bluuebunny/crossref_metadata_2025_split huggingface dataset:
A fully implicit scheme for simulating ionized gas flows using the gas dynamics electrodynamics coupled system
Authors: Panourgias Konstantinos T. , Ekaterinaris John A. 
Published: September 2014

SUMMARYThe flow of ionized gases under the influence of electromagnetic fields is governed by the coupled system of the compressible flow equations and the Maxwell equations. In this system, coupling of the flow with the electromagnetic field is obtained through nonlinear and stiff source terms, which may cause difficulties with the numerical solution of the coupled system. The discontinuous Galerkin finite element method is used for the numerical solution of this system. For the magnetic field vector, discontinuous Galerkin discretization is performed using a divergence‐free vector base for the magnetic field to preserve zero divergence in the element and retain the implicit constraint of a divergence‐free magnetic field vector down to very low level both globally and locally. To circumvent difficulties resulting from the presence of the stiff source terms, implicit time marching is used for the fully coupled system to avoid wrong wave shapes and propagation speeds that are obtained when the coupling source terms are lagged in time or by using splitting iterative schemes. Numerical solutions for benchmark problems computed on collocated meshes for the flow and electromagnetic field variables with this fully coupled monolithic approach showed good agreement with other numerical solutions and exact results. Copyright © 2014 John Wiley & Sons, Ltd.
Parathyroid hormone 1–34 enhances extracellular matrix deposition and organization during flexor tendon repair
Authors: Lee Daniel J. , Southgate Richard D. , Farhat Youssef M. , Loiselle Alayna E. , Hammert Warren C. , Awad Hani A. , O'Keefe Regis J. 
Published: September 2014

ABSTRACTParathyroid hormone (PTH) 1–34 is known to enhance fracture healing. Tendon repair is analogous to bone healing in its dependence on the proliferation and differentiation of mesenchymal stem cells, matrix formation, and tissue remodeling.1,2,3 We hypothesized that PTH 1–34 enhances tendon healing in a flexor digitorum longus (FDL) tendon repair model. C57Bl/6J mice were treated with either intraperitoneal PTH 1–34 or vehicle‐control (PBS). Tendons were harvested at 3–28 days for histology, gene expression, and biomechanical testing. The metatarsophalangeal joint range of motion was reduced 1.5–2‐fold in PTH 1–34 mice compared to control mice. The gliding coefficient, a measure of adhesion formation, was 2–3.5‐fold higher in PTH 1–34 mice. At 14 days post‐repair, the tensile strength was twofold higher in PTH 1–34 specimens, but at 28 days there were no differences. PTH 1–34 mice had increased fibrous tissue deposition that correlated with elevated expression of collagens and fibronectin as seen on quantitative PCR. PTH 1–34 accelerated the deposition of reparative tissue but increased adhesion formation. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 33:17–24, 2015.
Systemic absorption and metabolism of dietary procyanidin B4 in pigs
Authors: Bittner Katharina , Kemme Theresa , Peters Katharina , Kersten Susanne , Dänicke Sven , Humpf Hans‐Ulrich 
Published: September 2014

ScopeProcyanidins (PCs) are among the most abundant polyphenols in the human diet and they are reported to exhibit several beneficial health effects. However, the knowledge about their metabolic fate is rather limited. To investigate the systemic absorption and metabolism of dietary PC B4, a kinetic study using pigs as model system has been performed.Methods and resultsAfter oral application of a single dose of 10 mg/kg body weight PC B4, urine and plasma were collected over a period of 48 h. PC B4 and its possible metabolites were analyzed in physiological samples using HPLC‐MS/MS and GC‐MS. PC B4 was detected as intact molecule in urine as well as in plasma. Maximum reached plasma concentration of PC B4 (cmax) was 2.13 ng/mL (3.68 nM) and mean total urinary excretion related to the administered dose was 0.008 ± 0.003%. In addition to that the monomeric structural units catechin and epicatechin were determined as degradation products. Furthermore, methylated and conjugated monomeric metabolites were identified. Monomeric metabolites were identified to be the major fraction occurring in the systemic circulation. The analysis of phenolic acids did not show an increase of these possible further metabolites.ConclusionAfter oral administration, PC B4 is absorbed as intact molecule and it is excreted in urine. In addition, it is degraded to the monomeric subunits that are then further metabolized to methylated and glucuronidated conjugates in pigs.
Depletion of pericentrin in mouse oocytes disrupts microtubule organizing center function and meiotic spindle organization
Authors: Ma Wei , Viveiros Maria M. 
Published: September 2014

SUMMARYAccurate chromosome segregation is dependent on the formation and stability of the microtubule spindle apparatus. Meiotic spindle assembly in oocytes differs from the process used during mitosis, and is regulated by unique microtubule organizing centers (MTOCs) that lack centrioles. To gain insight into the molecular composition and function of acentriolar MTOCs in mouse oocytes, we assessed the role of a key MTOC‐associated protein, pericentrin (PCNT). In somatic cells, pericentrin functions as a scaffold that binds specific proteins at MTOCs, including γ‐tubulin, which is necessary for microtubule nucleation. Pericentrin is expressed in oocytes, but the conservation of its function is not known. Pericentrin localizes specifically to MTOCs during prophase‐I arrest in mouse oocytes recovered from pre‐ovulatory ovarian follicles, and remains associated with MTOCs at spindle poles during metaphase‐I and ‐II. To test function, specific siRNAs were used to knock down Pcnt transcripts in mouse oocytes. Efficient protein depletion was confirmed by Western blot as well as immunofluorescence analysis. Notably, meiotic spindle structure and chromosome alignment were disrupted in Pcnt‐depleted oocytes. Disorganized spindle structures with reduced microtubule density and misaligned chromosomes were observed in the majority of these oocytes (∼70%). In addition, γ‐tubulin localization to MTOCs was significantly reduced and microtubule regrowth, following cold treatment, was delayed in Pcnt‐depleted oocytes. Thus, pericentrin is a key functional component of the unique acentriolar MTOCs of mouse oocytes, and plays an important role in regulating meiotic spindle assembly and/or stability. Mol. Reprod. Dev. 81: 1019–1029, 2014. © 2014 Wiley Periodicals, Inc.
Proteogenomic strategies for identification of aberrant cancer peptides using large‐scale next‐generation sequencing data
Authors: Woo Sunghee , Cha Seong Won , Na Seungjin , Guest Clark , Liu Tao , Smith Richard D. , Rodland Karin D. , Payne Samuel , Bafna Vineet 
Published: September 2014

Cancer is driven by the acquisition of somatic DNA lesions. Distinguishing the early driver mutations from subsequent passenger mutations is key to molecular subtyping of cancers, understanding cancer progression, and the discovery of novel biomarkers. The advances of genomics technologies (whole‐genome exome, and transcript sequencing, collectively referred to as NGS (next‐generation sequencing)) have fueled recent studies on somatic mutation discovery. However, the vision is challenged by the complexity, redundancy, and errors in genomic data, and the difficulty of investigating the proteome translated portion of aberrant genes using only genomic approaches. Combination of proteomic and genomic technologies are increasingly being employed. Various strategies have been employed to allow the usage of large‐scale NGS data for conventional MS/MS searches. This paper provides a discussion of applying different strategies relating to large database search, and FDR (false discovery rate) ‐based error control, and their implication to cancer proteogenomics. Moreover, it extends and develops the idea of a unified genomic variant database that can be searched by any MS sample. A total of 879 BAM files downloaded from TCGA repository were used to create a 4.34 GB unified FASTA database that contained novel splice junctions, 38 464 deletions, 1 105 insertions, and 182 302 substitutions. Proteomic data from a single ovarian carcinoma sample (439 858 spectra) was searched against the database. By applying the most conservative FDR measure, we have identified 524 novel peptides and 65 578 known peptides at 1% FDR threshold. The novel peptides include interesting examples of doubly mutated peptides, frame‐shifts, and nonsample‐recruited mutations, which emphasize the strength of our approach.
Reactive Molecular Dynamics Simulations for a Better Insight in Plasma Medicine
Authors: Bogaerts Annemie , Yusupov Maksudbek , Van der Paal Jonas , Verlackt Christof C. W. , Neyts Erik C. 
Published: September 2014

AbstractIn this review paper, we present several examples of reactive molecular dynamics simulations, which contribute to a better understanding of the underlying mechanisms in plasma medicine on the atomic scale. This includes the interaction of important reactive oxygen plasma species with the outer cell wall of both gram‐positive and gram‐negative bacteria, and with lipids present in human skin. Moreover, as most biomolecules are surrounded by a liquid biofilm, the behavior of these plasma species in a liquid (water) layer is presented as well. Finally, a perspective for future atomic scale modeling studies is given, in the field of plasma medicine in general, and for cancer treatment in particular.
The Impact of Plasma‐modified Films with Sulfur Dioxide, Sodium Oxide on Food Pathogenic Microorganisms
Authors: Maćkiw Elżbieta , Mąka Łukasz , Ścieżyńska Halina , Pawlicka Marzena , Dziadczyk Paulina , Rżanek‐Boroch Zenobia 
Published: September 2014

AbstractIn this study, plasma modification was carried out in barrier discharge under atmospheric pressure. Sulfur dioxide and/or sodium oxide was used as the coating precursor. The results show that the films treated with a mixture of argon and sulfur dioxide inhibited microbial growth considerably better than those with coatings containing argon and sodium oxide. The highest levels of growth inhibition, of 86% for Staphylococcus aureus and 82% for Escherichia coli, were achieved with films carrying a sulfur‐containing coating (1.4% SO2). Copyright © 2014 John Wiley & Sons, Ltd.
Fully automated, high‐throughput instrumentation for measuring the δ13C value of methane and application of the instrumentation to rice paddy samples
Authors: Tokida Takeshi , Nakajima Yasuhiro , Hayashi Kentaro , Usui Yasuhiro , Katayanagi Nobuko , Kajiura Masako , Nakamura Hirofumi , Hasegawa Toshihiro 
Published: September 2014

RATIONALEThe stable carbon isotope ratio (13C/12C or δ13C value) of methane (CH4) produced in methanogenic environments contains information about primary source material, CH4 production pathways, degree of oxidation, and transport. However, the availability of δ13C‐CH4 data is severely limited because isotope analysis methods are low throughput, owing primarily to the need for manual processing steps. High‐throughput, fully automated measurement is necessary to facilitate the use of the δ13C signature in understanding CH4 biogeochemistry.METHODSWe modified a conventional continuous‐flow (CF) gas chromatography/combustion/isotope ratio mass spectrometry (IRMS) instrument system by incorporating (i) automated sample injection, (ii) a newly developed temperature‐control unit for preconcentration and cryofocus traps, and (iii) an automatic system for liquid‐nitrogen refilling. The system, which could run unattended for 1 day, was used to obtain δ13C‐CH4 data for CH4 samples collected from an irrigated rice paddy with an automated closed‐chamber system.RESULTSUsing the fully automated CF‐IRMS system, we measured δ13C‐CH4 data for 77 samples during a 21.5‐h continuous run (17 min per sample) with high precision (1σ = 0.11‰, reproducibility) and moderate consumption of liquid nitrogen (11 L). Application of the system to CH4 samples obtained from the rice paddy revealed distinct seasonal and diurnal variations in δ13C values with the highest temporal resolution ever reported.CONCLUSIONSA fully automated, high‐throughput system for the measurement of δ13C‐CH4 values was developed and used to analyze air samples obtained from a rice paddy. Our results demonstrate the high potential of this system for obtaining δ13C data useful for process‐level understanding of CH4 biogeochemistry with respect to spatiotemporal variation of CH4 sources and how that variation is affected by environmental and management factors. Copyright © 2014 John Wiley & Sons, Ltd.
A multilayer non‐repudiation system: a Suite‐B approach
Authors: Adibi Sasan 
Published: September 2014

AbstractSecurity provisioning is an essential part in the design of any communication systems, which becomes more critical for wireless systems. The consideration and comparisons of security algorithms in various Open Systems Interconnection layers is a difficult task, because there are many performance metrics involved. The aim of this novel research article is to present research results for the design of a wireless system revolving around the practical and low‐cost implementation of Suite‐B algorithms in different layers. Suite‐B, promulgated by the National Security Agency, is a set of cryptographic algorithms, including non‐repudiation. The end results include the deployment of Suite‐B algorithms at the application, transport, and network layers and the protocol flow at each layer. Copyright © 2014 John Wiley & Sons, Ltd.
Intravital Imaging of Mesenchymal Stem Cell Trafficking and Association With Platelets and Neutrophils
Authors: Teo Grace Sock Leng , Yang Zijiang , Carman Christopher V. , Karp Jeffrey M. , Lin Charles P. 
Published: September 2014

Abstract
Early events of mesenchymal stem/stromal cell (MSC) adhesion to and transmigration through the vascular wall following systemic infusion are important for MSC trafficking to inflamed sites, yet are poorly characterized in vivo. Here, we used intravital confocal imaging to determine the acute extravasation kinetics and distribution of culture-expanded MSC (2–6 hours postinfusion) in a murine model of dermal inflammation. By 2 hours postinfusion, among the MSC that arrested within the inflamed ear dermis, 47.8% ± 8.2% of MSC had either initiated or completed transmigration into the extravascular space. Arrested and transmigrating MSCs were equally distributed within both small capillaries and larger venules. This suggested existence of an active adhesion mechanism, since venule diameters were greater than those of the MSC. Heterotypic intravascular interactions between distinct blood cell types have been reported to facilitate the arrest and extravasation of leukocytes and circulating tumor cells. We found that 42.8% ± 24.8% of intravascular MSC were in contact with neutrophil-platelet clusters. A role for platelets in MSC trafficking was confirmed by platelet depletion, which significantly reduced the preferential homing of MSC to the inflamed ear, although the total percentage of MSC in contact with neutrophils was maintained. Interestingly, although platelet depletion increased vascular permeability in the inflamed ear, there was decreased MSC accumulation. This suggests that increased vascular permeability is unnecessary for MSC trafficking to inflamed sites. These findings represent the first glimpse into MSC extravasation kinetics and microvascular distribution in vivo, and further clarify the roles of active adhesion, the intravascular cellular environment, and vascular permeability in MSC trafficking. Stem Cells 2015;33:265–277
Annexin A3 as a Potential Target for Immunotherapy of Liver Cancer Stem-Like Cells
Authors: Pan Qiu-Zhong , Pan Ke , Wang Qi-Jing , Weng De-Sheng , Zhao Jing-Jing , Zheng Hai-Xia , Zhang Xiao-Fei , Jiang Shan-Shan , Lv Lin , Tang Yan , Li Yong-Qiang , He Jia , Liu Qing , Chen Chang-Long , Zhang Hong-Xia , Xia Jian-Chuan 
Published: September 2014

Abstract
Cancer stem-like cells/cancer-initiating cells (CSCs/CICs) are considered to represent a small population of cancer cells that is resistant to conventional cancer treatments and responsible for tumor recurrence and metastasis. The aim of this study was to establish CSC/CIC-targeting immunotherapy. In this study, we found that Annexin A3 (ANXA3) was preferentially expressed in CSCs/CICs derived from hepatocellular carcinoma (HCC) cells compared to non-CSCs/CICs. In HCC samples, high levels of ANXA3 correlated with expansion of CD133+ tumor cells representing CSCs/CICs in HCC; the combination of high levels of ANXA3 and CD133 was associated with progression of HCC. Overexpression of ANXA3 increased the proportion of CD133+ cells, enhancing their tumorigenicity. On the contrary, knockdown of ANXA3 decreased CD133+ cells and inhibited tumorigenicity. The mechanistic study revealed that ANXA3-mediated maintenance of HCC CSCs/CICs activity was likely involved with the HIF1A/Notch pathway. Using ANXA3 as a target, ANXA3-transfected dendritic cells could induce more functionally active T cells and these effector T cells could superiorly kill CD133+ HCC CSCs/CICs in vitro and in vivo. Taken together, our findings suggest that ANXA3 plays a role in HCC CSC/CIC maintenance, and that ANXA3 may represent a potential CSC/CIC-specific therapeutic target for improving the treatment of HCC. Stem Cells 2015;33:354–366
Arterialized Venous Flow-Through Flaps in the Reconstruction of Digital Defects: Case Series and Review of the Literature
Authors: Garlick Jared W. , Goodwin Isak A. , Wolter Keith , Agarwal Jayant P. 
Published: September 2014

Background Arterialized venous flow-through (AVFT) flaps are useful in reconstructing small soft tissue defects. Currently, no guidelines exist for the use of AVFT flaps for reconstructing soft tissue defects in the digits of the hand. We retrospectively reviewed our experience with AVFT flaps and developed a selection process for vascular anastomoses. Methods We reviewed the use of AVFT flaps in a series of ten consecutive patients requiring reconstruction of small soft tissue defects of the fingers. Results Between 2006 and 2012, ten consecutive digital reconstructions were performed using AVFT flaps. Flap sizes ranged from 5 to 13.5 cm2. Initial congestion was seen in all flaps and resolved within 3–7 days. Leeches were utilized in two cases. All cases achieved good functional results. Three illustrative cases from our series of ten are presented, each demonstrating key decision-making factors in selecting recipient and flap vessels for anastomosis. Conclusions AVFT flaps appear congested post-operatively, resolving in days to weeks and resulting in healthy coverage of digital soft tissue defects with good functionality. We suggest a selection process for the use of AVFT flaps in digital soft tissue reconstruction, based on dorsal vs. volar and proximal vs. distal defect location, and the flap's inherent venous architecture.
Debt, Cohabitation, and Marriage in Young Adulthood
Authors: Addo Fenaba R. 
Published: September 2014

Abstract
Despite growing evidence that debt influences pivotal life events in early and young adulthood, the role of debt in the familial lives of young adults has received relatively little attention. Using data from the NLSY 1997 cohort (N = 6,749) and a discrete-time competing risks hazard model framework, I test whether the transition to first union is influenced by a young adult’s credit card and education loan debt above and beyond traditional educational and labor market characteristics. I find that credit card debt is positively associated with cohabitation for men and women, and that women with education loan debt are more likely than women without such debt to delay marriage and transition into cohabitation. Single life may be difficult to afford, but marital life is unaffordable as well. Cohabitation presents an alternative to single life, but not necessarily a marital substitute for these young adults.
Strategies for Enhancing Perioperative Safety: Promoting Joy and Meaning in the Workforce
Authors: Morath Julianne , Filipp Rhonda , Cull Michael 
Published: September 2014

AbstractWorkforce safety is a precondition of patient safety, and safety from both physical and psychological harm in the workplace is the foundation for an environment in which joy and meaning can exist. Achieving joy and meaning in the workplace allows health care workers to continuously improve the care they provide. This requires an environment in which disrespectful and harmful behaviors are not tolerated or ignored. Health care leaders have an obligation to create workplace cultures that are characterized by respect, transparency, accountability, learning, and quality care. Evidence suggests, however, that health care settings are rife with disrespectful behavior, poor teamwork, and unsafe working conditions. Solutions for addressing workplace safety problems include defining core values, tasking leaders to act as role models, and committing to becoming a high‐reliability organization.
Three-dimensional instabilities of quasi-solitary waves in a falling liquid film
Authors: Kofman N. , Mergui S. , Ruyer-Quil C. 
Published: September 2014

AbstractThe stability of$\def \xmlpi #1{}\def \mathsfbi #1{\boldsymbol {\mathsf {#1}}}\let \le =\leqslant \let \leq =\leqslant \let \ge =\geqslant \let \geq =\geqslant \def \Pr {\mathit {Pr}}\def \Fr {\mathit {Fr}}\def \Rey {\mathit {Re}}\gamma _2$travelling waves at the surface of a film flow down an inclined plane is considered experimentally and numerically. These waves are fast, one-humped and quasi-solitary. They undergo a three-dimensional secondary instability if the flow rate (or Reynolds number) is sufficiently high. Rugged or scallop wave patterns are generated by the interplay between a short-wave and a long-wave instability mode. The short-wave mode arises in the capillary region of the wave, with a mechanism of capillary origin which is similar to the Rayleigh–Plateau instability, whereas the long-wave mode deforms the entire wave and is triggered by a Rayleigh–Taylor instability. Rugged waves are observed at relatively small inclination angles. At larger angles, the long-wave mode predominates and scallop waves are observed. For a water film the transition between rugged and scallop waves occurs for an inclination angle around 12°.
Model for the initiation of atomization in a high-speed laminar liquid jet
Authors: Umemura Akira 
Published: September 2014

AbstractA laminar water jet issuing at high speed from a short circular nozzle into air exhibits various instability features at different distances from the nozzle exit. Near the exit, the effects of gaseous friction and pressure are relatively weak. Deformation of the jet surface in this region is mainly due to the instability of a thin liquid shear layer flow, which relaxes from the velocity profile produced by the nozzle wall. In this paper, a model for this type of instability based on linear stability analysis is investigated to describe the process initiating the formation of liquid ligaments disintegrating into fine droplets near the nozzle exit. The modelling comprises identifying unstable waves excitable in the liquid shear layer and exploring a self-destabilizing mechanism by which unstable waves responsible for the formation of liquid ligaments are naturally reproduced from the upstream-propagating capillary waves produced by the growth of the unstable waves themselves. An expression for the location of ligament formation onset is derived that can be compared with experiments. The model also explains changes in jet instability features away from the nozzle exit and for very short nozzles.