bluuebunny/crossref_metadata_2025_split huggingface dataset:
The interplay between transient α‐helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts
Authors: Kjaergaard Magnus , Iešmantavičius Vytautas , Poulsen Flemming M. 
Published: September 2011

AbstractThe peptide backbones of disordered proteins are routinely characterized by NMR with respect to transient structure and dynamics. Little experimental information is, however, available about the side chain conformations and how structure in the backbone affects the side chains. Methyl chemical shifts can in principle report the conformations of aliphatic side chains in disordered proteins and in order to examine this two model systems were chosen: the acid denatured state of acyl‐CoA binding protein (ACBP) and the intrinsically disordered activation domain of the activator for thyroid hormone and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the γ‐gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation of γ‐gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The 13C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow a quantitative analysis of the ensemble of χ2‐angles of especially leucine residues in disordered proteins. The changes in the rotamer distributions upon denaturation correlate to the changes upon helix induction by the co‐solvent trifluoroethanol, suggesting that the side chain conformers are directly or indirectly related to formation of transient α‐helices.
An approach to crystallizing proteins by metal‐mediated synthetic symmetrization
Authors: Laganowsky Arthur , Zhao Minglei , Soriaga Angela B. , Sawaya Michael R. , Cascio Duilio , Yeates Todd O. 
Published: September 2011

AbstractCombining the concepts of synthetic symmetrization with the approach of engineering metal‐binding sites, we have developed a new crystallization methodology termed metal‐mediated synthetic symmetrization. In this method, pairs of histidine or cysteine mutations are introduced on the surface of target proteins, generating crystal lattice contacts or oligomeric assemblies upon coordination with metal. Metal‐mediated synthetic symmetrization greatly expands the packing and oligomeric assembly possibilities of target proteins, thereby increasing the chances of growing diffraction‐quality crystals. To demonstrate this method, we designed various T4 lysozyme (T4L) and maltose‐binding protein (MBP) mutants and cocrystallized them with one of three metal ions: copper (Cu2+), nickel (Ni2+), or zinc (Zn2+). The approach resulted in 16 new crystal structures—eight for T4L and eight for MBP—displaying a variety of oligomeric assemblies and packing modes, representing in total 13 new and distinct crystal forms for these proteins. We discuss the potential utility of the method for crystallizing target proteins of unknown structure by engineering in pairs of histidine or cysteine residues. As an alternate strategy, we propose that the varied crystallization‐prone forms of T4L or MBP engineered in this work could be used as crystallization chaperones, by fusing them genetically to target proteins of interest.
A tale of two GTPases in cotranslational protein targeting
Authors: Saraogi Ishu , Akopian David , Shan Shu‐Ou 
Published: September 2011

AbstractGuanosine triphosphatases (GTPases) comprise a superfamily of proteins that provide molecular switches to regulate numerous cellular processes. The “GTPase switch” paradigm, in which a GTPase acts as a bimodal switch that is turned “on” and “off” by external regulatory factors, has been used to interpret the regulatory mechanism of many GTPases. Recent work on a pair of GTPases in the signal recognition particle (SRP) pathway has revealed a distinct mode of GTPase regulation. Instead of the classical GTPase switch, the two GTPases in the SRP and SRP receptor undergo a series of conformational changes during their dimerization and reciprocal activation. Each conformational rearrangement provides a point at which these GTPases can communicate with and respond to their upstream and downstream biological cues, thus ensuring the spatial and temporal precision of all the molecular events in the SRP pathway. We suggest that the SRP and SRP receptor represent an emerging class of “multistate” regulatory GTPases uniquely suited to provide exquisite control over complex cellular pathways that require multiple molecular events to occur in a highly coordinated fashion.
Rational disruption of the oligomerization of the mini‐ferritin E. coli DPS through protein‐protein interface mutation
Authors: Zhang Yu , Fu Jing , Chee Sze Y. , Ang Emmiline X. W. , Orner Brendan P. 
Published: September 2011

AbstractDNA‐binding protein from starved cells (DPS), a mini‐ferritin capable of self‐assembling into a 12‐meric nano‐cage, was chosen as the basis for an alanine‐shaving mutagenesis study to investigate the importance of key amino acid residues, located at symmetry‐related protein‐protein interfaces, in controlling protein stability and self‐assembly. Nine mutants were designed through simple inspection, synthesized, and subjected to transmission electron microscopy, circular dichroism, size exclusion chromatography, and “virtual alanine scanning” computational analysis. The data indicate that many of these residues may be hot spot residues. Most remarkably, two residues, R83 and R133, were observed to shift the oligomerization state to ˜50% dimer. Based on the hypothesis that these two residues constitute a “hot strip,” located at the ferritin‐like threefold axis, the double mutant was generated which completely shuts down detectable formation of 12‐mer in solution, favoring a cooperatively folded dimer. The fact that this effect logically builds upon the single mutants emphasizes that complex self‐assembly has the potential to be manipulated rationally. This study should have an impact on the fundamental understanding of the assembly of DPS protein cages specifically and protein quaternary structure in general. In addition, as there is much interest in applying these and similar systems to the templation of nano‐materials and drug delivery, the ability to control this ferritin's oligomerization state and stability could prove especially valuable.
A historic account of the invasion of Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) in the continental United States, with remarks on their identification
Authors: Hauser Martin 
Published: September 2011

AbstractBACKGROUND: Drosophila suzukii is an oriental species first reported outside Asia from Hawaii in 1980. The first confirmed records for the continental United States were made in 2008 in California. The identification of this pest is difficult because very few published resources exist.RESULTS: It has since been recorded in Oregon, Washington, British Columbia, Alberta, Manitoba, Ontario, Quebec, Utah, Michigan, Wisconsin, Louisiana, North Carolina, South Carolina and Florida. Males are relatively easy to identify by the black apical wing spots and the single row of combs on the first and second tarsal segment of the fore leg. The male genitalia are also very characteristic and will aid in identifying teneral specimens. Females can be identified by the large ovipositor, which is 6–7 times as long as the diameter of the spermatheca. Immature stages can only be identified by molecular techniques.CONCLUSION: Although this species has been recorded from many US states and Canadian provinces, it has not been established in all of these places, and the main economic damage is restricted to the western part of North America. With the characters laid out in this paper, it should be possible to identify the pest with high certainty. Copyright © 2011 Society of Chemical Industry
New concepts in molecular and energy transport within carbon nanotubes: Thermopower waves and stochastically resonant ion channels
Authors: Shimizu Steven , Choi Wonjoon , Abrahamson Joel T. , Strano Michael S. 
Published: September 2011

AbstractOur laboratory has been interested in how carbon nanotubes can be utilized to illustrate new concepts in molecular and energy transfer. In the first example, we predict and demonstrate the concept of thermopower waves for energy generation. Coupling an exothermic chemical reaction with a thermally conductive CNT creates a self‐propagating reactive wave driven along its length. We realize such waves in multi‐walled nanotubes (MWNT) and show that they produce concomitant electrical pulses of high specific power >7 kW/kg. Such waves of high power density may find uses as unique energy sources. In the second system, we fabricate and study single‐walled nanotube (SWNT) ion channels for the first time and show that the longest, highest aspect ratio, and smallest diameter synthetic nanopore examined to date, a 500 µm SWNT, demonstrates oscillations in electro‐osmotic current at specific ranges of electric field, that are the signatures of coherence resonance, yielding self‐generated rhythmic and frequency‐locked transport. The observed oscillations in the current occur due to a coupling between stochastic pore blocking and a diffusion limitation that develops at the pore mouth during proton transport.
The study on the atomic force microscopy base nanoscale electrical discharge machining
Authors: Huang Jen‐Ching , Chen Chung‐Ming 
Published: September 2011

AbstractThis study proposes an innovative atomic force microscopy (AFM) based nanoscale electrical discharge machining (AFM‐based nanoEDM) system which combines an AFM with a self‐produced metallic probe and a high‐voltage generator to create an atmospheric environment AFM‐based nanoEDM system and a deionized water (DI water) environment AFM‐based nanoEDM system. This study combines wire‐cut processing and electrochemical tip sharpening techniques on a 40‐µm thick stainless steel sheet to produce a high conductive AFM probes, the production can withstand high voltage and large current. The tip radius of these probes is approximately 40 nm. A probe test was executed on the AFM using probes to obtain nanoscales morphology of Si wafer surface. The silicon wafer was as a specimen to carry out AFM‐base nanoEDM process in atmospheric and DI water environments by AFM‐based nanoEDM system. After experiments, the results show that the atmospheric and DI water environment AFM‐based nanoEDM systems operate smoothly. From experimental results, it can be found that the electric discharge depth of the silicon wafer at atmospheric environments is a mere 14.54 nm. In a DI water environment, the depth of electric discharge of the silicon wafer can reach 25.4 nm. This indicates that the EDM ability of DI water environment AFM‐based nanoEDM system is higher than that of atmospheric environment AFM‐based nanoEDM system. After multiple nanoEDM process, the tips become blunt. After applying electrochemical tip sharpening techniques, the tip radius can return to approximately 40 nm. Therefore, AFM probes produced in this study can be reused. SCANNING 34: 191–199, 2012. © 2011 Wiley Periodicals, Inc.
Primary teachers' attitudes toward science: A new theoretical framework
Authors: van Aalderen‐Smeets Sandra I. , Walma van der Molen Juliette H. , Asma Lieke J. F. 
Published: September 2011

AbstractAttention to the attitudes of preservice and inservice primary teachers toward science is of fundamental importance to research on primary science education. However, progress in this field of research has been slow due to the poor definition and conceptualization of the construct of primary teachers' attitude toward science. This poor theoretical background has led to the use of a multitude of different concepts and measurement instruments. The main goal of this article is to present a new and comprehensive theoretical framework for primary teachers' attitudes toward science. The framework is based on an extensive review of previously used concept definitions of the construct. It is argued that this framework should serve as a necessary conceptual basis for future research and interventions in this domain, as well as for the construction of valid measurement instruments. © 2011 Wiley Periodicals, Inc. Sci Ed 96:158–182, 2012
MiR-17 Modulates Osteogenic Differentiation Through a Coherent Feed-Forward Loop in Mesenchymal Stem Cells Isolated from Periodontal Ligaments of Patients with Periodontitis
Authors: Liu Yali , Liu Wenjia , Hu Chenghu , Xue Zengfu , Wang Guang , Ding Bofu , Luo Hailang , Tang Liang , Kong Xiangwei , Chen Xiaoyan , Liu Na , Ding Yin , Jin Yan 
Published: September 2011

Abstract
Chronic inflammatory diseases, such as rheumatoid arthritis and periodontitis, are the most common causes of bone tissue destruction. Recently, human periodontal ligament tissue-derived mesenchymal stem cells (PDLSCs), a population of multipotent stem cells, have been used to reconstruct tissues destroyed by chronic inflammation. However, the impact of the local inflammatory microenvironment on tissue-specific stem cells and the mechanisms controlling the effects of the local inflammatory environment remain poorly understood. In this study, we found that the multidifferentiation potential of mesenchymal stem cells (MSCs) isolated from periodontitis-affected periodontal ligament tissue (P-PDLSCs) was significantly lower than that of MSCs isolated from healthy human periodontal ligament tissue (H-PDLSCs). Inflammation in the microenvironment resulted in an inhibition of miR-17 levels, and a perturbation in the expression of miR-17 partly reversed the differentiation potential of PDLSCs in this microenvironment. Furthermore, inflammation in the microenvironment promoted the expression of Smad ubiquitin regulatory factor one (Smurf1), an important negative regulator of MSC osteogenic differentiation. Western blotting and 3′ untranslated regions (3′-UTR) reporter assays confirmed that Smurf1 is a direct target of miR-17 in PDLSCs. Our data demonstrate that excessive inflammatory cytokine levels, miR-17, and Smurf1 were all involved in a coherent feed-forward loop. In this circuit, inflammatory cytokines led to direct activation of Smurf1 and downregulation of miR-17, thereby increasing degradation of Smurf1-mediated osteoblast-specific factors. The elucidation of the molecular mechanisms governing MSC osteogenic differentiation in a chronic inflammatory microenvironment could provide us with a better knowledge of chronic inflammatory disorder and improve stem cell-mediated inflammatory bone disease therapy.
Construction of contiguous tetrasubstituted chiral carbon stereocenters via direct catalytic asymmetric aldol and mannich‐type reactions
Authors: Matsunaga Shigeki , Yoshino Tatsuhiko 
Published: September 2011

AbstractCatalytic asymmetric synthesis of unnatural amino acids with vicinal tetrasubstituted chiral carbon stereocenters is described. In the first part, direct catalytic asymmetric aldol reaction of simple non‐activated ketone electrophiles with α‐substituted α‐isothiocyanato ester donors was realized. A Mg/Schiff base catalyst promoted the aldol reaction, and α‐amino‐β‐hydroxy esters were obtained in up to 98% ee and 98:2 d.r. In the second part, the Mg/Schiff base catalyst and a Sr/Schiff base catalyst were utilized for stereodivergent direct asymmetric Mannich‐type reaction of ketimines. The Mg/Schiff base catalyst gave syn‐α,β‐diamino esters, while the Sr/Schiff base catalyst produced anti‐α,β‐diamino esters in good to high enantioselectivity, up to 97% ee. DOI 10.1002/tcr.201100020
Transtibial Ertl amputation for children and adolescents: A case series and literature review
Authors: Firth Gregory Bodley , Masquijo Julio Javier , Kontio Ken 
Published: September 2011

Purpose Despite advances in limb reconstruction, there are still a number of young patients who require trans-tibial amputation. Amputation osteoplasty is a technique first described by Ertl to enhance rehabilitation after trans-tibial amputation. The purpose of the study reported here was to evaluate the results of the original Ertl procedure in skeletally immature patients and to assess whether use of this procedure would result in a diminished incidence of bony overgrowth. Methods The cases of four consecutive patients (five amputations) treated between January 2005 and June 2008 were reviewed. Clinical evaluation consisted of the completion of the prosthesis evaluation questionnaire (PEQ) and physical examination. Radiographic analysis was performed to evaluate bone-bridge healing, bone overgrowth, and the development of genu varum as measured by the medial proximal tibial angle (MPTA). Results The best mean PEQ score in the question section was 91.8 (range 74–100) for ‘well being’ and the worst mean score was 66.6 (range 50–78) for ‘residual limb health’. Examination of the residual limbs revealed no bursae, and all knees were stable with full range of movement. All bony bridges united at an average age of 1.7 (range 1–2) months. One case required stump revision for bony overgrowth, and one case developed asymptomatic mild genu varum. Conclusions The original Ertl osteomyoplasty may serve as one of the options for treatment of trans-tibial amputation in older children. Clinical relevance Our results suggest that the Ertl osteomyoplasty is a feasible option in this challenging patient population.
Maternal cultural values and parenting practices: Longitudinal associations with Chinese adolescents’ aggression
Authors: Shuster Michael M. , Li Yan , Shi Junqi 
Published: September 2011

ABSTRACTInterrelations among cultural values, parenting practices, and adolescent aggression were examined using longitudinal data collected from Chinese adolescents and their mothers. Adolescents’ overt and relational aggression were assessed using peer nominations at Time 1 (7th grade) and Time 2 (9th grade). Mothers reported endorsement of cultural values (collectivism and social harmony) and parenting practices (psychological control and inductive reasoning) at Time 1. While controlling for Time 1 adolescent aggression, maternal collectivism and social harmony indirectly and longitudinally linked to adolescent aggression through maternal parenting practices. Specifically, maternal collectivism was positively related to inductive reasoning, which, in turn, negatively related to adolescent overt aggression at Time 2. Similarly, maternal social harmony negatively related to psychological control that positively predicted later adolescent relational aggression. Results of the present study shed light on mechanisms through which culture may indirectly influence adolescent aggression.
STRICT TOPOLOGY AS A MIXED TOPOLOGY ON LEBESGUE SPACES
Authors: MAGHSOUDI SAEID , NASR-ISFAHANI RASOUL 
Published: September 2011

AbstractLetXbe a locally compact space, and 𝔏∞0(X,ι) be the space of all essentially boundedι-measurable functionsfonXvanishing at infinity. We introduce and study a locally convex topologyβ1(X,ι) on the Lebesgue space 𝔏1(X,ι) such that the strong dual of (𝔏1(X,ι),β1(X,ι)) can be identified with$({\frak L}_0^\infty (X,\iota ),\|\cdot \|_\infty )$. Next, by showing thatβ1(X,ι) can be considered as a natural mixed topology, we deduce some of its basic properties. Finally, as an application, we prove thatL1(G) , the group algebra of a locally compact Hausdorff topological groupG, equipped with the convolution multiplication is a complete semitopological algebra under theβ1(G) topology.
Effects of constant and changing temperature conditions on diapause induction inHelicoverpa armigera(Lepidoptera: Noctuidae)
Authors: Mironidis G.K. , Savopoulou-Soultani M. 
Published: September 2011

AbstractThe effects of photoperiod and temperature on the induction and termination of facultative pupal diapause inHelicoverpa armigera(Lepidoptera: Noctuidae) were investigated under laboratory conditions. ExposingH. armigeralarvae to both constant and fluctuating temperature regimes with a mean of 25°C and 20°C resulted in a type-III photoperiodic response curve of a short-long day insect. The long-day critical daylengths for diapause induction were ten hours and 12 hours at the constant temperatures of 25°C and 20°C, respectively. Higher incidences of diapause and higher values both for the longer and the shorter critical photoperiods for diapause induction were observed at fluctuating regimes compared with the corresponding constant ones. At alternating temperatures, the incidence of diapause ranged from 4.2% to 33.3% and was determined by the temperature amplitude of the thermoperiod and by the interaction of cryophase or thermophase with the photoperiod.Helicoverpa armigeralarvae seem to respond to photoperiodic stimuli at temperatures >15°C and <30°C; all insects entered diapause at a constant temperature of 15°C, whereas none did so at a constant temperature of 30°C under all the photoperiodic regimes examined. Although chilling was not a prerequisite for diapause termination, exposure of diapausing pupae to chilling conditions significantly accelerated diapause development and the time of adult emergence. Therefore, temperature may be the primary factor controlling the termination of diapause inH. armigera.
On notions of determinism in topological dynamics
Authors: HOCHMAN MICHAEL 
Published: September 2011

AbstractWe examine the relations between topological entropy, invertibility, and prediction in topological dynamics. We show that topological determinism in the sense of Kamińsky, Siemaszko, and Szymański imposes no restriction on invariant measures except zero entropy. Also, we develop a new method for relating topological determinism and zero entropy, and apply it to obtain a multidimensional analog of this theory. We examine prediction in symbolic dynamics and show that while the condition that each past admits a unique future only occurs in finite systems, the condition that each past has a bounded number of futures imposes no restriction on invariant measures except zero entropy. Finally, we give a negative answer to a question of Eli Glasner by constructing a zero-entropy system with a globally supported ergodic measure in which every point has multiple preimages.
French immersion experience and reading skill development in at-risk readers
Authors: KRUK RICHARD S. , REYNOLDS KRISTIN A. A. 
Published: September 2011

ABSTRACTWe tracked the developmental influences of exposure to French on developing English phonological awareness, decoding and reading comprehension of English-speaking at-risk readers from Grade 1 to Grade 3. Teacher-nominated at-risk readers were matched with not-at-risk readers in French immersion and English language programs. Exposure to spoken French phonetic and syllabic forms and to written French orthographic and morphological forms by children attending French immersion programs was expected to promote phonological, decoding and reading comprehension achievement. Growth in all outcomes was found, with children in immersion experiencing higher final status in phonological awareness and more rapid growth and higher final status in decoding, using multilevel modeling. At-risk readers in French immersion experienced faster growth and higher final status in reading comprehension. Benefits to reading of exposure to an additional language are discussed in relation to cross-language transfer, phonological grain size and enhanced executive control processes.