bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transplantation of Achilles Tendon Treated With Bone Morphogenetic Protein 7 Promotes Meniscus Regeneration in a Rat Model of Massive Meniscal Defect
Authors: Ozeki Nobutake , Muneta Takeshi , Koga Hideyuki , Katagiri Hiroki , Otabe Koji , Okuno Makiko , Tsuji Kunikazu , Kobayashi Eiji , Matsumoto Kenji , Saito Hirohisa , Saito Tomoyuki , Sekiya Ichiro 
Published: July 2013

ObjectiveThis study was undertaken to examine whether bone morphogenetic protein 7 (BMP‐7) induces ectopic cartilage formation in the rat tendon, and whether transplantation of tendon treated with BMP‐7 promotes meniscal regeneration. Additionally, we analyzed the relative contributions of host and donor cells on the healing process after tendon transplantation in a rat model.MethodsBMP‐7 was injected in situ into the Achilles tendon of rats, and the histologic findings and gene profile were evaluated. Achilles tendon injected with 1 μg of BMP‐7 was transplanted into a meniscal defect in rats. The regenerated meniscus and articular cartilage were evaluated at 4, 8, and 12 weeks. Achilles tendon from LacZ‐transgenic rats was transplanted into the meniscal defect in wild‐type rats, and vice versa.ResultsInjection of BMP‐7 into the rat Achilles tendon induced the fibrochondrocyte differentiation of tendon cells and changed the collagen gene profile of tendon tissue to more closely approximate meniscal tissue. Transplantation of the rat Achilles tendon into a meniscal defect increased meniscal size. The rats that received the tendon treated with BMP‐7 had a meniscus matrix that exhibited increased Safranin O and type II collagen staining, and showed a delay in articular cartilage degradation. Using LacZ‐transgenic rats, we determined that the regeneration of the meniscus resulted from contribution from both donor and host cells.ConclusionOur findings indicate that BMP‐7 induces ectopic cartilage formation in rat tendons. Transplantation of Achilles tendon treated with BMP‐7 promotes meniscus regeneration and prevents cartilage degeneration in a rat model of massive meniscal defect. Native cells in the rat Achilles tendon contribute to meniscal regeneration.
ADAMTS‐4_v1 Is a Splice Variant of ADAMTS‐4 That Is Expressed as a Protein in Human Synovium and Cleaves Aggrecan at the Interglobular Domain
Authors: Wainwright Shane D. , Bondeson Jan , Caterson Bruce , Hughes Clare E. 
Published: July 2013

ObjectiveWe previously described a messenger RNA variant of ADAMTS4 (ADAMTS4_v1) in human synovial cell cocultures obtained from patients with osteoarthritis (OA). This RNA message has been found only in OA synovium and, if translated, would result in a protein identical to ADAMTS‐4, except that the C‐terminal spacer domain would be different. The purpose of this study was to determine whether ADAMTS4_v1 is translated into a protein, is expressed in vivo, and acts as a functional aggrecanase.MethodsPolyclonal antibodies were raised against unique C‐terminal sequences of ADAMTS‐4_v1. An immunohistochemical study of human OA synovium was performed. A mammalian expression vector coding for FLAG‐tagged human ADAMTS4 was mutated to contain the different sequences of ADAMTS4_v1, and the resultant plasmid was used to transfect HEK 293 cells. ADAMTS‐4_v1 produced by these cells was purified via the FLAG epitope, and the ability of this recombinant protein to cleave aggrecan, biglycan, and decorin was investigated.ResultsAn antibody specific for ADAMTS‐4_v1 was found to bind to the synovial membrane surface on cryosections, and the protein was detected in cell lysates from synovium obtained from OA patients. The recombinant ADAMTS‐4_v1 demonstrated enzyme activity toward the target substrate in a commercial aggrecanase 1 enzyme‐linked immunosorbent assay and was also found to cleave aggrecan at the pathologically important Glu373↓374Ala aggrecanase site.ConclusionADAMTS‐4_v1 is expressed as a protein in vivo in human OA synovium, functions as an aggrecanase, and cleaves other proteoglycan substrates. This splice variant may be a major contributor to loss of aggrecan from the superficial zone of OA cartilage.
Analytic hierarchy process application in selecting the mode of transport for a logistics company
Authors: Kumru Mesut , Kumru Pınar Yıldız 
Published: July 2013

SUMMARYAs a multi‐criteria decision‐making (MCDM) method, the analytic hierarchy process (AHP) has been used considerably to solve hierarchical or network‐based decision problems in socio‐economic fields. Following an in‐depth explanation of the transport function in logistics and an overview of the MCDM methods, the AHP model is employed in the paper for a logistics company in selecting the most suitable way of transportation between two given locations in Turkey. The criteria used in the selection of transportation modes are identified as the cost, speed, safety, accessibility, reliability, environmental friendliness, and flexibility. Several cost parameters (transportation, storage, handling, bosphorus crossover) are incorporated into the decision‐making process. The application is carried out in instructional character. The results of the study indicate that the railway transportation, which is not widely used in Turkey, is also an alternative and suitable means of transportation. Copyright © 2013 John Wiley & Sons, Ltd.
Micro‐computed tomography imaging and analysis in developmental biology and toxicology
Authors: Wise L. David , Winkelmann Christopher T. , Dogdas Belma , Bagchi Ansuman 
Published: July 2013

AbstractMicro‐computed tomography (micro‐CT) is a high resolution imaging technique that has expanded and strengthened in use since it was last reviewed in this journal in 2004. The technology has expanded to include more detailed analysis of bone, as well as soft tissues, by use of various contrast agents. It is increasingly applied to questions in developmental biology and developmental toxicology. Relatively high‐throughput protocols now provide a powerful and efficient means to evaluate embryos and fetuses subjected to genetic manipulations or chemical exposures. This review provides an overview of the technology, including scanning, reconstruction, visualization, segmentation, and analysis of micro‐CT generated images. This is followed by a review of more recent applications of the technology in some common laboratory species that highlight the diverse issues that can be addressed. Birth Defects Research (Part C) 99:71–82, 2013. © 2013 Wiley Periodicals, Inc.
Engineered genetic selection links in vivo protein folding and stability with asparagine‐linked glycosylation
Authors: Mansell Thomas J. , Guarino Cassandra , DeLisa Matthew P. 
Published: July 2013

AbstractPredicting the structural consequences of site‐specific glycosylation remains a major challenge due in part to the lack of convenient experimental tools for rapidly determining how glycosylation influences protein folding. To address this shortcoming, we developed a genetic selection that directly links the in vivo folding of asparagine‐linked (N‐linked) glycoproteins with antibiotic resistance. Using this assay, we identified three known or putative glycoproteins from Campylobacter jejuni (Peb3, CjaA, and Cj0610c) whose folding was significantly affected by N‐glycosylation. We also used the genetic selection to isolate a glycoengineered variant of the Escherichia coli colicin E7 immunity protein (Im7) whose intracellular folding and stability were enhanced as a result of N‐glycosylation. In addition to monitoring the effect of glycan attachment on protein folding in living cells, this strategy could easily be extended for optimizing protein folding in vivo and engineering glycosylation enzymes, pathways, and hosts for optimal performance.See accompanying commentary by Danielle Tullman‐Ercek DOI: 10.1002/biot.201300319
Peptide‐based ligand screening and functional analysis of protein kinase C
Authors: Ohashi Nami , Nomura Wataru , Narumi Tetsuo , Tamamura Hirokazu 
Published: July 2013

ABSTRACTProtein kinase C (PKC) plays an important role in cell signaling pathways and is implicated in disorders ranging from cancer to Alzheimer's disease. Highly potent PKC ligands as therapeutic drugs have not been developed to date and useful methodologies for controlling PKC activation in defined areas are necessary to analyze precise PKC functions in cells. Studies focused on the development of PKC ligand screening systems and methods for regulation of PKC activation have been performed in our laboratory. In this review, our ligand screening methods involving synthetic peptides and solvatochromic fluorescent dye‐labeled small compounds are summarized and the technique of spatio‐temporal manipulation of PKC activation by caging strategies is introduced. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 613–620, 2013.
Analysis of N‐amino‐imidazolin‐2‐one peptide turn mimic 4‐position substituent effects on conformation by X‐ray crystallography
Authors: Proulx Caroline , Lubell William D. 
Published: July 2013

ABSTRACTN‐Amino‐imidazolin‐2‐ones, a new class of turn mimics onto which side chains of different amino acids may be added conveniently, have been analyzed by X‐ray crystallography. 4‐Methyl and 4‐benzyl N‐amino‐imidazolin‐2‐one tetrapeptide models 2 and 3 were examined to study the influence of the 4‐position substituent on turn conformation and the chi dihedral angle of the neighbouring C‐terminal residue side‐chain. The nature of the 4‐position substituent caused substantial effects on the ψi + 2 main chain and C‐terminal Phe χ1 side‐chain dihedral angle values, giving a preference for β‐ and γ‐turn conformers for the methyl‐ and benzyl‐substituted imidazolin‐2‐ones, respectively. Conformational analysis in the solid state has provided insight to guide application of N‐amino‐imidazolin‐2‐ones in peptide mimicry. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 7–15, 2014.
When “IUPs” were “BAPs”: How to study the nonconformation of intrinsically unfolded polyaminoacid chains
Authors: Pastore Annalisa , Temussi Pierandrea 
Published: July 2013

ABSTRACTIdeas often recur. It has been pointed out recently that proteins are not always the well‐structured entities we have become accustomed to from crystallographic studies, but may be intrinsically unstructured or contain unstructured regions. This feature, far from making these proteins less interesting, is an essential requirement for their function. Fascinating though it may be, the concept of so‐called intrinsically unfolded (or unordered) proteins (IUPs), also often referred to as intrinsically disordered proteins (IDPs), is not new: it directly links back to the 1970s when the attention of many structural biologists was focused on biologically active peptides, which like IUPs lack a specific defined conformation. The recurrent nature of this concept may now be of topical interest since it suggests the transfer, upon suitable adaptation, of old tools to develop new ideas. Here, we review some of the approaches that were developed for the study of peptides and discuss how they could inspire powerful new methodologies for the study of IUPs. © 2013 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 100: 592–600, 2013.
Charge‐Transfer Solids Using Nucleobases: Supramolecular Architectures Composed of Cytosine and [Ni(dmit)2] Assembled by Multiple Hydrogen Bonds and Heteroatomic Contacts
Authors: Yoshida Yukihiro , Maesato Mitsuhiko , Ishikawa Manabu , Nakano Yoshiaki , Hiramatsu Takaaki , Yamochi Hideki , Saito Gunzi 
Published: July 2013

AbstractProtonated species of the nucleobase cytosine (C), namely the monoprotonated CH+ and the hemiprotonated CHC+, were used to obtain four charge‐transfer complexes of [Ni(dmit)2] (dmit: 1,3‐dithiole‐2‐thione‐4,5‐dithiolate). Diffusion methods afforded two semiconducting [Ni(dmit)2]− salts; (CH)[Ni(dmit)2](CH3CN) (1) and (CHC)[Ni(dmit)2] (2). In salt 1, the [Ni(dmit)2]− ions with a S=1/2 spin construct a uniform one‐dimensional array along the molecular long axis, and the significant intermolecular interaction along the face‐to‐face direction results in a spin‐singlet ground state. In contrast, salt 2 exhibits the Mott insulating behavior associated with uniform 1D arrays of [Ni(dmit)2]−, which assemble a two‐dimensional layer that is sandwiched between the layers of hydrogen‐bonded CHC+ ribbons. Multiple hydrogen bonds between CHC+ and [Ni(dmit)2]− seem to result in the absence of structural phase transition down to 0.5 K. Electrooxidation of [Ni(dmit)2]− afforded the polymorphs of the [Ni(dmit)2]0.5− salts, (CHC+)[{Ni(dmit)2}0.5−]2 (3 and 4), which are the first mixed‐valence salts of nucleobase cations with metal complex anions. Similar to 2, salt 3 contains CHC+ ribbons that are sandwiched between the 2D [Ni(dmit)2]0.5− layers. In the layer, the [Ni(dmit)2]0.5− ions form dimers with a S=1/2 spin and the narrow electronic bandwidth causes a semiconducting behavior. In salt 4, the CHC+ units form an unprecedented corrugated 2D sheet, which is sandwiched between the 2D [Ni(dmit)2]0.5− layers that involve ring‐over‐atom and spanning overlaps. In contrast to 3, salt 4 exhibits metallic behavior down to 1.8 K, associated with a wide bandwidth and a 2D Fermi surface. The ability of hydrogen‐bonded CHC+ sheets as a template for the anion radical arrangements is demonstrated.
Enthalpy and Entropy Barriers Explain the Effects of Topology on the Kinetics of Zeolite‐Catalyzed Reactions
Authors: Van der Mynsbrugge Jeroen , De Ridder Jeroen , Hemelsoet Karen , Waroquier Michel , Van Speybroeck Veronique 
Published: July 2013

AbstractThe methylation of ethene, propene, and trans‐2‐butene on zeolites H‐ZSM‐58 (DDR), H‐ZSM‐22 (TON), and H‐ZSM‐5 (MFI) is studied to elucidate the particular influence of topology on the kinetics of zeolite‐catalyzed reactions. H‐ZSM‐58 and H‐ZSM‐22 are found to display overall lower methylation rates compared to H‐ZSM‐5 and also different trends in methylation rates with increasing alkene size. These variations may be rationalized based on a decomposition of the free‐energy barriers into enthalpic and entropic contributions, which reveals that the lower methylation rates on H‐ZSM‐58 and H‐ZSM‐22 have virtually opposite reasons. On H‐ZSM‐58, the lower methylation rates are caused by higher enthalpy barriers, owing to inefficient stabilization of the reaction intermediates in the large cage‐like pores. On the other hand, on H‐ZSM‐22, the methylation rates mostly suffer from higher entropy barriers, because excessive entropy losses are incurred inside the narrow‐channel structure. These results show that the kinetics of crucial elementary steps hinge on the balance between proper stabilization of the reaction intermediates inside the zeolite pores and the resulting entropy losses. These fundamental insights into their inner workings are indispensable for ultimately selecting or designing better zeolite catalysts.
Intramolecular Participation of Amino Groups in the Cleavage and Isomerization of Ribonucleoside 3′‐Phosphodiesters: The Role in Stabilization of the Phosphorane Intermediate
Authors: Lain Luigi , Lönnberg Harri , Lönnberg Tuomas 
Published: July 2013

AbstractA dinucleoside‐3′,5′‐phosphodiester model, 5′‐amino‐4′‐aminomethyl‐5′‐deoxyuridylyl‐3′,5′‐thymidine, incorporating two aminomethyl functions in the 4′‐position of the 3′‐linked nucleoside has been prepared and its hydrolytic reactions studied over a wide pH range. The amino functions were found to accelerate the cleavage and isomerization of the phosphodiester linkage in both protonated and neutral form. When present in protonated form, the cleavage of the 3′,5′‐phosphodiester linkage and its isomerization to a 2′,5′‐linkage are pH‐independent and 50–80 times as fast as the corresponding reactions of uridylyl‐3′,5′‐uridine (3′,5′‐UpU). The cleavage of the resulting 2′,5′‐isomer is also accelerated, albeit less than with the 3′,5′‐isomer, whereas isomerization back to the 3′,5′‐diester is not enhanced. When the amino groups are deprotonated, the cleavage reactions of both isomers are again pH‐independent and up to 1000‐fold faster than the pH‐independent cleavage of UpU. Interestingly, the 2′‐ to 3′‐isomerization is now much faster than its reverse reaction. The mechanisms of these reactions are discussed. The rate accelerations are largely accounted for by electrostatic and hydrogen‐bonding interactions of the protonated amino groups with the phosphorane intermediate.
Particles motion in a cascading rotary drum dryer
Authors: Hamawand Ihsan , Yusaf Talal 
Published: July 2013

AbstractA mathematical model was built and used to show the motion of particles in a cascade rotary drum dryer. In a cascade rotary drum the flights pick up the particles at a number of points in the lower half of the drum while, in the upper half, the particles fall freely. A model is derived where the drag force exerted on the particles throughout the falling period is emphasised. The motion of the particles in a rotary drum is described by three actions: Cascade; Kiln and Bouncing. In this study a horizontal rotary drum was used where both the kiln and bouncing actions have minimal effect, therefore, the focus is on the cascade motion of the particles. A characteristic of the model is the “falling number” which is found to be dependent on the curtain properties. The model has demonstrated its ability to predict the effect of many important parameters such as drying medium velocity, drum rotation speed, particle size and feeding flow rate. It has been shown that increasing the drying medium velocity by 2.5 times results in an 85% decrease in the residence time. Also, the number of falling is shown to be limited and a function of the drum rotation speed, in this case 0.59 falling per second. An important feature of this model is the ability to predict the mean resident time, contact time interval and the resting time interval. The maximum error between the predicted and the measured data was <10%.
Axonal transcription factors: Novel regulators of growth cone‐to‐nucleus signaling
Authors: Ji Sheng‐Jian , Jaffrey Samie R. 
Published: July 2013

ABSTRACTDeveloping axons contain transcripts that are locally translated to influence the axonal proteome. Recent studies have shown that axonal transcripts include mRNAs encoding transcription factors. These mRNAs are translated to produce transcription factors that can be retrogradely trafficked back to the nucleus, where they regulate gene expression programs. These findings point to a novel mechanism of growth cone‐to‐nucleus signaling that occurs when growth cones encounter extracellular signaling molecules that stimulate local translation of these transcription factors, thereby influencing gene transcription. Here we summarize recent findings on local translation of transcription factors in axons and their roles in different neuronal processes such as neuronal specification, survival, and axon regeneration. Comprehensive axonal transcriptome studies have revealed transcripts that encode many more transcription factors and cofactors, suggesting a potentially broad role for this type of signaling. We review the progress on the approaches and tools that have been developed to study local translation and retrograde trafficking of transcription factors. We also highlight the challenges in the field and discuss the potential routes to resolving them. © 2013 Wiley Periodicals, Inc. Develop Neurobiol 74: 245–258, 2014
Identification of axon‐enriched MicroRNAs localized to growth cones of cortical neurons
Authors: Sasaki Yukio , Gross Christina , Xing Lei , Goshima Yoshio , Bassell Gary J. 
Published: July 2013

ABSTRACTThere is increasing evidence that localized mRNAs in axons and growth cones play an important role in axon extension and pathfinding via local translation. A few studies have revealed the presence of microRNAs (miRNAs) in axons, which may control local protein synthesis during axon development. However, so far, there has been no attempt to screen for axon‐enriched miRNAs and to validate their possible localization to growth cones of developing axons from neurons of the central nervous system. In this study, the localization of miRNAs in axons and growth cones in cortical neurons was examined using a “neuron ball” culture method that is suitable to prepare axonal miRNAs with high yield and purity. Axonal miRNAs prepared from the neuron ball cultures of mouse cortical neurons were analyzed by quantitative real‐time RT‐PCR. Among 375 miRNAs that were analyzed, 105 miRNAs were detected in axons, and six miRNAs were significantly enriched in axonal fractions when compared with cell body fractions. Fluorescence in situ hybridization revealed that two axon‐enriched miRNAs, miR‐181a‐1* and miR‐532, localized as distinct granules in distal axons and growth cones. The association of these miRNAs with the RNA‐induced silencing complex further supported their function to regulate mRNA levels or translation in the brain. These results suggest a mechanism to localize specific miRNAs to distal axons and growth cones, where they could be involved in local mRNA regulation. These findings provide new insight into the presence of axonal miRNAs and motivate further analysis of their function in local protein synthesis underlying axon guidance. © 2013 Wiley Periodicals, Inc. Develop Neurobiol 74: 397–406, 2014
Unexpected Coordination Behaviour of 3,5‐Di(2‐pyridyl)‐1,2,4‐oxadiazole
Authors: Klingele Julia , Kaase Dominic , Schmucker Maximilian , Meier Lea 
Published: July 2013

AbstractThe coordination behaviour of 3,5‐di(2‐pyridyl)‐1,2,4‐oxadiazole (L′) has been studied and compared with that of the 2,5‐di(2‐pyridyl)‐1,3,4‐chalcadiazolesLO,LSandLSe[LO= 2,5‐di(2‐pyridyl)‐1,3,4‐oxadiazole,LS= 2,5‐di(2‐pyridyl)‐1,3,4‐thiadiazole,LSe= 2,5‐di(2‐pyridyl)‐1,3,4‐selenadiazole]. LigandL′and the new complexes [CuII(L′)3](ClO4)2·1.5MeOH·H2O (1·1.5MeOH·H2O),1·MeCN, [CoII(L′)2(MeOH)2](ClO4)2(2), [CoII(LO)2(MeOH)2](ClO4)2(3), [CuII(L′)2Cl2] (4), [CuII(L′)2Br2] (5) and [CuII(LSe)2Cl2]·MeOH (6·MeOH) have been structurally characterised by single‐crystal X‐ray diffraction analyses. With the help of DFT calculations and the analyses of metal–ligand bond lengths of similar complexes ofL′,LO,LSandLSethe binding capacities have been determined asL′ <<LO <LS <LSe.
Reductive Deoxygenation of Alcohols: Catalytic Methods Beyond Barton–McCombie Deoxygenation
Authors: Herrmann Josef M. , König Burkhard 
Published: July 2013

AbstractDeoxygenation is an extensively studied field in organic chemistry, and over the last decades many methods such as the Barton–McCombie deoxygenation reaction or deoxygenation with alkali metals in liquid ammonia have been established. Within this microreview, we discuss different strategies for the chemoselective catalytic deoxygenation of alcohols with special attention to their scope and limitations. The deoxygenation of derivatives of alcohols and their direct deoxygenation as step‐economic alternative are covered with current examples. Catalytic methods can serve as convenient and economic alternatives for established methods in the reduction of carbon–oxygen single bonds.