bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergence analysis of a coherency‐constrained inversion for the separation of blended data
Authors: Doulgeris Panagiotis , Bube Kenneth , Hampson Gary , Blacquière Gerrit 
Published: June 2012

ABSTRACTBlended or simultaneous sources have been the focus of a good deal of interest recently. In conventional acquisition the time intervals between successive sources are large enough to avoid interference in time. In blended acquisition, temporal overlap between source responses is allowed. The procedure of retrieving data as if they were acquired in the conventional way is called deblending. This is an essential step if standard processing flows are to be applied.Several inversion techniques have been proposed for solving this ill‐posed problem. We study the properties of an iterative estimation and subtraction algorithm that integrates a coherency‐pass filter in a dedicated iteration. We begin by stating the problem we wish to solve and develop a new, more general, interpretation of the method. We then apply an algebraic analysis of the iteration to establish the convergence characteristics of the algorithm. In order to facilitate this analysis, the notion of leakage subspace is introduced, i.e., a subspace where energy that cannot be uniquely assigned to one of the sources resides. We find that a unique solution exists, if, and only if, there is no leakage subspace. If a unique solution does not exist, then the iteration converges to a least‐norm solution contaminated by the projection of the initial guess onto the leakage subspace. The insights gained by this analysis lead us to the development of a simple tool that can provide valuable information during the design of a blended survey. Finally we present results from the application of this method to real blended marine data and then draw our conclusions.
Multi‐source least‐squares reverse time migration
Authors: Dai Wei , Fowler Paul , Schuster Gerard T. 
Published: June 2012

ABSTRACTLeast‐squares migration has been shown to improve image quality compared to the conventional migration method, but its computational cost is often too high to be practical. In this paper, we develop two numerical schemes to implement least‐squares migration with the reverse time migration method and the blended source processing technique to increase computation efficiency. By iterative migration of supergathers, which consist in a sum of many phase‐encoded shots, the image quality is enhanced and the crosstalk noise associated with the encoded shots is reduced. Numerical tests on 2D HESS VTI data show that the multisource least‐squares reverse time migration (LSRTM) algorithm suppresses migration artefacts, balances the amplitudes, improves image resolution and reduces crosstalk noise associated with the blended shot gathers. For this example, the multisource LSRTM is about three times faster than the conventional RTM method. For the 3D example of the SEG/EAGE salt model, with a comparable computational cost, multisource LSRTM produces images with more accurate amplitudes, better spatial resolution and fewer migration artefacts compared to conventional RTM. The empirical results suggest that multisource LSRTM can produce more accurate reflectivity images than conventional RTM does with a similar or less computational cost. The caveat is that the LSRTM image is sensitive to large errors in the migration velocity model.
Gross cystic disease fluid protein‐15 and mammaglobin A expression determined by immunohistochemistry is of limited utility in triple‐negative breast cancer
Authors: Huo Lei , Zhang Jinxia , Gilcrease Michael Z , Gong Yun , Wu Yun , Zhang Hong , Resetkova Erika , Hunt Kelly K , Deavers Michael T 
Published: June 2012

Aims:  In addition to oestrogen and progesterone receptors, gross cystic disease fluid protein‐15 (GCDFP‐15) and mammaglobin A (MAM) are the most common markers used to identify breast origin by immunohistochemistry. GCDFP‐15 expression has been reported in approximately 60% of breast carcinomas and MAM expression in approximately 80%. Data on their expression in triple‐negative breast cancer (TNBC) are very limited. The aim of this study was to examine the expression of these markers in TNBC to determine their utility in pathological diagnosis.Methods and results:  We studied the immunohistochemical (IHC) expression of GCDFP‐15 and MAM in 63 primary and 118 metastatic TNBCs. GCDFP‐15 staining was present in 14% of primary and 21% of metastatic TNBCs. MAM staining was present in 25% of primary and 41% of metastatic TNBCs. The frequency of expression of GCDFP‐15 and/or MAM was 30% in primary and 43% in metastatic TNBCs, and many positive tumours had only focal staining.Conclusions:  Staining for GCDFP‐15 and/or MAM in triple‐negative carcinomas helps to confirm breast origin, but most tumours in this subgroup of breast carcinomas lack expression of either marker.
Overexpression of Toll‐Like Receptor 3 in Spleen is Associated with Experimental Arthritis in Rats
Authors: Zhu W. , Meng L. , Jiang C. , Xu J. , Wang B. , Han Y. , Lu S. 
Published: June 2012

AbstractThis study is to investigate the regulation of Toll‐like receptor (TLR) expression in systemic immune reactions in different arthritis rat models, which will provide evidence to understand the mechanisms of rheumatoid arthritis further. Arthritis‐susceptible DA rats were used to induce arthritis by pristane or collagen type II, and TLR2, 3, 4 and 7 expression levels in spleen were detected by real‐time quantitative polymerase chain reaction. TLR3 mRNA expression in spleen of both collagen‐induced arthritis and pristane‐induced arthritis (PIA) rats was increased significantly at 26 and 70 days after arthritis induction. The overexpression of TLR3 was confirmed by Western blotting. Methotrexate was administrated peritoneally to PIA rats, and phytol was applied subcutaneously to PIA rats. Both methotrexate and phytol treatment could alleviate arthritis severity and block TLR3 induction. However, in arthritis‐resistant E3 rats injected with pristane, TLR3 expression of spleen was unaltered. PIA in MHC congenic DA.1U rats had mild symptoms, whereas TLR3 mRNA expression in spleen of DA.1U rats showed an impaired induction at D26. So we conclude that overexpression of splenic TLR3 is strongly associated with arthritis in rats, which suggests that TLR3 should be a most vital TLR in spleen to regulate the initiation and development of experimental arthritis and may be as an intriguing therapeutic opportunity for human rheumatoid arthritis.
Sindbis Virus Replicase‐based DNA Vaccine Construct Encoding FMDV‐specific Multivalent Epitope Gene: Studies on its Immune Responses in Guinea Pigs
Authors: Dar P. A. , Ganesh K. , Nagarajan G. , Sarika S. , Reddy G. R. , Suryanarayana V. V. S. 
Published: June 2012

AbstractFoot‐and‐mouth disease (FMD) is still a perennial global menace affecting livestock health and production. It is imperative to figure out new ways to curb this disease. In this study, a sindbis virus replicase‐based DNA vaccine, pSinCMV‐Vac‐MEG990, encoding a multivalent epitope gene (representing tandemly linked VP1 C‐terminal halves of three foot‐and‐mouth disease virus (FMDV) serotypes) was constructed. In vitro transfection studies in BHK‐21 cells revealed that the construct was able to express FMDV‐specific antigen but does not overproduce the antigen. Immunization of guinea pigs with the construct at dose rate of 10, 5, 2 and 1 μg per animal through intramuscular route showed significant neutralizing antibody induction at all doses against all serotype tested as compared to non‐immunized controls. On viral challenge of guinea pigs 4 week post‐immunization with 1000 GPID50 of FMDV serotype A, it was observed that the immunization not only delayed the appearance and reduced the severity of FMD lesions significantly (P < 0.05) but also provided complete protection in several guinea pigs. In fact, two of six and one of six guinea pigs were completely protected in 10 and 5 μg immunized groups, respectively. These results suggest that the development of the replicase‐based DNA vaccine may provide a promising approach as an alternative vaccine strategy for controlling FMD.
Single Nucleotide Polymorphism in the Interleukin 12B Gene is Associated with Risk for Breast Cancer Development
Authors: Kaarvatn M. H. , Vrbanec J. , Kulic A. , Knezevic J. , Petricevic B. , Balen S. , Vrbanec D. , Dembic Z. 
Published: June 2012

AbstractWe analysed the association of a single nucleotide polymorphism (SNP) in the gene encoding the IL‐12 subunit p40 (IL12B, rs3212227, A>C) with breast cancer. The SNPs allelic and genotypic frequencies were compared between patients (n = 191) and healthy (n = 194) women in a case–control study from Croatia. The major allele (A) was associated with susceptibility to breast cancer (P = 0.003; OR = 1.67; 95% CI: 1.17–2.38). Likewise, the minor allele (C) was significantly correlated with protection (P = 0.003; OR = 0.60; 95% CI: 0.42–0.86). At the genotype level, AA homozygosity was significantly associated with predisposition to disease (P = 0.013; OR = 1.68, 95% CI: 1.09–2.59), whereas the minor allele homozygosity (CC) was correlated with protection to disease (P = 0.020, OR = 0.28, 95% CI: 0.09–0.91). The heterozygous genotype showed no significant correlation with disease. The product of the IL12B gene (IL‐12 p40) can either form a homodimeric cytokine or be part of two pro‐inflammatory (IL‐12 and IL‐23) cytokines. It is presently unclear whether the major allele is associated with higher or lower protein levels of IL‐12 p40 and IL‐12 p70, which are critical in inflammation and adaptive immune responses. However, as the A allele is high producer of IL12B (p40) mRNA, these results might imply that higher levels of IL‐12 p40 (either as homodimers or joined with one or both of the other two subunits) predispose to breast cancer.
Toll‐Like Receptor Gene Polymorphisms Confer Susceptibility to Graft‐Versus‐Host Disease in Allogenic Hematopoietic Stem Cell Transplantation
Authors: Sivula J. , Cordova Z. M. , Tuimala J. , Jaatinen T. , Partanen J. , Volin L. , Turpeinen H. 
Published: June 2012

AbstractGraft‐versus‐host disease (GvHD) is a major complication in hematopoietic stem cell transplantation (HSCT). The immune response against gut microbes is thought to be an important factor in the beginning of GvHD. Toll‐like receptors (TLR) recognize molecular structures of microbes and viruses and play central part in the innate immunity. We studied whether genetic variation in the TLR1, TLR2, TLR4, TLR5, TLR6 and TLR10 genes confers susceptibility to GvHD in 305 human leucocyte antigen‐identical sibling donor HSCT's performed in a single Finnish centre. The results showed that the genetic markers rs4833079 (P = 0.035) in TLR1, rs4837656 (P = 0.032) and rs17582214 (P = 0.029) in TLR4, rs10737416 (P = 0.048) in TLR5, rs6531656 (P = 0.035) in TLR6, and rs337629 (P = 0.005) in TLR10 were associated with the occurrence of acute GvHD. Interestingly, two markers in the TLR5 gene, rs2800230 (P = 0.010) and rs2800237 (P = 0.017), were associated with chronic GvHD. These results indicate that many genes of the TLR system are involved in the overall genetic risk for GvHD and emphasize the role of innate immunity in GvHD.
Transcriptome Analysis of the Interferon‐Signature Defining the Autoimmune Process of Sjögren’s Syndrome
Authors: Peck A. B. , Nguyen C. Q. 
Published: June 2012

AbstractSjögren’s syndrome (SS) of humans and SS‐like (SjS‐like) diseases in mouse models are characterized by chronic immune attacks against the salivary and lacrimal glands leading to exocrine dysfunction. One characteristic of SS and SjS‐like diseases repeatedly observed is a strong upregulated expression of both the type I (α/β) and type II (γ) interferons (IFNs). In addition, recent global transcriptome studies have identified a variety of IFN‐stimulated gene (ISG) transcripts differentially expressed in tissues of SS patients and mouse models exhibiting SjS‐like disease. Analyses of these transcriptome databases indicate that the sets of differentially expressed genes are highly restricted, suggesting that there is a unique specificity in ISGs activated (or suppressed) during development and onset of disease. As a result, these observations have led to both SS and SjS‐like diseases being designated as ‘interferon‐signature’ diseases. While SS and SjS‐like diseases may be designated as such, very little effort has been made to determine what an interferon‐signature might signify relative to autoinflammation and whether it might point directly to an underlying etiopathological mechanism. Here, we review these limited data and provide a model of how the products of these genes interact molecularly and biologically to define critical details of SS pathology.
Arabidopsis thaliana CENTRORADIALIS homologue(ATC) acts systemically to inhibit floral initiation in Arabidopsis
Authors: Huang Nien‐Chen , Jane Wann‐Neng , Chen Jychian , Yu Tien‐Shin 
Published: June 2012

SummaryFloral initiation is orchestrated by systemic floral activators and inhibitors. This remote‐control system may integrate environmental cues to modulate floral initiation. Recently, FLOWERING LOCUS T (FT) was found to be a florigen. However, the identity of systemic floral inhibitor or anti‐florigen remains to be elucidated. Here we show thatArabidopsis thaliana CENTRORADIALIS homologue(ATC), an ArabidopsisFThomologue, may act in a non‐cell autonomous manner to inhibit floral initiation. Analysis of theATCnull mutant revealed thatATCis a short‐day‐induced floral inhibitor. Cell type‐specific expression showed that companion cells and apex that expressATCare sufficient to inhibit floral initiation. Histochemical analysis showed that the promoter activity ofATCwas mainly found in vasculature but under the detection limit in apex, a finding that suggests thatATCmay move from the vasculature to the apex to influence flowering. Consistent with this notion, Arabidopsis seedling grafting experiments demonstrated thatATCmoved over a long distance and that floral inhibition byATCis graft transmissible. ATC probably antagonizes FT activity, because both ATC and FT interact with FD and affect the same downstream meristem identity genesAPETALA1, in an opposite manner. Thus, photoperiodic variations may trigger functionally oppositeFThomologues to systemically influence floral initiation.
Rhomboid proteins in the chloroplast envelope affect the level of allene oxide synthase in Arabidopsis thaliana
Authors: Knopf Ronit Rimon , Feder Ari , Mayer Kristin , Lin Albina , Rozenberg Mor , Schaller Andreas , Adam Zach 
Published: June 2012

SummaryRhomboids are intra‐membrane serine proteases whose sequences are found in nearly all organisms. They are involved in a variety of biological functions in both eukaryotes and prokaryotes. Localization assays revealed that two Arabidopsis thaliana rhomboid‐like proteases (AtRBL), AtRBL8 and AtRBL9, are targeted to the chloroplast. Using transgenic plants expressing epitope‐tagged AtRBL9, we localized AtRBL9 to the chloroplast inner envelope membrane, with both its N‐ and C‐termini facing the stroma. Mass spectrometry analyses confirmed this localization, and suggested that this is also the case for AtRBL8. Both are proteins of very low abundance. The results of size‐exclusion chromatography implied that AtRBL9 forms homo‐oligomers. In search of a putative function, a comparative proteomic analysis was performed on wild‐type and double‐knockout plants, lacking both AtRBL8 and AtRBL9, using the iTRAQ method. Of 180 envelope proteins, the level of only a few was either increased or decreased in the mutant line. One of the latter, allene oxide synthase, is involved in jasmonic acid biosynthesis. This observation provides an explanation for the recently reported aberration in flower morphology that is associated with the loss of AtRBL8.
New Antagonistic Strains of Non‐Pathogenic Agrobacterium vitis to Control Grapevine Crown Gall
Authors: Kawaguchi Akira , Inoue Koji 
Published: June 2012

AbstractGraft unions of nursery stock of grapevine (Vitis vinifera L.) collected in Japan yielded non‐pathogenic strains of Agrobacterium. On the basis of classic diagnostic tests, a sequence analysis and a previously reported multiplex PCR method, the non‐pathogenic strains ARK‐1, ARK‐2 and ARK‐3 were identified as Agrobacterium vitis. Stems of grapevine seedlings were inoculated with both a cell suspension of seven mixed strains of A. vitis (Ti) as a pathogen and one of a new strain or A. vitis strain VAR03‐1, one of the biological control agents against crown gall previously reported, as competitors to assay the suppression of tumour formation caused by the pathogen. In a test with a 1:1 cell ratio of pathogen/nonpathogen, strains ARK‐1, ARK‐2 and ARK‐3 reduced the tumour incidence.. In particular, strain ARK‐1 was strongest at inhibiting tumour formation in this study. Strain ARK‐1 established populations on roots of grapevine tree rootstock and persisted on roots for a year. ARK‐1, ARK‐2 and ARK‐3 did not produce a halo of inhibition against A. vitis (Ti) strain on YMA medium. Moreover, strain ARK‐1 did not reduce tumour incidence on the stems of grapevine when ARK‐1 was dead or only culture filtrate was used. This result indicates the possibility that these new strains inhibit grapevine crown gall in planta by a different mechanism other than VAR03‐1. In particular, one of the new strains, named ARK‐1, was most effective in inhibiting tumour formation on grapevine and appears to be a promising new agent to control grapevine crown gall.
Cell Cycle–dependent Dynamics of Cytoskeleton Involving Mitochondrial Redistribution in Hamster Embryos
Authors: Kabashima K , Yoshinaga D , Fang J , Matsuzaki M , Suzuki H 
Published: June 2012

ContentsMitochondria–cytoskeleton interactions were studied in the hamster embryos during interphase and M phase of the cell cycle. Two‐cell embryos were cultured for 1 h with nocodazole, cytochalasin D or in a combination of both inhibitors and then centrifuged at 10 000×g for 2 min. The control embryos were only centrifuged with no inhibitor treatment. Centrifuged embryos were fluorescently stained to examine the distribution of active mitochondria and nuclear configuration. In the control 2‐cell embryos, most mitochondria were accumulated at the perinuclear region with some at the cell cortex. Neither each inhibitor nor centrifugation did affect the distribution of mitochondria in interphase blastomeres. However, mitochondria were spun down towards the centrifugal pole in 71% (n = 41) of the interphase blastomeres treated with centrifugation following a combination of nocodazole plus cytochalasin D, suggesting that both microtubules and microfilaments may involve in mitochondrial redistribution during interphase of the cell cycle. In contrast, when M‐phase blastomeres were treated with all drug treatments applied, including cytochalasin D, mitochondria had been usually dislocated in a unipolar cluster, suggesting that microfilaments, not microtubules, may involve in the mitochondrial redistribution during M phase of the cell cycle. The data indicate that microfilaments function in mitochondrial redistribution regardless of the stages of the cell cycle and that microtubules may strongly associate with mitochondria during the interphase but dissociate from them during the M phase.
Effect of nitric oxide donors S‐nitroso‐N‐acetyl‐dl‐penicillamine, spermine NONOate and propylamine propylamine NONOate on intracellular pH in cardiomyocytes
Authors: Pravdic Danijel , Vladic Nikolina , Cavar Ivan , Bosnjak Zeljko J 
Published: June 2012

Summary
Previous studies suggest that exogenous nitric oxide (NO) and NO‐dependent signalling pathways modulate intracellular pH (pHi) in different cell types, but the role of NO in pHi regulation in the heart is poorly understood. Therefore, in the present study we investigated the effect of the NO donors S‐nitroso‐N‐acetyl‐dl‐penicillamine, spermine NONOate and propylamine propylamine NONOate on pHi in rat isolated ventricular myocytes.
Cells were isolated from the hearts of adult Wistar rats and pHi was monitored using the pH‐sensitive fluorescent indicator 5‐(and‐6)‐carboxy seminaphtharhodafluor (SNARF)‐1 (10 μmol/L) and a confocal microscope. To test the effect of NO donors on the Na+/H+ exchanger (NHE), basal pHi in Na+‐free buffer and pHi recovery from intracellular acidosis after an ammonium chloride (10 mmol/L) prepulse were monitored. The role of carbonic anhydrase was tested using acetazolamide (50 μmol/L). 4,4‐Diisothiocyanatostilbene‐2,2′‐disulphonic acid (0.5 mmol/L; DIDS) was used to inhibit the Cl−/OH− and Cl−/exchangers. Acetazolamide and DIDS were applied via the superfusion system 1 and 5 min before the NO donors.
All three NO donors acutely decreased pHi and this effect persisted until the NO donor was removed. In Na+‐free buffer, the decrease in basal pHi was increased, whereas inhibition of carbonic anhydrase and Cl−/OH− and Cl−/ exchangers did not alter the effects of the NO donors on pHi. After an ammonium preload, pHi recovery was accelerated in the presence of the NO donors.
In conclusion, exogenous NO decreases basal pHi, leading to increased NHE activity. Carbonic anhydrase and chloride‐dependent sarcolemmal and OH− transporters are not involved in the NO‐induced decrease in pHi in rat isolated ventricular myocytes.
Suspected macular degeneration in a captive western lowland gorilla (gorilla gorilla gorilla)
Authors: Steinmetz Andrea , Bernhard Andreas , Sahr Sabine , Oechtering Gerhard 
Published: June 2012

AbstractThe case of a 31‐year‐old captive female Western lowland gorilla (Gorilla gorilla gorilla) with decreased near vision but good distance vision is presented. Examination of the fundus revealed drusen‐like bodies in the macula presumably because of an age‐related macular degeneration (AMD).
Abundant immunoglobulin E‐positive cells in skin lesions support an allergic etiology of atopic dermatitis in the elderly
Authors: Tanei R. , Hasegawa Y. , Sawabe M. 
Published: June 2012

AbstractBackground/Objectives  Atopic dermatitis (AD) in the elderly is gradually increasing in industrialized countries in association with the aging of society. We report herein four cases of elderly AD {three extrinsic [immunoglobulin (Ig)E‐mediated allergy]; one intrinsic (non‐IgE‐allergy)} in which we investigated the presence of IgE+ cells in lesional skin.Methods/Results  Single immunohistochemical and double immunofluorescence stainings were performed for skin biopsy specimens from AD patients and non‐atopic control subjects with chronic eczema. In the lesional lichenified skin of patients with extrinsic elderly AD, numerous IgE+ cells were found among inflammatory cells infiltrates in the upper dermis. Comparative analysis of single immunohistochemistry results using serial paraffin and/or frozen sections found that many IgE+ cells showed identical distributions to tryptase+ mast cells. IgE+ cells coincident with CD1a+ Langerhans cells in the epidermis were found in small numbers only in frozen sections. Double immunofluorescence staining for IgE and CD11c revealed cells coexpressing IgE and CD11c with a dendritic morphology in the papillary and upper dermis. These IgE+ mast cells and IgE+ CD11c+ cells were also found in cured normal‐looking skin from a patient with extrinsic elderly AD after successful treatment. Although only a few weakly positive IgE+ cells were detected, no IgE+CD11c+ cells were found in specimens from patients with intrinsic elderly AD or non‐atopic chronic eczema.Conclusion  IgE‐mediated allergic inflammation may play an important role in the pathobiology of elderly AD, similar to other age groups of AD.