bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Concomitant Coronary Artery Disease on Atherosclerotic Plaques in the Aortic Arch in Patients With Severe Aortic Stenosis
Authors: Fujita Suwako , Sugioka Kenichi , Matsumura Yoshiki , Ito Asahiro , Hozumi Takeshi , Hasegawa Takao , Hanatani Akihisa , Naruko Takahiko , Ueda Makiko , Yoshiyama Minoru 
Published: April 2013

AbstractBackgroundCoronary artery disease (CAD) often occurs concurrently in patients with severe aortic stenosis (AS). However, the influence of concomitant CAD on the presence of atherosclerotic complex plaques in the aortic arch, which is associated with increased stroke risk, has not been fully assessed in patients with severe AS.HypothesisWe hypothesized that concomitant CAD would be associated with the presence of complex arch plaques in patients with severe AS.MethodsThe study population consisted of 154 patients with severe AS who had undergone transesophageal echocardiography (TEE) and coronary angiography (71 male; mean age, 72 ± 8 years; mean aortic valve area, 0.67 ± 0.15 cm2). Aortic arch plaques were assessed using TEE, and complex arch plaques were defined as large plaques (≥4 mm), ulcerated plaques, or mobile plaques.ResultsThe prevalence of aortic arch plaques (87% vs 70%; P = 0.03) and complex arch plaques (48% vs 20%; P < 0.001) was significantly greater in AS patients with CAD than in those without CAD. After adjustment for traditional atherosclerotic risk factors, we found that concomitant CAD was independently associated with the presence of complex arch plaques (odds ratio: 2.86, 95% confidence interval: 1.23‐6.68, P = 0.01).ConclusionsIn patients with severe AS, concomitant CAD is associated with severe atherosclerotic burden in the aortic arch. This observation suggests that AS patients with concomitant CAD are at a higher risk for stroke, and that careful evaluation of complex arch plaques by TEE is needed for the risk stratification of stroke in these patients.
D‐Glucuronic Acid Coated Gd(IO3)3·2H2O Nanomaterial as a Potential T1 MRI‐CT Dual Contrast Agent
Authors: Lee Eun Jung , Heo Woo Choul , Park Jang Woo , Chang Yongmin , Bae Ji‐Eun , Chae Kwon Seok , Kim Tae Jeong , Park Ji Ae , Lee Gang Ho 
Published: April 2013

AbstractTo date, only a few nanosystems have been investigated as T1 MRI‐CT dual contrast agents. The T1 MRI‐CT dual functionality of a material depends on its longitudinal water‐proton relaxivity (r1) and X‐ray absorption strength. We explored Gd(IO3)3·2H2O nanomaterial because Gd is the most powerful element for T1 MRI contrast agents, and both Gd and I absorb X‐ray radiation; Gd absorbs X‐ray radiation ca. 2.5 times more strongly than I. D‐Glucuronic acid coated Gd(IO3)3·2H2O nanomaterial showed a very large r1 of 52.3 s–1 mM–1 (r2/r1 = 1.21), which could be ascribed to hydrated water molecules in the lattice. Its X‐ray absorption intensity was also stronger than those of commercial molecular iodine CT contrast agents. This result clearly suggests that D‐glucuronic acid coated Gd(IO3)3·2H2O nanomaterial is a potential T1 MRI‐CT dual contrast agent.
Europium Polyoxometalates Encapsulated in Silica Nanoparticles – Characterization and Photoluminescence Studies
Authors: Neves Cristina S. , Granadeiro Carlos M. , Cunha‐Silva Luís , Ananias Duarte , Gago Sandra , Feio Gabriel , Carvalho Patricia A. , Eaton Peter , Balula Salete S. , Pereira Eulália 
Published: April 2013

AbstractThe incorporation of europium polyoxometalates into silica nanoparticles can lead to a biocompatible nanomaterial with luminescent properties suitable for applications in biosensors, biological probes, and imaging. Keggin‐type europium polyoxometalates Eu(PW11)x (x = 1 and 2) with different europium coordination environments were prepared by using simple methodologies and no expensive reactants. These luminescent compounds were then encapsulated into silica nanoparticles for the first time through the water‐in‐oil microemulsion methodology with a nonionic surfactant. The europium polyoxometalates and the nanoparticles were characterized by using several techniques [FTIR, FT‐Raman, 31P magic angle spinning (MAS) NMR, and TEM/energy‐dispersive X‐ray spectroscopy (TEM‐EDS), AFM, dynamic light scattering (DLS), and inductively coupled plasma MS (ICP‐MS) analysis]. The stability of the material and the integrity of the europium compounds incorporated were also examined. Furthermore, the photoluminescence properties of the Eu(PW11)x@SiO2 nanomaterials were evaluated and compared with those of the free europium polyoxometalates. The silica surface of the most stable nanoparticles was successfully functionalized with appropriate organosilanes to enable the covalent binding of oligonucleotides.
Preparation and physicochemical performances of poly[(vinylidene fluoride)‐co‐hexafluoropropylene]‐based composite polymer electrolytes doped with modified carbon nanotubes
Authors: Xiao Wei , Li Xinhai , Guo Huajun , Wang Zhixing , Li Yan , Yang Bo 
Published: April 2013

AbstractModified carbon nanotubes (m‐CNTs) were successfully prepared by the interactions between nitric and sulfuric acids and CNTs, which was confirmed using Fourier transform infrared spectroscopy. Poly[(vinylidene fluoride)‐co‐hexafluoropropylene]‐based composite polymer electrolyte (CPE) membranes doped with various amounts of m‐CNTs were prepared by phase inversion method. The desired CPEs were obtained by soaking the liquid electrolytes for 30 min. The physicochemical and electrochemical properties of the CPE membranes were investigated using scanning electron microscopy, X‐ray diffraction, thermogravimetry, electrochemical impedance spectroscopy and linear sweep voltammetry. The results show that the CPE membranes doped with 2.2 wt% m‐CNTs possess the smoothest surface and the highest decomposition temperature about 450 °C. Obviously, adding an appropriate amount of m‐CNTs into the polymer matrix can decrease the crystallinity and enhance the ionic conductivity; the temperature dependence of ionic conductivity follows the Arrhenius relation and the ionic conductivity at room temperature is up to 4.9 mS cm−1. The interfacial resistance can reach a stable value of about 415 Ω cm−2 after 10 days storage. The excellent rate and cycle performances with an electrochemical working window up to 5.4 V ensure that the CPEs doped with 2.2 wt% m‐CNTs can be considered as potential candidates as polymer electrolyte for lithium ion batteries. © 2013 Society of Chemical Industry
Simulation reveals two major docking pathways between the hexapeptide GDYMNM and the catalytic domain of the insulin receptor protein kinase
Authors: Huang Zunnan , Wong Chung F. 
Published: April 2013

AbstractExtending a previous mining‐minima approach to identifying the docking pathways between the hexapeptide GDYMNM and the catalytic domain of the insulin receptor tyrosine kinase (IRK), we found two major docking pathways connecting the binding pocket and the surface of the protein. One pathway was more likely to lead to phosphate transfer from ATP to the peptide as the distance between the γ‐phosphate of ATP and the hydroxyl oxygen of the target tyrosine approached one that could facilitate reaction. The movement of the peptide along the pathways was found to couple with residues in the activation loop of the protein. Although these residues might not affect binding affinity, they might influence the kinetics of peptide entrance and release. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric‐multithermal molecular dynamics method
Authors: Okumura Hisashi 
Published: April 2013

AbstractA multibaric‐multithermal molecular dynamics (MD) simulation of a 10‐residue protein, chignolin, was performed. All‐atom model with the Amber parm99SB force field was used for the protein and the TIP3P model was used for the explicit water molecules. This MD simulation covered wide ranges of temperature between 260 and 560 K and pressure between 0.1 and 600 MPa and sampled many conformations without getting trapped in local‐minimum free‐energy states. Folding events to the native β‐hairpin structure occurred five times and unfolding events were observed four times. As the temperature and/or pressure increases, fraction of folded chignolin decreases. The partial molar enthalpy change ΔH and partial molar volume change ΔV of unfolding were calculated as ΔH = 24.1 ± 4.9 kJ/mol and ΔV = −5.6 ± 1.5 cm3/mol, respectively. These values agree well with recent experimental results. Illustrating typical local‐minimum free‐energy conformations, folding and unfolding pathways were revealed. When chignolin unfolds from the β‐hairpin structure, only the C terminus or both C and N termini open first. It may undergo an α‐helix or 310‐helix structure and finally unfolds to the extended structure. Difference of the mechanism between temperature denaturation and pressure denaturation is also discussed. Temperature denaturation is caused by making the protein transferred to a higher entropy state and making it move around more with larger space. The reason for pressure denaturation is that water molecules approach the hydrophobic residues, which are not well hydrated at the folded state, and some hydrophobic contacts are broken. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Kinesin tail domains are intrinsically disordered
Authors: Seeger Mark A. , Zhang Yongbo , Rice Sarah E. 
Published: April 2013

AbstractKinesin motor proteins transport a wide variety of molecular cargoes in a spatially and temporally regulated manner. Kinesin motor domains, which hydrolyze ATP to produce a directed mechanical force along a microtubule, are well conserved throughout the entire superfamily. Outside of the motor domains, kinesin sequences diverge along with their transport functions. The nonmotor regions, particularly the tails, respond to a wide variety of structural and molecular cues that enable kinesins to carry specific cargoes in response to particular cellular signals. Here, we demonstrate that intrinsic disorder is a common structural feature of kinesins. A bioinformatics survey of the full‐length sequences of all 43 human kinesins predicts that significant regions of intrinsically disordered residues are present in all kinesins. These regions are concentrated in the nonmotor domains, particularly in the tails and near sites for ligand binding or post‐translational modifications. In order to experimentally verify these predictions, we expressed and purified the tail domains of kinesins representing three different families (Kif5B, Kif10, and KifC3). Circular dichroism and NMR spectroscopy experiments demonstrate that the isolated tails are disordered in vitro, yet they retain their functional microtubule‐binding activity. On the basis of these results, we propose that intrinsic disorder is a common structural feature that confers functional specificity to kinesins. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Overcoming sequence misalignments with weighted structural superposition
Authors: Khazanov Nickolay A. , Damm‐Ganamet Kelly L. , Quang Daniel X. , Carlson Heather A. 
Published: April 2013

AbstractAn appropriate structural superposition identifies similarities and differences between homologous proteins that are not evident from sequence alignments alone. We have coupled our Gaussian‐weighted RMSD (wRMSD) tool with a sequence aligner and seed extension (SE) algorithm to create a robust technique for overlaying structures and aligning sequences of homologous proteins (HwRMSD). HwRMSD overcomes errors in the initial sequence alignment that would normally propagate into a standard RMSD overlay. SE can generate a corrected sequence alignment from the improved structural superposition obtained by wRMSD. HwRMSD's robust performance and its superiority over standard RMSD are demonstrated over a range of homologous proteins. Its better overlay results in corrected sequence alignments with good agreement to HOMSTRAD. Finally, HwRMSD is compared to established structural alignment methods: FATCAT, secondary‐structure matching, combinatorial extension, and Dalilite. Most methods are comparable at placing residue pairs within 2 Å, but HwRMSD places many more residue pairs within 1 Å, providing a clear advantage. Such high accuracy is essential in drug design, where small distances can have a large impact on computational predictions. This level of accuracy is also needed to correct sequence alignments in an automated fashion, especially for omics‐scale analysis. HwRMSD can align homologs with low‐sequence identity and large conformational differences, cases where both sequence‐based and structural‐based methods may fail. The HwRMSD pipeline overcomes the dependency of structural overlays on initial sequence pairing and removes the need to determine the best sequence‐alignment method, substitution matrix, and gap parameters for each unique pair of homologs. Proteins 2012. © 2012 Wiley Periodicals, Inc.
Crystal packing modifies ligand binding affinity: The case of aldose reductase
Authors: Cousido‐Siah Alexandra , Petrova Tatiana , Hazemann Isabelle , Mitschler André , Ruiz Francesc X. , Howard Eduardo , Ginell Stephan , Atmanene Cédric , Van Dorsselaer Alain , Sanglier‐Cianférani Sarah , Joachimiak Andrzej , Podjarny Alberto 
Published: April 2013

AbstractThe relationship between the structures of protein–ligand complexes existing in the crystal and in solution, essential in the case of fragment‐based screening by X‐ray crystallography (FBS‐X), has been often an object of controversy. To address this question, simultaneous co‐crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; Kd = 6.5 nM) and IDD594 (594; Kd = 61 nM), which bind to h‐aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X‐ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122–130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B‐factors of the Loop A between the AR–594 and AR–FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X‐ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS‐X to validate this powerful screening technique, which is widely used. Proteins 2012. © 2012 Wiley Periodicals, Inc.
The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein
Authors: Baumketner Andrij 
Published: April 2013

AbstractUpon ATP binding, myosin motor protein is found in two alternative conformations, prerecovery state M* and postrecovery state M**. The transition from one state to the other, known as the recovery stroke, plays a key role in the myosin functional cycle. Despite much recent research, the microscopic details of this transition remain elusive. A critical step in the recovery stroke is the rotation of the converter domain from “up” position in prerecovery state to “down” position in postrecovery state that leads to the swing of the lever arm attached to it. In this work, we demonstrate that the two rotational states of the converter domain are determined by the interactions within a small structural motif in the force‐generating region of the protein that can be accurately modeled on computers using atomic representation and explicit solvent. Our simulations show that the transition between the two states is controlled by a small helix (SH1) located next to the relay helix and relay loop. A small translation in the position of SH1 away from the relay helix is seen to trigger the transition from “up” state to “down” state. The transition is driven by a cluster of hydrophobic residues I687, F487, and F506 that make significant contributions to the stability of both states. The proposed mechanism agrees well with the available structural and mutational studies. Proteins 2012; © 2012 Wiley Periodicals, Inc.
Small‐angle X‐ray scattering reveals architecture and A2B2 stoichiometry of the UvrA–UvrB DNA damage sensor
Authors: Pakotiprapha Danaya , Jeruzalmi David 
Published: April 2013

AbstractThe UvrA–UvrB (AB) protein complex operates in the bacterial nucleotide excision repair pathway as the main sensor of DNA damage. Crystallographic analysis of the AB complex revealed a linear UvrB–UvrA–UvrA–UvrB arrangement of subunits with an internal two‐fold axis that became incorporated into the crystal. Here, we have used small‐angle X‐ray scattering (SAXS) to show close correspondence between the crystal structure and the entity in solution. This result confirms the number and disposition of subunits in the crystallographic model and rules out other possible arrangements suggested by packing in the crystal. The current SAXS analysis failed to detect significant changes to the structure as a function of nucleotide. Proteins 2013. © 2012 Wiley Periodicals, Inc.
A hierarchical order within protein structures underlies large separations between strands in β‐sheets
Authors: Wathen Brent , Jia Zongchao 
Published: April 2013

AbstractProtein β‐sheets often involve nonlocal interactions between parts of the polypeptide chain that are separated by hundreds of residues, raising the question of how these nonlocal contacts form. A recent study of the smallest β‐sheets found that their formation was not driven by signals hidden in the primary sequence. Instead, the strands in these sheets were either local in sequence, or, when separated by large sequential distances, the intervening residues were found to fold into compact modules that anchored distant parts of the chain in close spatial proximity. Here, we examine larger β‐sheets to investigate the extensibility of this principle. From an analysis of the β‐sheets in a nonredundant protein dataset, we find that a highly ordered hierarchical relationship exists in the intervening structure between nonlocal β‐strands. This observation is almost universal: virtually all β‐sheets, no matter their complexity, appear to adopt an antiparallel model to manage the nonlocal aspects of their assembly, one where the chain, having left the vicinity of an unfinished β‐sheet, retraces its steps via the same route to complete the initial sheet. Exceptions typically involve unstructured regions at chain termini. Moreover, an analysis of the residues involved in nonlocal crossstrand interactions did not produce any evidence of a signal hidden in the sequence that might direct long‐range interactions. These results build on those reported for the smallest sheets, suggesting that sheet formation is either local in sequence or local in space following prior folding events that anchor disparate parts of the chain in close proximity. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Solution NMR structure of a sheddase inhibitor prodomain from the malarial parasite Plasmodium falciparum
Authors: He Yanan , Chen Yihong , Oganesyan Natalia , Ruan Biao , O'Brochta David , Bryan Philip N. , Orban John 
Published: April 2013

AbstractPlasmodium subtilisin 2 (Sub2) is a multidomain protein that plays an important role in malaria infection. Here, we describe the solution NMR structure of a conserved region of the inhibitory prodomain of Sub2 from Plasmodium falciparum, termed prosub2. Despite the absence of any detectable sequence homology, the protozoan prosub2 has structural similarity to bacterial and mammalian subtilisin‐like prodomains. Comparison with the three‐dimensional structures of these other prodomains suggests a likely binding interface with the catalytic domain of Sub2 and provides insights into the locations of primary and secondary processing sites in Plasmodium prodomains. Proteins 2012;. © 2012 Wiley Periodicals, Inc.
Nematotoxicity of drupacine and a Cephalotaxus alkaloid preparation against the plant‐parasitic nematodes Meloidogyne incognita and Bursaphelenchus xylophilus
Authors: Wen Yanhua , Meyer Susan L F , Masler Edward P , Zhang Fengxian , Liao Jinling , Wei Xiaoyi , Chitwood David J 
Published: April 2013

AbstractBackgroundSpecies of Cephalotaxus (the plum yews) produce nematotoxic compounds of unknown identity. Consequently, bioassay‐guided fractionation was employed to identify the compound(s) in Cephalotaxus fortunei twigs and leaves with activity against plant‐parasitic nematodes.ResultsA crude alkaloid extract, particularly drupacine, was responsible for much of the nematotoxicity. The ED50 of drupacine for Bursaphelenchus xylophilus was 27.1 µg mL−1, and for Meloidogyne incognita it was 76.3 µg mL−1. Immersion of M. incognita eggs in 1.0 mg mL−1 crude alkaloid extract (the highest tested concentration) reduced hatch by 36%; immersion of second‐stage juveniles (J2) resulted in 72–98% immobility. Crude alkaloid extract and drupacine suppressed protease activity in extracts of the microbivorous nematode Panagrellus redivivus by 50% and 80%, respectively. Application of 0.02–0.5 mg mL−1 crude alkaloid extract to soil with M. incognita inoculum did not significantly reduce pepper plant shoot length or weight, compared with nematode‐inoculated, water‐treated controls, but the number of eggs and J2 per root system respectively decreased by 69% and 73% at 0.5 mg mL−1.ConclusionDrupacine and a crude alkaloid extract suppress nematode hatch, activity of mixed life stages, and population numbers on plant roots. This is the first demonstration of nematotoxicity of crude Cephalotaxus alkaloids and drupacine. © 2013 Society of Chemical Industry
Vicarious Traumatization: Potential Hazards and Interventions for Disaster and Trauma Workers
Authors: Palm Kathleen M. , Polusny Melissa A. , Follette Victoria M. 
Published: April 2013

AbstractDisaster and trauma workers often disregard their own reactions and needs when focusing on caring for those directly exposed to traumatic events. This article discusses the concept of vicarious traumatization, a form of post-traumatic stress response sometimes experienced by those who indirectly are exposed to traumatic events. It includes an examination of how vicarious trauma reactions are experienced across different professions, and suggestions on how to limit or prevent vicarious traumatization. The authors review self-care strategies as well as training and organizational considerations that may be beneficial for individuals and organizations to address.
Pulse waveforms for 60 GHz M‐ary pulse position modulation communication systems
Authors: Zhang Hao , Lu Ting‐ting , Gulliver T. Aaron 
Published: April 2013

Pulse waveforms for 60 GHz impulse radio (IR) communication systems are investigated. The power spectral densities of the pulses are examined for compliance with Federal Communications Commission (FCC) spectral regulations. The error probability and capacity of M‐ary pulse position modulation (PPM) 60 GHz IR systems with a correlation receiver using different pulse waveforms are analysed. Both orthogonal and non‐orthogonal PPM is considered with additive white Gaussian noise and IEEE 802.15.3c channel models. Analytical and simulation results are presented, which show that an autocorrelation function that decays quickly provides a lower probability of error and better capacity. Among the pulse waveforms examined in this study, the truncated sinc pulse is the best in terms of compliance with FCC regulations and the PPM error probability and capacity.