bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new least‐squares minimization approach to depth and shape determination from magnetic data
Authors: Abdelrahman El‐Sayed M. , Abo‐Ezz Eid. R. , Essa Khalid S. , El‐Araby T.M. , Soliman Khaled S. 
Published: April 2007

ABSTRACTWe have developed a least‐squares minimization approach to depth determination using numerical second horizontal derivative anomalies obtained from magnetic data with filters of successive window lengths (graticule spacings). The problem of depth determination from second‐derivative magnetic anomalies has been transformed into finding a solution to a non‐linear equation of the form, f(z) = 0. Formulae have been derived for a sphere, a horizontal cylinder, a dike and a geological contact. Procedures are also formulated to estimate the magnetic angle and the amplitude coefficient.We have also developed a simple method to define simultaneously the shape (shape factor) and the depth of a buried structure from magnetic data. The method is based on computing the variance of depths determined from all second‐derivative anomaly profiles using the above method. The variance is considered a criterion for determining the correct shape and depth of the buried structure. When the correct shape factor is used, the variance of depths is less than the variances computed using incorrect shape factors.The method is applied to synthetic data with and without random errors, complicated regionals, and interference from neighbouring magnetic rocks. Finally, the method is tested on a field example from India. In all the cases examined, the depth and the shape parameters are found to be in good agreement with the actual parameters.
Localized cultural denoising of high‐resolution aeromagnetic data
Authors: Paoletti V. , Fedi M. , Florio G. , Rapolla A. 
Published: April 2007

ABSTRACTWe show how a denoising technique based on the wavelet transform can be used to deal with localized noise related to DC electrified railway lines. This method, which performs localized and sharp filtering of cultural noise, was applied to high‐resolution aeromagnetic data acquired in the Phlegrean volcanic area, southern Italy, in 1999 and 2001. The helicopter‐borne survey was aimed at giving new detailed insights into the distribution of the magnetization of the area and, therefore, into the volcanological characteristics of the region. The surveyed area is characterized by the presence of towns, buildings and DC electrified railway lines whose magnetic effects influenced the measurements and were responsible for some of the measured anomalies. This cultural noise has, therefore, to be minimized as much as possible in order to allow the data to be interpreted accurately. Due to the excellent space‐scale localization properties of the discrete wavelet transform, the cultural disturbance was removed very precisely, leaving the field in the adjacent areas unchanged.
Increased levels of interferon‐γ primed by culture filtrate proteins antigen and CpG‐ODN immunization do not confer significant protection against Mycobacterium tuberculosis infection
Authors: Morais da Fonseca Denise , Lopes Silva Célio , Oliveira e Paula Marina , Garcia Soares Edson , Marchal Gilles , Horn Cynthia , Deperon Bonato Vânia Luiza 
Published: April 2007

SummaryThe results of various animal model studies of tuberculosis (TB) suggest that culture filtrate proteins (CFPs), which are antigens secreted by Mycobacterium tuberculosis, are largely responsible for improvements in TB vaccines. The great obstacle to developing protein subunit vaccines is that adjuvants are required in order to stimulate relevant protective immune responses. Acting as immune adjuvants, CpG‐oligodeoxynucleotides (CpG‐ODNs) promote the activation of Th1 cells and of pro‐inflammatory cytokines. To evaluate the adjuvant role of CpG‐ODNs in conferring enhanced immunogenic capacity and protection against M. tuberculosis, we immunized mice with CFP antigen combined with synthetic CpG‐ODNs (CFP/CpG) or with incomplete Freund's adjuvant (IFA) (CFP/IFA). Immunization with CFP/CpG induced a T helper 1 (Th1)‐biased response accompanied by a higher immunoglobulin G2a (IgG2a) antibody/IgG1 antibody ratio, elevated production of interferon‐γ (IFN‐γ) by spleen cells and in lungs. However, CFP/IFA‐immunized mice presented higher levels of IgG1 antibodies, as well as increased production of IFN‐γ, interleukin (IL)‐5, and IL‐10 by spleen cells, together with lower levels of IFN‐γ in the lungs. Despite the stronger Th1 response seen in both groups, believed to be necessary for protection against TB, only mice immunized with CFP/IFA were protected after M. tuberculosis infection. Lung histology revealed that lung parenchyma were better preserved in CFP/IFA‐immunized mice, which also presented intense lymphocyte recruitment to the lesion, whereas CFP/CpG‐immunized mice presented severe pulmonary injury accompanied by necrosis. Based on the data presented, we discuss the widely accepted paradigm that high levels of IFN‐γ are directly correlated with protection against experimental TB.
Is a new paradigm emerging for oceanic island biogeography?
Authors: Heaney Lawrence R. 
Published: April 2007

AbstractFollowing several decades during which two dissimilar and incompatible models (equilibrium and vicariance) dominated island biogeography, recent publications have documented patterns that point the way towards a new paradigm that includes elements of both models, as well as some novel aspects. Many of these seminal contributions have been made possible by the recent development of robust, temporally calibrated phylogenies used in concert with increasingly precise and reliable geological reconstructions of oceanic regions. Although a new general model of oceanic island biogeography has not yet been proposed, in this brief overview I present six hypotheses that summarize aspects of the emerging paradigm. These hypotheses deal with: the frequency of dispersal over oceanic water barriers by terrestrial organisms; the existence of substantial variation in the amount of dispersal (and gene flow) within a given set of related species within a given archipelago; the frequency, extent and impact on species richness of diversification within archipelagos; the frequent correlation of island age and the age of the species that live on the island; the long‐term persistence of species on oceanic islands; and the occasional recolonization of continents by species from clades that diversified on islands. Identifying, testing, and seeking means of synthesizing these and other emerging hypotheses may allow a new conceptual paradigm to emerge.
The prevalence of tooth discolouration and the self‐satisfaction with tooth colour in a Chinese urban population
Authors: XIAO J. , ZHOU X. D. , ZHU W. C. , ZHANG B. , LI J. Y. , XU X. 
Published: April 2007

Summary  Objectives: To determine the prevalence of tooth discolouration, self‐satisfaction with tooth colour, and correlation with socio‐demographic‐behavioural factors in adults and teenagers in Chengdu, China. Design: A cross‐sectional survey.Participants: 405 Chinese urban adults and teenagers from a multistage random probability sample. Methods: Tooth colour was measured on the maxillary central incisors using a colorimeter. Tooth discolouration was determined according to the discolouration level figure and evaluation criteria. Self‐satisfaction with tooth colour was assessed on a five‐point qualitative scale. Data were coded and analyzed using SPSS software. Results: The mean values for L*, a* and b* were 70·67 (s.d. 1·91), 4·29 (s.d. 2·05) and 17·51 (s.d. 4·13), respectively. Age and sex were the most important factors associated with tooth colour (P < 0·05). About half of the study population (48·9%) suffered from some tooth discolouration, and 52·6% were dissatisfied with their tooth colour. Education and smoking were significant factors affecting self‐satisfaction with tooth colour (P < 0·05). Conclusions: Tooth discolouration is common among the Chinese, and many Chinese are dissatisfied with their tooth colour. Self‐satisfaction with tooth colour decreased with increasing severity of discolouration. Further research is needed to determine types of tooth discolouration among broader regions in China.
Contemporary pollen and seed dispersal in a Prunus mahaleb population: patterns in distance and direction
Authors: GARCÍA C. , JORDANO P. , GODOY J. A. 
Published: April 2007

AbstractPollination and seed dispersal determine the spatial pattern of gene flow in plant populations and, for those species relying on pollinators and frugivores as dispersal vectors, animal activity plays a key role in determining this spatial pattern. For these plant species, reported dispersal patterns are dominated by short‐distance movements with a significant amount of immigration. However, the contribution of seed and pollen to the overall contemporary gene immigration is still poorly documented for most plant populations. In this study we investigated pollination and seed dispersal at two spatial scales in a local population of Prunus mahaleb (L.), a species pollinated by insects and dispersed by frugivorous vertebrates. First, we dissected the relative contribution of pollen and seed dispersal to gene immigration from other parts of the metapopulation. We found high levels of gene immigration (18.50%), due to frequent long distance seed dispersal events. Second, we assessed the distance and directionality for pollen and seed dispersal events within the local population. Pollen and seed movement patterns were non‐random, with skewed distance distributions: pollen tended moved up to 548 m along an axis approaching the N–S direction, and seeds were dispersed up to 990 m, frequently along the SW and SE axes. Animal‐mediated dispersal contributed significantly towards gene immigration into the local population and had a markedly nonrandom pattern within the local population. Our data suggest that animals can impose distinct spatial signatures in contemporary gene flow, with the potential to induce significant genetic structure at a local level.
VZ CVn: a close binary system with γ Doradus-like variations
Authors: İbanoǧlu C. , Taş G. , Sipahi E. , Evren S. 
Published: April 2007

Abstract
We present new photometric two-colour observations of the double-lined close binary star VZ CVn. Combining two data sets obtained in 1971–72 and in 2006, the physical parameters of both components were derived. After removing the light variations due to the eclipses and proximity effects, a periodic variation in the more massive component with a dominant period of 1.068 76 d could be detected in the first photometric data set. In accordance with its position on the Hertzsprung–Russell diagram and both its pulsation period and pulsation constant of 0.62 d, the primary component of VZ CVn should be an excellent γ Doradus candidate. The less massive secondary component seems to have smaller radius with respect to its mass. Both components appear to have lower luminosities with respect to their masses; hence, their radiative properties seem to be different. The evolutionary status of the components is also discussed.
The ABC transporter AtPDR8 is a cadmium extrusion pump conferring heavy metal resistance
Authors: Kim Do‐Young , Bovet Lucien , Maeshima Masayoshi , Martinoia Enrico , Lee Youngsook 
Published: April 2007

SummaryCadmium (Cd) and lead (Pb) are widespread pollutants that are toxic to plant growth. The expression of AtPDR8 was upregulated in cadmium‐ or lead‐treated Arabidopsis thaliana. To test whether AtPDR8 is involved in heavy metal resistance, we examined transgenic Arabidopsis that over‐expressed AtPDR8 and RNAi plants that exhibited a severely reduced AtPDR8 transcript level, as well as T‐DNA insertion mutants of this ABC transporter. AtPDR8‐over‐expressing plants were more resistant to Cd2+ or Pb2+ than the wild‐type and had lower Cd contents. In contrast, AtPDR8 RNAi transgenic plants and T‐DNA insertion lines were more sensitive to Cd2+ or Pb2+ compared to wild‐type plants and had higher Cd contents. The GFP–AtPDR8 protein was targeted to the plasma membrane, and GUS activity was present in most cells but strongest in the root hair and epidermal cells. Cd extrusion was higher in the AtPDR8‐over‐expressing plants in a flux assay using isolated protoplasts and radioactive 109Cd, and was lower in the RNAi transgenic plants than in the wild‐type. Together, these data strongly support a role for AtPDR8 as an efflux pump of Cd2+ or Cd conjugates at the plasma membrane of Arabidopsis cells. As AtPDR8 has been suggested to be involved in the pathogen response and in the transport of chemicals that mediate pathogen resistance, this ABC protein is likely to transport a very broad range of substrates.
Infection of tobacco with different Pseudomonas syringae pathovars leads to distinct morphotypes of programmed cell death
Authors: Krzymowska Magdalena , Konopka‐Postupolska Dorota , Sobczak Miroslaw , Macioszek Violetta , Ellis Brian E. , Hennig Jacek 
Published: April 2007

SummaryTobacco plants (Nicotiana tabacum cv. Xanthi‐nc) infiltrated with either of two pathovars of Pseudomonas syringae– an avirulent strain of P. syringae pv. tabaci (Pst) or the non‐host pathogen P. syringae pv. maculicola M2 (Psm) – developed a hypersensitive response (HR). There were considerable differences in HR phenotype, timing and sequence of cell dismantling between the two pathosystems. Following Psm infiltration, the first macroscopic signs were visible at 4.5 h post‐infiltration (hpi). Simultaneously, increased plasma membrane permeability was observed, suggesting that the loss of cell membrane integrity initiates the macroscopic HR evoked by Psm. In contrast, after Pst treatment there was a distinct time lapse between the first signs of tissue collapse (9 hpi) and the occurrence of plasma membrane discontinuity (12 hpi). Ultrastructural studies of cells undergoing the HR triggered by Psm and Pst revealed distinct patterns of alterations in morphology of organelles. Moreover, while different forms of nuclear degeneration were observed in leaf zones infiltrated with Pst, we failed to detect any abnormalities in the nuclei of Psm‐treated tissue. In addition, application of synthetic caspase inhibitors (Ac‐DEVD‐CHO, Ac‐YVAD‐CMK) abolished HR induced by Pst, but not Psm. Our observations suggest that different cell death mechanisms are executed in response to Psm and Pst. Interestingly, pre‐inoculation with Pst, but not with Psm, induced a long‐distance acquired resistance (LDAR) response, even though locally a typical set of defense responses, including acquired resistance, was activated locally in response to Psm. The failure of Psm to induce LDAR may be due to the rapid degeneration of bundle sheath cells resulting from Psm infection.
A mutation in NLA, which encodes a RING‐type ubiquitin ligase, disrupts the adaptability of Arabidopsis to nitrogen limitation
Authors: Peng Mingsheng , Hannam Carol , Gu Honglan , Bi Yong‐Mei , Rothstein Steven J. 
Published: April 2007

SummaryAbundant nitrogen is required for the optimal growth and development of plants, while numerous biotic and abiotic factors that consume soil nitrogen frequently create a nitrogen limitation growth condition. To cope with this, plants have evolved a suite of adaptive responses to nitrogen limitation. However, the molecular mechanism governing the adaptability of plants to nitrogen limitation is totally unknown because no reported mutant defines this trait. Here we isolated an Arabidopsis mutant, nla (nitrogen limitation adaptation), and identified the NLA gene as an essential component in this molecular mechanism. Supplied with insufficient inorganic nitrogen (nitrate or ammonium), the nla mutant failed to develop the essential adaptive responses to nitrogen limitation, but senesced much earlier and more rapidly than did the wild type. Under other stress conditions including low phosphorus nutrient, drought and high temperature, the nla mutant did not show this early senescence phenotype, but closely resembled the wild type in growth and development. Map‐based cloning of NLA revealed that this gene encodes a RING‐type ubiquitin ligase, and nla is a deletion mutation which does not code for the RING domain in the NLA protein. The NLA protein is localized to the nuclear speckles, where this protein interacts with the Arabidopsis ubiquitin conjugase 8 (AtUBC8). In the nla mutant, the deletion of the RING domain from NLA altered its subcellular localization, disrupted the interaction between NLA and AtUBC8 and caused the early senescence phenotype induced by low inorganic nitrogen. All the results indicate that NLA is a positive regulator for the development of the adaptability of Arabidopsis to nitrogen limitation.
14th International HLA and Immunogenetics Workshop: Report on the Prospective Chronic Rejection Project
Authors: Ozawa M. , Terasaki P. I. , Lee J. H. , Castro R. , Alberu J. , Alonso C. , Alvarez I. , Toledo R. , Alvez H. , Monterio M. , Teixeira J. , Campbell P. , Ciszek M. , Charron D. , Gautreau C. , Christiansen F. , Conca R. , Gomez B. , Monteon F. , Grosse‐Wilde H. , Heinemann F. , Humar I. , Kamoun M. , Kimball P. , Kobayashi T. , Kupatawintu P. , Leech S. , LeFor W. , Mehra N. , Panigrahi A. , Naumova E. , Norman D. , Piazza A. , Poli F. , Colombo B. , Roy R. , Schonemann C. , Sireci G. , Tanabe K. , Ishida H. , Van den Berg‐Loonen E. , Zeevi A. 
Published: April 2007

AbstractAn international collaborative study of 45 transplant centers was undertaken at the 14th International HLA (human leukocyte antigen) and Immunogenetics Workshop to see if HLA antibodies detected posttransplant are predictive of chronic graft failure. With the newly developed assay, MICA (major histocompatibility complex class I‐related chain A) antibodies were also measured and their effect analyzed. Total of 5219 sera from patients who were more than 6 months posttransplant with functioning graft were tested for HLA antibodies by enzyme‐linked immunosorbent assay, flow cytometry, or Luminex. HLA antibodies were found in 27.2% of kidney patients, 23.6% in the liver, 52.7% in the heart, and 21.7% in the lung. The method of antibody testing did not have a marked influence on the frequency of antibodies detected. MICA antibodies were detected in 15% of kidneypatients, 30% of heart patients, and 31% of liver patients. Among 948 kidney patients who had HLA antibodies, 7.3% had rejected their graft within 1 year of testing, compared with 1.7% in 2615 patients without HLA antibodies (P= 0.8 × 10−17). Death occurred in 1.4% of total kidney patients and did not correlate to the presence of antibodies. We conclude that patients with posttransplant HLA antibodies indeed have a higher rate of chronic graft failure and that posttransplant antibodies are predictive of chronic rejection.
14th International HLA and Immunogenetics Workshop: Report of progress in methodology, data collection, and analyses
Authors: Single R. M. , Meyer D. , Mack S. J. , Lancaster A. , Erlich H. A. , Thomson G. 
Published: April 2007

AbstractThe Biostatistics Component of the 13th International Histocompatibility Workshop (IHWS) developed the PyPop (Python for Population Genomics) software framework for high‐throughput analysis and quality control (QC) assessments of highly polymorphic genotype data. Since its initial release, the software has had several new analysis modules added to it. These additions, combined with improved data filtering and QC modules, facilitate analyses of data at different levels (allele, haplotype, amino acid sequence, and nucleotide sequence). Since the 13th IHWS, much of the human leukocyte antigen (HLA) data from the workshop, QCed via PyPop and other methods, have been made publicly available through the Major Histocompatibility Complex database web site at the National Center for Biotechnology Information (http://ncbi.nih.gov/mhc/). The Anthropology/Human Genetic Diversity component (AHGDC) data have been used in a variety of studies. Prugnolle et al. used this data to corroborate a model of pathogen‐driven selection as a factor related to high levels of diversity at HLA loci. Using a comparative genomics approach contrasting results for HLA and non‐HLA markers, Meyer et al. analyzed a subset of the 13th IHWS AHGDC data and showed that HLA loci show detectable signs of both natural selection and the demographic history of populations.
PyPop update – a software pipeline for large‐scale multilocus population genomics
Authors: Lancaster A. K. , Single R. M. , Solberg O. D , Nelson M. P. , Thomson G. 
Published: April 2007

AbstractPopulation genetic statistics from multilocus genotype data inform our understanding of the patterns of genetic variation and their implications for evolutionary studies, generally, and human disease studies in particular. In any given population one can estimate haplotype frequencies, identify deviation from Hardy–Weinberg equilibrium, test for balancing or directional selection, and investigate patterns of linkage disequilibrium. Existing software packages are oriented primarily toward the computation of such statistics on a population‐by‐population basis, not on comparisons among populations and across different statistics. We developed PyPop (Python for Population Genomics) to facilitate the analyses of population genetic statistics across populations and the relationships among different statistics within and across populations. PyPop is an open‐source framework for performing large‐scale population genetic analyses on multilocus genotype data. It computes the statistics described above, among others. PyPop deploys a standard Extensible Markup Language (XML) output format and can integrate the results of multiple analyses on various populations that were performed at different times into a common output format that can be read into a spreadsheet. The XML output format allows PyPop to be embedded as part of a larger analysis pipeline. Originally developed to analyze the highly polymorphic genetic data of the human leukocyte antigen region of the human genome, PyPop has applicability to any kind of multilocus genetic data. It is the primary analysis platform for analyzing data collected for the Anthropological component of the 13th and 14th International Histocompatibility Workshops. PyPop has also been successfully used in studies by our group, with collaborators, and in publications by several independent research teams.
14th International HLA and Immunogenetics Workshop: Report on mapping microsatellite markers in the major histocompatibility complex region
Authors: Gourraud P‐A. , Hoffman D. , Cambon‐Thomsen A. , Feolo M. 
Published: April 2007

AbstractThis paper describes the use of the program e‐pcr to localize 687 known major histocompatability complex (MHC) microsatellite primer pairs to their sequence positions in several genomic assemblies across the MHC region. The sequences used were the Sequences of Sanger Institute’s MHC Haplotype Project: COX, PGF, QBL, as well as the Celera, and Reference (PGF across extended MHC) sequences from the NCBI genomic build 36. More than 95% (664/687) of the markers mapped unambiguously to the Reference assembly sequence. All primer pairs used in this analysis, and those were previously unknown to UniSTS, have now been assigned permanent public UniSTS identifiers. Mapping and descriptive data for each primer pair are available at the publicly accessible dbMHC microsatellite resource: http://www.ncbi.nlm.nih.gov/projects/mhc/xslcgi.fcgi?cmd=mssearch