bluuebunny/crossref_metadata_2025_split huggingface dataset:
ORC, MCM, and Histone Hyperacetylation at the Kaposi's Sarcoma-Associated Herpesvirus Latent Replication Origin
Authors: Stedman William , Deng Zhong , Lu Fang , Lieberman Paul M. 
Published: October 2004

ABSTRACT

The viral genome of Kaposi's sarcoma-associated herpesvirus (KSHV) persists as an extrachromosomal plasmid in latently infected cells. The KSHV latency-associated nuclear antigen (LANA) stimulates plasmid maintenance and DNA replication by binding to an ∼150-bp region within the viral terminal repeats (TR). We have used chromatin immunoprecipitation assays to demonstrate that LANA binds specifically to the replication origin sequence within the KSHV TR in latently infected cells. The latent replication origin within the TR was also bound by LANA-associated proteins CBP, double-bromodomain-containing protein 2 (BRD2), and the origin recognition complex 2 protein (ORC2) and was enriched in hyperacetylated histones H3 and H4 relative to other regions of the latent genome. Cell cycle analysis indicated that the minichromosome maintenance complex protein, MCM3, bound TR in late-G
1
/S-arrested cells, which coincided with the loss of histone H3 K4 methylation. Micrococcal nuclease studies revealed that TRs are embedded in a highly ordered nucleosome array that becomes disorganized in late G
1
/S phase. ORC binding to TR was LANA dependent when reconstituted in transfected plasmids. DNA affinity purification confirmed that LANA, CBP, BRD2, and ORC2 bound TR specifically and identified the histone acetyltransferase HBO1 (histone acetyltransferase binding to ORC1) as a potential TR binding protein. Disruption of ORC2, MCM5, and HBO1 expression by small interfering RNA reduced LANA-dependent DNA replication of TR-containing plasmids. These findings are the first demonstration that cellular replication and origin licensing factors are required for KSHV latent cycle replication. These results also suggest that the KSHV latent origin of replication is a unique chromatin environment containing histone H3 hyperacetylation within heterochromatic tandem repeats.
The Transmembrane Domains of the prM and E Proteins of Yellow Fever Virus Are Endoplasmic Reticulum Localization Signals
Authors: Op De Beeck Anne , Rouillé Yves , Caron Mélanie , Duvet Sandrine , Dubuisson Jean 
Published: October 2004

ABSTRACT
The immature flavivirus particle contains two envelope proteins, prM and E, that are associated as a heterodimer. Virion morphogenesis of the flaviviruses occurs in association with endoplasmic reticulum (ER) membranes, suggesting that there should be accumulation of the virion components in this compartment. This also implies that ER localization signals must be present in the flavivirus envelope proteins. In this work, we looked for potential subcellular localization signals in the yellow fever virus envelope proteins. Confocal immunofluorescence analysis of the subcellular localization of the E protein in yellow fever virus-infected cells indicated that this protein accumulates in the ER. Similar results were obtained with cells expressing only prM and E. Chimeric proteins containing the ectodomain of CD4 or CD8 fused to the transmembrane domains of prM or E were constructed, and their subcellular localization was studied by confocal immunofluorescence and by analyzing the maturation of their associated glycans. Although a small fraction was detected in the ER-to-Golgi intermediate and Golgi compartments, these chimeric proteins were located mainly in the ER. The C termini of prM and E form two antiparallel transmembrane α-helices. Interestingly, the first transmembrane passage contains enough information for ER localization. Taken altogether, these data indicate that, besides their role as membrane anchors, the transmembrane domains of yellow fever virus envelope proteins are ER retention signals. In addition, our data show that the mechanisms of ER retention of the flavivirus and hepacivirus envelope proteins are different.
Human Immunodeficiency Virus Type 1 (HIV-1)-Specific CD4
+
T Cells That Proliferate In Vitro Detected in Samples from Most Viremic Subjects and Inversely Associated with Plasma HIV-1 Levels
Authors: Boritz Eli , Palmer Brent E. , Wilson Cara C. 
Published: October 2004

ABSTRACT

Diminished in vitro proliferation of human immunodeficiency virus type 1 (HIV-1)-specific CD4
+
T cells has been associated with HIV-1 viremia and declining CD4
+
T-cell counts during chronic infection. To better understand this phenomenon, we examined whether HIV-1 Gag p24 antigen-induced CD4
+
T-cell proliferation might recover in vitro in a group of subjects with chronic HIV-1 viremia and no history of antiretroviral therapy (ART). We found that depletion of CD8
+
cells from peripheral blood mononuclear cells (PBMC) before antigen stimulation was associated with a 6.5-fold increase in the median p24-induced CD4
+
T-cell proliferative response and a 57% increase in the number of subjects with positive responses. These p24-induced CD4
+
T-cell proliferative responses from CD8-depleted PBMC were associated with expansion of the numbers of p24-specific, gamma interferon (IFN-γ)-producing CD4
+
T cells. Among the 20 viremic, treatment-naïve subjects studied, the only 5 subjects lacking proliferation-competent, p24-specific CD4
+
T-cell responses from CD8-depleted PBMC showed plasma HIV-1 RNA levels > 100,000 copies/ml. Furthermore, both the magnitude of p24-induced CD4
+
T-cell proliferative responses from CD8-depleted PBMC and the frequency of p24-specific, IFN-γ-producing CD4
+
T cells expanded from CD8-depleted PBMC were associated inversely with plasma HIV-1 RNA levels. Therefore, proliferation-competent, HIV-1-specific CD4
+
T cells that might help control HIV-1 disease may persist during chronic, progressive HIV-1 disease except at very high levels of in vivo HIV-1 replication.
Structure and Polymorphism of the UL6 Portal Protein of Herpes Simplex Virus Type 1
Authors: Trus Benes L. , Cheng Naiqian , Newcomb William W. , Homa Fred L. , Brown Jay C. , Steven Alasdair C. 
Published: October 2004

ABSTRACT
By electron microscopy and image analysis, we find that baculovirus-expressed UL6 is polymorphic, consisting of rings of 11-, 12-, 13-, and 14-fold symmetry. The 12-mer is likely to be the oligomer incorporated into procapsids: at a resolution of 16 Å, it has an axial channel, peripheral flanges, and fits snugly into a vacant vertex site. Its architecture resembles those of bacteriophage portal/connector proteins.
Vpr and Vpu Are Important for Efficient Human Immunodeficiency Virus Type 1 Replication and CD4
+
T-Cell Depletion in Human Lymphoid Tissue Ex Vivo
Authors: Rücker Elke , Grivel Jean-Charles , Münch Jan , Kirchhoff Frank , Margolis Leonid 
Published: October 2004

ABSTRACT

The relevance of the accessory
vpr
,
vpu
, and
nef
genes for human immunodeficiency virus type 1 (HIV-1) replication in human lymphoid tissue (HLT), the major site of viral replication in vivo, is largely unknown. Here, we show that an individual deletion of
nef
,
vpr
, or
vpu
significantly decreases HIV-1 replication and prevents CD4
+
T-cell depletion in ex vivo HLT. However, only combined defects in all three accessory genes entirely disrupt the replicative capacity of HIV-1. Our results demonstrate that
nef
,
vpr
, and
vpu
are all essential for efficient viral spread in HLT, suggesting an important role in AIDS pathogenesis.
EBNA2 Is Required for Protection of Latently Epstein-Barr Virus-Infected B Cells against Specific Apoptotic Stimuli
Authors: Lee Jae Myun , Lee Kyoung-Ho , Farrell Christopher J. , Ling Paul D. , Kempkes Bettina , Park Jeon Han , Hayward S. Diane 
Published: October 2004

ABSTRACTIn addition to functioning as a transcriptional transactivator, Epstein-Barr virus EBNA2 interacts with Nur77 to protect against Nur77-mediated apoptosis. Estrogen-regulated EBNA2 in EREB2-5 cells was replaced by either EBNA2 or EBNA2 with a deletion of conserved region 4 (EBNA2ΔCR4). Both EBNA2-converted and EBNA2ΔCR4-converted EREB2-5 cells grew in the absence of estrogen and expressed LMP1. Treatment with tumor necrosis factor alpha did not induce apoptosis of EBNA2- or EBNA2ΔCR4-expressing cells, but EBNA2ΔCR4 cells were susceptible to etoposide and 5-fluorouracil, Nur77-mediated inducers of apoptosis. Thus, EBNA2 protects B cells against specific apoptotic agents against which LMP1 is not effective.
Host Range Factor 1 from
Lymantria dispar
Nucleopolyhedrovirus (NPV) Is an Essential Viral Factor Required for Productive Infection of NPVs in IPLB-Ld652Y Cells Derived from
L. dispar
Authors: Ishikawa Hiroki , Ikeda Motoko , Alves Cristiano A. Felipe , Thiem Suzanne M. , Kobayashi Michihiro 
Published: October 2004

ABSTRACT

Host range factor 1 (HRF-1) of
Lymantria dispar
multinucleocapsid nucleopolyhedrovirus promotes
Autographa californica
MNPV replication in nonpermissive Ld652Y cells derived from
L. dispar
. Here we demonstrate that restricted
Hyphantria cunea
NPV replication in Ld652Y cells was not due to apoptosis but was likely due to global protein synthesis arrest that could be restored by HRF-1. Our data also showed that HRF-1 promoted the production of progeny virions for two other baculoviruses,
Bombyx mori
NPV and
Spodoptera exigua
MNPV, whose replication in Ld652Y cells is limited to replication of viral DNA without successful production of infectious progeny virions. Thus, HRF-1 is an essential viral factor required for productive infection of NPVs in Ld652Y cells.
Seminal Fluid Enhances Replication of Human T-Cell Leukemia Virus Type 1: Implications for Sexual Transmission
Authors: Moriuchi Masako , Moriuchi Hiroyuki 
Published: October 2004

ABSTRACT
Seminal fluid enhanced human T-cell leukemia virus type 1 (HTLV-1) infection by transactivating the HTLV-1 long terminal repeat promoter, which is chromosomally integrated in a cell-type-dependent manner. Our data may indicate a potential role for seminal fluid in the sexual transmission of HTLV-1 and imply complex features of regulation of HTLV-1 expression.
THE INFLUENCE OF DISPERSAL BEHAVIOUR ON METAPOPULATION VIABILITY
Authors: TYUTYUNOV YURI , DOMBROVSKY YURI , ARDITI ROGER , SURKOV FEODOR 
Published: October 2004

The dynamics of the metapopulation is described by a Markov chain with three possible states of each subpopulation: 0 (extinct), 1 (lower size), and 2 (carrying capacity). Migrations between subpopulations can depend both on the state of the source subpopulation (e.g., inversely) and the state of the target habitat. The strategies of conspecific attraction, when occupied patches receive a larger fraction of migrants, and conspecific repulsion, i.e., the preference for empty patches, are modelled. Emigration events affect the density of the source habitat. Immigration causes either a recolonisation of an empty patch or the transition from state 1 to state 2 of the target habitat. Application of queuing theory methods made it possible to obtain analytical formulas for extinction probability and persistence time. The effect of dispersal behaviour was investigated. The influence of random dispersal and of directional dispersal depends on population parameters. It is demonstrated that, while at high growth and mortality rates, conspecific repulsion provides better metapopulation viability, there exists a threshold value for the growth rate below which aggregation becomes favourable. Biological interpretation of these results is discussed and a classification of species is suggested associating population kinetic rates and dispersal strategy.
NORMAL FORMS FOR FUZZY LOGIC — AN APPLICATION OF KOLMOGOROV’S THEOREM
Authors: KREINOVICH VLADIK , NGUYEN HUNG T. , SPRECHER DAVID A. 
Published: October 2004

This paper addresses mathematical aspects of fuzzy logic. The main results obtained in this paper are: 1. the introduction of a concept of normal form in fuzzy logic using hedges; 2. using Kolmogorov’s theorem, we prove that all logical operations in fuzzy logic have normal forms; 3. for min-max operators, we obtain an approximation result similar to the universal approximation property of neural networks.
INTERVAL METHODS IN KNOWLEDGE REPRESENTATION
Authors: Kreinovich Vladik 
Published: October 2004

With this issue, we start a new section: short abstract of papers and books on interval methods in knowledge representation. The experience of several conferences on interval computations and fuzzy systems, including the 1995 International Workshop on Applications of Interval Computations (February 1995, El Paso, TX, USA), has shown that there are many areas of knowledge representation where interval methods are applied, and many interesting results of these applications, areas and results that are often not widely known to the knowledge representation community. These papers are published in different journals and conference proceedings, and it is difficult to trace them all. In view of this difficulty, we decided to provide the readers of IJUFKS with short abstract of these papers (something like an ongoing annotated bibliography). We strongly believe that the information about the current applications of interval methods is of interest to this community. For the reasons expressed above, we are currently, more probably, not covering all relevant papers. To increase the coverage, we need your help. If you know of any recent papers devoted to the applications of interval methods to knowledge representation, please send reference to Vladik Kreinovich at vladik@cs.utep.edu, or by regular mail to: Vladik Kreinovich, Department of Computer Science, University of Texas at El Paso, El Paso, TX 79968, USA. If you have writtend your own reviews of such papers, or if you would like to write such reviews, please contact Vladik as well. Authors, please send information and/or copies of your own applications papers (papers in French, Russian, and German are also welcome). Abstracts should ideally in LATEX or TEX, but ASCII is also acceptable This is a new section, and we want the readers' input about how to make it better. Any suggestions and recommendations will be highly welcome.
Hepatocyte Growth Factor Suppresses Vascular Medial Hyperplasia and Matrix Accumulation in Advanced Pulmonary Hypertension of Rats
Authors: Ono Masamichi , Sawa Yoshiki , Mizuno Shinya , Fukushima Norihida , Ichikawa Hajime , Bessho Kazuhiko , Nakamura Toshikazu , Matsuda Hikaru 
Published: October 2004

Background—Pulmonary hypertension (PH) is a progressive disease characterized by raised pulmonary vascular resistance, thought to be curable only through lung transplantation. Pathophysiologically, proliferation of pulmonary artery smooth muscle cells triggers pulmonary arterial stenosis and/or regurgitation, especially in advanced PH.Methods and Results—Using a rat model of advanced pulmonary vascular disease produced by injecting monocrotaline, we show that hepatocyte growth factor (HGF) targets pulmonary arterioles and blocks the progression of PH. In these rats, endogenous HGF production was dramatically downregulated during developing experimental PH, but c-Met/HGF receptor was abundant in the medial layers of pulmonary arterioles. HGF gene transfection 2 weeks after the monocrotaline injection resulted in milder medial hyperplasia in lung arterioles and inhibited overgrowth of pulmonary artery smooth muscle cells. Notably, exogenous HGF reduced lung expression levels of endothelin-1 and transforming growth factor-β, which are critically involved in PH-linked fibrogenic events. Overall, medial wall thickening of pulmonary arteries was almost completely prevented by HGF, and the total collagen deposition in the lung decreased; both effects contributed to the suppression of pulmonary artery hypertension.Conclusions—Our results suggest that the loss of endogenous HGF may be a feature of the pathogenesis of PH and that HGF supplementation may minimize pathological lung conditions, even advanced PH.
The Acquisition of Bulimia: Childhood Experience
Authors: Day Merrie 
Published: October 2004

AbstractThis article is concerned with the childhood experience that seems to be preparatory for the onset of bulimia. Three women's serial experiences of bulimia (reported in 4 interviews describing specific binge-purge episodes) were investigated and one pattern of experiencing that led to bulimia emerged. As the interview process deepened (interview 1 to interview 4), the data moved from symptom-related to life-related. The general structure that captured the essence of the lived experience of bulimia remained the same but the individual experiences varied as these women live out their unique lives. In understanding the totality of the phenomenon of bulimia, it is important to remember that although each of the six key constituents is described separately, in the life-world all the constituents merge together as they interact with each other and with the whole of the experience. These bulimic women reported having family backgrounds in which they experienced a sense of diminished self and dissatisfaction in interactions with significant others and self. They found themselves pressured to maintain a less than integrated life, and in rapid transition from 'awareful' behaving to automatic and anonymous functioning. A psychological hunger seems to possess them and this is lived out during the anonymous phase of their existence. Their need for the mastery and control ordinarily lacking in their lives becomes a symptomatic expression that has relevance for them in respect to the deep psychological pain that is only partially expressed. The phenomenal body and self are given priority over objective reality, resulting in distorted perceptions of "fatness" and feelings of terror of "fat."
The Self-Overcoming Subject: Freud's Challenge to the Cartesian Ontology
Authors: Fowler Steven 
Published: October 2004

AbstractTwo strands of enlightenment rationality—the mechanistic/deterministic and the self-overcoming—are distinguished, and the presence of the later in the work of Sigmund Freud is delineated. Beginning with Freud's investigations of hysteria, Freud's view of the person as a self-overcoming entity is spelled out in his theory of the unconscious and his theory of sexuality. It is argued that Freud provides, in the realm of empirical science, evidence that converges with the ontological conception of the person as a "being-in-the-world" developed by Heidegger in the philosophical classic, Being and Time.
‘Hottentots’ and the evolution of European racism
Authors: Hudson Nicholas 
Published: October 2004

Springing from the argument in recent scholarship that ‘race’ is a doctrine that emerged only in the post-Enlightenment, this essay develops a theory concerning the ideological history of ‘racism’, understood in its modern Western sense. While it is impossible to examine all forms of Western racism, the author focuses on evolving reactions in European travel accounts, belles-lettres and anthropology to the Khoikhoi, popularly known as ‘Hottentots’, a people that became proverbial as the most wretched and degraded of all ‘savages’. The question posed is why the Khoikhoi, a relatively peripheral and cooperative people, attracted this virulent hatred. Challenging the assumption of the small body of modern scholarship on the Khoikhoi, I maintain that this spite derived not simply from a sense of the Hottentots’ ‘Otherness’, but more accurately from the awareness that this people upset models of ethnicity that supported the Western vision of the non-European world. Europeans needed to neutralize the ideological threat represented by the Khoikhoi, a programme that culminated in the development of the modern science of ‘race’. ‘Race’, and its corresponding ideology of ‘racism’, I conclude, involves not merely the exclusion, but an approximation and appropriation of the ‘Other’ into Western systems of thought: the ultimate and fatal destiny of this highly distinct and independent culture.
Defining and Measuring the Productivity of Programming Languages
Authors: Kennedy Ken , Koelbel Charles , Schreiber Robert 
Published: October 2004

The goal of programming support systems is to make it possible for application developers to produce software faster, without any degradation in software quality. However, it is essential that this goal must not be achieved at the cost of performance: programs written in a high-level language and intended to solve large problems on highly parallel machines must not be egregiously less efficient than the same applications written in a lower-level language. Because this has been a traditional stumbling block for high-level languages, metrics for productivity analysis must explore the trade-off between programming effort and performance. To that end, we propose the use of two dimensionless ratios, relative power and relative efficiency, to measure the productivity of programming interfaces. In this paper we define these concepts, describe their application, and explore various ways for measuring them, including both empirical strategies and expert opinion. Rather than combine these metrics into a single number representing a universal productivity, we propose that they be represented graphically in at least two dimensions so that the trade-offs between abstraction and performance are clearly depicted. However, we also introduce a single problem-dependent parameter that allows us to reason about the relative productivity of two languages for a given problem.
Improved hit criteria for DNA local alignment
Authors: Noé Laurent , Kucherov Gregory 
Published: October 2004

Abstract
Background
The hit criterion is a key component of heuristic local alignment algorithms. It specifies a class of patterns assumed to witness a potential similarity, and this choice is decisive for the selectivity and sensitivity of the whole method.

Results
In this paper, we propose two ways to improve the hit criterion. First, we define the group criterion combining the advantages of the single-seed and double-seed approaches used in existing algorithms. Second, we introduce transition-constrained seeds that extend spaced seeds by the possibility of distinguishing transition and transversion mismatches. We provide analytical data as well as experimental results, obtained with the YASS software, supporting both improvements.

Conclusions
Proposed algorithmic ideas allow to obtain a significant gain in sensitivity of similarity search without increase in execution time. The method has been implemented in YASS software available at http://www.loria.fr/projects/YASS/.