bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic regional phase synchrony (DRePS)
Authors: Omidvarnia Amir , Pedersen Mangor , Walz Jennifer M. , Vaughan David N. , Abbott David F. , Jackson Graeme D. 
Published: March 2016

AbstractDynamic functional brain connectivity analysis is a fast expanding field in computational neuroscience research with the promise of elucidating brain network interactions. Sliding temporal window based approaches are commonly used in order to explore dynamic behavior of brain networks in task‐free functional magnetic resonance imaging (fMRI) data. However, the low effective temporal resolution of sliding window methods fail to capture the full dynamics of brain activity at each time point. These also require subjective decisions regarding window size and window overlap. In this study, we introduce dynamic regional phase synchrony (DRePS), a novel analysis approach that measures mean local instantaneous phase coherence within adjacent fMRI voxels. We evaluate the DRePS framework on simulated data showing that the proposed measure is able to estimate synchrony at higher temporal resolution than sliding windows of local connectivity. We applied DRePS analysis to task‐free fMRI data of 20 control subjects, revealing ultra‐slow dynamics of local connectivity in different brain areas. Spatial clustering based on the DRePS feature time series reveals biologically congruent local phase synchrony networks (LPSNs). Taken together, our results demonstrate three main findings. Firstly, DRePS has increased temporal sensitivity compared to sliding window correlation analysis in capturing locally synchronous events. Secondly, DRePS of task‐free fMRI reveals ultra‐slow fluctuations of ∼0.002–0.02 Hz. Lastly, LPSNs provide plausible spatial information about time‐varying brain local phase synchrony. With the DRePS method, we introduce a framework for interrogating brain local connectivity, which can potentially provide biomarkers of human brain function in health and disease. Hum Brain Mapp 37:1970–1985, 2016. © 2016 Wiley Periodicals, Inc.
Cell Polarity Proteins in Breast Cancer Progression
Authors: Rejon Carlis , Al‐Masri Maia , McCaffrey Luke 
Published: March 2016

ABSTRACTBreast cancer, one of the leading causes of cancer related death in women worldwide, is a heterogeneous disease with diverse subtypes that have different properties and prognoses. The developing mammary gland is a highly proliferative and invasive tissue, and some of the developmental programs may be aberrantly activated to promote breast cancer progression. In the breast, luminal epithelial cells exhibit apical–basal polarity, and the failure to maintain this organizational structure, due to disruption of polarity complexes, is implicated in promoting hyperplasia and tumors. Therefore, understanding the mechanisms underlying loss of polarity will contribute to our knowledge of the early stages leading to the pathogenesis of the disease. In this review, we will discuss recent findings that support the idea that loss of apical–basal cell polarity is a crucial step in the acquisition of the malignant phenotype. Oncogene induced loss of tissue organization shares a conserved cellular mechanism with developmental process, we will further describe the role of the individual polarity complexes, the Par, Crumbs, and Scribble, to couple cell division orientation and cell growth. We will examine symmetric or asymmetric cell divisions in mammary stem cell and their contribution to the development of breast cancer subtypes and cancer stem cells. Finally, we will highlight some of the recent advances in our understanding of the molecular mechanisms by which changes in epithelial polarity programs promote invasion and metastasis through single cell and collective cell modes. J. Cell. Biochem. 117: 2215–2223, 2016. © 2016 Wiley Periodicals, Inc.
Oxidation of amaranth dye by persulfate and peroxymonosulfate activated by ferrocene
Authors: Lin Kun‐Yi Andrew , Lin Jyun‐Ting , Jochems Andrew P 
Published: March 2016

AbstractBackgroundReadily‐available and efficient catalysts are preferable for activating oxidants such as persulfate (PSF) and peroxymonosulfate (PMS) for environmental remediation. Ferrocene (Fc), a stable and non‐toxic Fe2+‐bearing compound, is a promising heterogeneous catalyst for activation of PSF/PMS, that has not been previously investigated. In this study, the activation of PSF/PMS by Fc is evaluated using the oxidation of toxic amaranth dye as a model reaction.ResultsWhile an insignificant amount of amaranth dye was removed by Fc or PSF/PMS separately, the combination of Fc and the oxidants completely decolorized amaranth dye, indicating that Fc activated PSF/PMS. Fc‐activated PMS was found to be much more effective than Fc‐activated PSF for degrading amaranth. Elevated temperatures improved the degradation efficiency and kinetics, while the activation of PSF/PMS remained consistent under acidic conditions. Through examining the effects of inhibitors and electron paramagnetic resonance analyses, Fc was proven to activate PSF/PMS to generate sulfate radicals. Fc could also be re‐used for multiple cycles to activate PSF and PMS.ConclusionFc remained intact after the activation according to X‐ray diffraction, FT‐IR and X‐ray photoelectron spectroscopy analyses. These features make Fc an effective and readily‐available heterogeneous catalyst to activate PSF and PMS for advanced oxidation processes (AOPs). © 2016 Society of Chemical Industry
Identifying molecular phenotype of nucleus pulposus cells in human intervertebral disc with aging and degeneration
Authors: Tang Xinyan , Jing Liufang , Richardson William J. , Isaacs Robert E. , Fitch Robert D. , Brown Christopher R. , Erickson Melissa M. , Setton Lori A. , Chen Jun 
Published: March 2016

ABSTRACTPrevious study claimed that disc degeneration may be preceded by structure and matrix changes in the intervertebral disc (IVD) which coincide with the loss of distinct notochordally derived nucleus pulposus (NP) cells. However, the fate of notochordal cells and their molecular phenotype change during aging and degeneration in human are still unknown. In this study, a set of novel molecular phenotype markers of notochordal NP cells during aging and degeneration in human IVD tissue were revealed with immunostaining and flow cytometry. Furthermore, the potential of phenotype juvenilization and matrix regeneration of IVD cells in a laminin‐rich pseudo‐3D culture system were evaluated at day 28 by immunostaining, Safranin O, and type II collagen staining. Immunostaining and flow cytometry demonstrated that transcriptional factor Brachyury T, neuronal‐related proteins (brain abundant membrane attached signal protein 1, Basp1; Neurochondrin, Ncdn; Neuropilin, Nrp‐1), CD24, and CD221 were expressed only in juvenile human NP tissue, which suggested that these proteins may be served as the notochordal NP cell markers. However, the increased expression of CD54 and CD166 with aging indicated that they might be referenced as the potential biomarker for disc degeneration. In addition, 3D culture maintained most of markers in juvenile NP, and rescued the expression of Basp1, Ncdn, and Nrp 1 that disappeared in adult NP native tissue. These findings provided new insight into molecular profile that may be used to characterize the existence of a unique notochordal NP cells during aging and degeneration in human IVD cells, which will facilitate cell‐based therapy for IVD regeneration. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1316–1326, 2016.
Farmland Conversion Decreases Regional and National Land Quality in China
Authors: Song Wei , Liu Mingliang 
Published: March 2016

AbstractMaintaining sufficient farmland to ensure food security and a strong rural economy is crucial for China. At the national as well as regional levels, we compared the quality of the land converted from and to farmland during the period 1986–2005, thus quantifying the change in farmland quality directly attributable to land‐use conversion. Specifically, we compared land cover maps compiled for the initial and final years of the study period at a 1:250,000 scale by institutes of the Chinese Academy of Sciences, and combined this with national land quality assessment data compiled at the beginning of the period. Comparison of the land cover maps revealed that over the 20‐year period 12·9 Mha of farmland were converted to other land uses and 14·0 Mha of new farmland were brought under cultivation. Large net increases in farmland area occurred in Heilongjiang, Jilin, Liaoning, Xinjiang, and Inner Mongolia, together contributing 3·5 Mha of the net increase in farmland area. Several developed provinces, e.g. Beijing (−21·20%), Shanghai (−15·81%), Zhejiang (−9·85%), Guangdong (−7·79%), and Tianjin (−6·35%), experienced rapid farmland decreases. Although there was a net increase in farmland, the most suitable and productive farmland decreased by 1·8% while low‐quality farmland increased by 1·4%. Thus, focusing solely on maintaining the total farmland area did not prevent overall loss of a substantial amount of high‐quality farmland. Farmland protection policies should therefore take into account both farmland quantity and quality. Copyright © 2016 John Wiley & Sons, Ltd.
Accelerating fully phase‐encoded MRI near metal using multiband radiofrequency excitation
Authors: Artz Nathan S. , Wiens Curtis N. , Smith Matthew R. , Hernando Diego , Samsonov Alexey , Reeder Scott B. 
Published: March 2016

PurposeTo develop a multiband radiofrequency (RF) excitation strategy for simultaneous excitation of multiple RF offsets to accelerate fully phase‐encoded imaging near metallic prostheses.MethodsMultiband RF excitation was designed and incorporated into a spectrally resolved fully phase‐encoded (SR‐FPE) imaging scheme. A triband (−6, 0, 6 kHz) acquisition was compared with three separate single‐band acquisitions at the corresponding RF offsets with a phantom containing the head of a hip prosthesis. In vivo multiband data with continuous spectral coverage were acquired in the knee of a healthy volunteer with the head of a hip prosthesis placed posteriorly and in a volunteer with a total knee prosthetic implant.ResultsPhantom images acquired with triband excitation were essentially identical to the composite of three single‐band excitations, but with an acceleration factor of three. In vivo multiband images of the healthy knee with adjacent metal demonstrated very good depiction of knee anatomy. In vivo images of the total knee replacement were successfully acquired, allowing visualization of native tissue with far less signal dropout than 2D‐FSE.ConclusionsFPE imaging with multiband excitation is feasible in the presence of extreme off‐resonance. This approach can reduce scan time and/or increase off‐resonance coverage, enabling in vivo FPE imaging near metallic prostheses over a broad off‐resonance spectrum. Magn Reson Med 77:1223–1230, 2017. © 2016 International Society for Magnetic Resonance in Medicine
Quantitative susceptibility mapping detects abnormalities in cartilage canals in a goat model of preclinical osteochondritis dissecans
Authors: Wang Luning , Nissi Mikko J. , Toth Ferenc , Johnson Casey P. , Garwood Michael , Carlson Cathy S. , Ellermann Jutta 
Published: March 2016

PurposeTo use quantitative susceptibility mapping (QSM) to investigate changes in cartilage canals in the distal femur of juvenile goats after their surgical transection.MethodsChondronecrosis was surgically induced in the right medial femoral condyles of four 4‐day‐old goats. Both the operated and control knees were harvested at 2, 3, 5, and 10 weeks after the surgeries. Ex vivo MRI scans were conducted at 9.4 Tesla using TRAFF (relaxation time along a fictitious field)‐weighted fast spin echo imaging and QSM to detect areas of chondronecrosis and investigate cartilage canal abnormalities. Histological sections from these same areas stained with hematoxylin and eosin and safranin O were evaluated to assess the affected tissues.ResultsBoth the histological sections and the TRAFF‐weighted images of the femoral condyles demonstrated focal areas of chondronecrosis, evidenced by pyknotic chondrocyte nuclei, loss of matrix staining, and altered MR image contrast. At increasing time points after surgery, progressive changes and eventual disappearance of abnormal cartilage canals were observed in areas of chondronecrosis by using QSM.ConclusionAbnormal cartilage canals were directly visualized in areas of surgically induced chondronecrosis. Quantitative susceptibility mapping enabled investigation of the vascular changes accompanying chondronecrosis in juvenile goats. Magn Reson Med 77:1276–1283, 2017. © 2016 International Society for Magnetic Resonance in Medicine
A low‐communication, parallel algorithm for solving PDEs based on range decomposition
Authors: Appelhans David J. , Manteuffel Tom , McCormick Steve , Ruge John 
Published: March 2016

SummaryThis paper proposes a new, low‐communication algorithm for solving PDEs on massively parallel computers. The range decomposition (RD) algorithm exposes coarse‐grain parallelism by applying nested iteration and adaptive mesh refinement locally before performing a global communication step. Just a few such steps are observed to be sufficient to obtain accuracy within a small multiple of discretization error. The target applications are petascale and exascale machines, where hierarchical parallelism is required and traditional parallel numerical PDE communication patterns are costly because of message latency. The RD algorithm uses a partition of unity to equally distribute the error, and thus, the work. The computational advantages of this approach are that the decomposed problems can be solved in parallel without any communication until the partitioned solutions are summed. This offers potential advantages in the paradigm of expensive communication but very cheap computation. This paper introduces the method and explains the details of the communication step. Two performance models are developed, showing that the latency cost associated with a traditional parallel implementation of nested iteration is proportional to log(P)2, whereas the RD method reduces the communication latency to log(P), while maintaining similar bandwidth costs. Numerical results for two problems, Laplace and advection diffusion, demonstrate the enhanced performance, and a heuristic argument explains why the method converges quickly. Copyright © 2016 John Wiley & Sons, Ltd.
Combined homotopy and neighboring extremal optimal control
Authors: Gupta Rohit , Bloch Anthony M. , Kolmanovsky Ilya V. 
Published: March 2016

SummaryThis paper presents a new approach to trajectory optimization for nonlinear systems. The method exploits homotopy between a linear system and a nonlinear system and neighboring extremal optimal control, in combination with few iterations of a convergent optimizer at each step, to iteratively update the trajectory as the homotopy parameter changes. To illustrate the proposed method, a numerical example of a three‐dimensional orbit transfer problem for a spacecraft is presented. Copyright © 2016 John Wiley & Sons, Ltd.
Mesenchymal Stromal Cells Induce Peculiar Alternatively Activated Macrophages Capable of Dampening Both Innate and Adaptive Immune Responses
Authors: Chiossone Laura , Conte Romana , Spaggiari Grazia Maria , Serra Martina , Romei Cristina , Bellora Francesca , Becchetti Flavio , Andaloro Antonio , Moretta Lorenzo , Bottino Cristina 
Published: March 2016

AbstractMesenchymal stromal cells (MSCs) support hematopoiesis and exert immunoregulatory activities. Here, we analyzed the functional outcome of the interactions between MSCs and monocytes/macrophages. We showed that MSCs supported the survival of monocytes that underwent differentiation into macrophages, in the presence of macrophage colony-stimulating factor. However, MSCs skewed their polarization toward a peculiar M2-like functional phenotype (MMSC), through a prostaglandin E2-dependent mechanism. MMSC were characterized by high expression of scavenger receptors, increased phagocytic capacity, and high production of interleukin (IL)-10 and transforming growth factor-β. These cytokines contributed to the immunoregulatory properties of MMSC, which differed from those of typical IL-4-induced macrophages (M2). In particular, interacting with activated natural killer (NK) cells, MMSC inhibited both the expression of activating molecules such as NKp44, CD69, and CD25 and the production of IFNγ, while M2 affected only IFNγ production. Moreover, MMSC inhibited the proliferation of CD8+ T cells in response to allogeneic stimuli and induced the expansion of regulatory T cells (Tregs). Toll-like receptor engagement reverted the phenotypic and functional features of MMSC to those of M1 immunostimulatory/proinflammatory macrophages. Overall our data show that MSCs induce the generation of a novel type of alternatively activated macrophages capable of suppressing both innate and adaptive immune responses. These findings may help to better understand the role of MSCs in healthy tissues and inflammatory diseases including cancer, and provide clues for novel therapeutic approaches.
Heterologous expression and characterization of a new heme-catalase in Bacillus subtilis 168
Authors: Philibert Tuyishime , Rao Zhiming , Yang Taowei , Zhou Junping , Huang Genshu , Irene Komera , Samuel Niyomukiza 
Published: March 2016

Abstract
Reactive oxygen species (ROS) is an inherent consequence to all aerobically living organisms that might lead to the cells being lethal and susceptible to oxidative stress. Bacillus pumilus is characterized by high-resistance oxidative stress that stimulated our interest to investigate the heterologous expression and characterization of heme-catalase as potential biocatalyst. Results indicated that recombinant enzyme significantly exhibited the high catalytic activity of 55,784 U/mg expressed in Bacillus subtilis 168 and 98.097 µmol/min/mg peroxidatic activity, the apparent K m of catalytic activity was 59.6 ± 13 mM with higher turnover rate (K cat = 322.651 × 103 s−1). The pH dependence of catalatic and peroxidatic activity was pH 7.0 and pH 4.5 respectively with temperature dependence of 40 °C and the recombinant heme-catalase exhibited a strong Fe2+ preference. It was further revealed that catalase KatX2 improved the resistance oxidative stress of B. subtilis. These findings suggest that this B. pumilus heme-catalase can be considered among the industrially relevant biocatalysts due to its exceptional catalytic rate and high stability and it can be a potential candidate for the improvement of oxidative resistance of industrially produced strains.
Multivariate analysis of trace elements in shallow groundwater in Fuchu in western Tokyo Metropolis, Japan
Authors: Thuyet Dang Quoc , Saito Hirotaka , Saito Takeshi , Moritani Shigeoki , Kohgo Yuji , Komatsu Toshiko 
Published: March 2016

Abstract
A rapid increase in the use of ground source heat pump (GSHP) systems for heating and cooling of buildings potentially threatens to harm shallow groundwater quality. As a necessary preliminary step toward evaluating GSHP impact on shallow groundwater quality, this study used multivariate statistical analyses to investigate characteristics of trace elements in groundwater in Fuchu city in western Tokyo Metropolis. Water samples were collected twice a month from two aquifers at 30- and 45-m depths using four observation wells for more than a year. Concentrations of 14 trace elements (Li, B, Al, Cr, Mn, Fe, Ni, Cu, As, Se, Sr, Cd, Sb, and Pb) and Si as well as oxidation–reduction potential (ORP), dissolved oxygen (DO), electrical conductivity (EC), and pH were measured. All elements were under the environmental water quality criteria issued by the Japanese Ministry of the Environment. No clear seasonal trends were observed in the concentrations of 15 elements in groundwater. Principal component analyses showed the element properties were well characterized by three principal components (PC). PC1, which represents the more mobile trace elements in the groundwater, consisted of Li, B, Mn, Fe, As, and Si. PC2 included Al, Ni, Cd, and Sb, and represents ORP-insensitive properties. PC3 consisted of Pb, Cu, and Se, which are less mobile in groundwater. Samples collected from the same aquifer had high similarity in distribution and variation of the trace elements. This study proposes a useful statistical platform for assessing future effects of GSHP systems on shallow groundwater quality.
Establishing quantitative structure tribo-ability relationship model using Bayesian regularization neural network
Authors: Gao Xinlei , Dai Kang , Wang Zhan , Wang Tingting , He Junbo 
Published: March 2016

Abstract
Quantitative structure-activity relationship methods are used to study the quantitative structure triboability relationship (QSTR), which refers to the tribology capability of a compound from the calculation of structure descriptors. Here, we used the Bayesian regularization neural network (BRNN) to establish a QSTR prediction model. Two-dimensional (2D) BRNN–QSTR models can flexibly and easily estimate lubricant-additive antiwear properties. Our results show that electron transfer and heteroatoms (such as S, P, O, and N) in a lubricant-additive molecule improve the antiwear ability. We also found that molecular connectivity indices are good descriptors of 2D BRNN–QSTR models.
Analysis of local ice crystal growth in snow
Authors: KROL QUIRINE , LÖWE HENNING 
Published: March 2016

ABSTRACTThe structural evolution of snow under metamorphism is one of the key challenges in snow modeling. The main driving forces for metamorphism are curvature differences and temperature gradients, inducing water vapor transport and corresponding crystal growth, which is detectable by the motion of the ice/air interface. To provide quantitative means for a microscopic validation of metamorphism models, a VTK-based image analysis method is developed to track the ice/air interface in time-lapseμCT experiments to measure local interface velocities under both, isothermal and temperature gradient conditions. Using estimates of local temperatures from microstructure-based finite element simulations, a quantitative comparison of measured interface velocities with theoretical expressions is facilitated. For isothermal metamorphism, the data are compared with a kinetics and a diffusion limited growth law. In both cases the data are largely scattered but consistently show a mean curvature dependency of the interface velocity. For temperature gradient metamorphism, we confirm that the main contribution stems from the temperature gradient induced vapor flux, accompanied by effects of mean curvature as a secondary process. The scatter and uncertainties are discussed in view of the present theoretical understanding, the experimental setup and complications such as mechanical deformations.