bluuebunny/crossref_metadata_2025_split huggingface dataset:
Postnatal changes in the distribution and density of neuronal nuclei and doublecortin antigens in domestic chicks (Gallus domesticus)
Authors: Mezey Szilvia , Krivokuca Dragan , Bálint Eszter , Adorján András , Zachar Gergely , Csillag András 
Published: June 2011

AbstractTo understand better the rate of neurogenesis and the distribution of new neurons in posthatch domestic chicks, we describe and compare the expression of the neuronal nuclei protein (NeuN, a.k.a. Fox‐3) and doublecortin antigens in the whole brain of chicks 2 days, 8 days, and 14 weeks posthatch. In the forebrain ventricular and paraventricular zones, the density of bromodeoxyuridine‐, NeuN‐, and doublecortin‐labeled cells was compared between chicks 24 hours and 7 days after an injection of bromodeoxyuridine (2 and 8 days posthatch, respectively). The distribution of NeuN‐labeled neurons was similar to Nissl‐stained tissue, with the exception of some areas where neurons did not express NeuN: cerebellar Purkinje cells and olfactory bulb mitral cells. The ventral tegmental area of 2‐day‐old chicks was also faintly labeled. The distribution of doublecortin was similar at all timepoints, with doublecortin‐labeled profiles located throughout all forebrain areas as well as in the cerebellar granule cell layer. However, doublecortin labeling was not detectable in any midbrain or brainstem areas. Our data indicate that a significant number of new neurons is still formed in the telencephalon of posthatch domestic chicks, whereas subtelencephalic areas (except for the cerebellum) finish their neuronal expansion before hatching. Most newly formed cells in chicks leave the paraventricular zone after hatching, but a pool of neurons stays in the vicinity of the ventricular zone and matures in situ within 7 days. Proliferating cells often migrate laterally along forebrain laminae into still‐developing brain areas. J. Comp. Neurol., 2012. © 2011 Wiley Periodicals, Inc.
Device level communication libraries for high‐performance computing in Java
Authors: Taboada Guillermo L. , Touriño Juan , Doallo Ramón , Shafi Aamir , Baker Mark , Carpenter Bryan 
Published: June 2011

SUMMARYSince its release, the Java programming language has attracted considerable attention from the high‐performance computing (HPC) community because of its portability, high programming productivity, and built‐in multithreading and networking support. As a consequence, several initiatives have been taken to develop a high‐performance Java message‐passing library to program distributed memory architectures, such as clusters. The performance of Java message‐passing applications relies heavily on the communications performance. Thus, the design and implementation of low‐level communication devices that support message‐passing libraries is an important research issue in Java for HPC. MPJ Express is our Java message‐passing implementation for developing high‐performance parallel Java applications. Its public release currently contains three communication devices: the first one is built using the Java New Input/Output (NIO) package for the TCP/IP; the second one is specifically designed for the Myrinet Express library on Myrinet; and the third one supports thread‐based shared memory communications. Although these devices have been successfully deployed in many production environments, previous performance evaluations of MPJ Express suggest that the buffering layer, tightly coupled with these devices, incurs a certain degree of copying overhead, which represents one of the main performance penalties. This paper presents a more efficient Java message‐passing communications device, based on Java Input/Output sockets, that avoids this buffering overhead. Moreover, this device implements several strategies, both in the communication protocol and in the HPC hardware support, which optimizes Java message‐passing communications. In order to evaluate its benefits, this paper analyzes the performance of this device comparatively with other Java and native message‐passing libraries on various high‐speed networks, such as Gigabit Ethernet, Scalable Coherent Interface, Myrinet, and InfiniBand, as well as on a shared memory multicore scenario. The reported communication overhead reduction encourages the upcoming incorporation of this device in MPJ Express (http://mpj‐express.org). Copyright © 2011 John Wiley & Sons, Ltd.
Comparison of segmentation algorithms for fluorescence microscopy images of cells
Authors: Dima Alden A. , Elliott John T. , Filliben James J. , Halter Michael , Peskin Adele , Bernal Javier , Kociolek Marcin , Brady Mary C. , Tang Hai C. , Plant Anne L. 
Published: June 2011

AbstractThe analysis of fluorescence microscopy of cells often requires the determination of cell edges. This is typically done using segmentation techniques that separate the cell objects in an image from the surrounding background. This study compares segmentation results from nine different segmentation techniques applied to two different cell lines and five different sets of imaging conditions. Significant variability in the results of segmentation was observed that was due solely to differences in imaging conditions or applications of different algorithms. We quantified and compared the results with a novel bivariate similarity index metric that evaluates the degree of underestimating or overestimating a cell object. The results show that commonly used threshold‐based segmentation techniques are less accurate than k‐means clustering with multiple clusters. Segmentation accuracy varies with imaging conditions that determine the sharpness of cell edges and with geometric features of a cell. Based on this observation, we propose a method that quantifies cell edge character to provide an estimate of how accurately an algorithm will perform. The results of this study will assist the development of criteria for evaluating interlaboratory comparability. Published 2011 Wiley‐Liss, Inc.
The role of glutamate in my professional life: From molecular neuroplasticity to the relief of suffering
Authors: Irwin Scott A. 
Published: June 2011

AbstractThis invited address is offered in celebration of the career of Dr. William T. Greenough, especially the mentorship aspect of this illustrious career. It details how glutamate has been a thread throughout my professional career, including in my training with Bill. Our investigations of the role of metabotropic glutamate receptors in synaptic plasticity, specifically in relation to the fragile‐X mental retardation protein, are described. I then discuss how glutamate has played a role in my current professional life as a psychiatrist working in palliative care. Finally, I end with some words about how the training I received from Bill has had, and continues to have, an impact on my professional development. © 2011 Wiley Periodicals, Inc. Dev Psychobiol 53:482–488, 2011.
Evidence that angiogenesis lags behind neuron and astrocyte growth in experience‐dependent plasticity
Authors: Wallace Christopher S. , Withers Ginger S. , Farnand Alex , Lobingier Braden T. , McCleery Ellen J. 
Published: June 2011

AbstractBill Greenough's work on the cell biology of information storage suggests that we cannot understand the mechanism of long‐term memory without understanding the series of cellular transactions that drive coordinated structural changes in neurons, glia, and blood vessels. Here, we show that after 4 days of differential housing, neuropil of EC cortex has expanded significantly, but the vasculature has not, resulting in a dilution of the blood supply. Significant growth of neurons and astrocytes has been reported within this time period, suggesting expression of synaptic plasticity might involve temporally coordinated genomic responses by both neurons and glia. Given that astrocytes appear to couple neuronal and vascular growth during development, we hypothesize that they may also mediate the onset of angiogenesis in response to neural demand in the EC brain. Further, these results may imply that a neuron's capacity for plasticity could be constrained by the rate of vascular expansion. © 2011 Wiley Periodicals, Inc. Dev Psychobiol 53:435–442, 2011.
In vitro approaches to studying the metabolism of new psychoactive compounds
Authors: Peters Frank T. , Meyer Markus R. 
Published: June 2011

AbstractIn the last two decades, a large number of new drugs from several drug classes have appeared on the illicit drug market. While some of these compounds have meanwhile been scheduled as controlled substances, the majority of them are (still) sold as so‐called ‘legal highs’, mostly via the Internet. At the time they appear on the market the metabolism of these drugs is generally unknown. Therefore, it must be studied in order to obtain data necessary for analytical method development as well as toxicological risk assessment. In vitro metabolism studies of new designer drugs can be performed for identification and structure elucidation of new designer drug metabolites or to assess the qualitative and quantitative involvement of certain enzymes in the metabolism of a particular drug. In this review, the value of the following enzyme preparations for in vitro metabolism studies of new designer drugs will be discussed: liver microsomes, recombinant cDNA‐expressed enzymes, liver cytosol, S9 mix, and hepatocytes. This will cover the major metabolic enzymes: cytochrome P450 monooxygenases, flavin‐monooxygenases, monoamine oxidases, UDP‐glucuronyltransferases, sulfotransferases, and catechol‐O‐methyltransferases. Important analytical aspects such as the value of mass spectrometric techniques will also be covered. Copyright © 2011 John Wiley & Sons, Ltd.
Alkali‐like myosin light chain‐1 (myl1) is an early marker for differentiating fast muscle cells in zebrafish
Authors: Burguière A. C. , Nord H. , von Hofsten J. 
Published: June 2011

AbstractDuring myogenesis, muscle precursors become divided into either fast‐ or slow‐twitch fibres, which in the zebrafish occupy distinct domains in the embryo. Genes encoding sarcomeric proteins specific for fast or slow fibres are frequently used as lineage markers. In an attempt to identify and evaluate early definitive markers for cells in the fast‐twitch pathway, we analysed genes encoding proteins contributing to the fast sarcomeric structures. The previously uncharacterized zebrafish alkali‐like myosin light chain gene (myl1) was found to be expressed exclusively in cells in the fast‐twitch pathway initiated at an early stage of fast fibre differentiation. Myl1 was expressed earlier, and in a more fibre type restricted manner, than any of the previously described and frequently used fast myosin light and heavy chain and troponin muscle markers mylz2, mylz3, tnni2, tnnt3a, fMyHC1.3. In summary, this study introduces a novel marker for early differentiating fast muscle cells. Developmental Dynamics 240:1856–1863, 2011. © 2011 Wiley‐Liss, Inc.
The Prx1 limb enhancers: Targeted gene expression in developing zebrafish pectoral fins
Authors: Hernández‐Vega Amayra , Minguillón Carolina 
Published: June 2011

AbstractLimbs represent an excellent model to study the induction, growth, and patterning of several organs. A breakthrough to study gene function in various tissues has been the characterization of regulatory elements that allow tissue‐specific interference of gene function. The mouse Prx1 promoter has been used to generate limb‐specific mutants and overexpress genes in tetrapod limbs. Although zebrafish possess advantages that favor their use to study limb morphogenesis, there is no driver described suitable for specifically interfering with gene function in developing fins. We report the generation of zebrafish lines that express enhanced green fluorescent protein (EGFP) driven by the mouse Prx1 enhancer in developing pectoral fins. We also describe the expression pattern of the zebrafish prrx1 genes and identify three conserved non‐coding elements (CNEs) that we use to generate fin‐specific EGFP reporter lines. Finally, we show that the mouse and zebrafish regulatory elements may be used to modify gene function in pectoral fins. Developmental Dynamics 240:1977–1988, 2011. © 2011 Wiley‐Liss, Inc.
Does the European Pollutant Release and Transfer Register Enable Us to Understand the Environmental Performance of Firms?
Authors: Fikru Mahelet Getachew 
Published: June 2011

ABSTRACTThe study explores a new micro environmental data set, the European Pollutant Release and Transfer Register (E‐PRTR), by identifying limitations and potential strengths. We find that reporting requirements exclude on‐site abatement through end‐of‐the‐pipe techniques and cleaner technologies causing underestimation of firms' actual abatement. In addition, the lack of a mandatory section on production volume and firm size hinders data normalization and the use of control variables in economic analysis. Addressing the above limitations can make the E‐PRTR more usable for policy‐makers, environmentalists and academicians. Furthermore, the paper proposes a normalization procedure based on calculating how much beyond the threshold a firm has abated or emitted; and normalized values are used to approximate the environmental performance of firms. Analysis based on a sample of manufacturing firms suggests that industrial facilities in Europe have performed well in terms of abating a higher percentage of their gross pollution. Copyright © 2011 John Wiley & Sons, Ltd and ERP Environment.
Interleukin‐17‐educated monocytes suppress cytotoxic T‐cell function through B7‐H1 in hepatocellular carcinoma patients
Authors: Zhao Qiyi , Xiao Xiao , Wu Yan , Wei Yi , Zhu Ling‐Yan , Zhou Jia , Kuang Dong‐Ming 
Published: June 2011

AbstractSubstantial evidence indicates that inflammation is a critical component of tumor progression. The proinflammatory IL‐17‐producing cells have recently been detected in tumors, but the effect of IL‐17 on antigen‐presenting cells in tumors is presently unknown. We recently found that B7‐H1+ macrophages (Mφs) were enriched predominantly in the peritumoral stroma of hepatocellular carcinomas (HCCs). Here, we found a positive correlation between IL‐17‐producing cells and B7‐H1‐expressing Mφs in the same area. The B7‐H1+ monocytes/Mφs from HCC tissues expressed significantly more HLA‐DR, CD80, and CD86 than B7‐H1– cells. Accordingly, IL‐17 could activate monocytes to express B7‐H1 in a dose‐dependent manner. Although culture supernatants derived from hepatoma cells also induced B7‐H1 expression on monocytes, IL‐17 additionally increased hepatoma‐mediated B7‐H1 expression. Autocrine inflammatory cytokines released from IL‐17‐activated monocytes stimulated B7‐H1 expression. Moreover, these IL‐17‐exposed monocytes effectively suppressed cytotoxic T‐cell immunity in vitro; the effect could be reversed by blocking B7‐H1 on those monocytes. Consistent with this, cytotoxic T cells from HCC tissues expressed significant B7‐H1 receptor programmed death 1 (PD‐1) and exhibited an exhausted phenotype. These data reveal a fine‐tuned collaborative action between different stromal cells to counteract T‐cell responses in tumors. Such IL‐17‐mediated immune tolerance should be considered for the rational design of effective immune‐based anti‐cancer therapies.
Alternate pathways for Bcl6‐mediated regulation of B cell to plasma cell differentiation
Authors: Alinikula Jukka , Nera Kalle‐Pekka , Junttila Sini , Lassila Olli 
Published: June 2011

AbstractThe transcription factor Bcl6 regulates germinal center formation and differentiation of B cells into high‐affinity antibody‐producing plasma cells. The direct double‐negative regulatory circuit between Bcl6 and Blimp‐1 is well established. We now reveal alternative mechanisms for Bcl6‐mediated regulation of B‐cell differentiation to plasma cells and show with DT40 cells that Bcl6 directly promotes the expression of Bach2, a known suppressor of Blimp‐1. Moreover, Bcl6 suppresses Blimp‐1 expression through direct binding to the IRF4 gene, as well as by promoting the expression of MITF, a known suppressor of IRF4. We also provide evidence that Bcl6 is needed for the expression of AID and UNG, the indispensable proteins for somatic hypermutation and class‐switch recombination, and UNG appears to be a direct Bcl6 target. Our findings reveal a complex regulatory network in which Bcl6 acts as a key element dictating the transition of DT40 B cells to plasma cells.
Characterization of cocoa butter substitutes, milk fat and cocoa butter mixtures
Authors: Wang Fengyan , Liu Yuanfa , Jin Qingzhe , Meng Zong , Wang Xingguo 
Published: June 2011

AbstractThe melting properties and polymorphic behavior of binary and ternary blends of cocoa butter substitutes (CBS), cocoa butter (CB), and milk fat (MF) were studied by using pulsed nuclear magnetic resonance (NMR), differential scanning calorimetry (DSC), and X‐ray diffractometry (XRD). Hydrogenated palm kernel stearin (HPKS) and hydrogenated palm kernel olein (HPKO) were chosen as the two CBS feedstock fats. Both CBS/CB binary blends displayed significant eutectic behaviors. Multiple melting peaks and eutectic effects were observed at 30–50% addition levels of CB to HPKS. The range was broader in HPKO/CB blends. Dilution effect was observed in both CBS/MF blends while slight monotectic effect was also observed in HPKO/MF blends. Ternary phase diagrams and melting curves showed that eutectic effects existed in both ternary blends and the degree of interaction depended on the content of CB and MF. XRD results showed that when pure fat component in each blend exceeded 80%, its polymorphism dominated in the ternary blends. However, when CBS/CB or MF /CB were added at a comparative content (blends D and F), both β and β′ form existed.Practical applications: Phase properties of fat blends may have significant effects on the sensory characteristics and physical properties of the final products, such as hardness, brittleness, and the bloom formation. This study evaluates the melting properties and the polymorphic characteristics of fat blends of constituents with potential use in the manufacture of confectionery products. A comprehensive analysis of binary and ternary fat blends was conducted in order to provide a guide for compound chocolate production formulation.
Effects of microcapsule constitution on the quality of microencapsulated walnut oil
Authors: Calvo Patricia , Castaño Ángel Luis , Hernández María Teresa , González‐Gómez David 
Published: June 2011

AbstractThe encapsulation is a process by which small particles of core products are packaged within a wall material to form microcapsules. One of the most useful processes for drying thermosensitive substances that are unstable in aqueous solutions is the freeze‐drying technique (lyophilization), which involves conversion of liquid oils in the form of an emulsion into dry powders. In this paper, the chemical composition of walnut oil and microencapsulation conditions (microcapsule wall material composition) have been evaluated in order to assess the influence of the microencapsulation process on the quality and shelf‐life of microencapsulated walnut oil. Highest encapsulation yield was achieved when maltodextrin, carboxymethylcellulose, and lecithin were used as encapsulation agents and the ratio of oil–wall material was 1:1.5. Under these conditions all the oil was encapsulated. The presence of protein constituents in the microcapsule wall material extended the shelf‐life of the microencapsulated walnut oil regardless of the use of antioxidant additives.
Predicting the equilibrium bed slope in natural streams using a stochastic model for incipient sediment motion
Authors: Ferro Vito , Porto Paolo 
Published: June 2011

ABSTRACTIn this paper, a method to predict the equilibrium bed slope in natural streams based on the incipient motion criterion is proposed. The method is based on the criterion suggested by Gessler to simulate the grain size distribution of the armour coat using the concept of critical shear stress of a sediment mixture. In particular, a different expression of the probability for a single particle size to be part of the armour coat is firstly proposed; then, a simple two‐steps criterion is suggested to estimate the safety factor required by the proposed approach. The method is applied in three different Italian regions (Calabria, Basilicata, and Tuscany) and required several field campaigns involving the survey of 251 stream reaches upstream of grade‐control structures. The area including five Calabrian streams is firstly used to test the suitability of the two‐steps approach. In this area, considering the detailed information about the particle size of bed material, the effect of using a simplified grain size distribution for each torrent is also checked. The method is then applied within the two additional areas (Basilicata and Tuscany) in order to check the geographic influence on the prediction of the stable longitudinal profile. A comparison between measured and estimated values of the equilibrium bed slope showed a good agreement for the Calabrian streams, where the number of the investigated stream reaches is greater, and satisfactory results for the torrents located in Basilicata and Tuscany where the field data set is more limited. The overall results encourage the extension of the proposed method to additional field data and suggest the use of this approach by hydraulic designers in order to stabilize the longitudinal profile of natural streams. Copyright © 2011 John Wiley & Sons, Ltd.
Interactions of cadmium and zinc impact their toxicity to the earthworm Aporrectodea caliginosa
Authors: Qiu Hao , Vijver Martina G , Peijnenburg Willie J.G.M 
Published: June 2011

Abstract
Individual and binary mixture effects of Cd and Zn on mortality of the earthworm Aporrectodea caliginosa were investigated in one soil type. Mutual, systemic interactions of Cd and Zn were assessed over a broad range of concentration combinations. Exposures were expressed as measured total concentrations in soil, porewater concentrations, and CaCl2-extractable concentrations. The Cd-Zn and Zn-Cd interactions in soil were estimated by comparing partition coefficients (Kd) of one metal in the presence and absence of the second metal. Simple patterns of mixture toxicity (additive, antagonistic, or synergistic) were evaluated by the toxic unit approach. The more complex patterns (dose ratio dependent or dose level dependent) were quantified by the MIXTOX model. The partitioning of Cd and Zn between soil and pore water was affected neither by their concentration nor presence of the other metal, and metal partitioning remained linear at all exposure levels tested. The effect of the Cd and Zn mixtures on mortality of A. caliginosa was mainly antagonistic, and the magnitude of antagonism (1.1– 2.7 toxic units) was dependent upon both the relative concentrations of Cd and Zn and the concentration magnitudes. Interactions of both metals occurred at the organism level and were manifested in terms of effects (28-d median lethal concentrations). The present study highlights the importance of identifying the relative influence of various interactions from external exposure to internal assimilation in evaluating mixture toxicity. Environ. Toxicol. Chem. 2011;30:2084–2093. © 2011 SETAC