bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution and Distribution of Class II-Related Endogenous Retroviruses
Authors: Gifford Robert , Kabat Peter , Martin Joanne , Lynch Clare , Tristem Michael 
Published: April 2005

ABSTRACT
Endogenous retroviruses (ERVs) are widespread in vertebrate genomes and have been loosely grouped into “classes” on the basis of their phylogenetic relatedness to the established genera of exogenous retroviruses. Four of these genera—the lentiviruses, alpharetroviruses, betaretroviruses, and deltaretroviruses—form a well-supported clade in retroviral phylogenies, and ERVs that group with these genera have been termed class II ERVs. We used PCR amplification and sequencing of retroviral fragments from more than 130 vertebrate taxa to investigate the evolution of the class II retroviruses in detail. We confirm that class II retroviruses are largely confined to mammalian and avian hosts and provide evidence for a major novel group of avian retroviruses, and we identify additional members of both the alpha- and the betaretrovirus genera. Phylogenetic analyses demonstrated that the avian and mammalian viruses form distinct monophyletic groups, implying that interclass transmission has occurred only rarely during the evolution of the class II retroviruses. In contrast to previous reports, the lentiviruses clustered as sister taxa to several endogenous retroviruses derived from rodents and insectivores. This topology was further supported by the shared loss of both the class II PR-Pol frameshift site and the class II retrovirus G-patch domain.
Role of Genes That Modulate Host Immune Responses in the Immunogenicity and Pathogenicity of Vaccinia Virus
Authors: Jackson Shawn S. , Ilyinskii Petr , Philippon Valérie , Gritz Linda , Yafal Alicia Gómez , Zinnack Kimberly , Beaudry Kristin R. , Manson Kelledy H. , Lifton Michelle A. , Kuroda Marcelo J. , Letvin Norman L. , Mazzara Gail P. , Panicali Dennis L. 
Published: April 2005

ABSTRACTPoxvirus vaccine vectors, although capable of eliciting potent immune responses, pose serious health risks in immunosuppressed individuals. We therefore constructed five novel recombinant vaccinia virus vectors which contained overlapping deletions of coding regions for the B5R, B8R, B12R, B13R, B14R, B16R, B18R, and B19R immunomodulatory gene products and assessed them for both immunogenicity and pathogenicity. All five of these novel vectors elicited both cellular and humoral immunity to the inserted HIV-BH10envcomparable to that induced by the parental Wyeth strain vaccinia virus. However, deletion of these immunomodulatory genes did not increase the immunogenicity of these vectors compared with the parental vaccinia virus. Furthermore, four of these vectors were slightly less virulent and one was slightly more virulent than the Wyeth strain virus in neonatal mice. Attenuated poxviruses have potential use as safer alternatives to current replication-competent vaccinia virus. Improved vaccinia virus vectors can be generated by deleting additional genes to achieve a more significant viral attenuation.
Papillomavirus Subtypes Are Natural and Old Taxa: Phylogeny of Human Papillomavirus Types 44 and 55 and 68a and -b
Authors: Calleja-Macias Itzel E. , Kalantari Mina , Allan Bruce , Williamson Anna-Lise , Chung Lap-Ping , Collins Robert J. , Zuna Rosemary E. , Dunn S. Terence , Ortiz-Lopez Rocio , Barrera-Saldaña Hugo A. , Cubie Heather A. , Cuschieri Kate , Villa Luisa L. , Bernard Hans-Ulrich 
Published: April 2005

ABSTRACT
A human papillomavirus (HPV) type is defined as an HPV isolate whose L1 gene sequence is at least 10% different from that of any other type, while a subtype is 2 to 10% different from any HPV type. In order to analyze the phylogeny behind the subtype definition, we compared 49 isolates of HPV type 44 (HPV-44) and its subtype HPV-55, previously misclassified as a separate type, and 41 isolates of the subtype pair HPV-68a and -b, sampled from cohorts in four continents. The subtypes of each pair are separated by deep dichotomic branching, and three of the four subtypes have evolved large phylogenetic clusters of genomic variants forming a “star” phylogeny, with some branches specific for ethnically defined cohorts. We conclude that subtypes of HPV types are natural and old taxa, equivalent to types, which either diverged more recently than types or evolved more slowly.
Primary antibody deficiency and diagnostic delay: Table 1
Authors: Seymour B , Miles J , Haeney M 
Published: April 2005

Aims:To assess the occurrence of diagnostic delay in primary antibody deficiency in the period 1989–2002, since a similar study in 1989, and to assess the impact of UK national guidelines communicated in 1995.Methods:A retrospective case note review was performed of 89 consecutive patients with antibody deficiency referred to a regional referral centre for clinical immunology in north west England and north Wales. The delay in diagnosis and the estimated resulting morbidity in terms of infections were assessed.Results:Fifty six of the 89 patients experienced delay in diagnosis. The overall median delay was 2 years (mean, 4.4), resulting in substantial morbidity (equivalent to two major infections and one minor infection). This shows a moderate improvement since the previous study in 1989 and since the introduction of UK national guidelines in 1995. Respiratory infections are the most frequent presenting infections, and respiratory physicians the most common source of referral.Conclusions:There is still considerable delay in the diagnosis of primary antibody deficiency, but the data suggest an improvement in practice since the previous study in 1989 and the distribution of national guidelines in 1995.
Postmortem molecular diagnosis of sickle β thalassaemia: Figure 1
Authors: Kutlar F , Mirmow D , Glendenning M , Holley L , Kutlar A 
Published: April 2005

This report describes a case in which the diagnosis of sickle cell disease (SCD) was established after death. The diagnosis of sickle cell syndrome was made in a 68 year old black patient who was found to have sickled red blood cells in many organs at necropsy although the disease had not been diagnosed during her lifetime. DNA was isolated from a peripheral blood smear obtained on the day of the patient’s death. The β globin gene was polymerase chain reaction amplified and sequenced, revealing that the patient had S-β+thalassaemia. This study shows that blood smears are a suitable source for retrospective DNA analysis studies. This case illustrates that relatively “mild” forms of SCD can be overlooked, despite symptomatology suggestive of a sickle syndrome, and demonstrates the feasibility of the postmortem molecular diagnosis of haemoglobinopathies in such cases.
Expression and gene amplification of primary (A, B1, D1, D3, and E) and secondary (C and H) cyclins in colon adenocarcinomas and correlation with patient outcome
Authors: Bondi J , Husdal A , Bukholm G , Nesland J M , Bakka A , Bukholm I R K 
Published: April 2005

Background/Aims:Deregulation of cell cycle control is a hallmark of cancer. The primary cyclins (A, B1, D1, D3, and E) are crucial for cell cycle progression. Secondary cyclins (C and H) have putative indirect effects on cell cycle progression and have not previously been evaluated in colon cancer. This study examined cyclin protein expression and gene amplification in colon adenocarcinoma and the correlation with patient outcome.Methods:Immunohistochemistry and real time quantitative polymerase chain reaction were used to determine cyclin expression and gene amplification in 219 tumours. The results were compared with clinical variables and patient outcomes.Results:Cyclin H was overexpressed in all tumours, cyclin C in 88%, cyclin B1 in 58%, cyclin A in 83%, cyclin D3 in 36%, cyclin E in 25%, and cyclin D1 in 11% of the tumours. Extra gene copies of cyclin A were seen in 6.2% of the tumours, cyclin B1 in 9%, cyclin C in 26.9%, cyclin D1 in 55%, cyclin D3 in 20.5%, cyclin E in 19.1%, and cyclin H in 5.1%. A significant correlation between protein overexpression and gene amplification was seen for cyclin C only. High expression of cyclin A was independently associated with improved survival. Amplification of cyclin C was independently associated with an unfavourable prognosis.Conclusions:Amplification of the cyclin C gene was related to an unfavourable prognosis and high protein expression of cyclin A was associated with a better outcome in colon adenocarcinoma.
Processing of radical prostatectomy specimens for correlation of data from histopathological, molecular biological, and radiological studies: a new whole organ technique
Authors: Jhavar S G , Fisher C , Jackson A , Reinsberg S A , Dennis N , Falconer A , Dearnaley D , Edwards S E , Edwards S M , Leach M O , Cummings C , Christmas T , Thompson A , Woodhouse C , Sandhu S , Cooper C S , Eeles R A 
Published: April 2005

Aims:To develop a method of processing non-formalin fixed prostate specimens removed at radical prostatectomy to obtain fresh tissue for research and for correlating diagnostic and molecular results with preoperative imaging.Methods/Results:The method involves a prostate slicing apparatus comprising a tissue slicer with a series of juxtaposed planar stainless steel blades linked to a support, and a cradle adapted to grip the tissue sample and receive the blades. The fresh prostate gland is held in the cradle and the blades are moved through the cradle slits to produce multiple 4 mm slices of the gland in a plane perpendicular to its posterior surface. One of the resulting slices is preserved in RNAlaterTM. The areas comprising tumour and normal glands within this preserved slice can be identified by matching it to the haematoxylin and eosin stained sections of the adjacent slices that are formalin fixed and paraffin wax embedded. Intact RNA can be extracted from the identified tumour and normal glands within the RNAlater preserved slice. Preoperative imaging studies are acquired with the angulation of axial images chosen to be similar to the slicing axis, such that stained sections from the formalin fixed, paraffin wax embedded slices match their counterparts on imaging.Conclusions:A novel method of sampling fresh prostate removed at radical prostatectomy that allows tissue samples to be used both for diagnosis and molecular analysis is described. This method also allows the integration of preoperative imaging data with histopathological and molecular data obtained from the prostate tissue slices.
A study to determine plasma antioxidant concentrations in patients with Barrett’s oesophagus
Authors: Clements D M , Oleesky D A , Smith S C , Wheatley H , Hullin D A , Havard T J , Bowrey D J 
Published: April 2005

Background:Dietary questionnaire studies have suggested that patients with oesophageal adenocarcinoma are deficient in antioxidants. It is not known whether the same holds true for patients with the precursor lesion, Barrett’s oesophagus.Aims:To evaluate the hypothesis that patients with Barrett’s oesophagus are deficient in antioxidants compared with patients without evidence of Barrett’s oesophagus.Patients and methods:Plasma antioxidant profiles (copper, selenium, zinc; vitamins A, C, and E; carotenoids) were determined for patients with Barrett’s oesophagus (n  =  36), patients with erosive oesophagitis (n  =  32), and patient controls (n  =  35).Results:Patients with Barrett’s oesophagus had significantly lower plasma concentrations of selenium, vitamin C, β cryptoxanthine, and xanthophyll compared with the other groups.Conclusions:This study confirms the hypothesis that patients with Barrett’s oesophagus are deficient in certain antioxidants.
Different Effect of Cyclosporine A and Mycophenolate Mofetil on Passive Heymann Nephritis in the Rat
Authors: Blume Cornelia , Heise Gunhild , Hess Alexandra , Waldner Christoph , Grabensee Bernd , Schroer Karsten , Heering Peter 
Published: April 2005

<i>Background:</i> While cyclosporine A (CsA) is an effective therapy for nephrotic syndrome, it has nephrotoxic side effects. We compared the anti-proteinuric effects and nephrotoxicity in rats with passive Heymann nephritis (PHN) of CsA and mycophenolate mofetil (MMF). <i>Methods:</i> PHN was induced in female Wistar rats. Two treatment groups consisting of 8 rats each received either 25 mg of CsA or 25 mg of MMF/kg body weight/day and were compared with untreated controls. Kidney function and proteinuria were monitored over 4 weeks. Western blots were used for densitometric analysis of renal cyclooxygenase-2 (COX-2) protein expression. Thromboxane B<sub>2</sub> (TxB<sub>2</sub>) and 6-keto-PGF<sub>1α</sub> were determined by radioimmunoassays (RIAs) in renal tissue and urine. <i>Results:</i> Rats with PHN exhibited a marked proteinuria of 12.76 ± 4.42 vs. 0.73 ± 0.28 mg/24 h (p < 0.01) and showed increased glomerular concentrations of TxB<sub>2</sub> and 6-keto-PGF<sub>1α</sub> (992.6 ± 216.9 and 1,187.0 ± 54.2 pg/mg protein, respectively) compared with healthy controls (595 ± 196.17 and 729 ± 297.84, respectively) and a strongly induced COX-2 protein expression. CsA and MMF treatment reduced PHN-related proteinuria to 2.10 ± 1.47 and 1.47 ± 7.2 mg/24 h, respectively. In rats with PHN, CsA induced a significant deterioration of renal function and enhanced urine excretion of thromboxane A<sub>2</sub>, paralleled by a significant, twofold increase in COX-2 protein expression and renal prostaglandins. By contrast, MMF treatment in rats with PHN was not nephrotoxic and had no effect on prostaglandin production. COX-2 protein expression under MMF was suppressed. <i>Conclusion:</i> While the antiproteinuric efficacy of MMF and CsA in PHN was comparable, the absence of nephrotoxicity might favor MMF in the treatment of nephrotic syndrome. The CsA-induced increase in COX-2 expression and COX-2-dependent prostacyclin may indicate a mechanism that compensates nephrotoxicity in the diseased and CsA-exposed kidney.
Political Loyalty in the Biblical Account of 1 Samuel XX-XXII in the Light of Hittite Texts
Authors: Taggar-Cohen Ada 
Published: April 2005

AbstractThe historicity of the Book of Samuel has been critically denied, but comparison with Ancient Near Eastern documents may show that some of its stories can be placed in the context of its historical background. Hittite documents from the late second millennium BCE show striking similarities in the legal systems on which the concepts of royalty and loyalty are based. The relations between David and Jonathan (1 Sam. xx) are compared with the relations among the royalty described in the Hittite Bronze Tablet, while the execution of the priests of Nob (1 Sam. xxii) is interpreted as a justifiable reaction to the violation of the loyalty oath by the king's servants as prescribed in CTH 264.
Prophetaphobia: Fear and False Prophecy in Nehemiah VI
Authors: Shepherd David 
Published: April 2005

AbstractWhile it has long been recognized that Nehemiah vi is animated by the twin concerns of fear and false prophecy, the present study offers a new reading of this chapter which brings Nehemiah's account of his opponents' terror tactics into sharp focus. How does Nehemiah unmask Shemaiah as a false prophet? What were Nehemiah's real reasons for rejecting Shemaiah's prophetic oracle? Why does Noadiah, the prophetess, come in for special criticism from Nehemiah? The author suggests that Nehemiah's account of his enemies' actions and his own reactions may be brought into focus by viewing it through the lens of the Deuteronomic torah-instruction regarding the false prophet (Deut. xviii). By scrutinizing Nehemiah vi through this lens, the present study illustrates how many of the vexing interpretive questions which have long been asked of it, may best be answered by carefully attending to the text of the chapter itself.
Numbers Xi: seeing Moses plain
Authors: Reis Pamela Tamarkin 
Published: April 2005

AbstractThis essay presents an interpretation of Numbers xi that highlights its coherence and humor. Although source-critics see opposing views of Moses stitched together from separate sources by a later redactor—a bad Moses in the quail segment and a good Moses in the elders segment, this essay manifests the chapter's narrative integrity. A close literary analysis reveals an aesthetically-pleasing account, free of the disjunctions and non-sequiturs posited by other commentators; theme, puns, wordplay, and an ingenious man/quail metaphor unite all of the pericope's verses in a single favorable view of Moses. Far from revealing him as "snitch" and "informer," this holistic reading of the undivided text harmonizes with the rest of the Bible's consistent portrayal of Moses as the invariant champion of the Israelites, their never-failing mediator before God.
Subject trouble
Authors: Stoetzler Marcel 
Published: April 2005

In this essay I explore the role of dialectics for how social theory can take account of the problem of structure and agency, or, determination and freedom, in a critical and emancipatory way. I discuss the limits and possibilities of dialectical, and of anti-dialectical, criticisms of Hegelian dialectics. For this purpose, I look at Judith Butler’s discussion of dialectics and the concepts of ‘sex’ and ‘gender’ in her writings between 1987 ( Subjects of Desire; republished 1999) and 1990 ( Gender Trouble, republished 2000). Butler’s book Gender Trouble remains a key text of contemporary feminist theory. Butler formulates in this book a critique of Simone de Beauvoir’s The Second Sex based on her claim that Beauvoir makes a distinction between ‘sex’ and ‘gender’ that implies the notion of the sexed body as a pre-cultural entity. In her earlier writings, though, her evaluation of de Beauvoir had been much more positive. The change in Butler’s evaluation of de Beauvoir is part of her increasing rejection of dialectics: Butler rejected in Gender Trouble any form of Hegelian dialectics with reference to Luce Irigaray’s (1985) claim that it is ‘phallogocentric’. Although Butler subsequently returned to Hegelian themes, she seems never to have revoked this claim made in her most momentous work.I argue that this change in the theoretical structure of Butler’s argument weakens her critique of identity politics and I suggest reading Butler backwards, from Gender Trouble to the more open discussion of dialectics in her earlier texts. Drawing on Adorno’s Negative Dialectics and other formulations of critical theory, I argue that the valid aspects of the critique of Hegelian dialectics can better be formulated as a dialectical critique of dialectics (Adorno; Butler, 1987a) than as a rejection of dialectics (Derrida; Irigaray; Butler, 1990).Retracing the genealogy of Butler’s argument will be a necessary backdrop, too, for evaluating her more recent comments on the Hegelian and ‘Frankfurt School’ traditions such as her Adorno Lectures given in Frankfurt am Main, Germany, in November 2002.
In vivo analyses of early events in acute graft-versus-host disease reveal sequential infiltration of T-cell subsets
Authors: Beilhack Andreas , Schulz Stephan , Baker Jeanette , Beilhack Georg F. , Wieland Courtney B. , Herman Edward I. , Baker Enosh M. , Cao Yu-An , Contag Christopher H. , Negrin Robert S. 
Published: April 2005

AbstractGraft-versus-host disease (GVHD) is a major obstacle in allogeneic hematopoietic cell transplantation. Given the dynamic changes in immune cell subsets and tissue organization, which occur in GVHD, localization and timing of critical immunological events in vivo may reveal basic pathogenic mechanisms. To this end, we transplanted luciferase-labeled allogeneic splenocytes and monitored tissue distribution by in vivo bioluminescence imaging. High-resolution analyses showed initial proliferation of donor CD4+ T cells followed by CD8+ T cells in secondary lymphoid organs with subsequent homing to the intestines, liver, and skin. Transplantation of purified naive T cells caused GVHD that was initiated in secondary lymphoid organs followed by target organ manifestation in gut, liver, and skin. In contrast, transplanted CD4+ effector memory T (TEM) cells did not proliferate in secondary lymphoid organs in vivo and despite their in vitro alloreactivity in mixed leukocyte reaction (MLR) assays did not cause acute GVHD. These findings underline the potential of T-cell subsets with defined trafficking patterns for immune reconstitution without the risk of GVHD.
Advances in the biology and therapy of diffuse large B-cell lymphoma: moving toward a molecularly targeted approach
Authors: Abramson Jeremy S. , Shipp Margaret A. 
Published: April 2005

AbstractDiffuse large B-cell lymphoma (DLBCL) displays striking heterogeneity at the clinical, genetic, and molecular levels. Clinical prognostic models can define a population at high risk for relapse following empiric chemotherapy, although such models do not account for underlying biologic differences among tumors. Commonly observed genetic abnormalities that likely contribute to pathogenesis include translocations of BCL6, BCL2, cMYC, and FAS(CD95) mutations, and aberrant somatic hypermutation. Despite recent advances in empiric chemotherapy, including interval reduction of CHOP (cyclophosphamide, doxorubicin, vincristine, prednisone) and the incorporation of anti-CD20 monoclonal antibodies, a significant proportion of patients still die of their disease. Gene expression profiling has shed light on the molecular heterogeneity within DLBCL by highlighting similarities between subsets of tumors and normal B cells, identifying features associated with unfavorable responses to empiric combination chemotherapy, and defining robust subtypes with comprehensive transcriptional signatures. Such strategies have suggested distinct routes to lymphomagenesis and have identified promising rational therapeutic targets. Additional novel therapies under investigation include those targeting BCL6 and BCL2, as well as development of novel monoclonal antibody-based therapies. Our increasing molecular understanding of the heterogeneous subsets within DLBCL will likely improve the current empiric therapy of DLBCL by identifying rational therapeutic targets in specific disease subtypes.
A newly discovered human α-globin gene
Authors: Goh Sung-Ho , Lee Y. Terry , Bhanu Natarajan V. , Cam Margaret C. , Desper Richard , Martin Brian M. , Moharram Ramy , Gherman Robert B. , Miller Jeffery L. 
Published: April 2005

AbstractA previously undefined transcript with significant homology to the pseudo-α2 region of the α-globin locus on human chromosome 16 was detected as part of an effort to better define the transcriptional profiles of human reticulocytes. Cloning and sequencing of that transcript (GenBank AY698022; named μ-globin) revealed an insert with a 423-nucleotide open reading frame. BLASTP and ClustalW and phylogenetic analyses of the predicted protein demonstrated a high level of homology with the avian α-D globin. In addition, the heme- and globin-binding amino acids of μ-globin and avian α-D globin are largely conserved. Using quantitative real-time polymerase chain reaction (PCR), μ-globin was detected at a level of approximately 0.1% that measured for α-globin in erythroid tissues. Erythroid-specific expression was detected by Northern blot analysis, and maximal expression during the erythroblast terminal differentiation was also detected. Despite this highly regulated pattern of μ-globin gene transcription, μ-globin protein was not detected by mass spectrometry. These results suggest the human genome encodes a previously unrecognized globin member of the avian α-D family that is transcribed in a highly regulated pattern in erythroid cells. (Blood. 2005;106:1466-1472)