 2004

The spatial distribution and associated physical habitat of endangered freshwater pearl mussels (Margaritifera margaritifera) in a 145 km stretch of the River Spey, northeast Scotland, were investigated. The overall size of the SpeyM. margaritiferapopulation was estimated to be in the order of 10 million. Mussel distributions were compared with River Corridor Survey (RCS) macrohabitat data and found to be positively associated with coarse riverbed substrata, ‘fast‐flowing’ waters, riparian woodland, and river bends; and negatively associated with shingle bars, flood barriers, ‘slow‐flowing’ waters, eroding cliffs and aquatic macrophytes. Significant positive relationships between mussel density and channel slope, width and bank height, were also observed. Binary logistic regression models (based on four to six features) were used to predict the presence/absence of mussels or the occurrence of ‘optimal’ mussel habitat (i.e. mussel density >1 m−2) at any given site. Overall predictive success rates of 79% and 78% were achieved, respectively. Discriminant function models (based on five variables) were also used, with predictive success rates of 78% and 88%, respectively. Copyright © 2004 John Wiley & Sons, Ltd.
Likelihood‐based modelling of age‐related normal ranges for ordinal measurements: changes in visual acuity through early childhood
Authors: Wade A. M. , Salt A. T. , Proffitt R. V. , Heavens S. J. , Sonksen P. M.
Published: November 2004

This paper investigates the construction of age‐related standards for ordinal outcome data. Asymmetric logistic models are used to describe the age‐related changes in the cumulative probabilities for each ordinal level. Maximum likelihood estimation of model parameters allows the use of likelihood ratio tests to ascertain the appropriate model complexity. In contrast to methodologies for constructing age‐related standards where the outcome is continuous, we show how the methodology leads directly to centile estimation for individuals. The method is illustrated using visual acuity measurements collected from 2968 children between 2 and 9 years of age made on a 30‐point ordinal scale. We show how, in this instance, smoothing of parameters across ordinal categories leads to reduced validity of the centiles, justifying the need for specialized methodology for non‐continuous outcomes. Copyright © 2004 John Wiley & Sons, Ltd.
Evaluation of log‐rank tests for infrequent observations from a multi‐state process, with application to HPV vaccine efficacy
Authors: Kang Minhee , Lagakos Stephen W.
Published: November 2004

Genital infection by human papillomavirus (HPV) is a common sexually transmitted disease, with over 25 per cent prevalence among young women in the US. Infections are usually without symptoms and transient (or reversible), but a small proportion of infections persist and are believed to be responsible for nearly all cervical cancers and precursor lesions such as cervical intraepithelial neoplasia (CIN). Therefore, successful vaccines against persistent HPV infections could have a great impact in preventing cervical cancers. In trials being planned, ongoing, and recently completed, a log‐rank or a similar test may be employed to assess a vaccine effect in comparison to placebo, with an infection ‘event’ defined to capture persistent but not transient infections. However, it is not clear how best to define such an event, because (1) diagnostic tests cannot distinguish a persistent from a transient infection, (2) participants are only examined periodically, and (3) there can be misclassification errors in the detection of infections. This paper evaluates several definitions of persistent infection that are based on periodically observed infection statuses by postulating a multi‐state model for persistent and transient infections. The type I error and the power of tests on vaccine efficacy based on these operational definitions are then examined under various scenarios of how a vaccine might affect the infection–disease process. We find that none of the candidates performs satisfactorily, thus raising concerns that clinical trials based only on infection endpoints will not be reliable. Copyright © 2004 John Wiley & Sons, Ltd.
Analysis of clustered and interval censored data from a community‐based study in asthma
Authors: Bellamy Scarlett L. , Li Yi , Ryan Louise M. , Lipsitz Stuart , Canner Marina J. , Wright Rosalind
Published: November 2004

Many authors in recent years have proposed extensions of familiar survival analysis methodologies to apply in dependent data settings, for example, when data are clustered or subject to repeated measures. However, these extensions have been considered largely in the context of right censored data. In this paper, we discuss a parametric frailty model for the analysis of clustered and interval censored failure time data. Details are presented for the specific case where the underlying time to event data follow a Weibull distribution. Maximum likelihood estimates will be obtained using commercially available software and the empirical efficiency of these estimators will be explored via a simulation study. We also discuss a score test to make inferences about the magnitude and significance of over‐dispersion in clustered data settings. These methods will be illustrated using data from the East Boston Asthma Study. Copyright © 2004 John Wiley & Sons, Ltd.
Viscoamylographic Studies on Zea Mays [Mexican White Tuxpeño Maize] Partial Gelatinization with Calcium Hydroxide
Authors: Sánchez‐Tovar Salvador A. , Salazar‐Zazueta Alfredo , Mena‐Iniesta Baltasar , Durán‐de‐Bazúa Carmen
Published: November 2004

Mexicans staple food is maize “tortilla”, prepared by thermal‐alkaline processes. The sensory properties of “masa” and “tortilla” depend on the reactions occuring between lime and chemical compounds in maize. In the present study, the effect of different calcium hydroxide, Ca(OH)2, concentrations (0.0, 0.10, 0.30, 0.50 %, dry basis, d.b.) on the apparent viscosity and maximum gelatinization temperature of a cornstarch water slurry was assessed. This Mexican traditional thermal‐alkaline gelatinization reaction (TAGR) was evaluated in a Brabender Viscoamylograph. This small well‐mixed reactor was homogeneously heated, and apparent viscosity data from corn starch were recorded in Brabender Units BU). It was found that an increase in Ca(OH)2 concentrations considerably increases the apparent viscosity, thus reducing the time needed to reach the maximum gelatinization temperature. A mathematical model that represents the phenomena, that occur in the Viscoamylograph, was developed. In the model the Viscoamylograph was considered as a batch reactor and the apparent kinetic coefficients for the TAGR were obtained, including mass balances and thermal‐alkaline gelatinization rates, considering a spherical cornstarch granule formed by a starchy matrix. Activation energy found for this reaction was 1241 kJ.
Drops of water and of soap solution: Students' constraining mental models of the nature of matter
Authors: Eilam Billie
Published: November 2004

This study investigates how 25 junior high school students employed their bodies of knowledge and responded to problem cues while individually performing a science experiment and reasoning about a drops phenomenon. Line‐by‐line content analysis conducted on students' written ad hoc explanations aimed to reveal students' concepts and their relations within their explanations, and to construe students' mental models for the science phenomenon based on level of specification, models' correspondence with scientific claims, macro versus micro view of matter, and type of evidence used. We then inferred four types of knowledge representations for the nature of matter. Findings are discussed in terms of implications for science teaching. © 2004 Wiley Periodicals, Inc. J Res Sci Teach 41: 970–993, 2004
Enhancing the quality of argumentation in school science
Authors: Osborne Jonathan , Erduran Sibel , Simon Shirley
Published: November 2004

The research reported in this study focuses on the design and evaluation of learning environments that support the teaching and learning of argumentation in a scientific context. The research took place over 2 years, between 1999 and 2001, in junior high schools in the greater London area. The research was conducted in two phases. In phase 1, working with a group of 12 science teachers, the main emphasis was to develop sets of materials and strategies to support argumentation in the classroom, and to support and assess teachers' development with teaching argumentation. Data were collected by video‐ and audio‐recording the teachers' attempts to implement these lessons at the beginning and end of the year. During this phase, analytical tools for evaluating the quality of argumentation were developed based on Toulmin's argument pattern. Analysis of the data shows that there was significant development in the majority of teachers use of argumentation across the year. Results indicate that the pattern of use of argumentation is teacher‐specific, as is the nature of the change. In phase 2 of the project, the focus of this paper, teachers taught the experimental groups a minimum of nine lessons which involved socioscientific or scientific argumentation. In addition, these teachers taught similar lessons to a comparison group at the beginning and end of the year. The purpose of this research was to assess the progression in student capabilities with argumentation. For this purpose, data were collected from 33 lessons by video‐taping two groups of four students in each class engaging in argumentation. Using a framework for evaluating the nature of the discourse and its quality developed from Toulmin's argument pattern, the findings show that there was improvement in the quality of students' argumentation. This research presents new methodological developments for work in this field. © 2004 Wiley Periodicals, Inc. J Res Sci Teach 41: 994–1020, 2004
Design‐based science and student learning
Authors: Fortus David , Dershimer R. Charles , Krajcik Joseph , Marx Ronald W. , Mamlok‐Naaman Rachel
Published: November 2004

Design‐Based Science (DBS) is a pedagogy in which the goal of designing an artifact contextualizes all curricular activities. Design is viewed as a vehicle through which scientific knowledge and real‐world problem‐solving skills can be constructed. Following Anderson and Hogan's (1999) call to document the design of new science pedagogies, this goal of this article is twofold: (a) to describe DBS, and (b) to evaluate whether significant science knowledge was constructed during consecutive enactments of three DBS units. In this study, 92 students participated in the consecutive enactments of three different DBS units. The development of their scientific knowledge was assessed through posters and models constructed during the curricular enactments and by identical pre‐ and post‐instruction written tests. The posttests showed considerable gains compared with the pretests, while the models and posters show application of this newly constructed knowledge in solving a design problem. These positive results support efforts being made to restructure school science around inquiry‐based curricula in general and design‐based curricula in particular. © 2004 Wiley Periodicals, Inc. J Res Sci Teach 41: 1081–1110, 2004
When sex hurts, anxiety and fear orient attention towards pain
Authors: Payne Kimberley A. , Binik Yitzchak M. , Amsel Rhonda , Khalifé Samir
Published: November 2004

Hypervigilance for pain‐relevant stimuli has been associated with anxiety, fear of pain and anxiety sensitivity. This attentional bias has been primarily investigated in heterogeneous pain groups or pain‐free controls, but has not been examined in pain conditions where anxiety and fear are likely to play a central role. Due to the intimate and interpersonal nature of genital pain experienced during sexual intercourse, Vulvar Vestibulitis Syndrome (VVS) constitutes an ideal sample in which to investigate the role of cognitive and affective factors in pain perception and maintenance. Seventeen women suffering from VVS and an equal number of age and education matched control women completed an emotional Stroop and memory recall task in addition to a series of questionnaires assessing pain‐hypervigilance, state and trait anxiety, fear of pain, and anxiety sensitivity. VVS sufferers reported hypervigilance for coital pain and also exhibited a selective attentional bias towards pain stimuli on the emotional Stroop task as compared with controls. This effect was predicted by state and trait anxiety and fear of pain. According to these data, treament strategies for VVS should target anxiety and fear in addition to sensory systems.
Late Reconstruction of Neglected Metacarpal Shaft Defects Due to Gunshot Wound
Authors: AKMAZ IBRAHIM , KIRAL AHMET , PEHLIVAN OZCAN , MAHIROGULLARI MAHIR , SOLAKOGLU CAN , RODOP OSMAN , KUŞKUCU MESIH
Published: November 2004

We evaluated eight patients after delayed treatment of nine metacarpal bone defects due to gunshot injuries. The mean length of the metacarpal defects was 3 cm and the average time between the gunshot injury and the reconstruction surgery was 10 months. Although all of the patients had been treated with wound irrigation and debridement immediately following injury, no attempt had been made to repair the metacarpal defect or to maintain metacarpal length. As a result, serious shortening had occurred. After the original length of the metacarpal had been restored by distraction of the soft tissues (1 mm/day), a tri-cortical iliac bone graft was inserted into the bone defect. The average follow-up time was 15 months. Clinical and radiological union was established in all cases after an average of 12 weeks. The mean grip strength of the hand and the mean range of motion of the metacarpophalangeal joint increased by 24% and 60%, respectively.
Treatment of Cubital Tunnel Syndrome by Frontal Partial Medial Epicondylectomy. A Retrospective Series of 55 Cases
Authors: POPA M. , DUBERT TH.
Published: November 2004

The outcomes of 55 cases of cubital tunnel syndrome treated by a partial frontal epicondylectomy are presented at a mean follow-up of 38 months follow-up. According to McGowan classification, 25 cases were grade I (45%), 12 grade II (22%) and 18 grade III (33%). The results (Wilson and Krout classification) were excellent or good in 41 patients (75%), fair in nine patients and unchanged in five, without any worsening or recurrence. Total relief was reported in 80% of grade I, 75% of grade II and 66% of grade III patients. Seven painful scars and one persistent 15° elbow extension deficit were the only complications. The satisfaction rate was 93%. This technique preserves bony protection, the blood supply and gliding tissues for the nerve and nerve recovery were comparable to other surgical procedures. Residual pain at the osteotomy site was not a serious problem.
Holocene paleoenvironmental implications of diatom and organic carbon records from the southeastern Kara Sea (Siberian Margin)
Authors: Polyakova Yelena I. , Stein Ruediger
Published: November 2004

Diatom assemblages and organic carbon records from two sediment cores located within an estuarian bay of the inner Kara Sea trace changes in Yenisei River runoff and postglacial depositional environments. Paleosalinity and sea-ice reconstructions are based on modern relationships of local diatom assemblages and summer surface-water salinity. Approximately 15,500 cal yr B.P., rivers and bogs characterized the study area. When sea level reached the 38- to 40-m paleo-isobath approximately 9300 cal yr B.P., the coring site was flooded. From 9300–9100 cal yr B.P., estuarine conditions occurred proximal to the depocenter of fluvially derived material, and salinity was <7–8. Paleosalinity increased to 11–13 by 7500 cal yr B.P., following postglacial sea-level rise and the southward shift of the Siberian coast. Sharp decreases in diatom accumulation rates, total sediment, and organic carbon also occurred, suggesting the presence of brackish conditions and greater distance between the coast and study site. Maximum paleosalinity (up to 13) was recorded between 7500 and 6000 cal yr B.P., which was likely caused by the enhanced penetration of Atlantic waters to the Kara Sea. Stepwise decreases to modern salinity levels happened over the last 6000 cal yr.
Large‐scale hydraulic conductivities inferred from three‐dimensional groundwater flow and4He transport modeling in the Carrizo aquifer, Texas
Authors: Patriarche Delphine , Castro Maria Clara , Goblet Patrick
Published: November 2004

Through a series of groundwater flow and4He transport simulations, this study illustrates the conceptual and practical gains achieved by expanding a two‐dimensional (2‐D) model to a true 3‐D one through an application in the Carrizo aquifer and surrounding formations in southwestern Texas. The 3‐D simulations allow for a more detailed and accurate definition of the heterogeneities of the system by specifically identifying and differentiating processes that directly impact the three‐dimensional hydraulic conductivity field. It is shown that while hydraulic conductivity decreases exponentially along the regional groundwater flow direction, such decrease is better described as a function of depth rather than recharge distance. This relationship reflects the combined influences of differential compaction of the media as well as downdip lithological change. The intrinsic permeability derived from this relationship agrees with field information and with previous findings obtained for the continental crust for depths ≤2 km, suggesting that for large scales, decrease rate of permeability with depth is independent of the media. Results also suggest that the solution for groundwater flow simulations based on calibration of hydraulic heads depends on the ratio between hydraulic conductivities of different formations, indicating that an infinite number of solutions are available for calibration of 3‐D groundwater flow models. Understanding how geological processes directly affect the 3‐D hydraulic conductivity field at the regional scale is essential not only to hydrogeological applications but also at improving our understanding of the Earth's crust and mantle dynamics by allowing for a more accurate quantification of helium and heat fluxes.
Late Eocene to early Miocene ice sheet dynamics and the global carbon cycle
Authors: Lear C. H. , Rosenthal Y. , Coxall H. K. , Wilson P. A.
Published: November 2004

Paired benthic foraminiferal trace metal and stable isotope records have been constructed from equatorial Pacific Ocean Drilling Program Site 1218. The records include the two largest abrupt (<1 Myr) increases in the Cenozoic benthic oxygen isotope record: Oi‐1 in the earliest Oligocene (∼34 Ma) and Mi‐1 in the earliest Miocene (∼23 Ma). The paired Mg/Ca and oxygen isotope records are used to calculate seawater δ18O (δw). Calculated δw suggests that a large Antarctic ice sheet formed during Oi‐1 and subsequently fluctuated throughout the Oligocene on both short (<0.5 Myr) and long (2–3 Myr) timescales, between about 50 and 100% of its maximum earliest Oligocene size. The magnitudes of these fluctuations are consistent with estimates of sea level derived from sequence stratigraphy. The transient expansion of the Antarctic ice sheet at Mi‐1 is marked in the benthic δ18O record by two positive excursions between 23.7 and 22.9 Ma, each with a duration of 200–300 kyr. Bottom water temperatures decreased by ∼2°C over the 150 kyr immediately prior to both rapid δ18O excursions. However, the onset of each of these phases of ice growth is synchronous, within the resolution of the records, with the onset of a 2°C warming over ∼150 kyr. We suggest that the warming during these glacial expansions reflect increased greenhouse forcing prompted by a sudden decrease in global chemical weathering rates as Antarctic basement silicate rocks became blanketed by an ice sheet. This represents a negative feedback process that might have operated during major abrupt growth phases of the Antarctic ice sheet.
The invariant charges of the Nambu–Goto string and canonical quantization
Authors: Bahns Dorothea
Published: November 2004

It is shown that the algebra of diffeomorphism-invariant charges of the Nambu–Goto string cannot be quantized in the framework of canonical quantization. The argument is shown to be independent of the dimension of the underlying Minkowski space.
Magnetohydrodynamic simulations of turbulent magnetic reconnection
Authors: Fan Quan-Lin , Feng Xue-Shang , Xiang Chang-Qing
Published: November 2004

Turbulent reconnection process in a one-dimensional current sheet is investigated by means of a two-dimensional compressible one-fluid magnetohydrodynamic simulation with spatially uniform, fixed resistivity. Turbulence is set up by adding to the sheet pinch small but finite level of broadband random-phased magnetic field components. To clarify the nonlinear spatial-temporal nature of the turbulent reconnection process the reconnection system is treated as an unforced initial value problem without any anomalous resistivity model adopted. Numerical results demonstrate the duality of turbulent reconnection, i.e., a transition from Sweet–Parker-like slow reconnection to Petschek-like fast reconnection in its nonlinear evolutionary process. The initial slow reconnection phase is characterized by many independent microreconnection events confined within the sheet region and a global reconnection rate mainly dependent on the initially added turbulence and insensitive to variations of the plasma β and resistivity. The formation and amplification of the major plasmoid leads the following reconnection process to a rapid reconnection stage with a fast reconnection rate of the order of 0.1 or even larger, drastically changing the topology of the global magnetic field. That is, the presence of magnetohydrodynamic turbulence in large-scale current sheets can raise the reconnection rate from small values on the order of the Sweet–Parker rate to high values on the order of the Petscheck rate through triggering an evolution toward fast magnetic reconnection. Meanwhile, the backward coupling between the small- and large-scale magnetic field dynamics has been properly represented through the present high resolution simulation. The undriven turbulent reconnection model established here expresses a solid numerical basis for the previous schematic two-step magnetic reconnection models and a possible explanation of two-stage energy release process of solar explosives.
Composite systems and the role of the complex numbers in quantum mechanics
Authors: Niestegge Gerd
Published: November 2004

An axiomatic approach to the mathematical formalism of quantum mechanics, based upon a certain concept of conditional probability, has been proposed in two recent papers by the author. It leads to Jordan operator algebras and thus comes rather close to the standard Hilbert space model of quantum mechanics, but still includes the so-called exceptional Jordan algebras, for which a Hilbert space representation does not exist. This approach is now extended by defining a mathematical model of composite systems. Such a model is required for the study of the joint distribution of two quantum observables. A very general type of observables (not only the real-valued observables corresponding to the self-adjoint operators) is considered. The joint distribution is defined, using the concept of conditional probability, and exhibits a certain dependence on the succession of the observations which is different from the classical case and unknown so far in quantum mechanics. Finally, it turns out that, at least in the finite-dimensional case, a really satisfying model of the composite system exists only if each single system is modeled by a complex Jordan matrix algebra (or a direct sum), and the model then becomes the tensor product. This provides some reasoning why the exceptional Jordan algebras can be ruled out, why quantum mechanics needs the complex numbers and the complex Hilbert space, and why the tensor product is the right choice for the model of a composite system.
Autoregressive moving average model for analyzing edge localized mode time series on Axially Symmetric Divertor Experiment (ASDEX) Upgrade tokamak
Authors: Zvejnieks G. , Kuzovkov V. N. , Dumbrajs O. , Degeling A. W. , Suttrop W. , Urano H. , Zohm H.
Published: November 2004

An approach to analysis of time series of edge localized modes (ELMs) is proposed. It is based on the use of the autoregressive moving average model, which decomposes time series into deterministic and noise components. Despite the inclusion of nonlinearity in the model, the resulting deterministic equations for the ELM time series measured on Axially Symmetric Divertor Experiment Upgrade tokamak turn out to be linear. This contrasts with the findings on JAERI tokamak (JT-60U) and tokamak à configuration variable that ELMs exhibit features of chaotic dynamics, namely, the presence of unstable periodic orbits. This methodology for distinguishing chaotic behavior is examined, and found to be susceptible to misinterpretation.
Mimicking enzyme evolution by generating new (βα)
8
-barrels from (βα)
4
-half-barrels
Authors: Höcker Birte , Claren Jörg , Sterner Reinhard
Published: November 2004

Gene duplication and fusion events that multiply and link functional protein domains are crucial mechanisms of enzyme evolution. The analysis of amino acid sequences and three-dimensional structures suggested that the (βα)
8
-barrel, which is the most frequent fold among enzymes, has evolved by the duplication, fusion, and mixing of (βα)
4
-half-barrel domains. Here, we mimicked this evolutionary strategy by generating
in vitro
(βα)
8
-barrels from (βα)
4
-half-barrels that were deduced from the enzymes imidazole glycerol phosphate synthase (HisF) and
N
′[(5′-phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide isomerase (HisA). To this end, the gene for the C-terminal (βα)
4
-half-barrel (HisF-C) of HisF was duplicated and fused in tandem to yield HisF-CC, which is more stable than HisF-C. In the next step, by optimizing side-chain interactions within the center of the β-barrel of HisF-CC, the monomeric and compact (βα)
8
-barrel protein HisF-C*C was generated. Moreover, the genes for the N- and C-terminal (βα)
4
-half-barrels of HisF and HisA were fused crosswise to yield the chimeric proteins HisFA and HisAF. Whereas HisFA contains native secondary structure elements but adopts ill-defined association states, the (βα)
8
-barrel HisAF is a stable and compact monomer that reversibly unfolds with high cooperativity. The results obtained suggest a previously undescribed dimension for the diversification of enzymatic activities: new (βα)
8
-barrels with novel functions might have evolved by the exchange of (βα)
4
-half-barrel domains with distinct functional properties.
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates
Authors: Tusnády Gábor E. , Dosztányi Zsuzsanna , Simon István
Published: November 2004

Summary: The structure of integral membrane proteins is determined in the absence of the lipid bilayer; consequently the membrane localization of the protein is usually not specified in the corresponding PDB file. Recently, we have developed a new method called TMDET which determines the most possible localization of the membrane relative to the protein structure, and gives the annotation of the membrane embedded parts of the sequence. The entire Protein Data Bank has been scanned by the new TMDET algorithm resulting in the database of structurally determined transmembrane proteins (PDB_TM). Here we present the web interface of the TMDET algorithm to allow scientists to determine the membrane localization of structural data prior to deposition or to analyze model structures.

Availability: The TMDET server is available for academic users on http://www.enzim.hu/TMDET

Contact:  tusi@enzim.hu
A parallel graph decomposition algorithm for DNA sequencing with nanopores
Authors: Bokhari Shahid H. , Sauer Jon R.
Published: November 2004

Motivation: With the potential availability of nanopore devices that can sense the bases of translocating single-stranded DNA (ssDNA), it is likely that ‘reads’ of length ∼105 will be available in large numbers and at high speed. We address the problem of complete DNA sequencing using such reads.

We assume that ∼102 copies of a DNA sequence are split into single strands that break into randomly sized pieces as they translocate the nanopore in arbitrary orientations. The nanopore senses and reports each individual base that passes through, but all information about orientation and complementarity of the ssDNA subsequences is lost. Random errors (both biological and transduction) in the reads create further complications.

Results: We have developed an algorithm that addresses these issues. It can be considered an extreme variation of the well-known Eulerian path approach. It searches over a space of de Bruijn graphs until it finds one in which (a) the impact of errors is eliminated and (b) both possible orientations of the two ssDNA sequences can be identified separately and unambiguously.

Our algorithm is able to correctly reconstruct real DNA sequences of the order of 106 bases (e.g. the bacterium Mycoplasma pneumoniae) from simulated erroneous reads on a modest workstation in about 1 h. We describe, and give measured timings of, a parallel implementation of this algorithm on the Cray Multithreaded Architecture (MTA-2) supercomputer, whose architecture is ideally suited to this ‘unstructured’ problem. Our parallel implementation is crucial to the problem of rapidly sequencing long DNA sequences and also to the situation where multiple nanopores are used to obtain a high-bandwidth stream of reads.

Contact:  shb@acm.org
Circadian Rhythms of Ethylene Emission in Arabidopsis
Authors: Thain Simon C. , Vandenbussche Filip , Laarhoven Lucas J.J. , Dowson-Day Mandy J. , Wang Zhi-Yong , Tobin Elaine M. , Harren Frans J.M. , Millar Andrew J. , Van Der Straeten Dominique
Published: November 2004

Ethylene controls multiple physiological processes in plants, including cell elongation. Consequently, ethylene synthesis is regulated by internal and external signals. We show that a light-entrained circadian clock regulates ethylene release from unstressed, wild-type Arabidopsis (Arabidopsis thaliana) seedlings, with a peak in the mid-subjective day. The circadian clock drives the expression of multiple ACC SYNTHASE genes, resulting in peak RNA levels at the phase of maximal ethylene synthesis. Ethylene production levels are tightly correlated with ACC SYNTHASE 8 steady-state transcript levels. The expression of this gene is controlled by light, by the circadian clock, and by negative feedback regulation through ethylene signaling. In addition, ethylene production is controlled by the TIMING OF CAB EXPRESSION 1 and CIRCADIAN CLOCK ASSOCIATED 1 genes, which are critical for all circadian rhythms yet tested in Arabidopsis. Mutation of ethylene signaling pathways did not alter the phase or period of circadian rhythms. Mutants with altered ethylene production or signaling also retained normal rhythmicity of leaf movement. We conclude that circadian rhythms of ethylene production are not critical for rhythmic growth.
LIN, aMedicago truncatulaGene Required for Nodule Differentiation and Persistence of Rhizobial Infections
Authors: Kuppusamy Kavitha T. , Endre Gabriella , Prabhu Radhika , Penmetsa R. Varma , Veereshlingam Harita , Cook Douglas R. , Dickstein Rebecca , VandenBosch Kathryn A.
Published: November 2004

Ethyl methanesulfonate mutagenesis of the model legume Medicago truncatula has previously identified several genes required for early steps in nodulation. Here, we describe a new mutant that is defective in intermediate steps of nodule differentiation. The lin (lumpy infections) mutant is characterized by a 4-fold reduction in the number of infections, all of which arrest in the root epidermis, and by nodule primordia that initiate normally but fail to mature. Genetic analyses indicate that the symbiotic phenotype is conferred by a single gene that maps to the lower arm of linkage group 1. Transcriptional markers for early Nod factor responses (RIP1 and ENOD40) are induced in lin, as is another early nodulin, ENOD20, a gene expressed during the differentiation of nodule primordia. By contrast, other markers correlated with primordium differentiation (CCS52A), infection progression (MtN6), or nodule morphogenesis (ENOD2 and ENOD8) show reduced or no induction in homozygous lin individuals. Taken together, these results suggest that LIN functions in maintenance of rhizobial infections and differentiation of nodules from nodule primordia.
Processes Modulating Calcium Distribution in Citrus Leaves. An Investigation Using X-Ray Microanalysis with Strontium as a Tracer
Authors: Storey Richard , Leigh Roger A.
Published: November 2004

Citrus leaves accumulate large amounts of calcium that must be compartmented effectively to prevent stomatal closure by extracellular Ca2+ and interference with Ca2+-based cell signaling pathways. Using x-ray microanalysis, the distribution of calcium between vacuoles in different cell types of leaves of rough lemon (Citrus jambhiri Lush.) was investigated. Calcium was accumulated principally in palisade, spongy mesophyll, and crystal-containing idioblast cells. It was low in epidermal and bundle sheath cells. Potassium showed the reverse distribution. Rubidium and strontium were used as tracers to examine the pathways by which potassium and calcium reached these cells. Comparisons of strontium and calcium distribution indicated that strontium is a good tracer for calcium, but rubidium did not mirror the potassium distribution pattern. The amount of strontium accumulated was highest in palisade cells, lowest in bundle sheath and epidermal cells, and intermediate in the spongy mesophyll. Accumulation of strontium in palisade and spongy mesophyll was accompanied by loss of potassium from these cells and its accumulation in the bundle sheath. Strontium moved apoplastically from the xylem to all cell types, and manipulation of water loss from the adaxial leaf surface suggested that diffusion is responsible for strontium movement to this side of the leaf. The results highlight the importance of palisade and spongy mesophyll as repositories for calcium and suggest that calcium distribution between different cell types is the result of differential rates of uptake. This tracer technique can provide important information about the ion uptake and accumulation properties of cells in intact leaves.
Citrate-Permeable Channels in the Plasma Membrane of Cluster Roots from White Lupin
Authors: Zhang Wen-Hao , Ryan Peter R. , Tyerman Stephen D.
Published: November 2004

White lupin (Lupinus albus) is well adapted to phosphorus deficiency by developing cluster roots that release large amounts of citrate into the rhizosphere to mobilize the sparingly soluble phosphorus. To determine the mechanism underlying citrate release from cluster roots, we isolated protoplasts from different types of roots of white lupin plants grown in phosphorus-replete (+P) and phosphorus-deficient (−P) conditions and used the patch-clamp technique to measure the whole-cell currents flowing across plasma membrane of these protoplasts. Two main types of anion conductance were observed in protoplasts prepared from cluster root tissue: (1) an inwardly rectifying anion conductance (IRAC) activated by membrane hyperpolarization, and (2) an outwardly rectifying anion conductance (ORAC) that became more activated with membrane depolarization. Although ORAC was an outward rectifier, it did allow substantial inward current (anion efflux) to occur. Both conductances showed citrate permeability, with IRAC being more selective for citrate3− than Cl− (PCit/PCl = 26.3), while ORAC was selective for Cl− over citrate (PCl/PCit = 3.7). Both IRAC and ORAC were sensitive to the anion channel blocker anthracene-9-carboxylic acid. These currents were also detected in protoplasts derived from noncluster roots of −P plants, as well as from normal (noncluster) roots of plants grown with 25 μm phosphorus (+P). No differences were observed in the magnitude or frequency of IRAC and ORAC currents between the cluster roots and noncluster roots of −P plants. However, the IRAC current from +P plants occurred less frequently than in the −P plants. IRAC was unaffected by external phosphate, but ORAC had reduced inward current (anion efflux) when phosphate was present in the external medium. Our data suggest that IRAC is the main pathway for citrate efflux from white lupin roots, but ORAC may also contribute to citrate efflux.
Zeolin. A New Recombinant Storage Protein Constructed Using Maize γ-Zein and Bean Phaseolin
Authors: Mainieri Davide , Rossi Marika , Archinti Marco , Bellucci Michele , De Marchis Francesca , Vavassori Stefano , Pompa Andrea , Arcioni Sergio , Vitale Alessandro
Published: November 2004

The major seed storage proteins of maize (Zea mays) and bean (Phaseolus vulgaris), zein and phaseolin, accumulate in the endoplasmic reticulum (ER) and in storage vacuoles, respectively. We show here that a chimeric protein composed of phaseolin and 89 amino acids of γ-zein, including the repeated and the Pro-rich domains, maintains the main characteristics of wild-type γ-zein: It is insoluble unless its disulfide bonds are reduced and forms ER-located protein bodies. Unlike wild-type phaseolin, the protein, which we called zeolin, accumulates to very high amounts in leaves of transgenic tobacco (Nicotiana tabacum). A relevant proportion of the ER chaperone BiP is associated with zeolin protein bodies in an ATP-sensitive fashion. Pulse-chase labeling confirms the high affinity of BiP to insoluble zeolin but indicates that, unlike structurally defective proteins that also extensively interact with BiP, zeolin is highly stable. We conclude that the γ-zein portion is sufficient to induce the formation of protein bodies also when fused to another protein. Because the storage proteins of cereals and legumes nutritionally complement each other, zeolin can be used as a starting point to produce nutritionally balanced and highly stable chimeric storage proteins.
Vapour-diffusion protein crystallization in newly designed pore strips
Authors: Dekker Carien , Haire Lesley , Dodson Guy
Published: November 2004

Use of hanging drops in a pore rather than on cover slips increases the total surface accessible for evaporation. This will have an effect on the kinetics of crystallization and on the degree of convection, both of which could affect the nucleation rate. The crystallization of a set of well known proteins in pore strips has been tested. The results show that crystallization in pore strips is possible, and that nucleation is comparable with that in hanging drops despite the use of smaller volumes. Nonetheless, in about 25% of the cases, faster nucleation was observed. In a few cases, different crystal forms appeared, suggesting that pore crystallization may allow a different trajectory through the phase diagram compared with the hanging drop.
Sample management system for a vast amount of frozen crystals at SPring-8
Authors: Ueno Go , Hirose Raita , Ida Koh , Kumasaka Takashi , Yamamoto Masaki
Published: November 2004

The RIKEN Structural Genomics Beamlines at SPring-8 have been constructed for high-throughput protein crystallography. Beamline operation is automated, cooperating with the sample management system developed along with the beamline facilities. The system consists of a database of a large number of sample crystals, and sample handling robots, named SPACE (SPring-8 Precise Automatic Cryo-sample Exchanger), at the beamline and the laboratory. The system has been working reliably during the commissioning of the automatic beamline operation, started in October 2003.