bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation between fluorodeoxyglucose hotspots on pretreatment positron emission tomography/CT and preferential sites of local relapse after chemoradiotherapy for head and neck squamous cell carcinoma
Authors: Chaput Anne , Calais Jérémie , Robin Philippe , Thureau Sébastien , Bourhis David , Modzelewski Romain , Schick Ulrike , Vera Pierre , Salaün Pierre‐Yves , Abgral Ronan 
Published: March 2017

ABSTRACTBackgroundThe potential benefits of 18F‐fluoro‐2‐deoxy‐D‐glucose‐positron emission tomography/CT (FDG‐PET/CT) imaging for radiotherapy (RT) treatment planning of head and neck squamous cell carcinoma (HNSCC) are increasingly being recognized. It has been suggested that intratumoral subvolumes with high FDG avidity (“hotspots”) are potential targets for selected dose escalation. The purposes of this study were to demonstrate that pre‐RT FDG‐PET/CT can identify intratumoral sites at increased risk of local relapse after RT and to determine an optimal threshold to delineate smaller RT target volumes that would facilitate RT dose escalation without impaired tolerance.MethodsSeventy‐two consecutive patients with locally advanced HNSCC treated by RT ± chemotherapy were included in this study. All patients underwent FDG‐PET/CT at initial staging (PETA) and during systematic follow‐up (PETR). FDG‐PET/CT was coregistered on the initial CT scan with a rigid method. Various subvolumes (AX; × = 30%, 40%, 50%, 60%, 70%, 80%, and 90% standardized uptake value maximum [SUVmax] thresholds) within the primary tumor and in the subsequent local relapse (RX; × = 40% and 70% SUVmax thresholds) were compared together (Dice, Jaccard, overlap fraction, common volume/baseline volume, and common volume/recurrent volume).ResultsNineteen patients (26%) had local relapses. Using a 40% SUVmax threshold, the initial metabolic tumor volume was significantly higher in patients with local relapses than in controlled patients (10.4 ± 8.6 vs 5.1 ± 4.9 cc; p = .002) as well as total lesion glycolysis (117.9 ± 88.6 vs 60.6 ± 80.4; p = .013). For both methods, the overlap index among A30, A40, and A50 subvolumes on PETA and the whole metabolic volume of recurrence R40 and R70 on PETR showed a moderate agreement (0.52 to 0.43).ConclusionOur study does not find high overlap index values between the initial tumor and recurrence subvolumes, probably because of a suboptimal coregistration. Our results also confirm that metabolic tumor volume and total lesion glycolysis are independently correlated with recurrence‐free survival in patients with HNSCC. Further larger prospective studies with FDG‐PET/CT performed in the same RT position and with a validated elastic registration method are needed. © 2017 Wiley Periodicals, Inc. Head Neck 39: 1155–1165, 2017
Inhibition of multi‐species oral biofilm by bromide doped bioactive glass
Authors: Galarraga‐Vinueza M. E. , Passoni B. , Benfatti C. A. M. , Mesquita‐Guimarães J. , Henriques B. , Magini R. S. , Fredel M. C. , Meerbeek B. V. , Teughels W. , Souza J. C. M. 
Published: March 2017

AbstractBioactive glass is an attractive biomaterial that has shown excellent osteogenic and angiogenic effects for oral bone repairing procedures. However, anti‐biofilm potential related to such biomaterial has not been completely validated, mainly against multi‐species biofilms involved in early tissue infections. The aim of the present study was to evaluate the anti‐biofilm effect of 58 S bioactive glass embedding calcium bromide compounds at different concentrations. Bioactive glass free or containing 5, or 10 wt % CaBr2was synthesized by alkali sol‐gel method and then characterized by physco‐chemical analyses and scanning electron microscopy (SEM). Then, samples were tested by microbiological assays using optical density, real time q‐PCR, and SEM. Bioactive glass particles showed accurate chemical composition and an angular shape with a bimodal size distribution ranging from 0.6 to 110 µm. The mean particle size was around 29 µm. Anti‐biofilm effect was recorded for 5 wt % CaBr2‐doped bioactive glass againstS. mitis, V. parvula, P. gingivais, S. gordoni, A. viscosus, F, nucleatum, P. gingivais. F. nucleatum, andP. gingivalis. Such species are involved in the biofilm structure related to infections on hard and soft tissues in the oral cavity. The incorporation of calcium bromide into bioactive glass can be a strategy to enhance the anti‐biofilm potential of bioactive glasses for bone healing and infection treatment. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1994–2003, 2017.
Electrospun oriented gelatin‐hydroxyapatite fiber scaffolds for bone tissue engineering
Authors: Salifu Ali A. , Lekakou Constantina , Labeed Fatima H. 
Published: March 2017

AbstractTissue engineering of human fetal osteoblast cells was investigated on gelatin‐hydroxyapatite (HA), crosslinked, electrospun oriented fiber scaffolds at the different HA concentrations of 0, 10, 20, and 25 wt % in the dry fibers and different fiber diameter, pore size and porosity of scaffolds. Rheological tests and proton nuclear magnetic resonance spectroscopy were conducted for all solutions used for electrospinning. It was found that 25 wt % HA‐gelatin scaffolds electrospun at 20 kV led to the greatest cell attachment, cell proliferation and extracellular matrix (ECM) production while fiber orientation improved the mechanical properties, where crosslinked electrospun 25 wt % HA‐gelatin fiber scaffolds yielded a Young's modulus in the range of 0.5–0.9 GPa and a tensile strength in the range of 4–10 MPa in the fiber direction for an applied voltage of 20–30 kV, respectively, in the electrospinning of scaffolds. Biological characterization of cell seeded scaffolds yielded the rate of cell growth and ECM (collagen and calcium) production by the cells as a function of time; it included cell seeding efficiency tests, alamar blue cell proliferation assay, alkaline phosphate (ALP) assay, collagen assay, calcium colorimetric assay, fluorescence microscopy for live and dead cells, and scanning electron microscopy for cell culture from 1 to 18 days. After 18 days, cells seeded and grown on the 25 wt % HA‐gelatin scaffold, electrospun at 20 kV, reached production of collagen at 370 μg/L and calcium production at 0.8 mM. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1911–1926, 2017.
Tissue response to five commercially available peritoneal adhesion barriers—A systematic histological evaluation
Authors: Schmitt Volker H. , Mamilos Andreas , Schmitt Christine , Neitzer‐Planck Constanze N. E. , Rajab Taufiek K. , Hollemann David , Wagner Willi , Krämer Bernhard , Hierlemann Helmut , James Kirkpatrick C. , Brochhausen Christoph 
Published: March 2017

AbstractSeparating wounded serosa by physical barriers is the only clinically approved adjunct for postoperative adhesion prevention. Since the optimal adhesion barrier has not been found, it is essential to improve our pathogenic understanding of adhesion formation and to compare the effects of different barrier materials on tissue and cells. Wistar rats underwent standardized peritoneal damage and were treated either with Seprafilm, Adept, Intercoat, Spraygel, SupraSeal or remained untreated as a control. 14 days postoperatively, the lesions were explanted and histomorphologically analyzed using the European ISO score to evaluate material implants. Striking differences between the material groups were present regarding the inflammation, fibrosis, and foreign body reaction. According to the ISO score, Intercoat and Spraygel were considered as nonirritating to tissue. Adept, Seprafilm, and SupraSeal were assessed as mild‐irritating materials. Interestingly, the most effective material in adhesion prevention revealed moderate inflammation accompanied by minor fibrosis. The degree of inflammation to barrier materials does not predict the efficacy in the prevention of adhesions. Histopathological investigations are crucial to improve our understanding of the cellular mechanisms during adhesion formation and elucidate the tissue response to material approaches used in adhesion prevention. This will lead to improved antiadhesive strategies and the development of functional barrier biomaterials. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 598–609, 2018.
Assessment of Bone Health in Patients With Type 1 Gaucher Disease Using Impact Microindentation
Authors: Herrera Sabina , Pérez-López Jordi , Moltó-Abad Marc , Güerri-Fernández Roberto , Cabezudo Elena , Novelli Silvana , Esteve Jordi , Hernández Albert , Roig Inmaculada , Solanich Xavier , Prieto-Alhambra Daniel , Nogués Xavier , Díez-Pérez Adolfo 
Published: March 2017

ABSTRACT

Gaucher disease (GD), one of the most common lysosomal disorders (a global population incidence of 1:50,000), is characterized by beta-glucocerebrosidase deficiency. Some studies have demonstrated bone infiltration in up to 80% of patients, even if asymptomatic. Bone disorder remains the main cause of morbidity in these patients, along with osteoporosis, avascular necrosis, and bone infarcts. Enzyme replacement therapy (ERT) has been shown to improve these symptoms. This cross-sectional study included patients with type 1 Gaucher disease (GD1) selected from the Catalan Study Group on GD. Clinical data were collected and a general laboratory workup was performed. Bone mineral density (BMD) was measured at the lumbar spine and hip using dual-energy X-ray absorptiometry (DXA). Patients with bone infarcts or any other focal lesion in the area of indentation visible on imaging were excluded. Bone Material Strength index (BMSi) was measured by bone impact microindentation using an Osteoprobe instrument. Analysis of covariance (ANCOVA) models were fitted to adjust for age, sex, weight, and height. Sixteen patients with GD1 and 29 age- and sex-matched controls were included. GD1 was associated with significantly lower BMSi (adjusted beta –9.30; 95% CI, –15.18 to –3.42; p = 0.004) and reduced lumbar BMD (adjusted beta –0.14; 95% CI, –0.22 to –0.06; p = 0.002) and total hip BMD (adjusted beta –0.09; 95% CI, –0.15 to –0.03; p = 0.006), compared to GD1-free controls. Chitotriosidase levels were negatively correlated with BMSi (linear R2 = 51.6%, p = 0.004). Bone tissue mechanical characteristics were deteriorated in patients with GD1. BMSi was correlated with chitotriosidase, the marker of GD activity. Bone disorder requires special consideration in this group of patients, and microindentation could be an appropriate tool for assessing and managing their bone health. © 2017 American Society for Bone and Mineral Research.
Relocation of NPM Affects the Malignant Phenotypes of Hepatoma SMMC‐7721 Cells
Authors: Li Xiao , Xu Dong‐Hui , Liu Fan , Liu Guo‐Yan , Lu Kun , Deng Xiao‐Ling , Li Qi‐Fu , Shi Song‐Lin 
Published: March 2017

ABSTRACTNucleophosmin(NPM), heavily implicated in diverse solid tumors, is an important multifunctional protein mainly located in the nucleolus. Our previous study confirmed that NPM can also localize and accumulate in the cytoplasm of liver cancer cells. However, the role of cytoplasmic NPM (NPMc +) is unclear. Here, we showed that both nucleolar NPM and NPMc+ could promote cell proliferation, although the effect of NPMc+ was weaker than that of NPM. Cell adhesion ability of hepatoma cells was significantly reduced to a greater extent by NPMc+ expression. Nucleolar NPM enhanced cell migration and invasion, whereas NPMc+ impeded cell migration and invasion. The investigation of NPM interactional proteins by proteomic method demonstrated that the NPM was involved in multiple biological processes. By contrast, the interactional proteins of NPMc+ were mainly implicated in tRNA amino acylation regulation. The interactional network of NPMc+ was significantly small and simple. These results suggested that relocation of NPM altered its interactional network and consequently disturbed the primary functions, including cell proliferation, adhesion, migration, and invasion. NPM plays a promotional role in cancer and the reducing relocation may be a potential therapeutic target for hepatocellular carcinoma. J. Cell. Biochem. 118: 3225–3236, 2017. © 2017 Wiley Periodicals, Inc.
Orthogonally combined motion‐ and diffusion‐sensitized driven equilibrium (OC‐MDSDE) preparation for vessel signal suppression in 3D turbo spin echo imaging of peripheral nerves in the extremities
Authors: Cervantes Barbara , Kirschke Jan S. , Klupp Elizabeth , Kooijman Hendrik , Börnert Peter , Haase Axel , Rummeny Ernst J. , Karampinos Dimitrios C. 
Published: March 2017

PurposeTo design a preparation module for vessel signal suppression in MR neurography of the extremities, which causes minimal attenuation of nerve signal and is highly insensitive to eddy currents and motion.MethodsThe orthogonally combined motion‐ and diffusion‐sensitized driven equilibrium (OC‐MDSDE) preparation was proposed, based on the improved motion‐ and diffusion‐sensitized driven equilibrium methods (iMSDE and FC‐DSDE, respectively), with specific gradient design and orientation. OC‐MDSDE was desensitized against eddy currents using appropriately designed gradient prepulses. The motion sensitivity and vessel signal suppression capability of OC‐MDSDE and its components were assessed in vivo in the knee using 3D turbo spin echo (TSE). Nerve‐to‐vessel signal ratios were measured for iMSDE and OC‐MDSDE in 7 subjects.ResultsiMSDE was shown to be highly sensitive to motion with increasing flow sensitization. FC‐DSDE showed robustness against motion, but resulted in strong nerve signal loss with diffusion gradients oriented parallel to the nerve. OC‐MDSDE showed superior vessel suppression compared to iMSDE and FC‐DSDE and maintained high nerve signal. Mean nerve‐to‐vessel signal ratios in 7 subjects were 0.40 ± 0.17 for iMSDE and 0.63 ± 0.37 for OC‐MDSDE.ConclusionOC‐MDSDE combined with 3D TSE in the extremities allows high‐near‐isotropic‐resolution imaging of peripheral nerves with reduced vessel contamination and high nerve signal. Magn Reson Med 79:407–415, 2018. © 2017 Wiley Periodicals, Inc.
Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation
Authors: Kurimoto Eiji , Satoh Tadashi , Ito Yuri , Ishihara Eri , Okamoto Kenta , Yagi‐Utsumi Maho , Tanaka Keiji , Kato Koichi 
Published: March 2017

AbstractThe 26S proteasome is a large protein complex, responsible for degradation of ubiquinated proteins in eukaryotic cells. Eukaryotic proteasome formation is a highly ordered process that is assisted by several assembly chaperones. The assembly of its catalytic 20S core particle depends on at least five proteasome‐specific chaperones, i.e., proteasome‐assembling chaperons 1–4 (PAC1–4) and proteasome maturation protein (POMP). The orthologues of yeast assembly chaperones have been structurally characterized, whereas most mammalian assembly chaperones are not. In the present study, we determined a crystal structure of human PAC4 at 1.90‐Å resolution. Our crystallographic data identify a hydrophobic surface that is surrounded by charged residues. The hydrophobic surface is complementary to that of its binding partner, PAC3. The surface also exhibits charge complementarity with the proteasomal α4–5 subunits. This will provide insights into human proteasome‐assembling chaperones as potential anticancer drug targets.
Molecular dynamics simulations on networks of heparin and collagen
Authors: Kulke Martin , Geist Norman , Friedrichs Wenke , Langel Walter 
Published: March 2017

ABSTRACTSynthetic scaffolds containing collagen (Type I) are of increasing interest for bone tissue engineering, especially for highly porous biomaterials in combination with glycosaminoglycans. In experiments the integration of heparin during the fibrillogenesis resulted in different types of collagen fibrils, but models for this aggregation on a molecular scale were only tentative. We conducted molecular dynamic simulations investigating the binding of heparin to collagen and the influence of the telopeptides during collagen aggregation. This aims at explaining experimental findings on a molecular level. Novel structures for N‐ and C‐telopeptides were developed with the TIGER2 replica exchange algorithm and dihedral principle component analysis. We present an extended statistical analysis of the mainly electrostatic interaction between heparin and collagen and identify several binding sites. Finally, we propose a molecular mechanism for the influence of glycosaminoglycans on the morphology of collagen fibrils. Proteins 2017; 85:1119–1130. © 2017 Wiley Periodicals, Inc.
VoroMQA: Assessment of protein structure quality using interatomic contact areas
Authors: Olechnovič Kliment , Venclovas Česlovas 
Published: March 2017

ABSTRACTIn the absence of experimentally determined protein structure many biological questions can be addressed using computational structural models. However, the utility of protein structural models depends on their quality. Therefore, the estimation of the quality of predicted structures is an important problem. One of the approaches to this problem is the use of knowledge‐based statistical potentials. Such methods typically rely on the statistics of distances and angles of residue‐residue or atom‐atom interactions collected from experimentally determined structures. Here, we present VoroMQA (Voronoi tessellation‐based Model Quality Assessment), a new method for the estimation of protein structure quality. Our method combines the idea of statistical potentials with the use of interatomic contact areas instead of distances. Contact areas, derived using Voronoi tessellation of protein structure, are used to describe and seamlessly integrate both explicit interactions between protein atoms and implicit interactions of protein atoms with solvent. VoroMQA produces scores at atomic, residue, and global levels, all in the fixed range from 0 to 1. The method was tested on the CASP data and compared to several other single‐model quality assessment methods. VoroMQA showed strong performance in the recognition of the native structure and in the structural model selection tests, thus demonstrating the efficacy of interatomic contact areas in estimating protein structure quality. The software implementation of VoroMQA is freely available as a standalone application and as a web server at http://bioinformatics.lt/software/voromqa. Proteins 2017; 85:1131–1145. © 2017 Wiley Periodicals, Inc.
Comparative studies of the catalytic mechanisms of two chorismatases: CH‐fkbo and CH‐Hyg5
Authors: Dong Lihua , Liu Yongjun 
Published: March 2017

ABSTRACTChorismatase is an important enzyme involved in Shikimate pathway, which catalyzes the conversion of chorismate into pyruvate and (dihydro)‐benzoic acid derivatives. According to the outcomes of catalytic reactions, chorismatases can be divided into three subfamilies: CH‐Fkbo, CH‐Hyg5 and CH‐XanB2. Recently, the crystal structures of CH‐Fkbo and CH‐Hyg5 from Streptomyces hygroscopicus have been successfully obtained, allowing us to perform QM/MM calculations to explore the reaction details. Our calculation results support the proposal that CH‐Fkbo and CH‐Hyg5 employ different catalytic mechanisms and gave the mechanistic details. Fkbo follows a typical hydrolytic mechanism, which contains three consecutive steps, including the protonation step of the methylene group of substrate, the nucleophilic attack of the resulted carbocation by activated water and cleavage of C2′‐O8 bond of tetrahedral intermediate (hemiketal). The protonation of methylene group and the C2′‐O8 cleavage correspond to similar energy barriers (26.5 and 24.8 kcal/mol), suggesting both steps to be rate‐limiting. Whereas Hyg5 employs an intramolecular mechanism, in which the oxygen from C4 migrates to C3 via an arene oxide intermediate. The first step of Hyg5, which corresponds to the concerted protonation of methylene group and the cleavage of C3‐O8, is calculated to be rate‐limiting with an energy barrier of 26.3 kcal/mol. The nonconserved active site residue G240Hyg5 (or A244Fkb°) is suggested to be responsible for leading to different reaction mechanism in CH‐Fkbo and CH‐Hyg5. During the catalytic reaction, residue C327 plays an important role in directing the product selectivity in Hyg5 enzyme. Proteins 2017; 85:1146–1158. © 2017 Wiley Periodicals, Inc.
InterPred: A pipeline to identify and model protein–protein interactions
Authors: Mirabello Claudio , Wallner Björn 
Published: March 2017

ABSTRACTProtein–protein interactions (PPI) are crucial for protein function. There exist many techniques to identify PPIs experimentally, but to determine the interactions in molecular detail is still difficult and very time‐consuming. The fact that the number of PPIs is vastly larger than the number of individual proteins makes it practically impossible to characterize all interactions experimentally. Computational approaches that can bridge this gap and predict PPIs and model the interactions in molecular detail are greatly needed. Here we present InterPred, a fully automated pipeline that predicts and model PPIs from sequence using structural modeling combined with massive structural comparisons and molecular docking. A key component of the method is the use of a novel random forest classifier that integrate several structural features to distinguish correct from incorrect protein–protein interaction models. We show that InterPred represents a major improvement in protein–protein interaction detection with a performance comparable or better than experimental high‐throughput techniques. We also show that our full‐atom protein–protein complex modeling pipeline performs better than state of the art protein docking methods on a standard benchmark set. In addition, InterPred was also one of the top predictors in the latest CAPRI37 experiment.InterPred source code can be downloaded from http://wallnerlab.org/InterPred Proteins 2017; 85:1159–1170. © 2017 Wiley Periodicals, Inc.
Improving prediction of helix–helix packing in membrane proteins using predicted contact numbers as restraints
Authors: Li Bian , Mendenhall Jeffrey , Nguyen Elizabeth Dong , Weiner Brian E. , Fischer Axel W. , Meiler Jens 
Published: March 2017

ABSTRACTOne of the challenging problems in tertiary structure prediction of helical membrane proteins (HMPs) is the determination of rotation of α‐helices around the helix normal. Incorrect prediction of helix rotations substantially disrupts native residue–residue contacts while inducing only a relatively small effect on the overall fold. We previously developed a method for predicting residue contact numbers (CNs), which measure the local packing density of residues within the protein tertiary structure. In this study, we tested the idea of incorporating predicted CNs as restraints to guide the sampling of helix rotation. For a benchmark set of 15 HMPs with simple to rather complicated folds, the average contact recovery (CR) of best‐sampled models was improved for all targets, the likelihood of sampling models with CR greater than 20% was increased for 13 targets, and the average RMSD100 of best‐sampled models was improved for 12 targets. This study demonstrated that explicit incorporation of CNs as restraints improves the prediction of helix–helix packing. Proteins 2017; 85:1212–1221. © 2017 Wiley Periodicals, Inc.