bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping Martian Atmospheric Pressure with Ground-Based Near Infrared Spectroscopy
Authors: Chamberlain Sarah A. , Bailey Jeremy A. , Crisp David 
Published: November 2006

AbstractWe present images of Mars obtained in the 2.0 μm CO2 band with the United Kingdom Infrared Telescope (UKIRT). The images reveal topographic features of the Martian surface that are usually invisible in direct albedo images at visible or IR wavelengths, but agree remarkably well with the topography of the planet as mapped by the MOLA instrument on Mars Global Surveyor. The CO2 band depth is a measure of the absorbing column of CO2 and hence determined primarily by the surface atmospheric pressure. The surface pressure variations are detected with a sensitivity of 4–5 Pa. We compare our data with radiative transfer models and find that the measured CO2 variation with pressure is consistent with the models. We discuss the possibility that similar observations might be used to observe atmospheric pressure changes due to Martian weather systems.
ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats
Authors: Falkner J. A. , Falkner J. W. , Andrews P. C. 
Published: November 2006

AbstractMotivation: Effective use of proteomics data, specifically mass spectrometry data, relies on the ability to read and write the many mass spectrometer file formats. Even with mass spectrometer vendor-specific libraries and vendor-neutral file formats, such as mzXML and mzData it can be difficult to extract raw data files in a form suitable for batch processing and basic research. Introduced here are the ProteomeCommons.org Input and Output Framework, abbreviated to IO Framework, which is designed to abstractly represent mass spectrometry data. This project is a public, open-source, free-to-use framework that supports most of the mass spectrometry data formats, including current formats, legacy formats and proprietary formats that require a vendor-specific library in order to operate. The IO Framework includes an on-line tool for non-programmers and a set of libraries that developers may use to convert between various proteomics file formats.Availability: The current source-code and documentation for the ProteomeCommons.org IO Framework is freely available atContact: jfalkner@umich.edu
PrepMS: TOF MS data graphical preprocessing tool
Authors: Karpievitch Yuliya V. , Hill Elizabeth G. , Smolka Adam J. , Morris Jeffrey S. , Coombes Kevin R. , Baggerly Keith A. , Almeida Jonas S. 
Published: November 2006

AbstractSummary: We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings, experimentally determined to work well in most situations. These values, if desired, can be changed by the user. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection and visual data quality assessment.Availability: Stand-alone executable files and Matlab toolbox are available for download at:Contact: ykarpi@mdanderson.orgSupplementary information: Supplementary data are available at Bioinformatics online.
SNP2NMD: A database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay
Authors: Han Areum , Kim Woo-Yeon , Park Seong-Min 
Published: November 2006

AbstractSummary: Elucidating the effects of genetic polymorphisms on genes and gene networks is an important step in disease association studies. We developed the SNP2NMD database for human SNPs (single nucleotide polymorphisms) that result in PTCs (premature termination codons) and trigger nonsense-mediated mRNA decay (NMD). The SNP2NMD Web interfaces provide extensive genetic information on and graphical views of the queried SNP, gene, and disease terms.Availability: SNP2NMD is available from , or directly fromContact: kimplove@kribb.re.kr, lastmhc@kribb.re.krSupplementary information:
A Babel of Judicial Voices? Ruminations from the Bench
Authors: Higgins Rosalyn 
Published: November 2006

AbstractThis Keynote speech examines the implications of the multiplying of judicial institutions and the deepening of international law. Overlapping jurisdiction issues already exist among international courts and tribunals. This raises the question of ‘Whose view prevails?’ But the deepening of international law also requires any given court to ask itself, ‘Which of the many norms now developed are applicable?’ Alternative plausible applicable norms could lead to different solutions. It is ever more apparent that that law is more than ‘bright rules’ that simply need to be applied. This speech discusses potential solutions that have been proposed, such as instituting a judicial hierarchy, using certain provisions of the Vienna Convention on the Law of Treaties, and invoking a hierarchy of norms. It closes with a call for international judges to regard the multiplication of institutions and applicable norms as an opportunity rather than a problem, to read each other's judgments, respect each other's work and try to preserve unity unless context dictates otherwise.
Aminocyclopropane Carboxylic Acid Synthase Is a Regulated Step in Ethylene-Dependent Induced Conifer Defense. Full-Length cDNA Cloning of a Multigene Family, Differential Constitutive, and Wound- and Insect-Induced Expression, and Cellular and Subcellular Localization in Spruce and Douglas Fir
Authors: Ralph Steven G. , Hudgins J.W. , Jancsik Sharon , Franceschi Vincent R. , Bohlmann Jörg 
Published: November 2006

Abstract
In conifer stems, formation of chemical defenses against insects or pathogens involves specialized anatomical structures of the phloem and xylem. Oleoresin terpenoids are formed in resin duct epithelial cells and phenolics accumulate in polyphenolic parenchyma cells. Ethylene signaling has been implicated in the induction of these chemical defenses. Recently, we reported the cloning of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) from spruce (Picea spp.) and Douglas fir (Pseudotsuga menziesii). ACO protein was constitutively expressed in Douglas fir and only weakly induced upon wounding. We now cloned seven full-length and one near full-length cDNA representing four distinct 1-aminocyclopropane-1-carboxylic acid synthases (ACS; ACS1, ACS2, ACS3, and ACS4) from spruce and Douglas fir. Cloning of ACS has not previously been reported for any gymnosperm. Using gene-specific, quantitative real-time polymerase chain reaction, we measured constitutive expression for the four ACS genes and the single-copy ACO gene in various tissues of Sitka spruce (Picea sitchensis) and in white spruce (Picea glauca) somatic embryos. ACO and ACS4 were ubiquitously expressed at high levels; ACS1 was predominantly expressed in developing embryos and ACS2 and ACS3 were expressed only at very low levels. Insect attack or mechanical wounding caused strong induction of ACS2 and ACS3 in Sitka spruce bark, a moderate increase in ACO transcripts, but had no effect on ACS1 and ACS4. ACS protein was also strongly induced following mechanical wounding in Douglas fir and was highly abundant in resin duct epithelial cells and polyphenolic parenchyma cells. These results suggest that ACS, but not ACO, is a regulated step in ethylene-induced conifer defense.
TheArabidopsisHistidine Phosphotransfer Proteins Are Redundant Positive Regulators of Cytokinin Signaling
Authors: Hutchison Claire E. , Li Jie , Argueso Cristiana , Gonzalez Monica , Lee Eurie , Lewis Michael W. , Maxwell Bridey B. , Perdue Tony D. , Schaller G. Eric , Alonso Jose M. , Ecker Joseph R. , Kieber Joseph J. 
Published: November 2006

AbstractArabidopsis thaliana histidine phosphotransfer proteins (AHPs) are similar to bacterial and yeast histidine phosphotransfer proteins (HPts), which act in multistep phosphorelay signaling pathways. A phosphorelay pathway is the current model for cytokinin signaling. To assess the role of AHPs in cytokinin signaling, we isolated T-DNA insertions in the five AHP genes that are predicted to encode functional HPts and constructed multiple insertion mutants, including an ahp1,2,3,4,5 quintuple mutant. Single ahp mutants were indistinguishable from wild-type seedlings in cytokinin response assays. However, various higher-order mutants displayed reduced sensitivity to cytokinin in diverse cytokinin assays, indicating both a positive role for AHPs in cytokinin signaling and functional overlap among the AHPs. In contrast with the other four AHPs, AHP4 may play a negative role in some cytokinin responses. The quintuple ahp mutant showed various abnormalities in growth and development, including reduced fertility, increased seed size, reduced vascular development, and a shortened primary root. These data indicate that most of the AHPs are redundant, positive regulators of cytokinin signaling and affect multiple aspects of plant development.
Direct detection of transient α‐helical states in islet amyloid polypeptide
Authors: Williamson Jessica A. , Miranker Andrew D. 
Published: November 2006

AbstractThe protein islet amyloid polypeptide (IAPP) is a glucose metabolism associated hormone cosecreted with insulin by the β‐cells of the pancreas. In humans with type 2 diabetes, IAPP deposits as amyloid fibers. The assembly intermediates of this process are associated with β‐cell death. Here, we examine the rat IAPP sequence variant under physiological solution conditions. Rat IAPP is mechanistically informative for fibrillogenesis, as it samples intermediate‐like states but does not progress to form amyloid. A central challenge was the development of a bacterial expression system to generate isotopically labeled IAPP without terminal tags, but which does include a eukaryotic post‐translational modification. While optical spectroscopy shows IAPP to be natively unfolded, NMR chemical shifts of backbone and β‐carbon resonances reveal the sampling of α‐helical states across a continuous stretch comprising ∼40% of the protein. In addition, the manifestation of nonrandom coil chemical shifts is confirmed by the relative insensitivity of the amide proton chemical shifts to alterations in temperature. Intriguingly, the residues displaying helical propensity are conserved with the human sequence, suggesting a functional role for this conformational bias. The inability of rat IAPP to self assemble can be ascribed, in part, to several slowly exchanging conformations evident as multiple chemical shift assignments in the immediate vicinity of three proline residues residing outside of this helical region.
Improved outcome after relapse in children with acute myeloid leukaemia
Authors: Abrahamsson Jonas , Clausen Niels , Gustafsson Göran , Hovi Liisa , Jonmundsson Gudmundur , Zeller Bernward , Forestier Erik , Heldrup Jesper , Hasle Henrik ,   for the Nordic Society for Paediatric Haematology and Oncology (NOPHO)
Published: November 2006

SummaryIn the Nordic Society for Paediatric Haematology and Oncology paediatric study acute myeloid leukaemia (AML) 93, event‐free survival was 50% and overall survival was 66%, indicating that many patients were cured following relapse. Factors influencing outcome in children with relapsed AML were investigated. The study included all 146 children in the Nordic countries diagnosed with AML between 1988 and 2003, who relapsed. Data on disease characteristics and relapse treatment were related to outcome. Sixty‐six percentage achieved remission with survival after relapse (5 years) 34 ± 4%. Of 122 patients who received re‐induction therapy, 77% entered remission with 40 ± 5% survival. Remission rates were similar for different re‐induction regimens but fludarabine, cytarabine, granulocyte colony‐stimulating factor‐based therapy had low treatment‐related mortality. Prognostic factors for survival were duration of first complete remission (CR1) and stem cell transplantation (SCT) in CR1. In early relapse (<1 year in CR1), survival was 21 ± 5% compared with 48 ± 6% in late relapse. For children receiving re‐induction therapy, survival in early relapse was 29 ± 6% and 51 ± 6% in late. Patients treated in CR1 with SCT, autologous SCT or chemotherapy had a survival of 18 ± 9, 5 ± 5 and 41 ± 5%, respectively. Survival was 62 ± 6% in 64 children given SCT as part of their relapse therapy. A significant proportion of children with relapsed AML can be cured, even those with early relapse. Children who receive re‐induction therapy, enter remission and proceed to SCT can achieve a cure rate of 60%.
Epstein–Barr virus early‐antigen antibodies before allogeneic haematopoietic stem cell transplantation as a marker of risk of post‐transplant lymphoproliferative disorders
Authors: Agbalika Felix , Larghero Jerome , Esperou Helene , Marais Dominique , Robin Marie , Foïs Elena , De Latour Régis Peffault , Gluckman Eliane , Rocha Vanderson , Benbunan Marc , Socié Gerard , Marolleau Jean‐Pierre 
Published: November 2006

SummaryThe occurrence of post‐transplant lymphoproliferative disorders (PTLDs) after allogeneic haematopoietic stem cell transplantation (allo‐HSCT) represents a clinical problem. Pretransplant Epstein–Barr virus serological status and viral load was determined in 21 recipients and 28 control transplanted patients, with (+) and without (−) PTLD, respectively. Early‐antigen immunoglobulin G (EA‐IgG) was detected in 12/21 PTLD+ patients, but only 2/28 PTLD− patients (P = 0·00023, Odds ratio = 17·42). High viral load was detected in peripheral blood mononuclear cells at PTLD diagnosis, independently of deleted LMP1. Detection of EA‐IgG in allo‐HSCT recipients pretransplantation might be considered as risk factor for PTLD development.
Analysis of parotid glands of primary Sjögren's syndrome patients using proteomic technology reveals altered autoantigen composition and novel antigenic targets
Authors: Stea E A , Routsias J G , Samiotaki M , Panayotou G , Papalambros E , Moutsopoulos H M , Tzioufas A G 
Published: November 2006

Summary
Sjögren's syndrome (SS) is an autoimmune disease characterized by lymphocytic infiltration, destruction of the salivary and lacrimal glands and production of autoantibodies against a variety of cellular proteins. The aberrant immune response against these autoantigens may begin or extend to other proteins that are not yet defined. Several studies have shown that autoantibody production is taking place in the affected salivary glands. In the present study, using proteomic approaches, we aimed to: (a) identify new autoantigens in the salivary glands of primary SS (pSS) patients and (b) evaluate the epigenetic changes of known autoantigens. Total parotid gland extracts of pSS patients were analysed using two-dimensional gel electrophoresis, sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblot with pSS patients' sera or purified autoantibodies and immunoprecipitation using homologous IgG. Identification of the unknown proteins was performed using mass spectrometry (MS). Immunoblot analysis on two-dimensional gels using purified anti-La/SSB antibodies revealed that pSS salivary glands contain high levels of post-translationally modified La/SSB autoantigen, while the native form of the protein is recognized faintly, in contrast to normal controls. Moreover, salivary glands of pSS patients contain post-translationally modified actin that becomes immunogenic in the microenviroment of the affected tissue. The alteration of the physicochemical properties of self-proteins could thus contribute to the break of immune tolerance against them.
Circumferential wall tension due to hypertension plays a pivotal role in aorta remodelling
Authors: Prado Cibele M. , Rossi Marcos A. 
Published: November 2006

SummaryThe present study was carried out to investigate the role of hypertension in the genesis and localization of intimal lesions and medial remodelling found in the prestenotic segment in relation to a severe stenosis of the abdominal aorta just below the diaphragm. Male young rats were divided randomly into operated group, animals submitted to surgical abdominal aorta stenosis, and sham‐operated group, a control group of animals submitted to sham operation to simulate abdominal aorta stenosis. Aortas in the hypertensive prestenotic segment with increased circumferential wall tension associated with normal tensile stress, laminar flow/normal wall shear stress were characterized by enlarged heterogeneous endothelial cells elongated in the direction of the blood flow, diffusely distributed conspicuous neointimal plaques and medial thickening. The immunohistochemical analysis revealed an increased expression of eNOS, iNOS, nitrotyrosine and transforming growth factor‐β (TGF‐β) in endothelial cells and/or smooth muscle cells in this segment. Our findings suggest that increased circumferential wall tension due to hypertension plays a pivotal role in the remodelling of the prestenotic segment through biomechanical effects on oxidative stress and increased TGF‐β expression. Further studies are needed to clarify the intrinsic pathogenetic mechanism of focal distribution of the neointimal plaques in the hypertensive segment.
Neoproterozoic A‐type magmatism in the Western Sierras Pampeanas (Argentina): evidence for Rodinia break‐up along a proto‐Iapetus rift?
Authors: Baldo E. , Casquet C. , Pankhurst R.J. , Galindo C. , Rapela C.W. , Fanning C.M. , Dahlquist J. , Murra J. 
Published: November 2006

AbstractA‐type orthogneisses of mid Neoproterozoic age (774 ± 6 Ma, U‐Pb SHRIMP zircon age), are reported for the first time from the Grenvillian basement of the Western Sierras Pampeanas in Argentina. These anorogenic meta‐igneous rocks represent the latest event of Rodinia break‐up so far recognized in Grenvillian basement exposures across Andean South America. Moreover, they compare well with A‐type granitoids and volcanic rocks along the Appalachian margin of Laurentia (Blue Ridge), thus adding to former evidence that the Western Sierras Pampeanas Grenvillian basement was left on the conjugate rifted margin of eastern Laurentia during Rodinia break‐up and the consequent opening of the Iapetus ocean.
Fluid inclusion evidence for deep burial of the Tertiary accretionary wedge of the Carpathians
Authors: Hurai Vratislav , Marko František , Tokarski Antoni K. , Świerczewska Anna , Kotulová Júlia , Biroň Adrián 
Published: November 2006

AbstractHydrothermal quartz from mineralized joints of the Carpathian accretionary wedge contains immiscible aqueous, oil‐condensate, methane and carbon dioxide‐rich fluid inclusions. Distribution patterns of the inclusion trapping PT parameters point to a crack‐seal mechanism during upward and lateral migration of hot methane‐rich fluids from overpressured sediments at the base of the accretionary wedge. A simple equation is proposed to calculate depths from densities and trapping pressures of the buoyant inclusion fluids. In the Carpathian accretionary wedge, the paleofluid pressures of 52–306 MPa correspond to a 5‐ to 11‐km‐thick overburden. Prior to exhumation, thickness of the wedge must have attained 10–25 km, of which only c. 50% was preserved until recently. Anomalously high methane densities (up to 0.43 g cm−3) recorded in the lowermost nappe sheets are provisionally interpreted as a result of supralithostatic overpressure due to thermal cracking of oil and kerogen to methane and pyrobitumen at temperatures above 200 °C.
Apheresis products of the Amicus™ and the AS.TEC 204® cell separators are comparable with regard to dendritic cells derived from the mononuclear cell collection
Authors: Leitner G. C. , Koszik F. , Rudnicki T. , Buchta C. , Worel N. , Fischer M. B. , Schneeberger A. , Hoecker P. 
Published: November 2006

Background  In this study, we investigated the quality of autologous mononuclear cells (MNC) collected with two different cell separators using standard MNC‐apheresis procedure modalities. MNCs were purified by density gradient centrifugation and cultured according to standard protocols to generate dendritic cells (DC) and 1 × 107/ml immature DCs were pulsed with tumour lysate for 3 days and subsequently characterized by fluorescent‐activated cell sorter analysis.Results  No difference was found in the monocyte content of either apheresis product (P = 0·07) and in the overall yield of MNCs (P = 0·7). Mature DCs as defined by their phenotype revealed also no significant difference: Amicus‘, 118 × 106 cells ± 91 vs. AS.TEC 204®, 128 × 106 cells ± 137 (P = 0·55), respectively, although the contamination with platelets (threefold) and red cells (twofold) was significantly higher in the AS.TEC 204 group (P < 0·05) than in the Amicus group.Conclusion  The Amicus and the AS.TEC 204 are equally capable in providing MNCs for the generation of DCs and the amount of concomitantly collected red cells and platelets had no impact on the final DC yield.
Yield Formation and Plant Metabolism of Spring Barley in Response to Locally Injected Ammonium
Authors: Schittenhelm S. , Menge‐Hartmann U. 
Published: November 2006

AbstractThis study was conducted to elucidate the crop physiological basis for yield differences frequently observed in experiments comparing top‐dressing of N fertilizers with injection of ammonium or ammonium/urea solutions into the soil. The effects of diammonium phosphate (NH4‐N) injected at the two‐leaf stage, calcium nitrate (NO3‐N) broadcasted and incorporated before sowing, and a control without N fertilization (‐N) were assessed from measurements of growth, N‐uptake and N‐partitioning, light interception, gas exchange, leaf anatomy and the activity of key enzymes of N‐metabolism. The experiment was performed with spring barley (Hordeum vulgare L.) grown in 80‐l containers in a vegetation hall in Braunschweig, Germany. The plants in the NH4‐N treatment produced a 20 % higher grain yield than those in the NO3‐N treatment. The grain yield superiority of the NH4‐N plants was attributable to a higher number of ears per plant (+13 %) and more grains per ear (+6 %). The NH4‐N plants exhibited lower concentrations of inorganic cations than plants supplied with NO3‐N. In the NH4‐N treatment, the light penetrated more deeply into the crop canopy and the NH4‐N plants exhibited a higher leaf carbon exchange rate at the different leaf layers than the NO3‐N plants. It is concluded that as opposed to predominantly nitrate nutrition, provision of a persistent source of ammonium enables plants to take advantage of the positive yield effect of mixed N nutrition.
BMP‐15 regulation of ovulation quota in mammals
Authors: SHIMASAKI SHUNICHI 
Published: November 2006

Naturally occurring mutations in the oocyte‐specific factor, bone morphogenetic protein‐15 (BMP‐15), cause infertility in women and in ewes. In contrast to these monoovulatory mammals, the targeted deletion of BMP‐15 in polyovulatory mice results in subfertility with only minimal defects in the ovulation process. Given the established role of BMP‐15 in governing the progression of folliculogenesis, it is hypothesized that species‐specific differences in the BMP‐15 system are involved in species‐specific determination of ovulation quota and litter size. Recent data using in vitro cell transfection methodology indicate that, in contrast to human BMP‐15 which is successfully processed and secreted, the mouse BMP‐15 proprotein is resistant to proteolytic cleavage. Thus, no functional mature BMP‐15 is secreted in vitro. Further studies have shown that the functional mature form of BMP‐15 is barely detectable in mouse oocytes in vivo until just before ovulation, when it is markedly increased. The general hypothesis to emerge from these observations is that the species‐specific differences in the defects caused by mutations in the bmp15 gene between monoovulatory ewes and women and polyovulatory mice might be attributed to the timing of the production of BMP‐15 mature protein. (Reprod Med Biol 2006; 5: 245–248)