bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organization of the nitrergic neuronal system in the primitive bony fishesPolypterus senegalusandErpetoichthys calabaricus(Actinopterygii: Cladistia)
Authors: López Jesús M. , Lozano Daniel , Morona Ruth , González Agustín 
Published: October 2015

ABSTRACTCladistians are a group of basal actinopterygian fishes that constitute a good model for studying primitive brain features, most likely present in the ancestral bony fishes. The analysis of the nitrergic neurons (with the enzyme nitric oxide synthase; NOS) has helped in understanding important aspects of brain organization in all vertebrates studied. We investigated the nitrergic system of two cladistian species by means of specific antibodies against NOS and NADPH‐diaphorase (NADPH‐d) histochemistry, which, with the exception of the primary olfactory and terminal nerve fibers, labeled only for NADPH‐d, yielded identical results. Double immunohistochemistry was conducted for simultaneous detection of NOS with tyrosine hydroxylase, choline acetyltransferase, calbindin, calretinin, and serotonin, to establish accurately the localization of the nitrergic neurons and fibers and to assess possible interactions between these neuroactive substances. The pattern of distribution in both species showed only subtle differences in the density of labeled cells. Distinct groups of NOS‐immunoreactive cells were observed in pallial and subpallial areas, paraventricular region, tuberal and retromammillary hypothalamic areas, posterior tubercle, prethalamic and thalamic areas, optic tectum, torus semicircularis, mesencephalic tegmentum, interpeduncular nucleus, superior and middle reticular nuclei, magnocellular vestibular nucleus, solitary tract nucleus, nucleus medianus magnocellularis, the spinal cord and amacrine cells in the retina. Large neurons in cranial nerve sensory ganglia were also labeled. The comparison of these results with those from other vertebrates, using a neuromeric analysis, reveals a conserved pattern of organization of the nitrergic system from this primitive fish group to amniotes, including mammals. J. Comp. Neurol. 524:1770–1804, 2016. © 2015 Wiley Periodicals, Inc.
Sex differences in the photoperiodic regulation of RF‐Amide related peptide (RFRP) and its receptor GPR147 in the syrian hamster
Authors: Henningsen Jo B. , Poirel Vincent‐Joseph , Mikkelsen Jens D. , Tsutsui Kazuyoshi , Simonneaux Valérie , Gauer François 
Published: October 2015

ABSTRACTRF‐(Arg‐Phe) related peptides (RFRP‐1 and ‐3) are considered to play a role in the seasonal regulation of reproduction; however, the effect of the peptides depends on species and gender. This study aimed at comparing the RFRP system in male and female Syrian hamsters over long and short photoperiods to investigate the neuroanatomical basis of these differential effects. The neuroanatomical distribution of RFRP neurons and fibers, revealed using an antiserum recognizing RFRP‐1 and ‐3, as well as GPR147 mRNA, are similar in male and female Syrian hamsters. RFRP neurons are mainly found in the medial hypothalamus, whereas RFRP projections and GPR147 mRNA are observed in the preoptic area, anteroventral–periventricular nucleus, suprachiasmatic nucleus, paraventricular nucleus, bed nucleus of the stria terminalis, ventromedial hypothalamus, habenular nucleus, and arcuate nucleus. The number of RFRP neurons is higher in females than in males, and in both sexes, the number of RFRP neurons is reduced in short photoperiods. GPR147 mRNA levels are higher in females than in males and are downregulated in short photoperiods, particularly in females. Interestingly, the number of RFRP‐positive fibers in the anteroventral–periventricular nucleus is higher only in females adjusted to a short photoperiod. Our results suggest that the RFRP system, which is strongly regulated by photoperiod in both male and female Syrian hamsters, is particularly important in females, with a distinct role in the anteroventral–periventricular nucleus, possibly in the regulation of the preovulatory luteinizing hormone surge via kisspeptin neurons. J. Comp. Neurol. 524:1825–1838, 2016. © 2015 Wiley Periodicals, Inc.
Parallel construction of classification trees on a GPU
Authors: Strnad D. , Nerat A. 
Published: October 2015

SummaryAlgorithms for constructing tree‐based classifiers are aimed at building an optimal set of rules implicitly described by some dataset of training samples. As the number of samples and/or attributes in the dataset increases, the required construction time becomes the limiting factor for interactive or even functional use. The problem is emphasized if tree derivation is part of an iterative optimization method, such as boosting. Attempts to parallelize the construction of classification trees have therefore been presented in the past. This paper describes a parallel method for binary classification tree construction implemented on a graphics processing unit (GPU) using compute unified device architecture (CUDA). By employing node‐level, attribute‐level, and split‐level parallelism, the task parallel and data parallel sections of tree induction are mapped to the architecture of a modern GPU. The GPU‐based solution is compared with the sequential and multi‐threaded CPU versions on public access datasets, and it is shown that an order of magnitude acceleration can be achieved on this data‐intensive task using inexpensive commodity hardware. The influence of dataset characteristics on the efficiency of parallel implementation is also analyzed. Copyright © 2015 John Wiley & Sons, Ltd.
GSoC 2015 student contributions to GenApp and Airavata
Authors: Brookes Emre H. , Kapoor Abhishek , Patra Priyanshu , Marru Suresh , Singh Raminder , Pierce Marlon 
Published: October 2015

SummaryGenApp generates applications on an extensible set of target languages for scientific modules. GenApp utilizes JavaScript object notation (JSON) format for all definition files. To create an application, definition files are created for global directives, menu, and modules. Target languages have definition files detailing the steps‐mapping code fragments to output. Modules must be wrapped to accept and produce JSON as defined in the module's definition file. Execution models are not defined by GenApp; they are included in target language code fragments. Previously, GenApp included target languages of HTML5/PHP, Qt3/C++, and Qt4/C++ with execution models of direct local execution, a web server, or a web server accessible resource. A Google Summer of Code (GSoC) 2014 student demonstrated Airavata‐managed execution in GenApp's current target languages. Subsequently, Airavata's API and GenApp have evolved. Two GSoC‐2015 students updated the previous Airavata integration to support the current API and extend target languages to include Qt5/C++, Qt5/Android, and Java. GenApp was initially developed to wrap modules utilized in the small angles scattering field but is not restricted to this discipline. The GenApp philosophy is to minimize effort of the researcher to deploy modules and insure preservation in an evolving software landscape. Generated applications are in production and used by small angle scattering researchers. Copyright © 2015 John Wiley & Sons, Ltd.
The twisted crossed cube
Authors: Wang Xinyang , Liang Jiarong , Qi Deyu , Lin Weiwei 
Published: October 2015

SummaryThe topology of interconnection networks plays an important role in the performance of parallel and distributed computing systems. In this paper, we propose a new interconnection network called twisted crossed cube (TCQn) and investigate its basic network properties in terms of the regularity, connectivity, fault tolerance, recursiveness, hamiltonicity and ability to simulate other architectures, and so on. Then, we develop an effective routing algorithm Route (u, v) for TCQn that takes no more than d(u, v) + 1 steps for any two nodes (u, v) to communicate with each other, and the routing process shows that the diameter, wide diameter, and fault‐tolerant diameter of TCQn are about half of the corresponding diameters of the equivalent hypercube with the same dimension. In the end, by combining TCQn with crossed cube (CQn), we propose a preferable dynamic network structure, that is, the dynamic crossed cube, which has the same network diameter as TCQn/CQn and better properties in other respects, for example, its connection complexity is half of that of TCQn/CQn when the network scale is large enough, and the number of its average routing steps is also much smaller than that in TCQn/CQn. Copyright © 2015 John Wiley & Sons, Ltd.
Netrin‐1 induces local translation of down syndrome cell adhesion molecule in axonal growth cones
Authors: Jain Shruti , Welshhans Kristy 
Published: October 2015

ABSTRACTDown syndrome cell adhesion molecule (DSCAM) plays an important role in many neurodevelopmental processes such as axon guidance, dendrite arborization, and synapse formation. DSCAM is located in the Down syndrome trisomic region of human chromosome 21 and may contribute to the Down syndrome brain phenotype, which includes a reduction in the formation of long‐distance connectivity. The local translation of a select group of mRNA transcripts within growth cones is necessary for the formation of appropriate neuronal connectivity. Interestingly, we have found thatDscammRNA is localized to growth cones of mouse hippocampal neurons, and is dynamically regulated in response to the axon guidance molecule, netrin‐1. Furthermore, netrin‐1 stimulation results in an increase in locally translated DSCAM protein in growth cones. Deleted in colorectal cancer (DCC), a netrin‐1 receptor, is required for the netrin‐1‐induced increase inDscammRNA local translation. We also find that two RNA‐binding proteins—fragile X mental retardation protein (FMRP) and cytoplasmic polyadenylation element binding protein (CPEB)—colocalize withDscammRNA in growth cones, suggesting their regulation ofDscammRNA localization and translation. Finally, overexpression of DSCAM in mouse cortical neurons results in a severe stunting of axon outgrowth and branching, suggesting that an increase in DSCAM protein results in a structural change having functional consequences. Taken together, these results suggest that netrin‐1‐induced local translation ofDscammRNA during embryonic development may be an important mechanism to regulate axon growth and guidance in the developing nervous system. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 76: 799–816, 2016
Dendritic‐cell expression of Ship1 regulates Th2 immunity to helminth infection in mice
Authors: Gold Matthew J. , Antignano Frann , Hughes Michael R. , Zaph Colby , McNagny Kelly M. 
Published: October 2015

In mouse models of infection with the gastrointestinal parasite Trichuris muris, appropriate dendritic‐cell (DC) Ag sampling, migration, and presentation to T cells are necessary to mount a protective Th2‐polarized adaptive immune response, which is needed to clear infection. SH2‐containing inositol 5′‐phosphatase 1 (SHIP‐1) has been shown to be an important regulator of DC function in vitro through the negative regulation of the phosphoinositide 3‐kinase (PI3K) pathway, but its role in vivo is relatively unexplored. In the current work, mice with a specific deletion of SHIP‐1 in DCs (Ship1ΔDC) were infected with the parasite T. muris. Ship1ΔDC mice were susceptible to infection due to ineffective priming of Th2‐polarized responses. This is likely due to an increased production of interleukin (IL) 12p40 by SHIP‐1‐deficient DCs, as in vivo antibody blockade of IL‐12p40 was able to facilitate the clearing of infection in Ship1ΔDC mice. Our results describe a critical role for SHIP‐1 in regulating the ability of DCs to efficiently prime Th2‐type responses.
Changes in T‐cell subsets identify responders to FcR‐nonbinding anti‐CD3 mAb (teplizumab) in patients with type 1 diabetes
Authors: Tooley James E. , Vudattu Nalini , Choi Jinmyung , Cotsapas Chris , Devine Lesley , Raddassi Khadir , Ehlers Mario R. , McNamara James G. , Harris Kristina M. , Kanaparthi Sai , Phippard Deborah , Herold Kevan C. 
Published: October 2015

The mechanisms whereby immune therapies affect progression of type 1 diabetes (T1D) are not well understood. Teplizumab, an FcR nonbinding anti‐CD3 mAb, has shown efficacy in multiple randomized clinical trials. We previously reported an increase in the frequency of circulating CD8+ central memory (CD8CM) T cells in clinical responders, but the generalizability of this finding and the molecular effects of teplizumab on these T cells have not been evaluated. We analyzed data from two randomized clinical studies of teplizumab in patients with new‐ and recent‐onset T1D. At the conclusion of therapy, clinical responders showed a significant reduction in circulating CD4+ effector memory T cells. Afterward, there was an increase in the frequency and absolute number of CD8CM T cells. In vitro, teplizumab expanded CD8CM T cells by proliferation and conversion of non‐CM T cells. Nanostring analysis of gene expression of CD8CM T cells from responders and nonresponders versus placebo‐treated control subjects identified decreases in expression of genes associated with immune activation and increases in expression of genes associated with T‐cell differentiation and regulation. We conclude that CD8CM T cells with decreased activation and regulatory gene expression are associated with clinical responses to teplizumab in patients with T1D.
Whole brain fiber‐based comparison (FBC)—A tool for diffusion tensor imaging‐based cohort studies
Authors: Zimmerman‐Moreno Gali , Ben Bashat Dafna , Artzi Moran , Nefussy Beatrice , Drory Vivian , Aizenstein Orna , Greenspan Hayit 
Published: October 2015

AbstractWe present a novel method for fiber‐based comparison of diffusion tensor imaging (DTI) scans of groups of subjects. The method entails initial preprocessing and fiber reconstruction by tractography of each brain in its native coordinate system. Several diffusion parameters are sampled along each fiber and used in subsequent comparisons. A spatial correspondence between subjects is established based on geometric similarity between fibers in a template set (several choices for template are explored), and fibers in all other subjects. Diffusion parameters between groups are compared statistically for each template fiber. Results are presented at single fiber resolution. As an initial exploratory step in neurological population studies this method points to the locations affected by the pathology of interest, without requiring a hypothesis. It does not make any grouping assumptions on the fibers and no manual intervention is needed. The framework was applied here to 18 healthy subjects and 23 amyotrophic lateral sclerosis (ALS) patients. The results are compatible with previous findings and with the tract based spatial statistics (TBSS) method. Hum Brain Mapp 37:477–490, 2016. © 2015 Wiley Periodicals, Inc.
Efficient generation of endothelial cells from human pluripotent stem cells and characterization of their functional properties
Authors: Song Wei , Kaufman Dan S. , Shen Wei 
Published: October 2015

AbstractAlthough endothelial cells (ECs) have been derived from human pluripotent stem cells (hPSCs), large‐scale generation of hPSC‐ECs remains challenging and their functions are not well characterized. Here we report a simple and efficient three‐stage method that allows generation of approximately 98 and 9500 ECs on day 16 and day 34, respectively, from each human embryonic stem cell (hESC) input. The functional properties of hESC‐ECs derived in the presence and absence of a TGFβ‐inhibitory molecule SB431542 were characterized and compared with those of human umbilical vein endothelial cells (HUVECs). Confluent monolayers formed by SB431542 + hESC‐ECs, SB431542‐hESC‐ECs, and HUVECs showed similar permeability to 10,000 Da dextran, but these cells exhibited striking differences in forming tube‐like structures in 3D fibrin gels. The SB431542 + hESC‐ECs were most potent in forming tube‐like structures regardless of whether VEGF and bFGF were present in the medium; less potent SB431542‐hESC‐ECs and HUVECs responded differently to VEGF and bFGF, which significantly enhanced the ability of HUVECs to form tube‐like structures but had little impact on SB431542‐hESC‐ECs. This study offers an efficient approach to large‐scale hPSC‐EC production and suggests that the phenotypes and functions of hPSC‐ECs derived under different conditions need to be thoroughly examined before their use in technology development. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 678–687, 2016.
Cellulose‐based porous scaffold for bone tissue engineering applications: Assessment of hMSC proliferation and differentiation
Authors: Demitri Christian , Raucci Maria Grazia , Giuri Antonella , De Benedictis Vincenzo Maria , Giugliano Daniela , Calcagnile Paola , Sannino Alessandro , Ambrosio Luigi 
Published: October 2015

AbstractPhysical foaming combined with microwave‐induced curing was used in this study to develop an innovative device for bone tissue regeneration. In the first step of the process, a stable physical foaming was induced using a surfactant (i.e. pluronic) as blowing agent of a homogeneous blend of Sodium salt of carboxymethylcellulose (CMCNa) and polyethylene glycol diacrylate (PEGDA700) solution. In the second step, the porous structure of the scaffold was chemically stabilized by radical polymerization induced by a homogeneous rapid heating of the sample in a microwave reactor. In this step 2,2‐Azobis[2‐(2‐imidazolin‐2 yl)propane]Dihydrochloride was used as thermoinitiator (TI). CMCNa and PEGDA were mixed with different blends to correlate the properties of final product with the composition. The chemical properties of each sample were evaluated by spectroscopy analysis ATR‐IR (before and after curing) in order to maximize reaction yield, and optimize kinetic parameters (i.e. time curing, microwave power). The stability of the materials was evaluated in vitro by degradation test in Phosphate Buffered Saline. Biological analyses were performed to evaluate the effect of scaffold materials on cellular behavior in terms of proliferation and early osteogenic differentiation of human Mesenchymal Stem Cells. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 726–733, 2016.
A facile method to compare EFTEM maps obtained from materials changing composition over time
Authors: Casu Alberto , Genovese Alessandro , Di Benedetto Cristiano , Lentijo Mozo Sergio , Sogne Elisa , Zuddas Efisio , Falqui Andrea 
Published: October 2015

ABSTRACTEnergy Filtered Transmission Electron Microscopy (EFTEM) is an analytical tool that has been successfully and widely employed in the last two decades for obtaining fast elemental maps in TEM mode. Several studies and efforts have been addressed to investigate limitations and advantages of such technique, as well as to improve the spatial resolution of compositional maps. Usually, EFTEM maps undergo post‐acquisition treatments by changing brightness and contrast levels, either via dedicated software or via human elaboration, in order to maximize their signal‐to‐noise ratio and render them as visible as possible. However, elemental maps forming a single set of EFTEM images are usually subjected to independent map‐by‐map image treatment. This post‐acquisition step becomes crucial when analyzing materials that change composition over time as a consequence of an external stimulus, because the map‐by‐map approach doesn't take into account how the chemical features of the imaged materials actually progress, in particular when the investigated elements exhibit very low signals. In this article, we present a facile procedure applicable to whole sets of EFTEM maps acquired on a sample that is evolving over time. The main aim is to find a common method to treat the images features, in order to make them as comparable as possible without affecting the information there contained. Microsc. Res. Tech. 78:1090–1097, 2015. © 2015 Wiley Periodicals, Inc.
Dynamics of Biopolymers: Role of Hydration and Electrostatic Interactions
Authors: Roh Joon Ho 
Published: October 2015

This contribution highlights the recently developed microscopic picture of the effects of hydration and electrostatic interactions on subnanosecond dynamics of biopolymers protein and ribonucleic acid (RNA), studied by quasielastic neutron scattering spectroscopy. In contrast to the traditional concept of water‐slaved dynamics, more detailed analysis of the dynamics of different chemical structures (lysozyme vs transfer RNA; electrostatically unscreened vs screened) demonstrates that chemical and physical responses of biopolymers to hydration and charge screening determine the dynamic interactions. How the relationship of the dynamical flexibility and structural stability varies depending on water‐driven or charge screening‐driven folding into biologically active structures has also been discussed. However, the biological relevance of the fast conformational dynamics still remains elusive. Exploring the dynamic heterogeneity of biopolymers is proposed as a potential approach to the identification of biologically important dynamics.
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The effects of omega‐3 polyunsaturated fatty acids and genetic variants on methylation levels of the interleukin‐6 gene promoter
Authors: Ma Yiyi , Smith Caren E. , Lai Chao‐Qiang , Irvin Marguerite R. , Parnell Laurence D. , Lee Yu‐Chi , Pham Lucia D. , Aslibekyan Stella , Claas Steven A. , Tsai Michael Y. , Borecki Ingrid B. , Kabagambe Edmond K. , Ordovás José M. , Absher Devin M. , Arnett Donna K. 
Published: October 2015

ScopeOmega‐3 PUFAs (n‐3 PUFAs) reduce IL‐6 gene expression, but their effects on transcription regulatory mechanisms are unknown. We aimed to conduct an integrated analysis with both population and in vitro studies to systematically explore the relationships among n‐3 PUFA, DNA methylation, single nucleotide polymorphisms (SNPs), gene expression, and protein concentration of IL6.Methods and resultsUsing data in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study and the Encyclopedia of DNA Elements (ENCODE) consortium, we found that higher methylation of IL6 promoter cg01770232 was associated with higher IL‐6 plasma concentration (p = 0.03) and greater IL6 gene expression (p = 0.0005). Higher circulating total n‐3 PUFA was associated with lower cg01770232 methylation (p = 0.007) and lower IL‐6 concentration (p = 0.02). Moreover, an allele of IL6 rs2961298 was associated with higher cg01770232 methylation (p = 2.55 × 10−7). The association between n‐3 PUFA and cg01770232 methylation was dependent on rs2961298 genotype (p = 0.02), but higher total n‐3 PUFA was associated with lower cg01770232 methylation in the heterozygotes (p = 0.04) not in the homozygotes.ConclusionHigher n‐3 PUFA is associated with lower methylation at IL6 promoter, which may be modified by IL6 SNPs.