bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimized sample preparation for isotopic analyses of CO2 in air: systematic study of precision and accuracy dependence on driving variables during CO2 purification process
Authors: Bertolini T. , Rubino M. , Lubritto C. , D'Onofrio A. , Marzaioli F. , Passariello I. , Terrasi F. 
Published: July 2005

AbstractA systematic analysis of efficiency, reproducibility and accuracy of cryogenic purification of CO2 from air samples for isotopic analyses is presented. The technical characteristics of the cryogenic line are given in detail. To study the cryogenic process, three different operating parameters are considered: flow rate of the gas entering the line, pressure of the gas in the line, and CO2‐trap shape. Experimental results demonstrate that efficiency, reproducibility and accuracy strongly depend on the CO2trap shape. Moreover, a dependence of reproducibility and accuracy on the flow rate of the gas is found, but not on its pressure. High precision (≤0.02‰ for δ13C and ≤0.05‰ for δ18O) and good accuracy (<0.09‰ for δ13C and <0.14‰ for δ18O) is achieved after applying the N2O correction. Copyright © 2005 John Wiley & Sons, Ltd.
Loss of dopaminergic neurons by the induction of inducible nitric oxide synthase and cyclooxygenase‐2 via CD40: Relevance to Parkinson's disease
Authors: Okuno Tatsusada , Nakatsuji Yuji , Kumanogoh Atsushi , Moriya Masayuki , Ichinose Hiroshi , Sumi Hisae , Fujimura Harutoshi , Kikutani Hitoshi , Sakoda Saburo 
Published: July 2005

AbstractA glial reaction associated with up‐regulation of inflammatory molecules has been suggested to play an important role in dopaminergic neuron loss in Parkinson's disease (PD). Among inflammatory molecules, inducible nitric oxide synthase (iNOS) and cyclooxygenase‐2 (COX‐2) have been focused upon as key factors in the pathogenesis. However, the mechanism of how these molecules are induced in PD brains is not clearly understood. We focused on CD40, which is expressed on neural cells and could be implicated in the neuroinflammation by inducing inflammatory molecules. We showed that both iNOS and COX‐2 were up‐regulated in microglia and astrocytes by CD40 stimulation in association with a low dose of interferon‐γ (IFN‐γ) in vitro. Selective loss of dopaminergic neurons was induced by costimulation with CD40 and IFN‐γ in mesencephalic cultures, which was protected by selective inhibitors of iNOS and/or COX‐2. We also found in CD40‐stimulated astrocytes an increase of a low‐affinity IgE receptor CD23, which is known to induce iNOS expression. Together these data suggest that up‐regulated iNOS and COX‐2 via the CD40 pathway may lead to dopaminergic neuron loss and may participate in the neuroinflammaory pathway of PD. © 2005 Wiley‐Liss, Inc.
Variations in extracellular levels of dopamine, noradrenaline, glutamate, and aspartate across the sleep–wake cycle in the medial prefrontal cortex and nucleus accumbens of freely moving rats
Authors: Léna I. , Parrot S. , Deschaux O. , Muffat‐Joly S. , Sauvinet V. , Renaud B. , Suaud‐Chagny M.‐F. , Gottesmann C. 
Published: July 2005

AbstractWe used intracerebral microdialysis coupled with electrophysiologic recordings to determine relative changes in the concentrations of several neurotransmitters in the medial prefrontal cortex and nucleus accumbens of freely moving rats during waking, slow‐wave sleep, and rapid eye movement (REM) sleep. The concentrations of noradrenaline, dopamine, glutamate, and aspartate in 2‐min dialysate samples were analyzed by capillary electrophoresis combined with laser‐induced fluorescence detection. Changes in glutamate and aspartate concentrations were found only in the nucleus accumbens, in which a decrease was obtained during both slow‐wave sleep and REM sleep compared to waking. A progressive reduction in the release of noradrenaline was observed from waking to REM sleep in both structures. In contrast, dopamine concentrations were higher during waking and REM sleep compared to that during slow‐wave sleep. The latter results demonstrate that contrary to the findings of earlier electrophysiologic studies carried out on ventral tegmental area dopaminergic neurons, changes in the release of dopamine in projection areas occur across the sleep–wake cycle. The elevated levels of dopamine during waking and REM sleep in the medial prefrontal cortex and the nucleus accumbens could result from changes during these two states in afferent modulation at the level of cell bodies or at the level of dopaminergic terminals. © 2005 Wiley‐Liss, Inc.
CNS regeneration: A morphogen's tale
Authors: Vergara M. Natalia , Arsenijevic Yvan , Del Rio‐Tsonis Katia 
Published: July 2005

AbstractTissue regeneration will soon become an avenue for repair of damaged or diseased tissues as stem cell niches have been found in almost every organ of the vertebrate body including the CNS. In addition, different animals display an array of regenerative capabilities that are currently being researched to dissect the molecular mechanisms involved. This review concentrates on the different ways in which CNS tissues such as brain, spinal cord and retina can regenerate or display neurogenic potential and how these abilities are modulated by morphogens. © 2005 Wiley Periodicals, Inc. J Neurobiol 64: 491–507, 2005
Role of morphogens in brain growth
Authors: Tannahill David , Harris Laura W. , Keynes Roger 
Published: July 2005

AbstractDuring the last century, experiments on the chick embryo established that the ballooning expansion of the early forebrain and midbrain vesicles is dependent on the underlying axial (notochordal) mesoderm. Transient separation of the early midbrain primordium from the notochord causes subsequent collapse of both midbrain and forebrain (telencephalic) vesicles, accompanied by pronounced folding of the neural epithelium. More recent experiments have shown that vesicle collapse is caused by defective Sonic Hedgehog (Shh) signaling from the notochord and floor plate. Separation of the notochord from the brain causes loss of ventral Shh expression, resulting in reduced cell proliferation and increased cell death in the expanding neural epithelium, and culminating in vesicle collapse. These experiments are reviewed here, and set in the context of other studies illustrating the wide range of molecular and cellular processes that cause abnormal brain morphogenesis when perturbed. We also speculate that variation in the regulation of signaling pathways such as Hedgehog may have played a significant part in generating rapid morphogenetic changes during the evolution of the vertebrate brain. © 2005 Wiley Periodicals, Inc. J Neurobiol 64: 367–375, 2005
Morphogens and synaptogenesis in Drosophila
Authors: Marqués Guillermo 
Published: July 2005

AbstractDuring development and adult life synapses are remodeled in response to genetic programs and environmental cues. This synaptic plasticity is thought to be the basis of learning and memory. The larval neuromuscular junction of Drosophila is established during embryogenesis and grows during larval development to accommodate muscle growth and maintain synaptic homeostasis. This growth is dependent on bidirectional communication between the motoneuron and the muscle fiber. The best‐characterized retrograde signaling pathway is defined by Glass bottom boat (Gbb), a morphogen of the transforming growth factor‐β (TGF‐β) superfamily. Gbb acts as a muscle‐derived retrograde signal that activates the TGF‐β pathway presynaptically. This pathway includes the type II receptor Wishful thinking, type I receptors Thick veins and Saxophone, and the second messenger Smads Mothers against dpp (Mad) and Medea. Mutations that block this pathway result in small synapses that are morphologically aberrant and severely impaired functionally. An emerging anterograde signaling pathway is defined by Wingless, a morphogen of the Wnt family that acts as a motoneuron‐derived anterograde signal required for both pre‐ and postsynaptic development. In the absence of Wingless the neuronal microtubule cytoskeleton regulator Futsch is down‐regulated and synaptic growth impaired. Some of these morphogens have conserved roles in mammalian synaptogenesis, and genetic analysis suggests that additional signaling molecules are required for synaptic growth at the Drosophila neuromuscular junction. © 2005 Wiley Periodicals, Inc. J Neurobiol 64: 417–434, 2005
Morphing into cancer: The role of developmental signaling pathways in brain tumor formation
Authors: Fogarty Marie P. , Kessler Jessica D. , Wechsler‐Reya Robert J. 
Published: July 2005

AbstractMorphogens play a critical role in most aspects of development, including expansion and patterning of the central nervous system. Activating germline mutations in components of the Hedgehog and Wnt pathways have provided evidence for the important roles morphogens play in the genesis of brain tumors such as cerebellar medulloblastoma. In addition, aberrant expression of transforming growth factor‐β (TGF‐β) superfamily members has been demonstrated to contribute to progression of malignant gliomas. This review summarizes our current knowledge about the roles of morphogens in central nervous system tumorigenesis. © 2005 Wiley Periodicals, Inc. J Neurobiol 64: 458–475, 2005
Morphogens and cell survival during development
Authors: Mehlen Patrick , Mille Fréderic , Thibert Chantal 
Published: July 2005

AbstractThe notion of “morphogens” is an important one in developmental biology. By definition, a morphogen is a molecule that emanates from a specific set of cells that is present in a concentration gradient and that specifies the fate of each cell along this gradient. The strongest candidate morphogens are members of the transforming growth factor‐β (TGF‐β), Hedgehog (Hh), and Wnt families. While these morphogens have been extensively described as differentiation inducers, some reports also suggest their possible involvement in cell death and cell survival. It is frequently speculated that the cell death induction that is found associated with experimental removal of morphogens is the manifestation of abnormal differentiation signals. However, several recent reports have raised controversy about this death by default, suggesting that cell death regulation is an active process for shaping tissues and organs. In this review, we will present morphogens, with a specific emphasis on Sonic Hedgehog, a mammalian member of the Hh family, not as a positive regulators of cell differentiation but as key regulators of cell survival. © 2005 Wiley Periodicals, Inc. J Neurobiol 64: 357–366, 2005
Mechanisms of Hedgehog gradient formation and interpretation
Authors: Torroja Carlos , Gorfinkiel Nicole , Guerrero Isabel 
Published: July 2005

AbstractMorphogens are molecules that spread from localized sites of production, specifying distinct cell outcomes at different concentrations. Members of the Hedgehog (Hh) family of signaling molecules act as morphogens in different developmental systems. If we are to understand how Hh elicits multiple responses in a temporally and spatially specific manner, the molecular mechanism of Hh gradient formation needs to be established. Moreover, understanding the mechanisms of Hh signaling is a central issue in biology, not only because of the role of Hh in morphogenesis, but also because of its involvement in a wide range of human diseases. Here, we review the mechanisms affecting the dynamics of Hh gradient formation, mostly in the context of Drosophila wing development, although parallel findings in vertebrate systems are also discussed. © 2005 Wiley Periodicals, Inc. J Neurobiol 64: 334–356, 2005
Planar cell polarity and a potential role for a Wnt morphogen gradient in stereociliary bundle orientation in the mammalian inner ear
Authors: Dabdoub Alain , Kelley Matthew W. 
Published: July 2005

AbstractThe planar cell polarity (PCP) pathway, a noncanonical Wnt signaling pathway, is crucial for embryonic development in all animals as it is responsible for the regulation of coordinated orientation of structures within the plane of the various epithelia. In the mammalian cochlea, one of the best examples of planar polarity in vertebrates, stereociliary bundles located on mechanosensory hair cells within the sensory epithelium are all uniformly polarized. Generation of this polarity is important for hair cell mechanotransduction and auditory perception as stereociliary bundles are only sensitive to vibrations in their single plane of polarization. We describe the two step developmental process that results in the generation of planar polarity in the mammalian inner ear. Furthermore, we review evidence for the role of Wnt signaling, and the possible generation of a Wnt gradient, in planar polarity. © 2005 Wiley Periodicals, Inc. J Neurobiol 64: 446–457, 2005
Airway proteoglycans are differentially altered in fatal asthma
Authors: de Medeiros Matsushita Marcus , da Silva Luiz Fernando Ferraz , dos Santos Mario Adriano , Fernezlian Sandra , Schrumpf Jasmijn A , Roughley Peter , Hiemstra Pieter S , Saldiva Paulo Hilário Nascimento , Mauad Thais , Dolhnikoff Marisa 
Published: July 2005

AbstractIt has been suggested that airway remodelling is responsible for the persistent airway obstruction and decline in lung function observed in some asthmatic patients. The small airways are thought to contribute significantly to this functional impairment. Proteoglycans (PGs) are important components of the extracellular matrix (ECM) in the lungs. Besides controlling biophysical properties of the ECM, they play important roles in the regulation of some cytokines. Increased subepithelial PG deposition in the airways of mild asthmatics has been reported. However, there are no data on the PG content in small airways in asthma. This study has compared the content and distribution of PGs in large and small airways of patients who died of asthma with those in control lungs. Immunohistochemistry and image analysis were used to determine the content of lumican, decorin, biglycan, and versican in large (internal perimeter >6 mm) and small (internal perimeter ≤6 mm) airways of 18 patients who had died of asthma (A) and ten controls (C). The results were expressed as PG area (µm2)/epithelial basement membrane length (µm). The main differences between asthmatics and controls were observed in the small airways. There was a significant decrease in decorin and lumican contents in the external area of small airways in asthmatics (decorin: A = 1.05 ± 0.27 µm, C = 3.97 ± 1.17 µm, p = 0.042; lumican: A = 1.97 ± 0.37 µm, C = 5.66 ± 0.99 µm, p = 0.002). A significant increase in versican content in the internal area of small and large airways in asthmatics was also observed (small: A = 7.48 ± 0.84 µm, C = 5.16 ± 0.61 µm, p = 0.045; large: A = 18.38 ± 1.94 µm, C = 11.90 ± 2.86 µm, p = 0.028). The results show that PGs are differentially expressed in the airways of fatal asthma and may contribute to airway remodelling. These data reinforce the importance of the small airways in airway remodelling in asthma. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Chromosomal imbalances in wood dust‐related adenocarcinomas of the inner nose and their associations with pathological parameters
Authors: Korinth Dirk , Pacyna‐Gengelbach Manuela , Deutschmann Nicole , Hattenberger Sigurd , Bockmühl Ulrike , Dietel Manfred , Schroeder Heinz‐Georg , Donhuijsen Konrad , Petersen Iver 
Published: July 2005

AbstractComparative genomic hybridization (CGH) was used to screen 42 wood dust‐related sinonasal adenocarcinomas for chromosomal alterations. The tumour collection comprised 39 papillary‐tubular cylinder cell adenocarcinomas (PTCCs; six cases G1, 23 G2, and ten G3), two alveolar goblet cell adenocarcinomas (AGCs), and one signet ring cell adenocarcinoma (SRC), according to the Kleinsasser and Schroeder classification. Copy number changes were detected in 41 tumours (97.6%). The one carcinoma without imbalances was a PTCC‐G1. DNA gains were most frequently seen on chromosomes 12p (83%), 7q (74%), 8q (71%), and 20q (71%), 11q (61%), 22 (59%), and 1q (52%). Pronounced overrepresentations suggestive of high copy amplifications were detected on 8q (15 cases, 36%), 7q (six cases, 14%), 20q (five cases, 12%), 13q14 (three cases, 7%), 1q22, 5p, 12p and 20 (two cases, 5% each), and 2q24, 3q13, 3q22, 7p, 14q12, and 16q13 (one case, each 2%). Frequent chromosomal losses occurred at 5q (81%), 18q (76%), 4 (74%), 8p (61%), 9p (60%), 6q and 17p (52% each), and 3p, 13q, and 21 (50% each). There was a quantitative as well as a qualitative increase of alterations from PTCC‐G1 to PTCC‐G2 and finally PTCC‐G3, confirming the usefulness of histopathological grading. While PTCC‐G1 carried only a few alterations, namely gains on chromosomes 17 and 7 as well as losses of 4q and 13q, PTCC‐G2 already carried many of the above‐mentioned alterations, while PTCC‐G3 showed significantly more gains of 7q, 8q, and 12p, and losses of 8p and 17p. Additionally, the latter subgroup was particularly prone to carry pronounced DNA gains. These data provide further evidence for a recurrent pattern of chromosomal imbalances in sinonasal adenocarcinomas and highlight distinct aberrations that are associated with tumour differentiation and progression. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
BIC and miR‐155 are highly expressed in Hodgkin, primary mediastinal and diffuse large B cell lymphomas
Authors: Kluiver Joost , Poppema Sibrand , de Jong Debora , Blokzijl Tjasso , Harms Geert , Jacobs Susan , Kroesen Bart‐Jan , van den Berg Anke 
Published: July 2005

AbstractIn a previous study we demonstrated high expression of the non‐coding BIC gene in the vast majority of Hodgkin's lymphomas (HLs). Evidence suggesting that BIC is a primary microRNA transcript containing the mature microRNA‐155 (miR‐155) as part of a RNA hairpin is now accumulating. We therefore analysed HL cell lines and tissue samples to determine whether miR‐155 is also expressed in HL. High levels of miR‐155 could be demonstrated, indicating that BIC is processed into a microRNA in HL. Most non‐HL subtypes were negative for BIC as determined by RNA‐ISH. However, in diffuse large B cell lymphoma (DLBCL) and primary mediastinal B cell lymphoma (PMBL), significant percentages of positive tumour cells were observed in 12/18 and 8/8 cases. A higher proportion of tumour cells were positive for BIC in DLBCL with activated B cell‐like phenotype than in DLBCL with germinal centre B cell‐like phenotype. Differential BIC expression was confirmed by qRT‐PCR analysis. Northern blot analysis showed expression of miR‐155 in all DLBCL and PMBL derived cell lines and tissue samples analysed. In summary, we demonstrate expression of primary microRNA BIC and its derivative miR‐155 in HL, PMBL and DLBCL. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Carbonylation of milk powder proteins as a consequence of processing conditions
Authors: Fenaille François , Parisod Véronique , Tabet Jean‐Claude , Guy Philippe A. 
Published: July 2005

AbstractDuring industrial treatments, milk proteins could be oxidatively modified, thus leading to the formation of modified/oxidised amino acid residues. The apparition of such modified residues may contribute to the formation of new immunologically reactive structures. Some of these adducts could, in an advanced stage, lead to cross‐linked protein species whose proteolytic susceptibility would be drastically decreased. Such protein species, that are resistant to digestion, could also constitute major food allergens. Therefore, these oxidative protein modifications tend to increase the natural allergenicity of milk proteins. For these reasons, monitoring milk protein oxidative modifications could be very useful regarding both product quality and allergenicity issues. In the present paper, we highlight, using different analytical approaches, the preferential carbonylation of β‐lactoglobulin (β‐Lg) during industrial treatments of milk. This result is particularly interesting since native β‐Lg represents one of the major milk allergens.
The human platelet proteome mapped by peptide‐centric proteomics: A functional protein profile
Authors: Martens Lennart , Van Damme Petra , Van Damme Jozef , Staes An , Timmerman Evy , Ghesquière Bart , Thomas Grégoire R. , Vandekerckhove Joël , Gevaert Kris 
Published: July 2005

AbstractSeveral studies have been published in which holistic approaches were used to characterise the proteome and transcriptome of human platelets. The key intent being that a deeper understanding of the normal and aberrant physiological functions of platelets can only be achieved if most biomolecular building blocks are mapped. Here we present the application of recently developed novel technologies that overcome some of the shortcomings of gel‐based proteomics. Central in our approach is the so‐called combined fractional diagonal chromatography (COFRADIC)‐technology in which sets of representative peptides are sorted in a diagonal RP chromatographic system through a specific modification of their side chain. In this study we combined three different COFRADIC sorting techniques to analyse the proteome of human platelets. Methionyl, cysteinyl and amino terminal peptides were isolated and analysed by MS/MS. Merging the peptide identifications obtained after database searching resulted in a core set of 641 platelet proteins, which comprises the largest set identified today. In comparison to previously published platelet proteomes, we identified 404 novel platelet proteins containing a high number of hydrophobic membrane proteins and hypothetical proteins. Furthermore we discuss the observed characteristics and potential benefits of each of the different COFRADIC technologies for proteome analysis and highlight important issues that need to be considered when searching sequence databases using data obtained in peptide‐centric, non‐gel proteomics studies.
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories
Authors: Martens Lennart , Nesvizhskii Alexey I. , Hermjakob Henning , Adamski Marcin , Omenn Gilbert S. , Vandekerckhove Joël , Gevaert Kris 
Published: July 2005

AbstractWith the human Plasma Proteome Project (PPP) pilot phase completed, the largest and most ambitious proteomics experiment to date has reached its first milestone. The correspondingly impressive amount of data that came from this pilot project emphasized the need for a centralized dissemination mechanism and led to the development of a detailed, PPP specific data gathering infrastructure at the University of Michigan, Ann Arbor as well as the protein identifications database project at the European Bioinformatics Institute as a general proteomics data repository. One issue that crept up while discussing which data to store for the PPP concerns whether the raw, binary data coming from the mass spectrometers should be stored, or rather the more compact and already significantly processed peak lists. As this debate is not restricted to the PPP but relates to the proteomics community in general, we will attempt to detail the relative merits and caveats associated with centralized storage and dissemination of raw data and/or peak lists, building on the extensive experience gained during the PPP pilot phase. Finally, some suggestions are made for both immediate and future storage of MS data in public repositories.