bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissection of a Novel Nuclear Localization Signal in Open Reading Frame 29 of Varicella-Zoster Virus
Authors: Stallings Christina L. , Silverstein Saul
Published: September 2005

Open reading frame 29 (ORF29) of varicella-zoster virus (VZV) encodes a 120-kDa single-stranded DNA binding protein (ORF29p) that is not packaged in the virion and is expressed during latency. During lytic infection, ORF29p is localized primarily to infected cell nuclei. In contrast, ORF29p is found exclusively in the cytoplasm in neurons of the dorsal root ganglia obtained at autopsy from seropositive latently infected patients. ORF29p accumulates in the nuclei of neurons in dorsal root ganglia obtained at autopsy from patients with active zoster. The localization of this protein is, therefore, tightly correlated with the proposed VZV lytic/latent switch. In this report, we have investigated the nuclear import mechanism of ORF29p. We identified a novel nuclear targeting domain bounded by amino acids 9 to 154 of ORF29p that functions independent of other VZV-encoded factors. In vitro import assays in digitonin-permeabilized HeLa cells reveal that ORF29p is transported into the nucleus by a Ran-, karyopherin α- and β-dependent mechanism. These data are further supported by the demonstration that a glutathione
S
-transferase-karyopherin α fusion interacts with ORF29p, but not with a protein containing a point mutation in its nuclear localization signal (NLS). Therefore, the region of ORF29p responsible for its nuclear targeting is also involved in the association with karyopherin α. As a result of this interaction, this noncanonical NLS appears to hijack the classical cellular nuclear import machinery. Elucidation of the mechanisms governing ORF29p nuclear targeting could shed light on the VZV reactivation process.
Herpes Simplex Virus Tegument Protein VP22 Contains an Internal VP16 Interaction Domain and a C-Terminal Domain That Are Both Required for VP22 Assembly into the Virus Particle
Authors: Hafezi Wali , Bernard Emmanuelle , Cook Rachelle , Elliott Gillian
Published: September 2005

Many steps along the herpesvirus assembly and maturation pathway remain unclear. In particular, the acquisition of the virus tegument is a poorly understood process, and the molecular interactions involved in tegument assembly have not yet been defined. Previously we have shown that the two major herpes simplex virus tegument proteins VP22 and VP16 are able to interact, although the relevance of this to virus assembly is not clear. Here we have constructed a number of recombinant viruses expressing N- and C-terminal truncations of VP22 and have used them to identify regions of the protein involved in its assembly into the virus structure. Analysis of the packaging of these VP22 variants into extracellular virions revealed that the C terminus of VP22 is absolutely required for this process, with removal of the C-terminal 89 residues abrogating its incorporation. However, while these 89 residues alone were sufficient for specific incorporation of small amounts of VP22 into the tegument, efficient packaging of VP22 to the levels of full-length protein required an additional 52 residues of the protein. Coimmunoprecipitation assays indicated that these 52 residues also contained the interaction domain for VP16. Furthermore, analysis of the subcellular localization of the mutant forms of VP22 revealed that only those truncations that were efficiently assembled formed characteristic cytoplasmic trafficking complexes, suggesting that these complexes may represent the cellular location for VP22 assembly into the virus. Taken together, these results suggest that there are two determinants involved in the packaging of VP22—a C-terminal domain and an internal VP16 interaction domain, both of which are required for the efficient recruitment of VP22 to sites of virus assembly.
Inhibitors of Respiratory Syncytial Virus Replication Target Cotranscriptional mRNA Guanylylation by Viral RNA-Dependent RNA Polymerase
Authors: Liuzzi Michel , Mason Stephen W. , Cartier Mireille , Lawetz Carol , McCollum Robert S. , Dansereau Nathalie , Bolger Gordon , Lapeyre Nicole , Gaudette Yvon , Lagacé Lisette , Massariol Marie-Josée , Dô Florence , Whitehead Paul , Lamarre Lyne , Scouten Erika , Bordeleau Josée , Landry Serge , Rancourt Jean , Fazal Gulrez , Simoneau Bruno
Published: September 2005

Respiratory
syncytial virus (RSV) is a major cause of respiratory illness in
infants, immunocompromised patients, and the elderly. New antiviral
agents would be important tools in the treatment of acute RSV disease.
RSV encodes its own RNA-dependent RNA polymerase that is responsible
for the synthesis of both genomic RNA and subgenomic mRNAs. The viral
polymerase also cotranscriptionally caps and polyadenylates the RSV
mRNAs at their 5′ and 3′ ends, respectively. We have
previously reported the discovery of the first nonnucleoside
transcriptase inhibitor of RSV polymerase through high-throughput
screening. Here we report the design of inhibitors that have improved
potency both in vitro and in antiviral assays and that also exhibit
activity in a mouse model of RSV infection. We have isolated virus with
reduced susceptibility to this class of inhibitors. The mutations
conferring resistance mapped to a novel motif within the RSV L gene,
which encodes the catalytic subunit of RSV polymerase. This motif is
distinct from the catalytic region of the L protein and bears some
similarity to the nucleotide binding domain within nucleoside
diphosphate kinases. These findings lead to the hypothesis that this
class of inhibitors may block synthesis of RSV mRNAs by inhibiting
guanylylation of viral transcripts. We show that short transcripts
produced in the presence of inhibitor in vitro do not contain a
5′ cap but, instead, are triphosphorylated, confirming this
hypothesis. These inhibitors constitute useful tools for elucidating
the molecular mechanism of RSV capping and represent valid leads for
the development of novel anti-RSV
therapeutics.
Hepatocyte-Like Cells Transdifferentiated from a Pancreatic Origin Can Support Replication of Hepatitis B Virus
Authors: Wang Robert Yung-Liang , Shen Chia-Ning , Lin Min-Hui , Tosh David , Shih Chiaho
Published: September 2005

Recently, a rat pancreatic cell line (AR42J-B13) was shown to transdifferentiate to hepatocyte-like cells upon induction with dexamethasone (Dex). The aim of this study is to determine whether transdifferentiated hepatocytes can indeed function like bona fide liver cells and support replication of hepatotropic hepatitis B virus (HBV). We stably transfected AR42J-B13 cells with HBV DNA and examined the expression of hepatocyte markers and viral activities in control and transdifferentiated cells. A full spectrum of HBV replicative intermediates, including covalently closed circular DNA (cccDNA) and Dane particles, were detected only after induction with Dex and oncostatin M. Strikingly, the small envelope protein and RNA of HBV were increased by 40- to 100-fold upon induction. When HBV RNAs were examined by primer extension analysis, novel core- and precore-specific transcripts were induced by Dex which initiated at nucleotide (nt) 1820 and nt 1789, respectively. Most surprisingly, another species of core-specific RNA, which initiates at nt 1825, is always present at almost equal intensity before and after Dex treatment, a result consistent with Northern blot analysis. The fact that HBV core protein is dramatically produced only after transdifferentiation suggests the possibility of both transcriptional and translational regulation of HBV core antigen in HBV-transfected AR42J-B13 cells. Upon withdrawal of Dex, HBV replication and gene expression decreased rapidly—less than 50% of the cccDNA remained detectable in 1.5 days. Our studies demonstrate that the transdifferentiated AR42J-B13 cells can function like bona fide hepatocytes. This system offers a new opportunity for basic research of virus-host interactions and pancreatic transdifferentiation.
SAT: a Late NS Protein of Porcine Parvovirus
Authors: Zádori Zoltán , Szelei József , Tijssen Peter
Published: September 2005

The genomes of all members of the
Parvovirus
genus were found to contain a small open reading frame (ORF), designated SAT, with a start codon four or seven nucleotides downstream of the VP2 initiation codon. Green fluorescent protein or FLAG fusion constructs of SAT demonstrated that these ORFs were expressed. Although the SAT proteins of the different parvoviruses are not particularly conserved, they were all predicted to contain a membrane-spanning helix, and mutations in this hydrophobic stretch affected the localization of the SAT protein. SAT colocalized with calreticulin in the membranes of the endoplasmic reticulum and the nucleus. A knockout mutant (SAT
−
), with an unmodified VP sequence, showed a “slow-spreading” phenotype. These knockout mutants could be complemented with VP2
−
SAT
+
mutant. The SAT protein is a late nonstructural (NS) protein, in contrast to previously identified NS proteins, since it is expressed from the same mRNA as VP2.
Human Papillomavirus Type 16 E1
∧
E4 Contributes to Multiple Facets of the Papillomavirus Life Cycle
Authors: Nakahara Tomomi , Peh Woei Ling , Doorbar John , Lee Denis , Lambert Paul F.
Published: September 2005

The life cycle of human papillomaviruses (HPVs) is tightly linked to the differentiation program of the host's stratified epithelia that it infects. E1
∧
E4 is a viral protein that has been ascribed multiple biochemical properties of potential biological relevance to the viral life cycle. To identify the role(s) of the viral E1
∧
E4 protein in the HPV life cycle, we characterized the properties of HPV type 16 (HPV16) genomes harboring mutations in the E4 gene in NIKS cells, a spontaneously immortalized keratinocyte cell line that when grown in organotypic raft cultures supports the HPV life cycle. We learned that E1
∧
E4 contributes to the replication of the viral plasmid genome as a nuclear plasmid in basal cells, in which we also found E1
∧
E4 protein to be expressed at low levels. In the suprabasal compartment of organotypic raft cultures harboring E1
∧
E4 mutant HPV16 genomes there were alterations in the frequency of suprabasal cells supporting DNA synthesis, the levels of viral DNA amplification, and the degree to which the virus perturbs differentiation. Interestingly, the comparison of the phenotypes of various mutations in E4 indicated that the E1
∧
E4 protein-encoding requirements for these various processes differed. These data support the hypothesis that E1
∧
E4 is a multifunctional protein and that the different properties of E1
∧
E4 contribute to different processes in both the early and late stages of the virus life cycle.
Homotypic Interaction of Bunyamwera Virus Nucleocapsid Protein
Authors: Leonard Vincent H. J. , Kohl Alain , Osborne Jane C. , McLees Angela , Elliott Richard M.
Published: September 2005

The bunyavirus nucleocapsid protein, N, plays a central role in viral replication in encapsidating the three genomic RNA segments to form functional templates for transcription and replication by the viral RNA-dependent RNA polymerase. Here we report functional mapping of interacting domains of the Bunyamwera orthobunyavirus N protein by yeast and mammalian two-hybrid systems, immunoprecipitation experiments, and chemical cross-linking studies. N forms a range of multimers from dimers to high-molecular-weight structures, independently of the presence of RNA. Deletion of the N- or C-terminal domains resulted in loss of activity in a minireplicon assay and a decreased capacity for N to form higher multimers. Our data suggest a head-to-head and tail-to-tail multimerization model for the orthobunyavirus N protein.
A Role for Herpesvirus Entry Mediator as the Receptor for Herpes Simplex Virus 1 Entry into Primary Human Trabecular Meshwork Cells
Authors: Tiwari Vaibhav , Clement Christian , Scanlan Perry M. , Kowlessur Devanand , Yue Beatrice Y. J. T. , Shukla Deepak
Published: September 2005

The human eye is an important target for infection with herpes simplex virus 1 (HSV-1). Damage to cells forming the trabeculum of the eye by HSV-1 infection could contribute to the development of glaucoma, a major blinding disease. Primary cultures of human trabecular meshwork cells were used as an in vitro model to demonstrate the ability of HSV-1 to enter into and establish a productive infection of the trabeculum. Blocking of entry by anti-herpesvirus entry mediator (HVEM) antibody implicated HVEM as the major receptor for HSV-1 infection.
Kaposi's Sarcoma-Associated Herpesvirus Virion-Induced Transcription Activation of the ORF50 Immediate-Early Promoter
Authors: Lu Fang , Day Latasha , Lieberman Paul M.
Published: September 2005

Lytic cycle reactivation of Kaposi's sarcoma-associated herpesvirus (KSHV) can be initiated by transcription activation of the ORF50 immediate-early (IE) gene promoter (ORF50p). We provide evidence that KSHV virions stimulate transcription of ORF50p. Virion activation was resistant to UV inactivation and cycloheximide treatment. The virion-responsive element was mapped to core promoter region −150 to + 1 relative to the ORF50 initiation codon. Electrophoretic mobility shift assays and chromatin immunoprecipitation suggest that KSHV virions indirectly alter the protein composition and chromatin modifications at ORF50p. These data suggest that KSHV virions possess an IE
trans
-inducing function similar to that observed in alpha- and betaherpesviruses.
Pseudo-Gaucher cells in mycobacterial infection: a report of two cases: Figure 1
Authors: Dunn P , Kuo M-C , Sun C-F
Published: September 2005

This report describes two cases of mycobacterial infection with pseudo-Gaucher cells. Both patients had no clinical evidence of inherited Gaucher disease. The first case was a patient with AIDS andMycobacterium avium intracellulareinvolving the lung, spleen, and bone marrow. The bone marrow aspirates showed many histiocytes with needle-like inclusions. Acid fast staining showed that these histiocytes contained acid fast bacilli. Bone marrow biopsies revealed granulomatous lesions with aggregates of foamy histiocytes. The second case was an alcoholic patient withMycobacteriumkanasassiinfection involving the lung and lymph nodes. The lymph node aspirates showed infiltration of the same cells with acid fast bacilli in the cytoplasm.
Idiopathic pure red cell aplasia: first report on CD8 positive lymphocytosis in bone marrow biopsy sections: Figure 1
Authors: Ramadan K M A , Anderson J A M , McMullin M F , Markey G M
Published: September 2005

There is no information in the literature regarding the lymphocyte content or type in bone marrow biopsies from patients with “idiopathic” pure red cell aplasia (PRCA). This report describes the bone marrow biopsy sections of a patient with PRCA. A diffuse CD3 positive (CD8 positive, granzyme B negative) lymphocytosis of approximately 1500/mm3was revealed by immunohistochemical staining. The extent of the T cell increase was not evident from morphological examination of the bone marrow aspirate or biopsy, from flow cytometric analysis of the aspirate, or from the peripheral blood lymphocyte count. Therefore, immunohistochemical analysis should be performed routinely in this rare disease and the data acquired may help to inform the choice of treatment.
Cytogenetic differences in breast cancer samples between German and Japanese patients
Authors: Packeisen J , Nakachi K , Boecker W , Brandt B , Buerger H
Published: September 2005

Background:Japanese and German breast cancer cases differ substantially in the frequency ofegframplification.

Aims:To unravel further the cytogenetic differences between Japanese and German breast cancer cases.

Methods:Forty one Japanese breast cancer cases were evaluated by means of comparative genomic hybridisation (CGH). The results were compared with the CGH results from 161 German breast cancer cases.

Results:The mean number of genetic alterations/case was significantly higher in German premenopausal patients with breast cancer than in their Japanese counterparts. Japanese breast cancer cases revealed a higher number of chromosome 17p losses. Losses of 8p were associated with oestrogen receptor (ER) negativity in Japanese patients with breast cancer, whereas in the German patients gains of 3q and 6q were associated with the lack of ER expression.

Conclusions:The interethnic differences of invasive breast cancer are reflected by cytogenetic aberrations, which are also associated with the differential expression of the ER.
Dominantly inherited β thalassaemia intermedia caused by a new single nucleotide deletion in exon 2 of the β globin gene: Hb morgantown (β91 CTG>CG)
Authors: Luo H-Y , Tang W , Eung S H , Coad J E , Canfield P , Keller F , Crowell E H , Steinberg M H , Chui D H K
Published: September 2005

Family members in multiple generations of an Irish–American family were investigated for moderate to severe microcytic anaemia, inherited in an autosomal dominant fashion. A novel frameshift mutation of the β globin gene was discovered. This study highlights the importance of considering dominantly inherited β thalassemia in the investigation of anaemia, even in patients with ethnic backgrounds not usually associated with β thalassaemia.
Suppressor of cytokine signalling 2 (SOCS-2) expression in breast carcinoma
Authors: Farabegoli F , Ceccarelli C , Santini D , Taffurelli M
Published: September 2005

Aims:To investigate SOCS-2 (suppressor of cytokine signalling 2) protein expression in breast carcinoma samples in relation to biopathological parameters and survival.

Methods:A polyclonal antibody against SOCS-2 was used to study 50 archival breast carcinoma samples, collected from 1993 to 1995. The presence of SOCS-2 protein was investigated in relation to clinical and biological parameters used in breast cancer pathology. Fluorescence in situ hybridisation (FISH) was used to study whether SOCS-2 expression was related to SOCS-2 gene copy number.

Results:SOCS-2 protein was expressed in 34 of 50 breast carcinoma samples and was positively associated with low grade, low nuclear grade, and p27 protein. SOCS-2 expression was inversely related to Ki-67, cyclin A, retinoblastoma protein (pRb), and the epidermal growth factor receptor (EGFR). No relation with overall survival was demonstrated. SOCS-2 amplification was found in three samples. No relation between the number of FISH signals and SOCS-2 expression was found.

Conclusions:The significant correlation seen between SOCS-2 expression, grade, nuclear grade, p27, Ki-67, cyclin A, pRb, and EGFR labelling strongly supports the hypothesis that SOCS-2 loss might be related to cell proliferation and tumour growth in breast carcinoma. Gene copy number changes did not seem to play a role in SOCS-2 regulation and expression; other mechanisms might be involved and deserve further study.
Best practice in primary care pathology: review 1
Authors: Smellie W S A , Wilson D , McNulty C A M , Galloway M J , Spickett G A , Finnigan D I , Bareford D A , Greig M A , Richards J
Published: September 2005

This first best practice review examines four series of common primary care questions in laboratory medicine, namely: (i) measurement and monitoring of cholesterol and of liver and muscle enzymes in patients in the context of lipid lowering drugs, (ii) diagnosis and monitoring of vitamin B12/folate deficiency, (iii) investigation and monitoring of paraprotein bands in blood, and (iv) management ofHelicobacter pyloriinfection. The review is presented in a question–answer format, referenced for each question series. The recommendations represent a précis of guidance found using a standardised literature search of national and international guidance notes, consensus statements, health policy documents, and evidence based medicine reviews, supplemented by MEDLINE EMBASE searches to identify relevant primary research documents. They are not standards but form a guide to be set in the clinical context. Most are consensus rather than evidence based. They will be updated periodically to take account of new information.
A shift to a peripheral Th2-type cytokine pattern during the carcinogenesis of cervical cancer becomes manifest in CIN III lesions
Authors: Bais A G , Beckmann I , Lindemans J , Ewing P C , Meijer C J L M , Snijders P J F , Helmerhorst T J M
Published: September 2005

Background:A shifted balance between T helper 1 (Th1)-type and Th2-type cytokines has been hypothesised in cervical dysplasia

Aims:To evaluate possible deregulation of the cytokine network by estimating the expression of peripheral cytokines in different stages of cervical disease and in relation to the presence or absence of high risk human papillomavirus (HR-HPV).

Methods:Twenty one HR-HPV positive women with high grade cervical intraepithelial neoplasia (CIN II–III) and 12 patients with invasive cervical carcinoma formed the study groups. Two control groups consisted of 10 HR-HPV positive and 11 HR-HPV negative women without CIN. Differences in leucocyte subgroups were evaluated by a differential leucocyte count. Plasma concentrations of tumour necrosis factor α (TNFα), TNFα receptors TNFRI and TNFRII, interferon γ (IFNγ), interleukin 2 (IL-2), IL-12, IL-4, and IL-10 were determined by enzyme linked immunosorbent assays.

Results:Leucocyte counts in patients with CIN III and carcinoma were significantly higher than in controls. Plasma IFNγ concentrations were significantly lower in patients with CIN III and carcinoma than in women with CIN II or controls. Plasma concentrations of IL-12, IL-2, IL-4, and TNFα did not differ significantly between groups, but significantly lower plasma concentrations of TNFRII were found in CIN III and carcinoma compared with CIN II. IL-10 was detected with increased frequency in the plasma of patients with CIN III and carcinoma.

Conclusions:These results indicate that a shift to a Th2-type cytokine pattern during the carcinogenesis of cervical cancer occurs in women with CIN III lesions.
Gene amplification and protein expression of EGFR and HER2 by chromogenic in situ hybridisation and immunohistochemistry in atypical adenomatous hyperplasia and adenocarcinoma of the lung
Authors: Awaya H , Takeshima Y , Furonaka O , Kohno N , Inai K
Published: September 2005

Aims:To investigate the importance of gene amplification and EGFR (epidermal growth factor receptor) and HER2 protein expression during the progression of adenocarcinoma of the lung.

Methods:EGFR and HER2 gene amplification was examined in atypical adenomatous hyperplasia (AAH), bronchioloalveolar carcinoma (BAC), and adenocarcinoma with mixed subtypes (MX) by chromogenic in situ hybridisation (CISH), and protein expression was examined by immunohistochemistry using paraffin wax embedded tissues.

Results:EGFR and HER2 gene amplification was found in four and two of 86 cases, respectively, and was detected only in the invasive components of MX. EGFR and HER2 protein expression was seen in 24 and 18 of 86 cases, respectively. EGFR and HER2 proteins were not expressed in AAH but were expressed in one BAC case each. EGFR and HER2 proteins were expressed in 23 and 17 of 55 adenocarcinomas with MX. EGFR and HER2 protein expression was seen more often in the invasive components than in the BAC components of MX, and increased significantly as lesions progressed from AAH to BAC, early MX, and overt MX. Because EGFR and HER2 protein expression was frequently seen without gene amplification, other mechanisms apart from gene amplification may be associated with protein expression.

Conclusions:EGFR and HER2 gene amplification may be a late event and EGFR and HER2 protein expression may be associated with the development of adenocarcinoma of the lung.
The influence of extent of surgical margin positivity on prostate specific antigen recurrence
Authors: Emerson R E , Koch M O , Jones T D , Daggy J K , Juliar B E , Cheng L
Published: September 2005

Background:Positive surgical margins are an adverse prognostic factor in patients undergoing prostatectomy for prostate cancer. The extent of margin positivity varies and its influence on clinical outcome is uncertain.

Aims:To evaluate the linear extent of margin positivity and the number and location of positive sites as prognostic indicators in a series of prostatectomy specimens evaluated with the whole mount technique.

Methods:Eighty six consecutive margin positive prostatectomy specimens were evaluated, and all pathology data were collected prospectively. The linear extent of margin positivity was measured with an ocular micrometer and the total extent of all positive sites was summed. The total number of sites with positive margins and anatomical sites of the positive margins were analysed.

Results:The linear extent of margin positivity ranged from 0.01 to 68 mm (mean, 6.8; median, 3.0) and was associated with prostate specific antigen (PSA) recurrence in univariate logistic regression (p = 0.031). In addition, the extent of margin positivity weakly correlated with preoperative PSA (p = 0.017) and tumour volume (p = 0.013), but not with age, prostate weight, Gleason score, pathological stage, or perineural invasion. The total number of positive sites was significantly higher in patients with PSA recurrence (p = 0.037). The location of the positive margin site was not associated with PSA recurrence. The extent of margin positivity correlated with PSA recurrence in univariate analysis, although it had only marginal predictive value when adjusted for Gleason score (p = 0.076).

Conclusions:The extent of margin positivity correlates with PSA recurrence in univariate analysis, although it has no predictive value independent of Gleason score.
Molecular pathology of ataxia telangiectasia
Authors: Taylor A M R , Byrd P J
Published: September 2005

Ataxia telangiectasia (A-T) is one of a group of autosomal recessive cerebellar ataxias. Presentation is usually by the age of 2 years and ataxia of both upper and lower limbs develops, such that by early teenage most patients require a wheelchair for mobility. Speech and eye movement are also affected. Other important features are t(7;14) translocations, immunodeficiency, a high serum α fetoprotein concentration, growth retardation, telangiectasia—most noticeably on the bulbar conjunctiva—and a very high risk of developing a lymphoid tumour. Patients also show an increased sensitivity to ionising radiation. The classic form of A-T results from the presence of two truncatingATMmutations, leading to total loss of the ATM protein, a protein kinase. Importantly, A-T shows clinical heterogeneity, including milder forms where neurological progression may be slower or of later onset. In these cases there is a correlation between the preservation of neurological function, decreased radiosensitivity, and the degree of retained ATM protein kinase activity. Considerable scope remains for understanding the progress of the disorder in relation to the types ofATMmutation present.
Marsh stars in Liverpool
Authors: Agarwal A , Helliwell T R
Published: September 2005

Introduction/Methods:After the recognition of contaminating algae on histopathological sections stained by periodic acid Schiff (PAS) and Grocott methods, a detailed audit was undertaken to assess the extent of contamination and its possible source.

Results:The contaminating organism was a member of the staurastrum genus of Chlorophyta, star shaped organisms commonly found in fresh water marshes. The organisms were seen on sections stained by the diastase-PAS, PAS, or Grocott methods and on cytological preparations between July 2003 and May 2004. It is unlikely that contamination of water baths or concentrated staining solutions was to blame, and a more general contamination of the laboratory water supply is the most likely source.

Conclusions:Contaminating organisms may appear on histological and cytological material and their nature and source should be investigated. Although in this instance, confusion with pathologically important organisms was minimal, algae may occasionally cause significant disease.
KSHV/HHV-8 associated lymph node based lymphomas in HIV seronegative subjects. Report of two cases with anaplastic large cell morphology and plasmablastic immunophenotype
Authors: Carbone A , Gloghini A , Vaccher E , Marchetti G , Gaidano G , Tirelli U
Published: September 2005

Background:Kaposi sarcoma associated herpesvirus (KSHV)/human herpesvirus 8 (HHV-8) associated lymphomas, which often develop in human immunodeficiency virus (HIV) infected patients with advanced AIDS, present predominantly as primary effusion lymphoma (PEL) or, less frequently, as “solid” extracavitary based lymphomas, associated with serous effusions. These last lymphomas, also called “solid PEL”, have been reported before the development of an effusion lymphoma and after resolution of PEL. Interestingly, KSHV/HHV-8 associated lymphomas that present as solid or extracavitary based lesions in HIV seropositive patients without serous effusions have been reported recently.

Methods/Results:This paper provides evidence for the existence of a previously undescribed KSHV/HHV-8 associated lymphoma in HIV seronegative patients without serous effusions. These lymphomas exhibit a predilection for the lymph nodes and display anaplastic large cell morphology. These tumours were completely devoid of common cell type specific antigens, including epithelial and melanocytic cell markers. B and T cell associated antigens and other commonly used lymphoid markers were absent or weakly demonstrable in a fraction of the tumour cells. Conversely, immunohistochemical studies showed strong immunostaining with plasma cell reactive antibodies.

Conclusions:Analysis of viral infection and immunohistological studies are of primary importance to define this lymph node based KSHV/HHV-8 associated lymphoma with anaplastic large cell morphology and plasmablastic immunophenotype occurring in HIV seronegative patients without serous effusions.
The fall and rise of bison populations in Wood Buffalo National Park: 1971 to 2003
Authors: Bradley Mark , Wilmshurst John
Published: September 2005

Two hypotheses have been proposed to explain the decline of bison (Bison bison (L., 1758)) abundance in Wood Buffalo National Park (WBNP). The "disease–predation" hypothesis proposes that tuberculosis (Mycobacterium bovis (Karlson and Lessel 1970)) and brucellosis (Brucella abortus (Schmidt 1901)) reduce bison survival and reproduction, resulting in a low-density, predator-regulated equilibrium. The "habitat dispersion hypothesis" proposes that bison in one area of WBNP, the Peace–Athabasca Delta (Delta), have an increased risk of predation because they are concentrated in large meadows with high temporal and spatial predictability. We incorporate bison census data, calf and yearling segregation counts, reproductive rates, adult survival rates, and adult disease incidence in a stochastic population model to show that the historical decline of bison in WBNP would have occurred regardless of disease prevalence. Our model shows that survival of juveniles, the age class that is least susceptible to disease effects, was likely an important determinant of historical changes in population size. We also demonstrate that the population decline was most pronounced in the Delta and that juvenile survival was lower in the Delta, despite evidence that disease incidence was lower in the Delta than in the rest of WBNP. Lastly, the current population trend in WBNP is one of rapid increase, even in the presence of disease.
Factors affecting nest-site selection of Sabine's Gulls in the eastern Canadian Arctic
Authors: Stenhouse Iain J , Gilchrist H Grant , Montevecchi William A
Published: September 2005

The selection of breeding habitat is of prime importance for individual fitness. Among birds, natural selection should favour the ability to recognize and select habitat suitable for nesting and rearing chicks. This study compares the characteristics of Sabine's Gull, Xema sabini (Sabine, 1819), nest sites with random points across a coastal tundra environment on Southampton Island, Nunavut, Canada. The availability of terrestrial invertebrate prey was also examined among habitats. Sabine's Gull nests were nonrandomly distributed in relation to vegetation, substrate, and proximity to water. Gulls nested within approximately 1 km of the coastline and selected sites with the greatest proportions of moss and standing water (i.e., they nested close to the edge of small freshwater ponds near shore). However, there were no detectable differences in characteristics between successful and unsuccessful nests within preferred habitat. The dynamics of terrestrial invertebrate prey communities varied between years, but the volume of invertebrates in Sabine's Gull nesting habitat was intermediate between the most productive habitats and the least productive habitats in both years. However, nest-site selection in Sabine's Gulls may also be influenced by the availability of aquatic invertebrates (not examined in this study) and their proximity to the marine coastline, where chicks are taken to be reared.
Behavioral thermoregulation by maturing adult sockeye salmon (Oncorhynchus nerka) in a stratified lake prior to spawning
Authors: Newell Jennifer C , Quinn Thomas P
Published: September 2005

Adult sockeye salmon, Oncorhynchus nerka (Walbaum in Artedi, 1792), return to Lake Washington several months prior to spawning, spending the warmest months of the year in the lake. We proposed that the fish selected a temperature range ideal for final sexual maturation and energy conservation prior to swimming upstream to spawn. The temperature preferences of the adult sockeye salmon in Lake Washington are attributable to physiological factors, as they are not avoiding predators or seeking prey and are not limited by dissolved oxygen. At the Hiram M. Chittenden Locks, 257 sockeye salmon were tagged with temperature loggers in the summer of 2003, and 38 tags with readable data were recovered. The fish spent an average of 6 days swimming through the ship canal's warm water (ca. 18 °C) and then experienced a drop to temperatures of 13 °C or lower when they entered the lake and descended below the thermocline. Fish remained in the lake for an average of 83 days before migrating upstream to spawn, as indicated by a sudden increase in recorded temperature. Approximately 92% of temperature records in the lake were 9–11 °C, corresponding to depths of 18–30 m. The salmon rarely occupied the cooler and warmer waters available to them. Finally, the apparent thermal preference decreased over the summer, perhaps as a function of sexual maturation.
Factors affecting escape behavior of Iberian green frogs (Rana perezi)
Authors: Martín José , Luque-Larena Juán José , López Pilar
Published: September 2005

Theoretical models and empirical evidence suggest that prey should not flee immediately upon detecting an approaching predator, but instead should adjust their escape response to minimize the costs of flight. Similarly, after deciding to escape, animals should tend to adjust the magnitude and characteristics of their escape response according to the perceived level of predation risk. Although these hypotheses have been tested in some prey types, it remains for their applicability to a wider range of taxa to be ascertained and for a larger variety of microhabitat and environmental conditions to be considered. We simulated predator approaches to Iberian green frogs (Rana perezi Seoane, 1885) in the field. Frogs were approached while they were foraging alone at the edge of water, and they escaped by jumping into the water. Results showed that escape decisions of frogs are influenced by microhabitat variables and body size. Both the approach distance allowed to the predator and the distance jumped by the frogs in response to the approach were positively correlated with the initial distance of the frog from the water's edge; they were also dependent on vegetation cover at the edge of and in the water. Small frogs appeared to rely on crypsis more than large frogs and allowed shorter predator approach distances. They also remained still on the water surface after jumping more often than large frogs. We conclude that such flexibility in the escape response may allow frogs to reduce predation risk without incurring excessive costs.
Competition potential between sympatric woodland caribou and wood bison in southwestern Yukon, Canada
Authors: Fischer Lisa A , Gates C Cormack
Published: September 2005

Wood bison (Bison bison athabascae Rhoads, 1898) were reintroduced to the Aishihik Lake area in the southwestern Yukon, where a population of woodland caribou (Rangifer tarandus caribou (Gmelin, 1788)) existed. These species co-occurred in nearby Beringia over several hundred thousand years and in the study area throughout most of the Holocene. We hypothesized that resource-selection patterns should differ widely between species at all scales because co-evolution should have resulted in strong patterns of resource partitioning. We compared winter utilization distributions of both species based on aerial survey data and assessed differential resource selection at the scales of landscape and distributional overlap. We also assessed differential resource use within feeding sites and compared late-winter diets of the two species. We found 41% overlap in 95% utilization distributions but only 6% overlap in 50% utilization distributions. Strong differences were measured for use of space and terrain, including elevation, slope, and distance from permanent water bodies. Bison strongly selected for or used graminoids, while caribou selected for or used lichens at each scale. Overlap in winter diet between the two species was 10%. At current densities, exploitative competition in winter between these species is unlikely.
STUDY OF ELASTIN SEQUENCES WITH SOLVENT INDUCED FORCE FIELD
Authors: ARKIN HANDAN
Published: September 2005

Conformational structures of two common repeat motifs Val1-Pro2-Gly3-Val4-Gly5 and Gly1-Leu2-Gly3-Gly4 of tropoelastin are investigated by using the multicanonical simulation procedure with solvation effects included energy force field. The effects of solvation energy term on the conformations are determined by analyzing Ramachandran plots. By minimizing the energy structures along the trajectory, the thermodynamically most stable low-energy microstates of the molecule in aqueous solution are determined and the root mean square deviations of these structures with respect to the global minimum are calculated.
JUNCTION FORMATION IN CROSSED NANOTUBES UNDER PRESSURE: MOLECULAR-DYNAMICS SIMULATIONS
Authors: TAŞCI EMRE , MALCIOĞLU OSMAN BARIŞ , ERKOÇ ŞAKİR
Published: September 2005

Junction formation in crossed C (10,0) single wall carbon nanotubes under pressure has been investigated, using classical molecular-dynamics simulations at 1 K. It has been found that a stable mechanical junction was formed by means of placing two crossed single wall carbon nanotubes between two rigid graphene layers which move toward each other.
SELF-SIMILAR LOG-PERIODIC STRUCTURES IN WESTERN STOCK MARKETS FROM 2000
Authors: BARTOLOZZI M. , DROŻDŻ S. , LEINWEBER D. B. , SPETH J. , THOMAS A. W.
Published: September 2005

The presence of log-periodic structures before and after stock market crashes is considered to be an imprint of an intrinsic discrete scale invariance (DSI) in this complex system. The fractal framework of the theory leaves open the possibility of observing self-similar log-periodic structures at different time scales. In the present work, we analyze the daily closures of four of the most important indices worldwide since 2000: the DAX for Germany and the NASDAQ-100, the S&P 500 and the Dow Jones for the United States. The qualitative behavior of these different markets is similar during the temporal frame studied. Evidence is found for decelerating log-periodic oscillations of duration about two years and starting in September 2000. Moreover, a nested sub-structure starting in May 2002 is revealed, bringing more evidence to support the hypothesis of self-similar, log-periodic behavior. Ongoing log-periodic oscillations are also revealed. A Lomb analysis over the aforementioned periods indicates a preferential scaling factor λ~2. Higher order harmonics are also present. The spectral pattern of the data has been found to be similar to that of a Weierstrass-type function, used as a prototype of a log-periodic fractal function.
FIRST-PRINCIPLES STUDY OF DOPED SINGLE WALL CARBON NANOTUBES
Authors: MAO YU-LIANG , YAN XIAO-HONG , XIAO YANG , CAO JUE-XIAN , XIANG JUN
Published: September 2005

We investigate boron and nitrogen substitutional doping single wall carbon nanotubes (SWCNTs) by first-principles calculations. The optimized geometres of boron and nitrogen substituted SWCNTs exhibit bamboo-like structures. Boron and nitrogen impurities form acceptor and donor states in semiconductor SWCNTs. The highest occupied molecular orbital (HOMO) indicates the trend of forming inter-tube bonds in doping SWCNTs. It may start a new way to form inter-tube bonds by doping in SWCNTs.
EXPERT SYSTEM FOR THRESHOLD SPECTRA ANALYSIS OF NITROGEN MOLECULES
Authors: PETROVIĆ VIOLETA , BOČVARSKI V.
Published: September 2005

The electron method spectroscopy consists in the detection of very low energy electrons formed in electron–molecule collisions. The advantage of this method over the method of optical spectroscopy lies in the possibility to study optically forbidden states, so the complexity of spectrum rises steeply, which makes its analysis more difficult. Besides electron states, there are also a vibrational states in threshold spectra analysis, and those had to be identified and classified. This paper presents an expert system developed to automate, speed up and improve the N 2 threshold spectra analysis.
THE EFFECT OF DELAY TIMES ON THE OPTIMAL VELOCITY TRAFFIC FLOW BEHAVIOR
Authors: EZ-ZAHRAOUY H. , BENRIHANE Z. , BENYOUSSEF A.
Published: September 2005

We have numerically investigated the effect of the delay times τf and τs of a mixture of fast and slow vehicles on the fundamental diagram (the current-density relation) of the optimal velocity model. The optimal velocity function of the fast cars depends not only on the headway of each car but also on the headway of the immediately preceding one. It is found that the small delay times have almost no effects, while, for sufficiently large delay time τs, the current profile displays qualitatively five different forms, depending on τf, τs and the fractions df and ds of the fast and slow cars, respectively. The velocity (current) exhibits first-order transitions at low and/or high densities, from freely moving phase to the congested state, and from congested state to a jamming one, respectively. The minimal current appears in intermediate values of τs. Furthermore, there exist a critical value of τf above which the metastability and hysteresis appear. The spatial-temporal traffic patterns near the congested-jamming first-order transition is also presented.
COMPLEX BEHAVIOR OF FUZZY LOGISTIC RULE 90 AUTOMATON
Authors: SANCHEZ JUAN R.
Published: September 2005

A dynamical system falling in between the elementary binary cellular automata and the coupled map lattices is presented. It is composed by a one-dimensional cellular automaton in which the values within each cell are continuous instead of discrete. However, in this case, the coupling between cells is made through a logistic map instead of making the fuzzification of the disjunctive normal form describing the corresponding Boolean rule. The system resembles the CA rule 90 evolution, since the future value of a cell depends only on a combination of the values of the nearest neighbors cells. The basic dynamical and stability properties of the system are analyzed. The system displays different types from attractors (fixed points, cycles and chaotic attractors), depending on the growth rate parameter used for the logistic map coupling. If the cell values are binary, i.e., only values 0 and 1 are allowed within each cell, the dynamical evolution of the rule 90 automaton is recovered.
OPINION DYNAMICS AND DECISION OF VOTE IN BIPOLAR POLITICAL SYSTEMS
Authors: CARUSO FILIPPO , CASTORINA PAOLO
Published: September 2005

A model of the opinion dynamics underlying the political decision is proposed. The analysis is restricted to a bipolar scheme with a possible third political area. The interaction among voters is local but the final decision strongly depends on global effects such as the rating of the governments. As in the realistic case, the individual decision making process is determined by the most relevant personal interests and problems. The phenomenological analysis of the national vote in Italy and Germany has been carried out and a prediction of the next Italian vote as a function of the government rating is presented.
SOLVATION EFFECTS ON FREE ENERGY SURFACE OF POLYALANINE
Authors: GÖKOĞLU GÖKHAN , ARKIN HANDAN , AKTÜRK ETHEM , ÇELIK TARIK
Published: September 2005

We have simulated 10-residue polyalanine chain by multicanonical method to visualize the 3D topographic picture of the free energy landscape over the whole range of temperatures, hence to show the funnel along the folding pathway exhaustively. We have simulated and compared the system in vacuo and in solvent, and examined the changes in the free energy landscape due to the solvent effects, which are taken into account by commonly used model Accessible Surface Area.
YANGIAN SYMMETRIES OF MATRIX MODELS AND SPIN CHAINS: THE DILATATION OPERATOR OF ${\mathcal N} = 4$ SYM
Authors: AGARWAL A. , RAJEEV S. G.
Published: September 2005

We present an analysis of the Yangian symmetries of various bosonic sectors of the dilatation operator of [Formula: see text] SYM. The analysis is presented from the point of view of Hamiltonian matrix models. In the various SU (n) sectors, we give a modified presentation of the Yangian generators, which are conserved on states of any size. A careful analysis of the Yangian invariance of the full SO(6) sector of the scalars is also presented in this paper. We also study the Yangian invariance beyond first order perturbation theory. Following this, we derive the continuum limits of the various matrix models and reproduce the sigma model actions for fast moving strings reported in some papers. We motivate the constructions of continuum sigma models (corresponding to both the SU (n) and SO (n) sectors) as variational approximations to the matrix model Hamiltonians. These sigma models retain the semiclassical counterparts of the original Yangian symmetries of the dilatation operator. The semiclassical Yangian symmetries of the sigma models are worked out in detail. The zero curvature representation of the equations of motion and the construction of the transfer matrix for the SO (n) sigma model obtained as the continuum limit of the one loop bosonic dilatation operator is carried out, and the similar constructions for the SU (n) case are also discussed.
BUILDING BLOCKS OF PHYSICAL STATES IN A NONCRITICAL 3-BRANE ON R × S3
Authors: HAMADA KEN-JI
Published: September 2005

The physical states in a worldvolume model of a noncritical 3-brane are systematically constructed using techniques of four-dimensional conformal field theories on R × S3 developed recently. Invariant combinations of creation modes under a special conformal transformation provide building blocks of physical states. Any state can be created by acting with such building blocks on a conformally invariant vacuum in an invariant way under the other conformal charges: the Hamiltonian and rotation generators on S3. We explicitly construct building blocks for scalar, vector and gravitational fields, and classify them as finite types.