bluuebunny/crossref_metadata_2025_split huggingface dataset:
“OUR DEEP, DEAR SILENCE”: MARRIAGE AND LYRICISM IN THESONNETS FROM THE PORTUGUESE
Authors: Williams Rhian 
Published: February 2009

SonnetXLIof Elizabeth Barrett Browning'sSonnets from the Portugueseis candid about its ambition to write love poetry that will last:— Oh, to shootMy soul's full meaning into future years, —Thattheyshould lend it utterance, and saluteLove that endures, with Life that disappears! – (Barrett Browning 397)This is a rare moment in the sequence of hope enunciated. Although littered with apparently unfettered exclamations of the newly loved and newly loving – “I seemed not one | For such man's love!” (XXXII), “Beloved, I onlylove thee!” (IX) – therhetorical modeof theSonnets from the Portuguesealso feels reticent, provisional, even transient: “This said, ‘I am thine’ – and so, its ink has paled | With lying at my heart that beats too fast” (XXVIII). Yet the sequence's desire for endurance may be reconciled with its frequent return to moments of erasure – “My letters! – all dead paper, . . . mute and white! –” (XXVIII) – by attending to the generative effects of silence in this most ambivalent of sonnet performances. Indeed, the sequence appears to fall in with Daniel Barenboim's logic, which would dictate that if ensuing years are to produce, as the sonnet anticipates, “utterance” – to form sound – the sonnet itself must provide the pre-silence. If silence is the pulse of “Love that endures” (passing over from life to love), then theSonnets from the Portuguesebecome, perhaps, an exercise in learning, in Derrida's terms, “how to be silent.” Despite such elevated investment, however, silence clearly troubles our reading of this sonnet sequence; not only does it threaten to undermine the efficacy of a sequence celebrated for theenunciationof love, but it also gestures at a broader Victorian discourse in which silence and “woman-love,” as sonnet XIII names it, are more frequently brought together as an effect of systemized suppression. But, I suggest that these sonnets are, in fact, pushing us to reconsider how we read silence; perhaps surprisingly, this is revealed by paying attention to the sequence's careful anticipation of marriage. Indeed, establishing a conjugal perspective on these poems reveals a radical dynamic in which silencing, in fact, gives way to finding, as Derrida asks, “how to say something.”
Statistical methods of background correction for Illumina BeadArray data
Authors: Xie Yang , Wang Xinlei , Story Michael 
Published: February 2009

Abstract
Motivation: Advances in technology have made different microarray platforms available. Among the many, Illumina BeadArrays are relatively new and have captured significant market share. With BeadArray technology, high data quality is generated from low sample input at reduced cost. However, the analysis methods for Illumina BeadArrays are far behind those for Affymetrix oligonucleotide arrays, and so need to be improved.
Results: In this article, we consider the problem of background correction for BeadArray data. One distinct feature of BeadArrays is that for each array, the noise is controlled by over 1000 bead types conjugated with non-specific oligonucleotide sequences. We extend the robust multi-array analysis (RMA) background correction model to incorporate the information from negative control beads, and consider three commonly used approaches for parameter estimation, namely, non-parametric, maximum likelihood estimation (MLE) and Bayesian estimation. The proposed approaches, as well as the existing background correction methods, are compared through simulation studies and a data example. We find that the maximum likelihood and Bayes methods seem to be the most promising.
Contact: yang.xie@utsouthwestern.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Potato spindle tuber viroid in Cape Gooseberry (Physalis peruviana) from Turkey and Germany
Authors: Verhoeven J. Th. J. , Botermans M. , Roenhorst J. W. , Westerhof J. , Meekes E. T. M. 
Published: February 2009

Since the recent identification of Potato spindle tuber viroid (PSTVd) in vegetatively propagated ornamental plant species (4), many growers have asked to have their mother plants tested for this viroid. In December of 2007, a grower from Turkey submitted cuttings of cape gooseberry (Physalis peruviana) to be tested for PSTVd. Initial testing by real-time reverse transcription (RT)-PCR according to Boonham et al. (1) indicated the presence of either Mexican papita viroid, PSTVd, or Tomato chlorotic dwarf viroid in four samples. To identify the viroid(s) present, isolated RNA from these samples was used for RT-PCR (2), and products of the expected full genome size for the three viroids were amplified from each sample. One of the PCR products was sequenced (GenBank Accession No. EU862230) and analysis of the 357 nt sequence indicated it was most related to PSTVd sequences belonging to the so-called ‘Oceanian’ strain of the viroid (3), with 99.7% identity to GenBank Accession No. AY962324. Therefore, the viroid was identified as PSTVd. Pathogenicity of this PSTVd genotype was demonstrated when 4 weeks after mechanical inoculation with sap extracts seedlings of tomato cv. Money-maker showed the expected viroid symptoms of chlorosis and stunting, and the presence of the viroid in these plants was confirmed by RT-PCR (2). In March of 2008, by use of RT-PCR (2) and sequencing of the PCR product (GenBank Accession No. EU862231), PSTVd was identified in young seedlings of P. peruviana from a German grower. The German isolate differed at only three nucleotide positions from the Turkish isolate. The identification of PSTVd in young seedlings indicates that seeds had been source of infection, whereas in the case of the PSTVd infected cuttings from Turkey, the infection originated from infected mother plants. To our knowledge, these are the first reports of PSTVd in P. peruviana. Although infected P. peruviana plants did not show symptoms, they might act as sources of inoculum for crops like potato and tomato, which may suffer serious damage. References: (1) N. Boonham et al. J. Virol. Methods 116:139, 2004. (2) A. M. Shamloul et al. Can. J. Plant Pathol. 19:89, 1997. (3) J. Th. J. Verhoeven et al. Eur. J. Plant Pathol. 110:823, 2004. (4) J. Th. J. Verhoeven et al. Plant Pathol. 57:399, 2008.
First Report of the Soybean Cyst Nematode, Heterodera glycines, on Soybean in Zhejiang, Eastern China
Authors: Zheng J. , Zhang Y. , Li X. , Zhao L. , Chen S. 
Published: February 2009

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is a destructive pest of soybean. Damage to soybean by SCN was first reported from northeastern China in 1899 (1). SCN has been documented in Anhui, Beijing, Hebei, Heilongjiang, Henan, Jiangsu, Jilin, Liaoning, Neimenggu, Shaanxi, Shandong, and Shanxi provinces in mainland China (1). These provinces are situated in the Heilongjiang and Songhuajing valleys in northeastern China and the eastern region of the Yangtze and Yellow rivers in northern China and have cold to temperate climates. In June of 2008, cyst-forming nematodes were detected in two soybean-growing areas of Hangzhou and Xiaoshan in Zhejiang Province, in subtropical eastern China. The soybean plants at the Hangzhou site showed symptoms of stunting and chlorosis, whereas no aboveground or root symptoms were observed on soybean plants at the Xiaoshan site, except for the presence of SCN females on the roots. The two populations had the same morphological and molecular characters. The cysts were lemon shaped with posterior protuberance, ambifenestrate, underbridge and bullae strongly developed, and lateral field of second-stage juveniles consisted of four incisures. The key morphometrics of cysts were fenestra length (41 to 52 μm) and width (33 to 48 μm), vulval silt (47 to 55 μm), and underbridge length (79 to 94 μm), all of which were coincident with that of SCN (2). Amplification of rDNA-internal transcribed spacer (ITS) region using primers TW81 (5′-GTT TCC GTA GGT GAA CCT GC-3′) and AB28 (5′-ATA TGC TTA AGT TCA GCG GGT-3′) yielded a PCR fragment of approximately 1,030 bp. The digestion patterns of the PCR fragments of the ITS region with AluI, AvaI, CfoI, MvaI, and RsaI showed identical restriction profiles to H. glycines (3), and the sequences exhibited 100% similarity with those of H. glycines isolates, Accession No. AY667456 from GenBank. Morphological and molecular identification confirmed that the two populations of cyst-forming nematodes from Zhejiang are SCN. To our knowledge, this is the first report of SCN in Zhejiang, now the most southern location in mainland China with confirmed infestation of SCN. References: (1) Z. X. Liu et al. Int. J. Nematol. 7:18, 1997. (2) R. H. Mulvey. Can. J. Zool. 50:1277, 1972. (3) J. Zheng et al. Russ. J. Nematol. 8:109, 2000.
Laparoscopic Transdiaphragmatic Access to the Apex of the Left Ventricle of the Heart
Authors: Thompson Jess L. , Suri Rakesh M. , McKellar Stephen H. , Schaff Hartzell V. 
Published: February 2009

Objective Delivery of a collapsable aortic valve prosthesis via the left ventricular (LV) apex has proven problematic clinically. We describe our experience with a novel technique for a laparoscopic transdiaphragmatic approach to the LV outflow tract (LVOT). Methods Laparoscopic transabdominal access to the left ventricle was achieved in four live swine and one human cadaver using three abdominal laparoscopic trocars. Pericardioscopy and cardioscopy were performed. A hemostatic purse-string suture was placed laparoscopically at the apex of the left ventricle in one pig, and an instrument passed through the purse-string and into the LVOT. After the procedure, a thoracotomy was performed and the heart explanted for gross examination. Results Transdiaphragmatic exposure of the LV apex was accomplished at a mean of 23 minutes. Hemodynamic stability was maintained in all animals and the pleural cavities were not violated. Pericardioscopy allowed visualization of both right and left pulmonary veins along with the left atrial appendage. In situ cardioscopy confirmed that access to the LVOT and the aortic annulus was possible from the LV apex entry site. Conclusions Laparoscopic transdiaphragmatic approach to the LVOT is a possible route for minimally invasive beating heart aortic valve implantation. This strategy permits a straight transapical line of access to the aortic valve; avoiding the potential for cardiac torsion via a thoracotomy.
Inhibition of SNF1-Related Protein Kinase1 Activity and Regulation of Metabolic Pathways by Trehalose-6-Phosphate
Authors: Zhang Yuhua , Primavesi Lucia F. , Jhurreea Deveraj , Andralojc P. John , Mitchell Rowan A.C. , Powers Stephen J. , Schluepmann Henriette , Delatte Thierry , Wingler Astrid , Paul Matthew J. 
Published: February 2009

Abstract
Trehalose-6-phosphate (T6P) is a proposed signaling molecule in plants, yet how it signals was not clear. Here, we provide evidence that T6P functions as an inhibitor of SNF1-related protein kinase1 (SnRK1; AKIN10/AKIN11) of the SNF1-related group of protein kinases. T6P, but not other sugars and sugar phosphates, inhibited SnRK1 in Arabidopsis (Arabidopsis thaliana) seedling extracts strongly (50%) at low concentrations (1–20 μ m). Inhibition was noncompetitive with respect to ATP. In immunoprecipitation studies using antibodies to AKIN10 and AKIN11, SnRK1 catalytic activity and T6P inhibition were physically separable, with T6P inhibition of SnRK1 dependent on an intermediary factor. In subsequent analysis, T6P inhibited SnRK1 in extracts of all tissues analyzed except those of mature leaves, which did not contain the intermediary factor. To assess the impact of T6P inhibition of SnRK1 in vivo, gene expression was determined in seedlings expressing Escherichia coli otsA encoding T6P synthase to elevate T6P or otsB encoding T6P phosphatase to decrease T6P. SnRK1 target genes showed opposite regulation, consistent with the regulation of SnRK1 by T6P in vivo. Analysis of microarray data showed up-regulation by T6P of genes involved in biosynthetic reactions, such as genes for amino acid, protein, and nucleotide synthesis, the tricarboxylic acid cycle, and mitochondrial electron transport, which are normally down-regulated by SnRK1. In contrast, genes involved in photosynthesis and degradation processes, which are normally up-regulated by SnRK1, were down-regulated by T6P. These experiments provide strong evidence that T6P inhibits SnRK1 to activate biosynthetic processes in growing tissues.
Rituximab‐based immunosuppression for autoimmune haemolytic anaemia in infants
Authors: Svahn Johanna , Fioredda Francesca , Calvillo Michaela , Molinari Angelo C. , Micalizzi Concetta , Banov Laura , Schmidt Madalina , Caprino Daniela , Marinelli Doretta , Gallisai Domenico , Dufour Carlo 
Published: February 2009

SummaryWe report a case series of four infants with severe autoimmune haemolytic anaemia (AIHA) who responded to treatment with rituximab and cyclosporine after having failed first line therapy with high‐dose steroid (prednisolone 4–8 mg/kg/d). Rituximab was started at 11–90 d from onset due to continued haemolysis; three infants also received cyclosporine A. Three of four infants reached complete response, defined as normal haemoglobin, reticulocytes and negative indices of haemolysis, at 7–21 months from diagnosis. In long‐term follow‐up two infants remained disease‐free with normal immunology, one had undefined immunodeficiency and one had autoimmune lymphoproliferative syndrome.
Composition of the immunoglobulin classic antigen‐binding site regulates allergic airway inflammation in a murine model of experimental asthma
Authors: Kerzel S. , Wagner J. , Rogosch T. , Yildirim A.‐Ö. , Sikula L. , Fehrenbach H. , Garn H. , Maier R. F. , Schroeder Jr H. W. , Zemlin M. 
Published: February 2009

SummaryBackground
When bound to mast cell FcɛRI, IgE serves as antigen receptor for allergic reactions, permitting specific identification of the allergen. Although the core of the classic antigen‐binding site is heavy chain complementarity determining region 3 (CDR‐H3), recent studies suggest that allergens might also bind IgE in a superantigen‐like fashion outside the classic antigen‐binding site.Objective
We sought to evaluate the contribution of the classic CDR‐H3‐centric antigen‐binding site to the development of an allergic phenotype.Methods
Using a murine model of experimental asthma, we characterized a gene‐targeted mouse strain expressing an altered range of CDR‐H3s (ΔD‐iD mice) in response to the hydrophobic allergen ovalbumin (OVA). Mutant and wild‐type (wt) mice were sensitized intraperitoneally with OVA; non‐sensitized mice served as controls.Results
We found the composition of the classic CDR‐H3‐centric antigen‐binding site to be critical for the development of characteristic aspects of allergic asthma. (i) Compared with wt animals, ΔD‐iD mice showed a significantly less pronounced OVA ‐induced rise in allergen‐specific IgE levels and hence in total serum IgE levels. (ii) In addition, ΔD‐iD mice demonstrated a significant reduction in eosinophilic airway inflammation, as well as in interleukin‐4 (IL‐4), IL‐5 and IL‐13 levels in BAL fluids.Conclusion
Allergic sensitization and airway inflammation depend on the composition of the predominant CDR‐H3 repertoire, suggesting that the classic CDR‐H3‐centric antigen‐binding site plays a crucial role in creating the immunological interface between allergen and IgE. Our results further emphasize a central role of IgE, not only in mediating but also in regulating the allergic immune response.
T‐cell seeding: neonatal transfer of anti‐myelin basic protein T‐cell lines renders Fischer rats susceptible later in life to the active induction of experimental autoimmune encephalitis
Authors: Volovitz Ilan , Mor Felix , Machlenkin Athur , Goldberger Ofir , Marmor Yotvat , Eisenbach Lea , Cohen Irun 
Published: February 2009

SummaryFischer strain rats resist active induction of experimental autoimmune encephalomyelitis (EAE) following immunization with guinea‐pig myelin basic protein (MBP) in complete Freund’s adjuvant (CFA). Nevertheless, we now report that an encephalitogenic CD4+ anti‐MBP T‐cell line could be developed from actively immunized Fischer rats. Adoptive transfer of the activated line mediated acute EAE in adult Fischer rats, but not in 1‐day‐old rats. Moreover, we found that both resting and activated anti‐MBP T cells injected 1 day post‐natally rendered these rats susceptible later in life to the active induction of EAE by immunization with MBP/CFA. The actively induced EAE manifested the accelerated onset of a secondary, memory‐type response. Resting anti‐MBP T cells injected even up to 2 weeks post‐natally produced no clinical signs but seeded 50–100% of the recipients for an active encephalitogenic immune response to MBP. An earlier T‐cell injection (1–2 days) produced a higher incidence and stronger response. The transferred resting T cells entered the neonatal spleen and thymus and proliferated there but did not change the total anti‐MBP precursor number in adults. Splenocytes harvested from rats that were injected neonatally but not exposed to MBP in vivo proliferated strongly and produced significant amounts of interferon‐γ to MBP in vitro. Similar results were observed in rats injected with resting T‐cell lines reactive to ovalbumin, suggesting that the neonatal injection of resting T cells specific for a self or for a foreign antigen can seed the immune system with the potential for an enhanced effector response to that antigen later in life.
Adenosine regulates CD8 T‐cell priming by inhibition of membrane‐proximal T‐cell receptor signalling
Authors: Linnemann Carsten , Schildberg Frank A. , Schurich Anna , Diehl Linda , Hegenbarth Silke I. , Endl Elmar , Lacher Svenja , Müller Christa E. , Frey Jürgen , Simeoni Luca , Schraven Burkhart , Stabenow Dirk , Knolle Percy A. 
Published: February 2009

SummaryAdenosine is a well‐described anti‐inflammatory modulator of immune responses within peripheral tissues. Extracellular adenosine accumulates in inflamed and damaged tissues and inhibits the effector functions of various immune cell populations, including CD8 T cells. However, it remains unclear whether extracellular adenosine also regulates the initial activation of naïve CD8 T cells by professional and semi‐professional antigen‐presenting cells, which determines their differentiation into effector or tolerant CD8 T cells, respectively. We show that adenosine inhibited the initial activation of murine naïve CD8 T cells after αCD3/CD28‐mediated stimulation. Adenosine caused inhibition of activation, cytokine production, metabolic activity, proliferation and ultimately effector differentiation of naïve CD8 T cells. Remarkably, adenosine interfered efficiently with CD8 T‐cell priming by professional antigen‐presenting cells (dendritic cells) and semi‐professional antigen‐presenting cells (liver sinusoidal endothelial cells). Further analysis of the underlying mechanisms demonstrated that adenosine prevented rapid tyrosine phosphorylation of the key kinase ZAP‐70 as well as Akt and ERK1/2 in naïve αCD3/CD28‐stimulated CD8 cells. Consequently, αCD3/CD28‐induced calcium‐influx into CD8 cells was reduced by exposure to adenosine. Our results support the notion that extracellular adenosine controls membrane‐proximal T‐cell receptor signalling and thereby also differentiation of naïve CD8 T cells. These data raise the possibility that extracellular adenosine has a physiological role in the regulation of CD8 T‐cell priming and differentiation in peripheral organs.
Alpha‐1 Antitrypsin (AAT) and Alpha‐fetoprotein (AFP) in Sera of Patients with Germ Cell Neoplasm
Authors: HAIJE W. G. , TALERMAN A. , BAGGERMAN L. 
Published: February 2009

Serum alpha‐fetoprotein (AFP) and serum alpha‐1 antitrypsin (AAT) was determined in 24 patients with germ cell neoplasms of the gonads and extra‐gonadal sites.Although when serial determinations are performed a correlation between AAT and AFP can be seen, 71 determinations of AAT as well as AFP in the serum of the patients with germ cell tumours gave the following results: when the AFP‐concentration was below 20 ng/ml, the AAT values were always below the upper limit of the normal range (4.0 g/l); with AFP‐values well above 20 ng/ml, the AAT concentration was elevated (>4.0 g/l) in only 33% of the cases; in all the sera with an elevated AAT‐level, the AFP‐concentration was—mostly considerably—enhanced; and in 45% of the sera with normal (or lowered) AAT, there was a diagnostically meaningful elevation of the AFP‐concentration. In addition data from 9 patients with tumours not of germ cell origin undergoing therapy showed considerable variations of AAT‐values at normal AFP concentrations.It is therefore considered that although there is evidence that AAT is produced by EST, serum AAT is not a useful monitor of disease activity in these patients, especially when compared with serum AFP.
Protein Synthesis in Yolk Sac Tumor: Histochemical Studies of Human and Rat Yolk Sac Tumor
Authors: ENDO Y. , URANO Y. , TSUCHIDA Y. , ASAKA T. , KANEKO Y. , KANEKO M. , SAKASHITA S. , TSUKADA Y. , WATABE H. , HIRAI H. , ODA T. 
Published: February 2009

Synthesis of various serum proteins, such as albumin, prealbumin, α1‐antitrypsin, transferrin and α‐fetoprotein, by human and rat yolk sac tumors was studied by indirect immunofluorescence and immunoperoxidase techniques. These serum proteins were found to be present in the cytoplasm of tumor cells forming the lining of vitelline cysts, as well as Schiller‐Duval bodies and vacuolated meshwork on histological sections. Two of these tumors were cultured. Immunopathological studies revealed that albumin, prealbumin, α1‐antitrypsin, transferrin and α‐fetoprotein were found in the cytoplasm of these cultured tumor cells. The immunofluorescence of these proteins was also found on the PAS‐positive granules, which existed intra‐ and extra‐cellularly.The ability to synthesize these serum proteins of these tumor cells was not affected by tissue culture and was maintained during subcloning.It was demonstrated by electron microscope ferritin antibody technique that α‐fetoprotein was mainly synthesized on the ribosomes of the rough endoplasmic reticula of rat yolk sac tumor cells.
Usefulness and Limitation of Carcinoembryonic Proteins as Therapeutic and Prognostic Markers in Malignant Tumors
Authors: OHKURA H. , MUKOJIMA T. , ISHII M. , HATTORI N. 
Published: February 2009

Patients with germ cell tumors, hepatomas and other malignant tumors were studied throughout their courses of surgical, radiological and medical treatments with serial determinations of AFP, CEA, HCG and basic fetoprotein (BFP), which was newly found by M. Ishii.In general, these carcinoembryonic or trophoblastic markers were observed to be well correlated with the fate of the tumor in the body and to be useful in evaluating the effect of treatment or in predicting the prognosis of the patient. Except for a postoperative transient increase in serum BFP and CEA, the levels fell after surgery and rose again with recurrence of the tumor. Although we had some patients with teratocarcinoma, hepatoma or gastric carcinoma, whose serum AFP showed a transient parallelism with their clinical courses, an obvious dissociation in these markers occurred later in their course. Similar dissociations were also observed with these carcinofetal or trophoblastic markers in patients with chemotherapy or radiotherapy for their teratocarcinomas.We conclude that each carcinoembryonic protein is a useful but limited marker for malignancy but should be used clinically in combination with other tumor markers.