bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Modified Type‐12 Impact Sensitivity Test Apparatus for Explosives
Authors: Phillips Jason J. 
Published: April 2012

AbstractThis investigation is to improve the Type‐12 impact sensitivity test apparatus through the merging of basic split‐Hopkinson pressure bar principles with existing impact sensitivity testing methods. This is accomplished mainly through the addition of resistance strain gage equipment. Upon completion of the modifications to the apparatus, incident pressure waves created by impact are recorded, as well as sharp pressure releases suspected to be caused by rapid mechanical failure of energetic material samples. To solve data acquisition issues during the initial testing attempts with the modified equipment, the Type‐12 tooling is further adapted by installing a high‐density polyethylene (HDPE) bushing through which the striker bar is inserted. A series of sensitivity tests are then conducted using RDX to determine if this alteration affected the normal operation of the instrument. It is found that this modification to the apparatus creates a 46 % reduction in the standard deviation of H50 results in comparison to the standard tooling.
A “Link‐Psi” strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable
Authors: Shandiz Ali T. , Baxa Michael C. , Sosnick Tobin R. 
Published: April 2012

AbstractUsing a combined crosslinking‐ψ analysis strategy, we examine whether the structural content of the transition state of ubiquitin can be altered. A synthetic dichloroacetone crosslink is first introduced across two β strands. Whether the structural content in the transition state ensemble has shifted towards the region containing the crosslink is probed by remeasuring the ψ value at another region (ψ identifies the degree to which an inserted bi‐Histidine metal ion binding site is formed in the transition state). For sites around the periphery of the obligate transition state nucleus, we find that the resulting changes in ψ values are near or at our detection limit, thereby indicating that the structural content of the transition state has not measurably changed upon crosslinking. This work demonstrates the utility of the simultaneous application of crosslinking and ψ‐analysis for examining potential transition state heterogeneity in globular proteins.
Template‐based structure prediction and classification of transcription factors in Arabidopsis thaliana
Authors: Lu Tao , Yang Yuedong , Yao Bo , Liu Song , Zhou Yaoqi , Zhang Chi 
Published: April 2012

AbstractTranscription factors (TFs) play important roles in plants. However, there is no systematic study of their structures and functions of most TFs in plants. Here, we performed template‐based structure prediction for all TFs in Arabidopsis thaliana, with their full‐length sequences as well as C‐terminal and N‐terminal regions. A total of 2918 model structures were obtained with a high confidence score. We find that TF families employ only a smaller number of templates for DNA‐binding domains (DBD) but a diverse number of templates for transcription regulatory domains (TRD). Although TF families are classified according to DBD, their sizes have a significant correlation with the number of unique non‐DNA‐binding templates employed in the family (Pearson correlation coefficient of 0.74). That is, the size of TF family is related to its functional diversity. Network analysis reveals new connections between TF families based on shared TRD or DBD templates; 81% TF families share DBD and 67% share TRD templates. Two large fully connected family clusters in this network are observed along with 69 island families. In addition, 25 genes with unknown functions are found to be DNA‐binding and/or TF factors according to predicted structures. This work provides a global view of the classification of TFs based on their DBD or TRD templates, and hence, a deeper understanding of DNA‐binding and regulatory functions from structural perspective. All structural models of TFs are deposited in the online database for public usage at http://sysbio.unl.edu/AthTF.
Active site residues critical for flavin binding and 5,6‐dimethylbenzimidazole biosynthesis in the flavin destructase enzyme BluB
Authors: Yu Ta‐Yi , Mok Kenny C. , Kennedy Kristopher J. , Valton Julien , Anderson Karen S. , Walker Graham C. , Taga Michiko E. 
Published: April 2012

AbstractThe “flavin destructase” enzyme BluB catalyzes the unprecedented conversion of flavin mononucleotide (FMN) to 5,6‐dimethylbenzimidazole (DMB), a component of vitamin B12. Because of its unusual chemistry, the mechanism of this transformation has remained elusive. This study reports the identification of 12 mutant forms of BluB that have severely reduced catalytic function, though most retain the ability to bind flavin. The “flavin destructase” BluB is an unusual enzyme that fragments the flavin cofactor FMNH2 in the presence of oxygen to produce 5,6‐dimethylbenzimidazole (DMB), the lower axial ligand of vitamin B12 (cobalamin). Despite the similarities in sequence and structure between BluB and the nitroreductase and flavin oxidoreductase enzyme families, BluB is the only enzyme known to fragment a flavin isoalloxazine ring. To explore the catalytic residues involved in this unusual reaction, mutants of BluB impaired in DMB biosynthesis were identified in a genetic screen in the bacterium Sinorhizobium meliloti. Of the 16 unique point mutations identified in the screen, the majority were located in conserved residues in the active site or in the unique “lid” domain proposed to shield the active site from solvent. Steady‐state enzyme assays of 12 purified mutant proteins showed a significant reduction in DMB synthesis in all of the mutants, with eight completely defective in DMB production. Ten of these mutants have weaker binding affinities for both oxidized and reduced FMN, though only two have a significant effect on complex stability. These results implicate several conserved residues in BluB's unique ability to fragment FMNH2 and demonstrate the sensitivity of BluB's active site to structural perturbations. This work lays the foundation for mechanistic studies of this enzyme and further advances our understanding of the structure‐function relationship of BluB.
The bacterial outer membrane β‐barrel assembly machinery
Authors: Kim Kelly H. , Aulakh Suraaj , Paetzel Mark 
Published: April 2012

Abstractβ‐Barrel proteins found in the outer membrane of Gram‐negative bacteria serve a variety of cellular functions. Proper folding and assembly of these proteins are essential for the viability of bacteria and can also play an important role in virulence. The β‐barrel assembly machinery (BAM) complex, which is responsible for the proper assembly of β‐barrels into the outer membrane of Gram‐negative bacteria, has been the focus of many recent studies. This review summarizes the significant progress that has been made toward understanding the structure and function of the bacterial BAM complex.
The interface of protein structure, protein biophysics, and molecular evolution
Authors: Liberles David A. , Teichmann Sarah A. , Bahar Ivet , Bastolla Ugo , Bloom Jesse , Bornberg‐Bauer Erich , Colwell Lucy J. , de Koning A. P. Jason , Dokholyan Nikolay V. , Echave Julian , Elofsson Arne , Gerloff Dietlind L. , Goldstein Richard A. , Grahnen Johan A. , Holder Mark T. , Lakner Clemens , Lartillot Nicholas , Lovell Simon C. , Naylor Gavin , Perica Tina , Pollock David D. , Pupko Tal , Regan Lynne , Roger Andrew , Rubinstein Nimrod , Shakhnovich Eugene , Sjölander Kimmen , Sunyaev Shamil , Teufel Ashley I. , Thorne Jeffrey L. , Thornton Joseph W. , Weinreich Daniel M. , Whelan Simon 
Published: April 2012

AbstractAbstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state‐of‐the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high‐throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction.
Hemostatic gelatin sponge is a superior matrix to matrigel for establishment of LNCaP human prostate cancer in nude mice
Authors: Cui Lingling , Chen Pingping , Tan Zongqing , Li Wenjie , Dong Zhongyun 
Published: April 2012

AbstractBACKGROUNDMatrigels, solubilized basement membrane preparations, are often used to support tumor development in animal models. However, tumors formed by a mixture of tumor cells and Matrigel may vary significantly. The purpose of this study was to compare tumor development and growth of LNCaP human prostate cancer cells mixed with Matrigel or in gelatin sponges.METHODSLNCaP cells were mixed with Matrigel or absorbed into VETSPON, a gelatin sponge, and inoculated into the subcutis of nude mice. Tumor incidence and growth rate were determined. Gene expression and cell growth and survival in tumor lesions were evaluated by immunohistochemistry (IHC), immunoblotting, and RT‐PCR.RESULTSAll mice (12/12) inoculated with LNCaP cells in VETSPON produced tumors, compared to 70% (19/27) of mice injected with the cells with Matrigel. Tumor volume also varied less with VETSPON implants. No significant differences were observed in gene expression, cell growth, apoptosis, and microvessel density in tumors established from the two types of implants. However, in samples collected on days 1 and 4, more cells in Matrigel implants than those in VETSPON implants were stained positive for cleaved‐caspase 3 and ‐PARP1. Expression of VEGF‐A, HIF‐1α, and Bcl‐2 was elevated in the early VETSPON implants.CONCLUSIONThese data indicate that VETSPON promotes tumor cell survival at the early stage of implantation and suggest that the gelatin sponge is superior to Matrigel in supporting development and progression of human prostate cancer in nude mice. This model should be useful for preclinical studies in nude mice using LNCaP cells. Prostate 72:1669–1677, 2012. © 2012 Wiley Periodicals, Inc.
Low dosed interferon alpha augments the anti‐tumor potential of histone deacetylase inhibition on prostate cancer cell growth and invasion
Authors: Hudak Lukasz , Tezeeh Patrick , Wedel Steffen , Makarević Jasmina , Juengel Eva , Tsaur Igor , Bartsch Georg , Wiesner Christoph , Haferkamp Axel , Blaheta Roman A. 
Published: April 2012

AbstractWe evaluated whether low‐dosed interferon alpha (IFNa) may augment the anti‐tumor potential of the histone deacetylase (HDAC)‐inhibitor valproic acid (VPA) on prostate cancer cells in vitro and in vivo. PC‐3, DU‐145, or LNCaP prostate cancer cells were treated with VPA (1 mM), IFNa (200 U/ml), or with the VPA‐IFNa combination. Tumor cell growth, cell cycle progression, and cell cycle regulating proteins were then investigated by the MTT assay, flow cytometry, and western blotting. Tumor cell adhesion to endothelium or to immobilized extracellular matrix proteins, as well as migratory properties of the cells, were evaluated. Integrin α and β adhesion molecules and alterations of cell signaling pathways were analyzed. Finally, effects of the drug treatment on prostate cancer growth in vivo were determined in the NOD/SCID mouse model. VPA reduced tumor cell adhesion, migration, and growth in vitro. A much stronger anti‐cancer potential was evoked by the VPA‐IFNa combination, although IFNa in itself did not block growth or adhesion. The same effect was seen when tumor growth was evaluated in vivo. Molecular analysis revealed distinct elevation of histone H3 acetylation caused by VPA which was further up‐regulated by VPA‐IFNa, whereas IFNa alone did not alter H3 acetylation. The combinatorial benefit became obvious in Akt phosphorylation, p21 and p27 and integrin α1, α3, and β1 expression. Application of low‐dosed IFNa to a VPA based regimen profoundly boosts the anti‐tumor properties of VPA. The combined use of VPA and low‐dosed IFNa may therefore be an innovative option in treating advanced prostate cancer. Prostate 72:1719–1735, 2012. © 2012 Wiley Periodicals, Inc.
Quantitative impact assessment of spray coverage and pest behavior on contact pesticide performance
Authors: Martini Xavier , Kincy Natalie , Nansen Christian 
Published: April 2012

AbstractBACKGROUND: Standard procedures for evaluation of pesticide performance do not take into account pest behavioral response or incomplete spray coverage. In this study, a series of laboratory experiments was conducted with two non‐systemic miticides (propargite and hexythiazox) applied to cotyledon cotton plants, which were subsequently infested with spider mites. The results of these laboratory experiments are discussed through a comprehensive pest population dynamics model.RESULTS: When cotton leaves were submerged in miticide solutions, both miticides provided effective control of spider mites. In a two‐choice test it was demonstrated that propargite was repellent to spider mites, but not hexythiazox. Finally, the spray coverage on cotton plants was varied, and, for both miticides, significantly positive relationships between spray coverage and spider mite mortality were shown. However, propargite required higher spray coverage (20%) than hexythiazox (10%) to control spider mites. A theoretical model showed that, without repellency, the pesticide performance is positively correlated with target pest mobility. If the pesticide is repellent, the probability of exposure decreases, especially for a less mobile pest.CONCLUSION: With an experimental and theoretical modeling approach, it was demonstrated how the combination of behavioral avoidance and low spray coverage can markedly reduce pesticide performance. Copyright © 2012 Society of Chemical Industry
Structure–activity relationships of eugenol derivatives against Aedes aegypti (Diptera: Culicidae) larvae
Authors: Barbosa Juliana DF , Silva Viviane B , Alves Péricles B , Gumina Giuseppe , Santos Roseli LC , Sousa Damião P , Cavalcanti Sócrates CH 
Published: April 2012

AbstractBACKGROUND: Dengue fever is a severe public health problem for several countries. In order to find effective larvicides to aid control programs, the structure‐activity relationships of eugenol derivatives against Aedes aegypti (Diptera: Culicidae) larvae were evaluated. Additionally, the composition and larvicidal activity of Syzygium aromaticum essential oil was assessed.RESULTS: Four compounds representing 99.05% of S. aromaticum essential oil have been identified. The essential oil was active against Ae. aegypti larvae (LC50 = 62.3 and 77.0 ppm, field‐collected and Rockefeller larvae respectively). The larvicidal activity of eugenol, the major compound of the essential oil, was further evaluated (LC50 = 93.3 and 71.9 ppm, field‐collected and Rockefeller larvae respectively). The larvicidal activity and structure‐activity relationships of synthetic derivatives of eugenol were also assessed. The larvicidal activity of the derivatives varied between 62.3 and 1614.9 ppm. Oxidation of eugenol allylic bond to a primary alcohol and removal of the phenolic proton resulted in decreased potency. However, oxidation of the same double bond in 1‐benzoate‐2‐methoxy‐4‐(2‐propen‐1‐yl)‐phenol resulted in increased potency.CONCLUSION: Structural characteristics were identified that may contribute to the understanding of the larvicidal activity of phenylpropanoids. The present approach may help future work in the search for larvicidal compounds. Copyright © 2012 Society of Chemical Industry
Composition and biological activity of essential oils against Metopolophium dirhodum (Hemiptera: Aphididae) cereal crop pest
Authors: Sánchez Chopa Carolina , Descamps Lilian R 
Published: April 2012

AbstractBACKGROUND: Natural pesticides based on plant essential oils may represent alternative crop protectants. This study analysed the chemical constituents and bioactivities of essential oils from Schinus areira L., Rosmarinus officinalis L. and Tagetes terniflora Kunth against winged and wingless adults of Metopolophium dirhodum (Walk.).RESULTS: The major component of S. areira was α‐phellandrene, that of R. officinalis was 1,8‐cineole and that of T. terniflora was cis‐ocimene. Rosemary essential oil was more effective than the others in immersion method tests. In contact toxicity, the rosemary oil was the most toxic to wingless adults and the S. areira leaf oil was the most toxic to winged adults. All the EOs produced some degrees of repellency in adults and effects on the reproduction and demographic parameters.CONCLUSION: These results showed that the essential oils from S. areira, R. officinalis and T. terniflora could be used as an alternative in the management of M. dirhodum. Copyright © 2012 Society of Chemical Industry
Spectral selection of spatial modes in edge‐emitting lasers
Authors: Savenko I. G. , Gordeev N. Yu. , Iorsh I. V. , Kaliteevski M. A. , Maximov M. V. , Zhukov A. E. 
Published: April 2012

AbstractWe have analytically considered the way of high‐order lateral modes suppression in edge‐emitting lasers by integrating into the cavity a spectral filter based on the set of etched micrometer‐size features. We have found optimal features location and numerically calculated their spectral and loss properties for single‐mode laser and investigated the effect robustness against size fluctuation (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Host country uncertainty, intra‐MNC production shifts, and subsidiary performance
Authors: Lee Seung‐Hyun , Song Sangcheol 
Published: April 2012

AbstractThis study examines whether or not production shifts occur among the foreign subsidiaries of multinational corporations (MNCs) under the influence of differing macroeconomic conditions in their host countries. This study compares intra‐MNC production shifts under the influence of exchange rate changes across different host countries. Our findings indicate that the increase of a subsidiary's production at the time of its host country currency depreciation decreases the production of other subsidiaries within the same MNC network. Our empirical evidence also shows that MNC subsidiaries that engage in production shifts with other affiliated subsidiaries command a higher performance. Copyright © 2012 John Wiley & Sons, Ltd.
Studying Polymer/Fullerene Intermixing and Miscibility in Laterally Patterned Films with X‐Ray Spectromicroscopy
Authors: He Xiaoxi , Collins Brian A. , Watts Benjamin , Ade Harald , McNeill Christopher R. 
Published: April 2012

AbstractFilms of the fullerene derivatives [6,6]‐phenyl‐C61‐butyric acid methyl ester (PC61BM) and [6,6]‐phenyl‐C71‐butyric acid methyl ester (PC71BM) are patterned on silicon nitride membranes using photolithography to study, with X‐ray spectromicroscopy, the lateral, solid‐state diffusion of fullerene derivatives into conjugated polymer films. After patterning of the fullerene film, a film of conjugated polymer is laminated on top and the structure is annealed in order to study lateral intermixing and facilitate measurement of fullerene miscibility. Lateral intermixing of polymer and fullerene readily occurs for poly(2,5‐bis(3‐tetradecylthiophen‐2‐yl)thieno[3,2‐b]thiophene) (PBTTT) and regiorandom poly(3‐hexylthiophene) (RRa‐P3HT). A 42 wt.% miscibility of PC61BM in PBTTT is measured, while miscibilities of 20 and 41 wt.% are measured for PC61BM and PC71BM, respectively, in RRa‐P3HT, thereby demonstrating a significant difference in the miscibilities of these two fullerene derivatives. For regioregular poly(3‐hexylthiophene) (RR‐P3HT), incomplete lateral intermixing of fullerene and RR‐P3HT is observed with PCBM crystallite formation competing with the lateral diffusion of PCBM molecules into the polymer film.
IGF-II Promotes Stemness of Neural Restricted Precursors
Authors: Ziegler Amber N. , Schneider Joel S. , Qin Mei , Tyler William A. , Pintar John E. , Fraidenraich Diego , Wood Teresa L. , Levison Steven W. 
Published: April 2012

Abstract
Insulin-like growth factor (IGF)-I and IGF-II regulate brain development and growth through the IGF type 1 receptor (IGF-1R). Less appreciated is that IGF-II, but not IGF-I, activates a splice variant of the insulin receptor (IR) known as IR-A. We hypothesized that IGF-II exerts distinct effects from IGF-I on neural stem/progenitor cells (NSPs) via its interaction with IR-A. Immunofluorescence revealed high IGF-II in the medial region of the subventricular zone (SVZ) comprising the neural stem cell niche, with IGF-II mRNA predominant in the adjacent choroid plexus. The IGF-1R and the IR isoforms were differentially expressed with IR-A predominant in the medial SVZ, whereas the IGF-1R was more abundant laterally. Similarly, IR-A was more highly expressed by NSPs, whereas the IGF-1R was more highly expressed by lineage restricted cells. In vitro, IGF-II was more potent in promoting NSP expansion than either IGF-I or standard growth medium. Limiting dilution and differentiation assays revealed that IGF-II was superior to IGF-I in promoting stemness. In vivo, NSPs propagated in IGF-II migrated to and took up residence in periventricular niches while IGF-I-treated NSPs predominantly colonized white matter. Knockdown of IR or IGF-1R using shRNAs supported the conclusion that the IGF-1R promotes progenitor proliferation, whereas the IR is important for self-renewal. Q-PCR revealed that IGF-II increased Oct4, Sox1, and FABP7 mRNA levels in NSPs. Our data support the conclusion that IGF-II promotes the self-renewal of neural stem/progenitors via the IR. By contrast, IGF-1R functions as a mitogenic receptor to increase precursor abundance.
Disclosure of potential conflicts of interest is found at the end of this article.