bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating nonpolar surface area and liquid chromatography/mass spectrometry response: an application for site occupancy measurements for enzyme intermediates in polyketide biosynthesis
Authors: Randall Shan M. , Koryakina Irina , Williams Gavin J. , Muddiman David C. 
Published: October 2014

RATIONALESite occupancy measurements using liquid chromatography/mass spectrometry (LC/MS) are reported throughout the literature. However, site occupancy quantification suffers from ionization bias between modified and unmodified peptides containing the active site. In this study, we explore the MS signal as a function of nonpolar surface area (NPSA) in order to better understand this bias in electrospray response. The correlation between hydrophobicity and LC/MS response was evaluated and applied to study enzyme intermediates in polyketide synthases.METHODSSite occupancy methods were developed to study acyltransferase activity. To further evaluate these methods, several standard peptides containing one cysteine residue were modified with alkylation reagents of increasing hydrophobicity to study the MS signal as a function of NPSA.RESULTSA consistent trend in MS response was observed which is dependent on the NPSA of the analyte. An optimal NPSA zone was observed for the peptides studied.CONCLUSIONSNonpolar surface area can be used as metric to determine relative LC/MS response for peptides and evaluate site occupancy measurements. Copyright © 2014 John Wiley & Sons, Ltd.
A robust automated markerless registration framework for neurosurgery navigation
Authors: Jiang Long , Zhang Shaoting , Yang Jie , Zhuang Xiahai , Zhang Lixia , Gu Lixu 
Published: October 2014

AbstractBackgroundThe registration of a pre‐operative image with the intra‐operative patient is a crucial aspect for the success of navigation in neurosurgery.MethodsFirst, the intra‐operative face is reconstructed, using a structured light technique, while the pre‐operative face is segmented from head CT/MRI images. In order to perform neurosurgery navigation, a markerless surface registration method is designed by aligning the intra‐operative face to the pre‐operative face. We propose an efficient and robust registration approach based on the scale invariant feature transform (SIFT), and compare it with iterative closest point (ICP) and coherent point drift (CPD) through a new evaluation standard.ResultsOur registration method was validated by studies of 10 volunteers and one synthetic model. The average symmetrical surface distances (ASDs) for ICP, CPD and our registration method were 2.24 ± 0.53, 2.18 ± 0.41 and 2.30 ± 0.69 mm, respectively. The average running times of ICP, CPD and our registration method were 343.46, 3847.56 and 0.58 s, respectively.ConclusionOur system can quickly reconstruct the intra‐operative face, and then efficiently and accurately align it to the pre‐operative image, meeting the registration requirements in neurosurgery navigation. It avoids a tedious set‐up process for surgeons. Copyright © 2014 John Wiley & Sons, Ltd.
Exploiting the European Union trusted service status list for certificate validation in STORK: design, implementation, and lessons learnt
Authors: Berbecaru Diana , Lioy Antonio 
Published: October 2014

SummarySince December 2009, the European Union Trusted Service Status Lists (TSLs) have been specified and adopted across European Union countries in order to enable the verification of digital signatures with legal values. This paper deals with the exploitation of TSLs in real digital services, other than electronic signatures, that is for certificate validation service. In particular, we used such lists in the service provided by the pan‐European Secure identTities acRoss boRders linKed identity management infrastructure in order to validate X.509 public key certificates. In addition, we propose an XML data structure to be used in conjunction with a TSL, in the form of a Trust Service Association (TrSA) file, to hold trust relationships between different services in a TSL. The TrSA file in conjunction with the TSLs may be used directly by the service providers or users to validate certificates. For the generation of the TSLs, we propose also a tool for automatic generation of the TSLs, named TSLGenerator. Copyright © 2014 John Wiley & Sons, Ltd.
Imaging inclusion complex formation in starch granules using confocal laser scanning microscopy
Authors: Manca Marianna , Woortman Albert J. J. , Loos Katja , Loi Maria A. 
Published: October 2014

AbstractThe tendency of amylose to form inclusion complexes with guest molecules has been an object of wide interest due to its fundamental role in food processing. Here we investigated the features of starch granules from several botanical sources using confocal laser scanning microscopy (CLSM) and uncovered the interactions between amylose and fluorescent lipophilic molecules below gelatinization temperature. In natural starch granules, we reveal complexation of lipophilic molecules labeled with fluorescein with amylose located at the periphery of the granules, appearing as a bright well‐defined luminescent rim. This phenomenon is occurring below the gelatinization point for very low concentration of aliphatic chains. Control experiments performed with the fluorescein dye show staining of the whole granule, evidencing non‐specific interactions. Similarly, experiments performed with waxy granules show a broader luminescent rim when interacting with the lipid‐dye molecules.
Human Adipose-Derived Stem Cells Ameliorate Cigarette Smoke-Induced Murine Myelosuppression via Secretion of TSG-6
Authors: Xie Jie , Broxmeyer Hal E. , Feng Dongni , Schweitzer Kelly S. , Yi Ru , Cook Todd G. , Chitteti Brahmananda R. , Barwinska Daria , Traktuev Dmitry O. , Van Demark Mary J. , Justice Matthew J. , Ou Xuan , Srour Edward F. , Prockop Darwin J. , Petrache Irina , March Keith L. 
Published: October 2014

AbstractObjective: Bone marrow-derived hematopoietic stem and progenitor cells (HSC/HPC) are critical to homeostasis and tissue repair. The aims of this study were to delineate the myelotoxicity of cigarette smoking (CS) in a murine model, to explore human adipose-derived stem cells (hASC) as a novel approach to mitigate this toxicity, and to identify key mediating factors for ASC activities. Methods: C57BL/6 mice were exposed to CS with or without i.v. injection of regular or siRNA-transfected hASC. For in vitro experiments, cigarette smoke extract was used to mimic the toxicity of CS exposure. Analysis of bone marrow HPC was performed both by flow cytometry and colony-forming unit assays. Results: In this study, we demonstrate that as few as 3 days of CS exposure results in marked cycling arrest and diminished clonogenic capacity of HPC, followed by depletion of phenotypically defined HSC/HPC. Intravenous injection of hASC substantially ameliorated both acute and chronic CS-induced myelosuppression. This effect was specifically dependent on the anti-inflammatory factor TSG-6, which is induced from xenografted hASC, primarily located in the lung and capable of responding to host inflammatory signals. Gene expression analysis within bone marrow HSC/HPC revealed several specific signaling molecules altered by CS and normalized by hASC. Conclusion: Our results suggest that systemic administration of hASC or TSG-6 may be novel approaches to reverse CS-induced myelosuppression. Stem Cells 2015;33:468–478
Syntheses and Characterization of Silver Phenylphosphonates and Phenylarsonates, AgxH4–x(O3PPh)2 (x = 1–4) and AgxH4–x(O3AsPh)2 (x = 2, 4)
Authors: Padalwar Nitin Balkrushna , Akkisetty Bhaskar , Vidyasagar Kanamaluru 
Published: October 2014

AbstractSix phenylphosphonates and phenylarsonates of silver, Ag(HO3PPh)(H2O3PPh) (1), Ag2(HO3PPh)2 (2), Ag3(O3PPh)(HO3PPh) (3), Ag4(O3PPh)2 (4), Ag2(HO3AsPh)2 (5), and Ag4(O3AsPh)2 (6) were isolated and structurally characterized by single‐crystal X‐ray diffraction. The 1:2 silver phenylphosphonate, Ag(HO3PPh)(H2O3PPh) (1) has ladder‐type structural framework of known isostructural ammonium phenylphosphonate, whereas the remaining five compounds have layered structures. The silver ions are four‐coordinated in compounds 1–5 and both three‐ and four‐coordinated in compound 6. The two silver phenylarsonates are not isostructural with their phenylphosphonate analogues. Polycrystalline samples of compounds 2, 4, 5 and 6 are synthesized and characterized by powder XRD, thermogravimetric and spectroscopic techniques.
Chemical Reactions followed by in situ Neutron Powder Diffraction
Authors: Hansen Thomas C. , Kohlmann Holger 
Published: October 2014

AbstractIn situ neutron powder diffraction is a very convenient tool for the investigation of chemical reactions, whenever crystalline solids are involved. It may give insight into reaction pathways, thus allowing for strategic synthesis planning, revealing particular intermediate steps and quantifying the reaction kinetics. Although the method is rather straightforward, one is bound to a small number of available neutron sources and the few sufficiently high intensity powder diffractometers there, most of which are briefly described herein. The high penetration depth of thermal neutrons allows for a large range of complex sample environments; however neutron absorption and parasitic scattering have to be carefully considered in the construction of dedicated in situ equipment. Some specific types of sample environment, specially designed for in situ neutron powder diffraction will be discussed such as electrochemical cells, autoclaves for the study of solvothermal reactions, and gas‐solid reaction cells. Several examples from inorganic chemistry are being presented, ranging from metal hydrides, nitrides, oxides, and halides, to intermetallic compounds or metal organic frameworks, many of them of importance in applications, e.g. in lithium ion batteries, as magnetic or hard materials, high strength alloys, hydrogen storage, ferroelectric or superconducting materials, or as solid catalysts. In situ neutron powder diffraction often paves the way to a better reaction control in chemical synthesis, to the discovery of metastable compounds or gives insight into technologically relevant processes. These successful applications in inorganic chemistry demonstrate the usefulness of the method of in situ neutron powder diffraction and may encourage the reader to consider neutron diffraction in the repertoire of analytic tools.
Posterosuperior Lesion has a High Risk of Lateral and Central Nodal Metastasis in Solitary Papillary Thyroid Cancer
Authors: Lee Dong Jin , Lee Kyu Ho , Kim Jin Hwan , Kwon Kee Hwan , Yoon Dae Young , Rho Young Soo 
Published: October 2014

AbstractBackgroundPreoperative nodal assessment of papillary thyroid cancer (PTC) is very important because 60 to 70 % of all disease recurrence in the neck can occur in the lymph nodes. This study explored the association between ultrasonographic intrathyroidal location and the nodal metastasis pattern in solitary PTC.MethodsData from 218 patients who underwent total thyroidectomy with or without neck dissection for previously untreated PTC between 2006 and 2010 were retrospectively analyzed. Only patient data for which both preoperative ultrasound findings and postoperative pathologic reports were available were included. Multifocal cases, cases with extrathyroidal extension, and distant metastasis were excluded. The association between nodal metastasis pattern and clinical or pathologic features of solitary PTCs was analyzed, as was the association between ultrasonographic intrathyroidal location and central or lateral nodal metastasis in solitary PTC.ResultsMass size larger than 2 cm (p < 0.001, Odds ratio (OR) 4.117) and central nodal metastasis (p < 0.001, OR 3.984) were related with lateral neck metastasis in multivariate analysis. Male sex (p = 0.001, OR 3.012) and capsular invasion (p < 0.001, OR 4.720) were related with central neck metastasis in multivariate analysis. When analyzing ultrasonographic location of intrathyroidal solitary lesion, posterosuperiorly located lesion was strongly associated with both lateral and central neck metastasis. (p < 0.001 and p = 0.002, respectively).ConclusionsPosterosuperior location of intrathyroidal solitary PTC has a high risk of lateral and central nodal metastasis when compared to other locations. For such patients, careful preoperative evaluation of nodal status should be done.
Ceramic Liner Fracture and Impingement in Total Hip Arthroplasty
Authors: Steinhoff Amy , Hakim Victor , Walker Richard H. , Colwell Clifford W. , Copp Steven N. 
Published: October 2014

Background Ceramic-on-ceramic bearing surfaces were developed to provide an alternate to metal-on-polyethylene to decrease wear-induced osteolysis in total hip arthroplasty patients. In an effort to decrease the risk of ceramic acetabular component fracture or damage during implantation, a raised metal rim was added. Questions/Purposes How many fractures or impingements have occurred in our population of patients with ceramic liners with raised rims? Methods With IRB-approved consent, a case series was reviewed from a single center registry and 4 of 169 patients were identified who had revision hip surgery with the ceramic liner with a raised metal rim: one for ceramic liner fracture and three for metallosis, pain, and squeaking. Implant alignment and operative findings were reviewed. Results One ceramic liner fracture and three cases of metallosis from impingement of the femoral neck on the posterior elevated metal rim of the acetabular liner were observed at revision. The femoral neck in each patient had a divot that corresponded to a divot in the posterosuperior liner rim. Three of the four patients had audible squeaking or clicking prior to revision. A total of 3% of patients in this series had clinically significant impingement with this implant type. Conclusion Acoustic phenomenon in a ceramic on ceramic bearing surface should be investigated with a cross-table lateral radiograph to evaluate component position. If symptomatic impingement is demonstrated, revision should be considered to avoid failure from metallosis or fracture.
Direct Polymerization of Vernonia Oil through Cationic Means
Authors: Biswas Atanu , Cheng H. N. , Klasson K. Thomas , Liu Zengshe , Berfield Janet , Ayorinde F. O. 
Published: October 2014

AbstractVernonia oil is obtained by extraction from Vernonia galamensis seeds. It is a triglyceride containing 70–80 % vernolic acid (12,13‐epoxy‐9‐decenoic acid). With approximately three epoxy groups per molecule, vernonia oil is a good raw material for new product development and many derivatives have been reported. In this work we report for the first time direct polymerization of vernonia oil through cationic means. The reaction entails the use of fluorosulfonic acid as a catalyst and 25–35 °C. Depending on the level of acid catalyst used, the products can range from a viscous oil to a completely insoluble resin. These products have been characterized by NMR and FT‐IR. The polymer may perhaps find applications as a thickener in lubricants and oil‐based commercial formulations.
Positional‐Species Composition of Triacylglycerols from the Arils of Mature Euonymus Fruits
Authors: Sidorov Roman A. , Pchelkin Vasily P. , Zhukov Anatoly V. , Vereshchagin Andrei G. , Tsydendambaev Vladimir D. 
Published: October 2014

AbstractPositional‐species composition (PSC) of 1,2,3‐triacyl‐sn‐glycerols (TAG) from the arils of mature fruits of 13 species of Euonymus L. genus was established. The residues of six major fatty acids (FA), palmitic, stearic, hexadecenoic (H), octadecenoic (O), linoleic (L), and linolenic, were present in the TAG. PSC of TAG was determined by their partial lipase hydrolysis. By using hierarchical cluster and principal component analyses, it was definitely demonstrated that separate taxonomic units forming this genus were significantly distinguished as regards PSC of TAG. In particular, the Euonymus subgenus greatly exceeded the Kalonymus subgenus in both total content of L in TAG and in the rate of its incorporation into their mid‐position, while TAG of Kalonymus were marked by a prevalence of O‐TAG and sn‐2‐O isomers. Thus, these subgenera were significantly distinct in the rate of incorporation of O and L residues in the sn‐2 position of TAG molecules. Meanwhile, the TAG from the Euonymus section species were marked by an enhanced concentration of H and the incorporation of H in UUU TAG was much more active than in other TAG types. As for positional‐type composition of TAG, saturated FA were always virtually absent in the sn‐2 position of Euonymus aril TAG.
Three-dimensional instabilities of a stratified cylinder wake
Authors: Bosco M. , Meunier P. 
Published: October 2014

AbstractThis paper describes experimentally, numerically and theoretically how the three-dimensional instabilities of a cylinder wake are modified by the presence of a linear density stratification. The first part is focused on the case of a cylinder with a small tilt angle between the cylinder’s axis and the vertical. The classical mode A well-known for a homogeneous fluid is still present. It is more unstable for moderate stratifications but it is stabilized by a strong stratification. The second part treats the case of a moderate tilt angle. For moderate stratifications, a new unstable mode appears, mode S, characterized by undulated layers of strong density gradients and axial flow. These structures correspond to Kelvin–Helmholtz billows created by the strong shear present in the critical layer of each tilted von Kármán vortex. The last two parts deal with the case of a strongly tilted cylinder. For a weak stratification, an instability (mode RT) appears far from the cylinder, due to the overturning of the isopycnals by the von Kármán vortices. For a strong stratification, a short wavelength unstable mode (mode L) appears, even in the absence of von Kármán vortices. It is probably due to the strong shear created by the lee waves upstream of a secondary recirculation bubble. A map of the four different unstable modes is established in terms of the three parameters of the study: the Reynolds number, the Froude number (characterizing the stratification) and the tilt angle.
Study on high-Weber-number droplet collision by a parallel, adaptive interface-tracking method
Authors: Kuan Chih-Kuang , Pan Kuo-Long , Shyy Wei 
Published: October 2014

AbstractWe have established a parallel, adaptive interface-tracking framework in order to conduct, based on the framework, direct simulation of binary head-on droplet collision in the high-Weber-number regime (from 200 to 1500) that exhibits complex topological changes and substantial length scale variations. The overall algorithms include a combined Eulerian and Lagrangian solver to track moving interfaces, conservative Lagrangian mesh modification and reconstruction, cell-based unstructured adaptive mesh refinement (AMR) in the Eulerian solver, and associated Eulerian and Lagrangian domain partitions to minimize communication overhead. Based on the combined computational and experimental efforts, we have resolved for the first time the free-surface instabilities of the colliding droplets at such high Weber number. We detail the characteristics of coalescence, stretch, end pinching, fingering, free-surface movement and drop breakup. The Taylor–Culick rim is present soon after the collision. Furthermore, we observe two types of longitudinal instabilities on the rim, namely, the Rayleigh–Taylor (RT)-type instability in the initial deceleration phase of the circular sheet right after droplet coalescence, and later the Rayleigh–Plateau (RP) instabilities. As the Taylor–Culick rim disintegrates in the retraction phase, fingering effect is profound and resulting in wider droplet size distribution.
Dynamics of fluid flow over a circular flexible plate
Authors: Hua Ru-Nan , Zhu Luoding , Lu Xi-Yun 
Published: October 2014

AbstractThe dynamics of viscous fluid flow over a circular flexible plate are studied numerically by an immersed boundary–lattice Boltzmann method for the fluid flow and a finite-element method for the plate motion. When the plate is clamped at its centre and placed in a uniform flow, it deforms by the flow-induced forces exerted on its surface. A series of distinct deformation modes of the plate are found in terms of the azimuthal fold number from axial symmetry to multifold deformation patterns. The developing process of deformation modes is analysed and both steady and unsteady states of the fluid–structure system are identified. The drag reduction due to the plate deformation and the elastic potential energy of the flexible plate are investigated. Theoretical analysis is performed to elucidate the deformation characteristics. The results obtained in this study provide physical insight into the understanding of the mechanisms on the dynamics of the fluid–structure system.
Diets high in resistant starch and arabinoxylan modulate digestion processes and SCFA pool size in the large intestine and faecal microbial composition in pigs
Authors: Nielsen Tina S. , Lærke Helle N. , Theil Peter K. , Sørensen Jens F. , Saarinen Markku , Forssten Sofia , Bach Knudsen Knud E. 
Published: October 2014

The effects of a high level of dietary fibre (DF) either as arabinoxylan (AX) or resistant starch (RS) on digestion processes, SCFA concentration and pool size in various intestinal segments and on the microbial composition in the faeces were studied in a model experiment with pigs. A total of thirty female pigs (body weight 63·1 (sem4·4) kg) were fed a low-DF, high-fat Western-style control diet (WSD), an AX-rich diet (AXD) or a RS-rich diet (RSD) for 3 weeks. Diet significantly affected the digestibility of DM, protein, fat, NSP and NSP components, and the arabinose:xylose ratio, as well as the disappearance of NSP and AX in the large intestine. RS was mainly digested in the caecum. AX was digested at a slower rate than RS. The digesta from AXD-fed pigs passed from the ileum to the distal colon more than twice as fast as those from WSD-fed pigs, with those from RSD-fed pigs being intermediate (P< 0·001). AXD feeding resulted in a higher number ofFaecalibacterium prausnitzii,Roseburia intestinalis,Blautia coccoides–Eubacterium rectale,Bifidobacteriumspp. andLactobacillusspp. in the faeces sampled at week 3 of the experimental period (P< 0·05). In the caecum, proximal and mid colon, AXD feeding resulted in a 3- to 5-fold higher pool size of butyrate compared with WSD feeding, with the RSD being intermediate (P <0·001). In conclusion, the RSD and AXD differently affected digestion processes compared with the WSD, and the AXD most efficiently shifted the microbial composition towards butyrogenic species in the faeces and increased the large-intestinal butyrate pool size.