bluuebunny/crossref_metadata_2025 huggingface dataset:
Reproducibility of first‐pass cardiovascular magnetic resonance myocardial perfusion
Authors: Larghat Abdulghani M. , Maredia Neil , Biglands John , Greenwood John P. , Ball Stephen G. , Jerosch‐Herold Michael , Radjenovic Aleksandra , Plein Sven
Published: January 2013

Purpose:

To assess the reproducibility of semiquantitative and quantitative analysis of first‐pass myocardial perfusion cardiovascular magnetic resonance (CMR) in healthy volunteers.

Materials and Methods:

Eleven volunteers underwent myocardial perfusion CMR during adenosine stress and rest on 2 separate days. Perfusion data were acquired in a single mid‐ventricular section in two cardiac phases to permit cardiac phase reproducibility comparisons. Semiquantitative analysis was performed to derive normalized upslopes of myocardial signal intensity profiles (myocardial perfusion index, MPI). The quantitative analysis estimated absolute myocardial blood flow (MBF) using Fermi‐constrained deconvolution. The perfusion reserve index was calculated by dividing stress by rest data. Two observers performed all the measurements independently. One observer repeated all first scan measurements 4 weeks later.

Results:

The reproducibility of perfusion CMR was highest for semiquantitative analysis with an intraobserver coefficient of variability (CoV) of 3%–7% and interobserver CoV of 4%–10%. Semiquantitative interstudy comparison was less reproducible (CoV of 13%–27%). Quantitative intraobserver CoV of 10%–18%, interobserver CoV of 8%–15% and interstudy CoV of 20%–41%. Reproducibility of systolic and diastolic phases and the endocardial and epicardial myocardial layer showed similar reproducibility on both semiquantitative and quantitative analysis.

Conclusion:

The reproducibility of CMR myocardial perfusion estimates is good, but varies between intraobserver, interobserver, and interstudy comparisons. In this study semiquantitative analysis was more reproducible than quantitative analysis. J. Magn. Reson. Imaging 2013;37:865–874. © 2013 Wiley Periodicals, Inc.
Satisfaction With the Initial Police Response and Development of Posttraumatic Stress Disorder Symptoms in Victims of Domestic Burglary
Authors: Kunst M. J. J. , Rutten S. , Knijf E.
Published: January 2013

The current study used a prospective design to investigate the association between early symptoms, satisfaction with the initial police response, and development of posttraumatic stress disorder (PTSD) symptomatology in victims of domestic burglary (n = 95). Early symptoms and satisfaction with the initial police response were assessed through telephone interviews conducted within the first month after the burglary and PTSD symptoms 4 to 6 weeks after baseline. Separate regression models were tested for satisfaction with performance and satisfaction with procedure. Results suggested that early symptoms were a risk factor for PTSD symptomatology (β = .50, p < .001 and β = .48, p < .001) above and beyond levels of peritraumatic distress (β = .21, p < .05 and β = .22, p < .05) and irrespective of level of satisfaction (β = −.02, ns and β = −.10, ns). Victims with high levels of early symptoms, however, were clearly at an increased risk of PTSD symptomatology if they scored low on satisfaction at baseline. Results were discussed in light of the framework of therapeutic jurisprudence.
Primary inner ear schwannomas: A case series and systematic review of the literature
Authors: Van Abel Kathryn M. , Carlson Matthew L. , Link Michael J. , Neff Brian A. , Beatty Charles W. , Lohse Christine M. , Eckel Laurence J. , Lane John I. , Driscoll Colin L.
Published: January 2013

Objectives/Hypothesis

To describe the natural history of primary inner ear schwannomas (PIES) and evaluate management outcomes and relationship between PIES location, clinical presentation, and time to diagnosis.

Study Design

Retrospective chart review and systematic review of the literature.

Methods

Vestibular schwannoma confined to or arising from the inner ear were included. PIES classification was based on anatomic subsite(s) involved. Detailed clinical history and outcomes were recorded.

Results

In a systematic review (1933–2011), including 14 patients from the authors' institution (1999–2009), a total of 72 studies comprising 234 patients were evaluated. Mean follow‐up was 32.8 ± 39.1 months (range, 0–183 months). The cochlea was the most commonly involved subsite (51%). Hearing loss was the most frequent presenting symptom (99%). Vertigo and abnormal balance were more common among tumors involving the vestibular system (P < .01). Average delay between symptom onset and diagnosis was 7.0 ± 8.0 years (median, 5 years; range, 0–40 years). Recent onset hearing loss was more likely to elicit an earlier diagnosis (P = .01). The majority of patients were observed without treatment (53%). Tumor progression was seen in 52% of patients.

Conclusions

PIES are rare tumors and most commonly involve the cochlea. Tumor location is often associated with clinical presentation and correlates with delay between symptom onset and diagnosis. A watch‐and‐scan approach is the management strategy of choice in the absence of intractable vertigo or extensive tumor growth. The majority of patients report stable or improved symptoms over time, regardless of treatment. Laryngoscope, 123:1957–1966, 2013
Shrinking Hydrogel‐DNA Spots Generates 3D Microdots Arrays
Authors: Le Goff Gaelle C. , Blum Loïc J. , Marquette Christophe A.
Published: January 2013

This report describes a straightforward approach for the achievement of sub‐100 micrometers size hydrogel dots supporting DNA immobilization. Hydrogel‐DNA spots are arrayed and UV‐crosslinked on PolyShrink, an innovative polymer material having the remarkable property of isotropically shrinking under high temperature. Curing the microarray enables then spot miniaturization, resulting in 6 µm thick and 60 µm wide hydrogel dots in which oligonucleotides are immobilized in a 3D hydrophilic environment. The probe immobilization within the hydrogel network and its capacity to detect targets specifically and quantitatively is demonstrated using chemiluminescent as well as colorimetric detection techniques. The hydrogel material improves probe accessibility within the spot, leading to an enhanced sensitivity.

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Emulsion Self‐Assembly Synthesis of Chitosan/Poly(lactic‐co‐glycolic acid) Stimuli‐Responsive Amphiphiles
Authors: Niu Xufeng , Wang Lizhen , Chen Pin , Li Xiaoming , Zhou Gang , Feng Qingling , Fan Yubo
Published: January 2013

An amphiphilic graft copolymer using chitosan (CS) as a hydrophilic main chain and poly(lactic‐co‐glycolic acid) (PLGA) as a hydrophobic side chain is prepared through an emulsion self‐assembly synthesis. CS aqueous solution is used as a water phase and PLGA in chloroform is served as an oil phase. A water‐in‐oil (W/O) emulsion is fabricated in the presence of the surfactant span‐80. The self‐assembly reaction is performed between PLGA and CS under the condensation of EDC. Fourier transform IR (FTIR) spectroscopy reveals that PLGA is grafted onto the backbone of CS through the interactions between end carboxyl and amino groups of the two components. 1H NMR spectroscopy directly indicates the grafting content of PLGA in the CS‐graft‐PLGA (CS‐g‐PLGA) copolymer is close to 25%. X‐ray diffraction (XRD) confirms that the copolymer exhibits an amorphous structure. The CS‐g‐PLGA amphiphile can self‐assemble to form micelles with size in the range of ≈100–300 nm, which makes it easy to apply in various targeted‐drug‐release and biomaterial fields.
Temporal Gödel‐Gentzen and Girard translations
Authors: Kamide Norihiro
Published: January 2013

A theorem for embedding a first‐order linear‐time temporal logic LTL into its intuitionistic counterpart ILTL is proved using Baratella‐Masini's temporal extension of the Gödel‐Gentzen negative translation of classical logic into intuitionistic logic. A substructural counterpart LLTL of ILTL is introduced, and a theorem for embedding ILTL into LLTL is proved using a temporal extension of the Girard translation of intuitionistic logic into intuitionistic linear logic. These embedding theorems are proved syntactically based on Gentzen‐type sequent calculi.
Complex calcaneal defect reconstruction with osteotomized free fibula–flexor hallucis longus osteomuscular flap
Authors: Lykoudis Efstathios G. , Gantsos Apostolos , Dimou Apostolos Od.
Published: January 2013

Complex calcaneal defects represent a reconstructive challenge since calcaneous plays a key role in standing and gait. We report the case of a 35‐year‐old patient with a complex calcaneal defect due to chronic osteomyelitis after a high energy Gustillo type IIIB calcaneal fracture that was reconstructed with a free fibula–flexor hallucis longus osteomuscular flap. The fibula was osteotomized into two segments, which were used to reconstruct the bone defect, and the muscular component of the flap was used for coverage of the reconstructed calcaneal skeleton. Fifteen days later permanent skin coverage was ensured with a local random pattern rhomboid skin flap. Early and late postoperative periods were uneventful. Bone maturation was radiographically evident at a follow up of 12 weeks, and complete bone incorporation at 3 years. Full weight bearing was possible at 6 months postop. Final follow up, at 3 years postop, verified a very good functional and aesthetic outcome. © 2012 Wiley Periodicals, Inc. Microsurgery, 2013.
Anomalous behavior of bilinear quadrilateral finite elements for modeling cohesive cracks with XFEM/GFEM
Authors: Ahmed A. , Sluys L.J.
Published: January 2013

The performance of partition‐of‐unity based methods such as the generalized finite element method or the extended finite element method is studied for the simulation of cohesive cracking. The focus of investigation is on the performance of bilinear quadrilateral finite elements using these methods. In particular, the approximation of the displacement jump field, representing cohesive cracks, by extended finite element method/generalized finite element method and its effect on the overall behavior at element and structural level is investigated. A single element test is performed with two different integration schemes, namely the Newton‐Cotes/Lobatto and the Gauss integration schemes, for the cracked interface contribution. It was found that cohesive crack segments subjected to a nonuniform opening in unstructured meshes (or an inclined crack in a structured finite element mesh) result in an unrealistic crack opening. The reasons for such behavior and its effect on the response at element level are discussed. Furthermore, a mesh refinement study is performed to analyze the overall response of a cohesively cracked body in a finite element analysis. Copyright © 2013 John Wiley & Sons, Ltd.
Skeletal muscle adiposity is associated with serum lipid and lipoprotein levels in Afro‐Caribbean men
Authors: Miljkovic I. , Kuipers A.L. , Kuller L.H. , Sheu Y. , Bunker C.H. , Patrick A.L. , Wheeler V.W. , Evans R.W. , Zmuda J.M.
Published: January 2013

Objective: When compared with other ethnic groups, African ancestry individuals have lower triglycerides and higher High‐density lipoprotein cholesterol (HDL‐C) levels, although the mechanisms for these differences remain unclear. A comprehensive array of factors potentially related to fasting serum lipid and lipoprotein levels in African ancestry men was evaluated.

Design and Methods: Men (1,821) underwent dual‐energy X‐ray absorptiometry measures of total body fat and quantitative computed tomography assessments of calf skeletal muscle adiposity [subcutaneous and intermuscular adipose tissue (AT), and muscle density as a measure of intra‐muscular AT].

Results: Multivariable linear regression analysis identified age (−), total body fat (+), subcutaneous AT (−), fasting glucose (+), fasting insulin (+), diastolic blood pressure (+), and non‐African ancestry (+) as independent correlates of triglycerides (all P < 0.05). Total body fat (+), intra‐muscular AT (−), and diastolic blood pressure (+) were independent correlates of Low‐density lipoprotein cholesterol (LDL‐C) (all P < 0.001). Age (+), waist circumference (−), fasting insulin (−), physical activity (+), and alcohol intake (+) were independent correlates of HDL‐C (all P < 0.05).

Conclusions: A novel relationship between skeletal muscle adiposity and serum lipid and lipoprotein levels in African ancestry men, independent of total and central adiposity was illuminated. In African ancestry populations, genetic factors are likely a significant determinant of triglycerides levels.
Influence of a clinical lifestyle‐based weight loss program on the metabolic risk profile of metabolically normal and abnormal obese adults
Authors: Liu Rebecca H. , Wharton Sean , Sharma Arya M. , Ardern Chris I. , Kuk Jennifer L.
Published: January 2013

Objective

It is unclear whether all obese individuals should be prescribed weight loss (WL) treatment. The effect of a clinically significant WL of 5% on metabolic factors among metabolically normal and abnormal overweight and obese (MNO and MAO) individuals was examined.

Design and Methods

The sample included 392 overweight and obese adults from the Wharton Medical Clinic. MAO was defined as having one or more clinically relevant aberrations in glucose, triglycerides, blood pressure (BP), high‐density lipoprotein‐C, low‐density lipoprotein‐C, preexisting, or current medication use for metabolic conditions.

Results

Of the 392 patients, 21.2% of the sample was MNO at baseline and 41.3% of the sample attained a 5% WL. Regardless of initial metabolic health status, improvements in most risk factors were observed with a 5% WL in comparison with those who did not lose weight. Even MAO patients who did not achieve a 5% WL still significantly improved BP and cholesterol over the treatment period.

Conclusions

A clinically significant WL is beneficial for the cardiometabolic risk profile of both MNO and MAO. However, a 5% WL is not necessarily required to improve the cardiometabolic risk profile of MAO. Thus, lifestyle‐based WL provides beneficial metabolic effects for all overweight and obese individuals, particularly those with significant metabolic aberrations.
Electron transfer dissociation (ETD): The mass spectrometric breakthrough essential for O‐GlcNAc protein site assignments—a study of the O‐GlcNAcylated protein Host Cell Factor C1
Authors: Myers Samuel A. , Daou Salima , Affar El Bachir , Burlingame Al
Published: January 2013

The development of electron‐based, unimolecular dissociation MS, i.e. electron capture and electron transfer dissociation (ECD and ETD, respectively), has greatly increased the speed and reliability of labile PTM site assignment. The field of intracellular O‐GlcNAc (O‐linked N‐acetylglucosamine) signaling has especially advanced with the advent of ETD MS. Only within the last five years have proteomic‐scale experiments utilizing ETD allowed the assignment of hundreds of O‐GlcNAc sites within cells and subcellular structures. Our ability to identify and unambiguously assign the site of O‐GlcNAc modifications using ETD is rapidly increasing our understanding of this regulatory glycosylation and its potential interaction with other PTMs. Here, we discuss the advantages of using ETD, complimented with collisional‐activation MS, in a study of the extensively O‐GlcNAcylated protein Host Cell Factor C1 (HCF‐1). HCF‐1 is a transcriptional coregulator that forms a stable complex with O‐GlcNAc transferase and controls cell cycle progression. ETD, along with higher energy collisional dissociation (HCD) MS, was employed to assign the PTMs of the HCF‐1 protein isolated from HEK293T cells. These include 19 sites of O‐GlcNAcylation, two sites of phosphorylation, and two sites bearing dimethylarginine, and showcase the residue‐specific, PTM complexity of this regulator of cell proliferation.
A simple integrated system for rapid analysis of sialic‐acid‐containing N‐glycopeptides from human serum
Authors: Zhu Jun , Wang Fangjun , Cheng Kai , Dong Jing , Sun Deguang , Chen Rui , Wang Liming , Ye Mingliang , Zou Hanfa
Published: January 2013

Terminal sialylation is very important in cancer biology and has been extensively investigated for the discovery of potential clinical biomarkers of cancers. In this study, we presented a novel approach, by using of Ti(IV)‐IMAC, to enrich sialic‐acid‐containing N‐glycopeptides for the analysis of terminal sialylation. Compared with conventional method using TiO2, this approach obtained 2.5 times more glycopeptides and glycosylation sites. Then, a simple integrated system combining filter‐aided sample preparation, ACN‐improved digestion, and Ti(IV)‐IMAC enrichment was established for efficient analysis. In this system, protein digestion, glycopeptide enrichment, and deglycosylation were integrated and were performed sequentially in a single filter unit without any need for desalting, lyophilization, or sample transfer procedures. As a result, the number of identifications was improved by 1.5‐fold and the total processing time was drastically reduced to only 7–8 h. By using this system, fast and efficient analysis of human serum sialylated N‐glycoproteome was achieved. From only 1 μL of human serum, 217 unique glycopeptides and 194 glycosylation sites were successfully identified.
The therapeutic potential of mesenchymal stem cell‐derived extracellular vesicles
Authors: Katsuda Takeshi , Kosaka Nobuyoshi , Takeshita Fumitaka , Ochiya Takahiro
Published: January 2013

Extracellular vesicles (EVs), membrane vesicles that are secreted by a variety of mammalian cell types, have been shown to play an important role in intercellular communication. The contents of EVs, including proteins, microRNAs, and mRNAs, vary according to the cell type that secreted them. Accordingly, researchers have demonstrated that EVs derived from various cell types play different roles in biological phenomena. Considering the ubiquitous presence of mesenchymal stem cells (MSCs) in the body, MSC‐derived EVs may take part in a wide range of events. In particular, MSCs have recently attracted much attention due to the therapeutic effects of their secretory factors. MSC‐derived EVs may therefore provide novel therapeutic approaches. In this review, we first summarize the wide range of functions of EVs released from different cell types, emphasizing that EVs echo the phenotype of their parent cell. Then, we describe the various therapeutic effects of MSCs and pay particular attention to the significance of their paracrine effect. We then survey recent reports on MSC‐derived EVs and consider the therapeutic potential of MSC‐derived EVs. Finally, we discuss remaining issues that must be addressed before realizing the practical application of MSC‐derived EVs, and we provide some suggestions for enhancing their therapeutic efficiency.
Examining factors that influence erroneous phosphorylation site localization via competing fragmentation and rearrangement reactions during ion trap CID‐MS/MS and ‐MS3
Authors: Cui Li , Reid Gavin E.
Published: January 2013

Factors influencing the magnitude of competing fragmentation and intramolecular phosphate group rearrangement reactions during CID‐MS/MS and CID‐MS3 of protonated phosphopeptide ions in ion trap mass spectrometers, and their effect on phosphorylation site localization using automated search algorithms, have been examined by systematically varying the peptide composition, the identity, number, and position of the phosphorylated “donor” and nonphosphorylated “acceptor” residues, and the proton mobility of the precursor ion charge states for a synthetic phosphopeptide library. CID‐MS3 of product ions formed via combined neutral losses of HPO3 and H2O, rather than direct loss of H3PO4 from phosphotyrosine containing peptides yielded incorrect phosphorylation site assignments, while correct phosphorylation site assignments for phosphothreonine and phosphoserine containing peptides were highly dependant on the relative abundance of these competing fragmentation pathways. Abundant phosphate group rearrangement product ions were observed from CID‐MS/MS of multiply protonated phosphopeptide ions, with increased rearrangement under nonmobile or partially mobile protonation conditions, and as a function of the identity and number of the donor and acceptor residues. A clear inverse trend was observed between the amplitude of these rearrangement reactions and the confidence for phosphorylation site localization, and rearrangement played a contributing role in erroneous phosphorylation site assignment for several peptides.
How maltose influences structural changes to bind to maltose‐binding protein: Results from umbrella sampling simulation
Authors: Mascarenhas Nahren Manuel , Kästner Johannes
Published: January 2013

A well‐studied periplasmic‐binding protein involved in the abstraction of maltose is maltose‐binding protein (MBP), which undergoes a ligand‐induced conformational transition from an open (ligand‐free) to a closed (ligand‐bound) state. Umbrella sampling simulations have been us to estimate the free energy of binding of maltose to MBP and to trace the potential of mean force of the unbinding event using the center‐of‐mass distance between the protein and ligand as the reaction coordinate. The free energy thus obtained compares nicely with the experimentally measured value justifying our theoretical basis. Measurement of the domain angle (N‐terminal‐domain – hinge – C‐terminal‐domain) along the unbinding pathway established the existence of three different states. Starting from a closed state, the protein shifts to an open conformation during the initial unbinding event of the ligand then resides in a semi‐open conformation and later resides predominantly in an open‐state. These transitions along the ligand unbinding pathway have been captured in greater depth using principal component analysis. It is proposed that in mixed‐model, both conformational selection and an induced‐fit mechanism combine to the ligand recognition process in MBP. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Toward optimal fragment generations for ab initio protein structure assembly
Authors: Xu Dong , Zhang Yang
Published: January 2013

Fragment assembly using structural motifs excised from other solved proteins has shown to be an efficient method for ab initio protein‐structure prediction. However, how to construct accurate fragments, how to derive optimal restraints from fragments, and what the best fragment length is are the basic issues yet to be systematically examined. In this work, we developed a gapless‐threading method to generate position‐specific structure fragments. Distance profiles and torsion angle pairs are then derived from the fragments by statistical consistency analysis, which achieved comparable accuracy with the machine‐learning‐based methods although the fragments were taken from unrelated proteins. When measured by both accuracies of the derived distance profiles and torsion angle pairs, we come to a consistent conclusion that the optimal fragment length for structural assembly is around 10, and at least 100 fragments at each location are needed to achieve optimal structure assembly. The distant profiles and torsion angle pairs as derived by the fragments have been successfully used in QUARK for ab initio protein structure assembly and are provided by the QUARK online server at http://zhanglab.ccmb. med.umich.edu/QUARK/. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Coarse‐grained and all‐atom modeling of structural states and transitions in hemoglobin
Authors: Tekpinar Mustafa , Zheng Wenjun
Published: January 2013

Hemoglobin (Hb), an oxygen‐binding protein composed of four subunits (α1, α2, β1, and β2), is a well‐known example of allosteric proteins that are capable of cooperative ligand binding. Despite decades of studies, the structural basis of its cooperativity remains controversial. In this study, we have integrated coarse‐grained (CG) modeling, all‐atom simulation, and structural data from X‐ray crystallography and wide‐angle X‐ray scattering (WAXS), aiming to probe dynamic properties of the two structural states of Hb (T and R state) and the transitions between them. First, by analyzing the WAXS data of unliganded and liganded Hb, we have found that the structural ensemble of T or R state is dominated by one crystal structure of Hb with small contributions from other crystal structures of Hb. Second, we have used normal mode analysis to identify two distinct quaternary rotations between the α1β1 and α2β2 dimer, which drive the transitions between T and R state. We have also identified the hot‐spot residues whose mutations are predicted to greatly change these quaternary motions. Third, we have generated a CG transition pathway between T and R state, which predicts a clear order of quaternary and tertiary changes involving α and β subunits in Hb. Fourth, we have used the accelerated molecular dynamics to perform an all‐atom simulation starting from the T state of Hb, and we have observed a transition toward the R state of Hb. Further analysis of crystal structural data and the all‐atom simulation trajectory has corroborated the order of quaternary and tertiary changes predicted by CG modeling. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Crystal structure and nucleic acid‐binding activity of the CRISPR‐associated protein Csx1 of Pyrococcus furiosus
Authors: Kim Young Kwan , Kim Yeon‐Gil , Oh Byung‐Ha
Published: January 2013

In many prokaryotic organisms, chromosomal loci known as clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR‐associated (CAS) genes comprise an acquired immune defense system against invading phages and plasmids. Although many different Cas protein families have been identified, the exact biochemical functions of most of their constituents remain to be determined. In this study, we report the crystal structure of PF1127, a Cas protein of Pyrococcus furiosus DSM 3638 that is composed of 480 amino acids and belongs to the Csx1 family. The C‐terminal domain of PF1127 has a unique β‐hairpin structure that protrudes out of an α‐helix and contains several positively charged residues. We demonstrate that PF1127 binds double‐stranded DNA and RNA and that this activity requires an intact β‐hairpin and involve the homodimerization of the protein. In contrast, another Csx1 protein from Sulfolobus solfataricus P2 that is composed of 377 amino acids does not have the β‐hairpin structure and exhibits no DNA‐binding properties under the same experimental conditions. Notably, the C‐terminal domain of these two Csx1 proteins is greatly diversified, in contrast to the conserved N‐terminal domain, which appears to play a common role in the homodimerization of the protein. Thus, although P. furiosus Csx1 is identified as a nucleic acid‐binding protein, other Csx1 proteins are predicted to exhibit different individual biochemical activities. Proteins 2013. © 2012 Wiley Periodicals, Inc.
HIV‐1 ENV gp120 structural determinants for peptide triazole dual receptor site antagonism
Authors: Tuzer Ferit , Madani Navid , Kamanna Kantharaju , Zentner Isaac , LaLonde Judith , Holmes Andrew , Upton Elizabeth , Rajagopal Srivats , McFadden Karyn , Contarino Mark , Sodroski Joseph , Chaiken Irwin
Published: January 2013

Despite advances in HIV therapy, viral resistance and side‐effects with current drug regimens require targeting new components of the virus. Dual antagonist peptide triazoles (PT) are a novel class of HIV‐1 inhibitors that specifically target the gp120 component of the viral spike and inhibit its interaction with both of its cell surface protein ligands, namely the initial receptor CD4 and the co‐receptor (CCR5/CXCR4), thus preventing viral entry. Following an initial survey of 19 gp120 alanine mutants by ELISA, we screened 11 mutants for their importance in binding to, and inhibition by the PT KR21 using surface plasmon resonance. Key mutants were purified and tested for their effects on the peptide's affinity and its ability to inhibit binding of CD4 and the co‐receptor surrogate mAb 17b. Effects of the mutations on KR21 viral neutralization were measured by single‐round cell infection assays. Two mutations, D474A and T257A, caused large‐scale loss of KR21 binding, as well as losses in both CD4/17b and viral inhibition by KR21. A set of other Ala mutants revealed more moderate losses in direct binding affinity and inhibition sensitivity to KR21. The cluster of sensitive residues defines a PT functional epitope. This site is in a conserved region of gp120 that overlaps the CD4 binding site and is distant from the co‐receptor/17b binding site, suggesting an allosteric mode of inhibition for the latter. The arrangement and sequence conservation of the residues in the functional epitope explain the breadth of antiviral activity, and improve the potential for rational inhibitor development. Proteins 2013. © 2012 Wiley Periodicals, Inc.
The translocation kinetics of antibiotics through porin OmpC: Insights from structure‐based solvation mapping using WaterMap
Authors: Tran Que‐Tien , Williams Sarah , Farid Ramy , Erdemli Gül , Pearlstein Robert
Published: January 2013

Poor permeability of the lipopolysaccharide‐based outer membrane of Gram‐negative bacteria is compensated by the existence of protein channels (porins) that selectively admit low molecular weight substrates, including many antibiotics. Improved understanding of the translocation mechanisms of porin substrates could help guide the design of antibiotics capable of achieving high intracellular exposure. Energy barriers to channel entry and exit govern antibiotic fluxes through porins. We have previously reported a hypothesis that the costs of transferring protein solvation to and from bulk medium underlie the barriers to protein‐ligand association and dissociation, respectively, concomitant with the gain and loss of protein‐ligand interactions during those processes. We have now applied this hypothesis to explain the published rates of entry (association) and exit (dissociation) of six antibiotics to/from reconstituted E. coli porin OmpC. WaterMap was used to estimate the total water transfer energies resulting from transient occupation by each antibiotic. Our results suggest that solvation within the porin cavity is highly energetically favorable, and the observed moderately fast entry rates of the antibiotics are consistent with replacement of protein‐water H‐bonds. The observed ultrafast exit kinetics is consistent with the lack of intrachannel solvation sites that convey unfavorable resolvation during antibiotic dissociation. These results are aligned with known general relationships between antibiotic efficacy and physicochemical properties, namely unusually low logP, reflecting an abundance of H‐bond partners. We conclude that antibiotics figuratively “melt” their way through porin solvation at a rate determined by the cost of exchanging protein‐solvent for protein‐antibiotic H‐bonds. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Solution structures of polcalcin Phl p 7 in three ligation states: Apo‐, hemi‐Mg2+‐bound, and fully Ca2+‐bound
Authors: Henzl Michael T. , Sirianni Arthur G. , Wycoff Wei G. , Tan Anmin , Tanner John J.
Published: January 2013

Polcalcins are small EF‐hand proteins believed to assist in regulating pollen‐tube growth. Phl p 7, from timothy grass (Phleum pratense), crystallizes as a domain‐swapped dimer at low pH. This study describes the solution structures of the recombinant protein in buffered saline at pH 6.0, containing either 5.0 mM EDTA, 5.0 mM Mg2+, or 100 μM Ca2+. Phl p 7 is monomeric in all three ligation states. In the apo‐form, both EF‐hand motifs reside in the closed conformation, with roughly antiparallel N‐ and C‐terminal helical segments. In 5.0 mM Mg2+, the divalent ion is bound by EF‐hand 2, perturbing interhelical angles and imposing more regular helical structure. The structure of Ca2+‐bound Phl p 7 resembles that previously reported for Bet v 4—likewise exposing apolar surface to the solvent. Occluded in the apo‐ and Mg2+‐bound forms, this surface presumably provides the docking site for Phl p 7 targets. Unlike Bet v 4, EF‐hand 2 in Phl p 7 includes five potential anionic ligands, due to replacement of the consensus serine residue at –x (residue 55 in Phl p 7) with aspartate. In the Phl p 7 crystal structure, D55 functions as a helix cap for helix D. In solution, however, D55 apparently serves as a ligand to the bound Ca2+. When Mg2+ resides in site 2, the D55 carboxylate withdraws to a distance consistent with a role as an outer‐sphere ligand. 15N relaxation data, collected at 600 MHz, indicate that backbone mobility is limited in all three ligation states. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Computational protein design suggests that human PCNA‐partner interactions are not optimized for affinity
Authors: Fridman Yearit , Gur Eyal , Fleishman Sarel J. , Aharoni Amir
Published: January 2013

Increasing the affinity of binding proteins is invaluable for basic and applied biological research. Currently, directed protein evolution experiments are the main approach for generating such proteins through the construction and screening of large mutant libraries. Proliferating cell nuclear antigen (PCNA) is an essential hub protein that interacts with many different partners to tightly regulate DNA replication and repair in all eukaryotes. Here, we used computational design to generate human PCNA mutants with enhanced affinity for several different partners. We identified double mutations in PCNA, outside the main partner binding site, that were predicted to increase PCNA‐partner binding affinities compared to the wild‐type protein by forming additional hydrophobic interactions with conserved residues in the PCNA partners. Affinity increases were experimentally validated with four different PCNA partners, demonstrating that computational design can reveal unexpected regions where affinity enhancements in natural systems are possible. The designed PCNA mutants can be used as a valuable tool for further examination of the regulation of PCNA‐partner interactions during DNA replication and repair both in vitro and in vivo. More broadly, the ability to engineer affinity increases toward several PCNA partners suggests that interaction affinity is not an evolutionarily optimized trait of this system. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Simulation of the mutation F76del on the von Hippel–Lindau tumor suppressor protein: Mechanism of the disease and implications for drug development
Authors: Limaverde‐Sousa Gabriel , de Andrade Barreto Ester , Ferreira Carlos Gil , Cláudio Casali‐da‐Rocha José
Published: January 2013

The von Hippel–Lindau tumor suppressor protein (pVHL) plays a central role in the oxygen‐sensing pathway by regulating the degradation of the hypoxia‐inducible factor (HIF‐1α). The capture of HIF‐1α by pVHL is regulated by an oxygen‐dependent hydroxylation of a specific conserved prolyl residue. The VHL gene is mutated in the von Hippel–Lindau cancer predisposition syndrome, which is characterized by the development of highly vascularized tumors and is associated with constitutively high levels of HIF‐1α. The disturbance of the dynamic coupling between HIF‐1α and pVHL bearing the commonly found mutation F76del was experimentally confirmed but the mechanism of such complex disruption is still not clear. Performing unbiased molecular dynamics simulations, we show that the F76del mutation may enlarge the HIF binding pocket in pVHL and induce the formation of an internal cavity in the hydrophobic core of the β‐domain, which can lead to a partial destabilization of the β‐sheets S1, S4, and S7 and a consequent loss of hydrogen bonds with a conserved recognition motif in HIF. The newly formed cavity has a significant druggability score and may be a suitable target for stabilizing ligands. Studies of this nature may help to fill the information gap between genotype–phenotype correlations with details obtained at atomic level and provide basis for future development of drug candidates, such as pharmacological chaperones, with the specific aim of reverting the dysfunction of such pathological protein complexes found in patients with VHL. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Enhanced critical current density in MgB2 prepared by reaction of MgB4 and Mg
Authors: Tan K. L. , Lim K. P. , Halim A. S. , Chen S. K.
Published: January 2013

Instead of reacting B and Mg powders, MgB4 was used as precursor to react with Mg to obtain the polycrystalline samples of nominal composition MgxB2 (x = 1.2, 1.5, and 1.7). Upon increasing the sintering temperature to 750 °C, the reaction between MgB4 and Mg was thermodynamically intensified leading to the formation of larger MgB2 weight fraction as estimated from X‐ray diffraction (XRD) data using the Rietveld method. Despite no further improvement to the weight fraction of this phase by increasing the excess nominal Mg, it was shown that the critical current density (Jc) was enhanced by almost one order of magnitude. At 5 K, 2 T, Jc for the sample Mg1.5B2 is estimated to be 4.5 × 105 A cm−2. The enhancement of Jc is attributed to the collective effect of improved grain connectivity and flux pinning by unreacted Mg. Incorporation of nano‐SiC for reaction resulted in a more gradual drop of Jc with applied magnetic field. Hence, Jc can be tailored to meet the range of fields intended for various applications via optimization of excess nominal Mg and dopant additions.
Defect and analysis effects in the infrared optical properties of silicon
Authors: Smith D. Y. , Karstens W. , Shiles E. , Inokuti Mitio
Published: January 2013

The infrared optical properties of silicon reported by different workers disagree by far more than the precision of the measurements. Further, their extrapolations conflict with THz measurements. These inconsistencies are commonly attributed to crystal defects or impurities, but lack of reliable intrinsic silicon values hampers separation of host and defect effects. We have developed tests based on linear‐response theory to address this. Tests include requiring that the refractive index is an even function of photon energy, and comparing the coefficients of a Taylor expansion of the IR index with the moments of the electronic absorption above the band gap. The latter is sufficiently well known for silicon that predictions for the intercept, slope, and curvature, of the index may be used to test infrared measurements for consistency. Thus, we identified the sources of conflict as: (i) A physically inconsistent assumption for index parity commonly made in analysis of channel‐spectra. (ii) Defect and free‐carrier absorption. Eliminating data sets with these shortcomings resolved the conflict between measurements and allowed us to develop a composite set of IR optical constants for silicon that is a best fit to reliable measurements from microwaves to the visible.
Valence‐band effective‐potential evolution for coupled holes
Authors: Flores‐Godoy J. J. , Mendoza‐Álvarez A. , Diago‐Cisneros L. , Fernández‐Anaya G.
Published: January 2013

We present the metamorphosis in the effective‐potential profile of layered heterostructures, for several III–V semiconductor binary compounds, when the band mixing of light and heavy holes increases. A root‐locus‐like procedure is directly applied to an eigenvalue quadratic problem obtained from a multichannel system of coupled modes, in the context of the multiband effective mass approximation. By letting grow valence‐band mixing, it is shown that the standard fixed‐height rectangular potential energy for the scatterer distribution is a reliable test‐run input for heavy holes. On the contrary, this scheme is no longer valid for light holes and a mutable effective band offset profile has to be considered instead whenever the in‐plane kinetic energy changes.
Vibrational spectroscopic studies on pure and metal‐covered metal oxide surfaces
Authors: Noei Heshmat , Jin Lanying , Qiu Hengshan , Xu Mingchun , Gao Youkun , Zhao Jianli , Kauer Max , Wöll Christof , Muhler Martin , Wang Yuemin
Published: January 2013

Metal oxides and metal nanoparticles dispersed on oxide substrates have gained increasing interest in surface science because of their widespread applications, especially in heterogeneous catalysis. In this review we summarize our recent vibrational spectroscopic studies on pure and metal‐covered oxide surfaces (ZnO, TiO2, Au/ZnO and Cu/ZnO) using a number of small molecules (H2, CO, CO2, NO and HCOOH) as probes and/or reactants. High‐resolution electron energy loss spectroscopy (HREELS) turned out to be a powerful tool to investigate well‐defined oxide and metal/oxide model systems. The application of a novel ultrahigh vacuum IR spectroscopy (UHV‐FTIRS) apparatus allowed us to record high‐quality IR data on oxide surfaces of both single crystals and polycrystalline powder particles. We will particularly focus on following important issues: (i) the interaction of hydrogen with ZnO; (ii) structure and reactivity of polar and nonpolar ZnO surfaces; (iii) the role of defects in surface chemistry of oxides; (iv) the origin of significant difference in photocatalytic activity between anatase and rutile TiO2 and (v) the interaction between metal nanoparticles and oxide supports. We will demonstrate that the data from HREELS and UHV‐FTIRS provide detailed insight into structural, electronic and chemical properties of the studied systems.
Failure mode and effects analysis in designing a virtual reality‐based training simulator for bilateral sagittal split osteotomy
Authors: Sofronia R. E. , Knott T. , Davidescu A. , Savii G. G. , Kuhlen T. , Gerressen M.
Published: January 2013

Background

Virtual reality‐based simulators offer a cost‐effective and efficient alternative to traditional medical training and planning. Developing a simulator that enables the training of medical skills and also supports recognition of errors made by the trainee is a challenge. The first step in developing such a system consists of error identification in the real procedure, in order to ensure that the training environment covers the most significant errors that can occur. This paper focuses on identifying the main system requirements for an interactive simulator for training bilateral sagittal split osteotomy (BSSO).

Methods

An approach is proposed based on failure mode and effects analysis (FMEA), a risk analysis method that is well structured and already an approved technique in other domains.

Results

Based on the FMEA results, a BSSO training simulator is currently being developed, which centres upon the main critical steps of the procedure (sawing and splitting) and their main errors.

Conclusions

FMEA seems to be a suitable tool in the design phase of developing medical simulators. Herein, it serves as a communication medium for knowledge transfer between the medical experts and the system developers. The method encourages a reflective process and allows identification of the most important elements and scenarios that need to be trained. Copyright © 2013 John Wiley & Sons, Ltd.
An efficient online trajectory generating method for underactuated crane systems
Authors: Sun Ning , Fang Yongchun
Published: January 2013

In this paper, a trajectory planning approach is proposed for underactuated overhead cranes. Different from existing trajectory planning methods, the presented approach generates trajectory commands online without the necessity of iterative optimization, which is convenient for practical implementation. We demonstrate the performance of the proposed method, including swing elimination and precise trolley positioning, with rigorous Lyapunov‐based mathematical analysis. Both numerical simulation and experimental results suggest that the presented method is feasible and efficient for practical applications. Copyright © 2013 John Wiley & Sons, Ltd.
Self‐Organized Graphene Nanosheets with Corrugated, Ordered Tip Structures for High‐Performance Flexible Field Emission
Authors: Jeong Hee Jin , Jeong Hae Deuk , Kim Ho Young , Jeong Seung Yol , Han Joong Tark , Lee Geon‐Woong
Published: January 2013

Patterned reduced graphene oxide (rGO) films with vertically aligned tip structures are fabricated by a straightforward self‐assembly method. The size, uniformity of the patterns, and alignment of the tips are successfully controlled according to the concentration of a GO/octadecylamine (ODA)‐dispersed solution. The surface energy difference between the GO/ODA solution and a self‐assembled water droplet is a critical parameter for determining the pattern structure. Numerous rGO nanosheets are formed so as to be vertically aligned with respect to the substrate during film fabrication at GO concentrations below 2.0 g/L. These samples provide high field‐emission characteristics. The patterned rGO arrays are highly flexible with preservation of the field emission properties, even at large bending angles. This is attributed to the high crystallinity, emitter density, and good chemical stability of the rGO arrays, as well as the strong interactions between the rGO arrays and the substrate.
Dynamic Migration and Cell-Cell Interactions of Early Reprogramming Revealed by High-Resolution Time-Lapse Imaging
Authors: Megyola Cynthia M. , Gao Yuan , Teixeira Alexandra M. , Cheng Jijun , Heydari Kartoosh , Cheng Ee-Chun , Nottoli Timothy , Krause Diane S. , Lu Jun , Guo Shangqin
Published: January 2013

Discovery of the cellular and molecular mechanisms of induced pluripotency has been hampered by its low efficiency and slow kinetics. Here, we report an experimental system with multicolor time-lapse microscopy that permits direct observation of pluripotency induction at single cell resolution, with temporal intervals as short as 5 minutes. Using granulocyte-monocyte progenitors as source cells, we visualized nascent pluripotent cells that emerge from a hematopoietic state. We engineered a suite of image processing and analysis software to annotate the behaviors of the reprogramming cells, which revealed the highly dynamic cell-cell interactions associated with early reprogramming. We observed frequent cell migration, which can lead to sister colonies, satellite colonies, and colonies of mixed genetic makeup. In addition, we discovered a previously unknown morphologically distinct two-cell intermediate of reprogramming, which occurs prior to other reprogramming landmarks. By directly visualizing the reprogramming process with E-cadherin inhibition, we demonstrate that E-cadherin is required for proper cellular interactions from an early stage of reprogramming, including the two-cell intermediate. The detailed cell-cell interactions revealed by this imaging platform shed light on previously unappreciated early reprogramming dynamics. This experimental system could serve as a powerful tool to dissect the complex mechanisms of early reprogramming by focusing on the relevant but rare cells with superb temporal and spatial resolution.