bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of measured and computed portal dose for IMRT treatment
Authors: Cilla Savino , Viola Pietro , Azario Luigi , Grimaldi Luca , Craus Maurizio , D'Onofrio Guido , Fidanzio Andrea , Deodato Francesco , Macchia Gabriella , Digesù Cinzia , Morganti Alessio G. , Piermattei Angelo
Published: February 2007

A new 2D array Seven 29™ model (PTW, Freiburg), equipped with 729 vented plane‐parallel ion chambers, projected for pretreatment verification of radiotherapy plans, was used as a detector for the transmitted or portal dose measurements below a Rando phantom. The dosimetric qualities of the 2D array make it attractive for measuring transmitted dose maps from step‐and‐shoot intensity‐modulated radiotherapy (IMRT). It is well known that for step‐and‐shoot IMRT beams that use a small number of monitor units (MUs) per sequence, the early and recent electronic portal imaging devices (EPIDs) present a different response at X‐ray start‐up that affects the accuracy of the measured transmitted dose. The comparison of portal doses measured to those calculated by a commercial treatment‐planning system (TPS) can verify correct dose delivery during treatment. This direct validation was tested by irradiating a simulated head tumor in a Rando anthropomorphic phantom by step‐and‐shoot IMRT beams. The absolute transmitted doses on a plane orthogonal to the beam central axis below the phantom were measured by the 2D array calibrated in terms of dose to water and compared with the computed portal dose extracted by custom software. In a previous paper, the comparison between the IMRT portal doses, computed by a commercial TPS and measured by a linear array that supplied a 1 mm spatial dose resolution, was carried out. The γ‐index analysis supplied an agreement of more than 95% of the dose point with acceptance criteria, in terms of dose difference, , and distance agreement, , equal to 4% and 4 mm, respectively. In this paper, we verify the possible use of the PTW 2D array for measurements of the transmitted doses during several fractions of head and neck tumor radiotherapy. There are two advantages in the use of this 2D array as a portal dose device for the IMRT quality assurance program: first is the ability to perform absolute dose comparisons for hundreds of measurement positions to verify the correct dose delivery in several fractions of the therapy; second is the efficiency in time to detect these kinds of dose distributions within the field of view area of the CT scanner.

PACS number: 87.53.Xd
Book Review
Authors: Jackson Edward F.
Published: February 2007

Imaging Systems for Medical Diagnostics: Fundamentals, Technical Solutions, Applications for Systems Applying Ionizing Radiation, Nuclear Magnetic Resonance and Ultrasound, Arnulf Oppelt, Editor, Publicis Corporate Publishing, John Wiley and Sons Distributor, ISBN 3‐9578‐226‐2 (cloth) $145
Dose modification factors for 192Ir high‐dose‐rate irradiation using Monte Carlo simulations
Authors: Kassas Bassel , Mourtada Firas , Horton John L. , Lane Richard G. , Buchholz Thomas A. , Strom Eric A.
Published: February 2007

A recently introduced brachytherapy system for partial breast irradiation, MammoSite, consists of a balloon applicator filled with contrast solution and a catheter for insertion of an high‐dose‐rate (HDR) source. In using this system, the treatment dose is typically prescribed to be delivered 1 cm from the balloon's surface. Most treatment‐planning systems currently in use for brachytherapy procedures use water‐based dosimetry with no correction for heterogeneity. Therefore, these systems assume that full scatter exists regardless of the amount of tissue beyond the prescription line. This assumption might not be a reasonable one, especially when the tissue beyond the prescription line is thin. In such a case, the resulting limited scatter could cause an underdose to be delivered along the prescription line. We used Monte Carlo simulations to investigate how the thickness of the tissue between the surface of the balloon and the skin or lung affected the treatment dose delivery. Calculations were based on a spherical water phantom with a diameter of 30 cm and balloons with diameters of 4 cm, 5 cm, and 6 cm. The dose modification factor is defined as the ratio of the dose rate at the typical prescription distance of 1 cm from the balloon's surface with full scatter obtained using the water phantom to the dose rate with a finite tissue thickness (from 0 cm to 10 cm) beyond the prescription line. The dose modification factor was found to be dependent on the balloon diameter and was 1.098 for the 4‐cm balloon and 1.132 for the 6‐cm balloon with no tissue beyond the prescription distance at the breast–skin interface. The dose modification factor at the breast–lung interface was 1.067 for the 4‐cm balloon and 1.096 for the 6‐cm balloon. Even 5 cm of tissue beyond the prescription distance could not result in full scatter. Thus, we found that considering the effect of diminished scatter is important to accurate dosimetry. Not accounting for the dose modification factor may result in delivering a lower dose than is prescribed.

PACS number: 87.53.Jw
Book Review
Authors: Smith René J.
Published: February 2007

Editors Note: This book is written in Spanish and the review is given in both English and Spanish. Both reviews were written by the same individual and essentially have the same content.

Code of Practice for Quality Control of Treatment Planning Systems (TPS) in Radiation Therapy, by José Miguel Delgado Rodríguez, Feliciano García Vicente, Esther Millán Cebrián. Sociedad Española de Física Médica. Ramírez de Arellano Editores, S. L. 2005, Madrid, Spain; available. secretaria@sefm.es, 50ε

Protocolo para Control de Calidad en Sistemas de Planificación de Terapia con Radiaciones Ionizantes, por José Miguel Delgado Rodríguez, Feliciano García Vicente, Esther Millán Cebrián. Sociedad Española de Física Médica. Ramírez de Arellano Editores, S. L. 2005, Madrid, Spain.

secretaria@sefm.es, 50ε
Book Review
Authors: Smathers James. B.
Published: February 2007

Structural Shielding Design and Evaluation for Megavoltage X‐ and Gamma Ray Radiotherapy Facilities; National Council on Radiation Protection and Measurements (NCRP Report 151); Issued December 2005, ISBN‐13: 987‐0‐29600‐87‐1; Price $100 USD (hard copy), $80 (down loadable PDF), $170 (combined package)
Expression of the Human Hepatitis B Virus Large Surface Antigen Gene in Transgenic Tomato Plants
Authors: Lou Xiao-Ming , Yao Quan-Hong , Zhang Zhen , Peng Ri-He , Xiong Ai-Sheng , Wang Hua-Kun
Published: February 2007

The original hepatitis B virus (HBV) large surface antigen gene was synthesized. In order to optimize the expression of this gene in tomato plants, the tobacco pathogenesis-related protein S signal peptide was fused to the 5′ end of the modified gene and the sequence encoding amino acids S, E, K, D, E, and L was placed at the 3′ end. The gene encoding the modified HBV large surface antigen under the control of a fruit-specific promoter was constructed and expressed in transgenic tomato plants. The expression of the antigen from transgenic plants was confirmed by PCR and reverse transcriptase PCR. Enzyme-linked immunoassays using a monoclonal antibody directed against human serum-derived HBsAg revealed that the maximal level of HBsAg was about 0.02% of the soluble protein in transgenic tomato fruit. The amount of HBsAg in mature fruits was found to be 65- to 171-fold larger than in small or medium fruits and leaf tissues. Examination of transgenic plant samples by transmission electron microscopy proved that HBsAg had been expressed and had accumulated. The HBsAg protein was capable of assembling into capsomers and virus-like particles. To our knowledge, this is the first time the HBV large surface antigen has been expressed in plants. This work suggests the possibility of producing a new alternative vaccine for human HBV.
Long-Lasting Protective Immune Response to the 19-Kilodalton Carboxy-Terminal Fragment ofPlasmodium yoeliiMerozoite Surface Protein 1 in Mice
Authors: Jeamwattanalert Pimmada , Mahakunkijcharoen Yuvadee , Kittigul Leera , Mahannop Pakpimol , Pichyangkul Sathit , Hirunpetcharat Chakrit
Published: February 2007

Merozoite surface protein 1 (MSP1) is the major protein on the surface of the plasmodial merozoite, and its carboxy terminus, the 19-kDa fragment (MSP119), is highly conserved and effective in induction of a protective immune response against malaria parasite infection in mice and monkeys. However, the duration of the immune response has not been elucidated. As such, we immunized BALB/c mice with a standard four-dose injection of recombinantPlasmodium yoeliiMSP119formulated with Montanide ISA51 and CpG oligodeoxynucleotide (ODN) and monitored the MSP119-specific antibody levels for up to 12 months. The antibody titers persisted constantly over the period of time without significant waning, in contrast to the antibody levels induced by immunization with Freund's adjuvant, where the antibody levels gradually declined to significantly lower levels 12 months after immunization. Investigation of immunoglobulin G (IgG) subclass longevity revealed that only the IgG1 antibody level (Th2 type-driven response) decreased significantly by 6 months, while the IgG2a antibody level (Th1 type-driven response) did not change over the 12 months after immunization, but the boosting effect was seen in the IgG1 antibody responses but not in the IgG2a antibody responses. After challenge infection, all immunized mice survived with negligibly patent parasitemia. These findings suggest that protective immune responses to MSP119following immunization using oil-based Montanide ISA51 and CpG ODN as an adjuvant are very long-lasting and encourage clinical trials for malaria vaccine development.
Use of a Novel Chimeric Mouse Model with a Functionally Active Human Immune System To Study Human Immunodeficiency Virus Type 1 Infection
Authors: An Dong Sung , Poon Betty , Fang Raphael Ho Tsong , Weijer Kees , Blom Bianca , Spits Hergen , Chen Irvin S. Y. , Uittenbogaart Christel H.
Published: February 2007

The goal of this study was to develop a small-animal model to study human immunodeficiency virus type 1 (HIV-1) pathogenesis in blood and primary and secondary lymphoid organs. Rag2
−/−
γ
c
−/−
mice that are neonatally injected with human CD34
+
cells develop a functional human immune system (HIS), with human hematopoietic cells being found in the thymuses, peripheral blood, spleens, and bone marrow of the animals (hereafter these animals are referred to as HIS-Rag2
−/−
γ
c
−/−
mice). HIS-Rag2
−/−
γ
c
−/−
mice were infected with small amounts of CCR5-tropic HIV-1. Viral replication and immunophenotypic changes in the human cells in peripheral blood and lymphoid organs were examined. The productive infection of human cells in peripheral blood, thymus and spleen tissue, and bone marrow was detected. Ratios of CD4
+
T cells to CD8
+
T cells in the infected animals declined. Although no specific anti-HIV-1 immune responses were detected, immunoglobulin M (IgM) and IgG antibodies to an unidentified fetal calf serum protein present in the virus preparation were found in the inoculated animals. Thus, we have shown that the HIS-Rag2
−/−
γ
c
−/−
mouse model can be used for infection with low doses of CCR5-tropic HIV-1, which is most commonly transmitted during primary infections. HIS-Rag2
−/−
γ
c
−/−
mice can serve as a small-animal model for investigating HIV-1 pathogenesis and testing potential HIV-1 therapies, and studies with this model may replace some long and costly studies with nonhuman primates.
Comparative Evaluation of Enzyme-Linked Immunosorbent Assays Based on Crude and Recombinant Leishmanial Antigens for Serodiagnosis of Symptomatic and Asymptomatic
Leishmania infantum
Visceral Infections in Dogs
Authors: Porrozzi Renato , Santos da Costa Marcos V. , Teva Antonio , Falqueto Aloísio , Ferreira Adelson L. , dos Santos Claudiney D. , Fernandes Ana Paula , Gazzinelli Ricardo T. , Campos-Neto Antonio , Grimaldi Gabriel
Published: February 2007

The diagnosis of visceral leishmaniasis remains difficult in rural areas where the disease is endemic, and serologic methods still need assessment, as they are not very sensitive for the detection of asymptomatic infectious dogs. Here we present data on the development of enzyme-linked immunosorbent assay (ELISA)-based methods for the detection of antibodies against recombinant leishmanial antigens (namely, the recombinant K26 [rK26] and rK39 antigens from
Leishmania infantum
and the rA2 protein from
Leishmania donovani
) in comparison to ELISAs employing crude soluble antigen (CSA). The assays utilized sera from known negative controls (
n
= 25) and clinically asymptomatic (
n
= 50) and symptomatic (
n
= 50) dogs with confirmed
L. infantum
infections. Additional studies were also done using sera from animals harboring other infections (
n
= 14) for the evaluation of cross-reactivity. Our study indicated that rK26 and rK39 used in ELISAs provided very high sensitivities for the detection of symptomatic dogs (94% and 100%, respectively), followed by CSA (88%) and rA2 (70%). Conversely, rA2 was more sensitive for asymptomatic dogs (88%) than rK39 and rK26 (both 66%) and CSA (30%). Some cross-reactivity in sera from dogs with other infections (
Leishmania braziliensis
and
Leptospira interrogans
) was identified, but the rA2 protein provided the greatest specificity (98%). Data further indicate that all three recombinant proteins must be used in parallel to detect essentially all infected dogs. Efforts should be made to develop a cheap and reliable serologic test based on epitope selection from these diagnostic markers for the sensitive detection of
L. infantum
-infected dogs.
Detection of Human Papillomavirus Type 16-Specific T Lymphocytes by a Recombinant Vaccinia Virus-Based Enzyme-Linked Immunospot Assay
Authors: Kim Kevin H. , Greenfield William , Shotts Ezekiel , Nakagawa Mayumi
Published: February 2007

Cell-mediated immunity, particularly that induced by T cells, is thought to have a key role in controlling infection. The enzyme-linked immunospot (ELISPOT) assay has been successfully adapted to detect T-cell immune response to a variety of pathogens. However, it still remains a challenge to detect antigen-specific T cells when the numbers of circulating cells are low, such as in a local cervical infection caused by genital human papillomavirus (HPV). The goal of this study was to develop a protocol for enhanced detection of HPV-specific CD8
+
T cells by examining a number of the variables involved in performing an ELISPOT assay. Since blood samples consistently positive for HPV-specific T cells are difficult to obtain, previously described human papillomavirus type 16 (HPV16) E6 52-61 (FAFRDLCIVY)-specific T-cell clone cells (13) seeded in peripheral blood mononuclear cells from an HLA-B57-positive blood donor were used. The variables examined were the amounts of primary and secondary anti-gamma interferon antibodies, amounts of antigen-presenting monocytes and recombinant vaccinia virus expressing the HPV16 E6 protein, and amounts of exogenous cytokines added (recombinant human interleukin-2 [rhIL-2] and rhIL-7). The amounts of antigen-presenting monocytes, followed by the concentration of exogenous rhIL-2, had the most pronounced and significant effects in enhancing sensitivity of the ELISPOT assay. Blood samples from six patients being monitored for abnormal Pap smear results and from 12 healthy volunteers were examined using the enhanced conditions.
Toxin Profiles and Resistances to Macrolides and Newer Fluoroquinolones as Epidemicity Determinants of Clinical Isolates of
Clostridium difficile
from Warsaw, Poland
Authors: Pituch Hanna , van Leeuwen Willem , Maquelin Kees , Wultańska Dorota , Obuch-Woszczatyński Piotr , Nurzyńska Grazyna , Kato Haru , Reijans Martin , Meisel-Mikołajczyk Felicja , Łuczak Mirosław , van Belkum Alex
Published: February 2007

Amplified fragment length polymorphism genotypes, antibiotic resistance profiles, and toxin profiles of
Clostridium difficile
strains from Warsaw were determined. The isolates segregate in six major genotypes, coinciding with toxin profiles. Most of the toxin A-negative toxin B-positive toxin CDT-negative strains possess
ermB
, and several strains were resistant to fluoroquinolones. Resistograms and toxin types of
C. difficile
strains are epidemicity determinants.
Development of a Loop-Mediated Isothermal Amplification Assay for Rapid Detection of BK Virus
Authors: Bista Bipin Raj , Ishwad Chandra , Wadowsky Robert M. , Manna Pradip , Randhawa Parmjeet Singh , Gupta Gaurav , Adhikari Meena , Tyagi Rakhi , Gasper Gina , Vats Abhay
Published: February 2007

Loop-mediated isothermal amplification (LAMP) is a novel method for rapid amplification of DNA. Its advantages include rapidity and minimal equipment requirement. The LAMP assay was developed for BK virus (BKV), which is a leading cause of morbidity in renal transplant recipients. The characteristics of the assay, including its specificity and sensitivity, were evaluated. BKV LAMP was performed using various incubation times with a variety of specimens, including unprocessed urine and plasma samples. A ladder pattern on gel electrophoresis, typical of successful LAMP reactions, was observed specifically only for BKV and not for other viruses. The sensitivity of the assay with 1 h of incubation was 100 copies/tube of a cloned BKV fragment. Additionally, a positive reaction was visually ascertained by a simple color reaction using SYBR green dye. BKV LAMP was also successful for urine and plasma specimens without the need for DNA extraction. Due to its simplicity and specificity, the LAMP assay can potentially be developed for “point of care” screening of BKV.
Development of Methods for Coordinate Measurement of Total Cell-Associated and Integrated Human Immunodeficiency Virus Type 1 (HIV-1) DNA Forms in Routine Clinical Samples: Levels Are Not Associated with Clinical Parameters, but Low Levels of Integrated HIV-1 DNA May Be Prognostic for Continued Successful Therapy
Authors: Carr J. M. , Cheney K. M. , Coolen C. , Davis A. , Shaw D. , Ferguson W. , Chang G. , Higgins G. , Burrell C. , Li P.
Published: February 2007

We have adapted our established
Alu
PCR assay for proviral DNA and PCR for total cellular DNA to a real-time PCR format and applied these to human immunodeficiency virus (HIV)-positive specimens collected for routine determination of the plasma viral load (pVL). In a cohort of five patients, measurements of integrated viral load (iVL) and cell-associated viral load (cVL) in CD4
+
cells isolated by a single positive selection step were not indicative of HIV DNA levels in the circulation, and further analysis was performed on peripheral blood mononuclear cells (PBMC). In a cohort of 46 samples total cVL was quantitated in most samples, but iVL could be quantitated in only 47.8%, since in 26% iVL was undetectable and in 21.7% the results were invalid due to high levels of unintegrated HIV DNA. There was no correlation of cVL or iVL with pVL, CD4 count, or duration of successful antiretroviral treatment. Out of 26 patients with undetectable pVL, 4 patients failed therapy within the subsequent 12 months and had higher than average iVL, but this was not the case for cVL. Among nine patients with long-term undetectable pVL, no consistent decline in cVL or iVL was seen with time, and changes in cVL and iVL within a patient could be concordant or discordant. These results show that cVL and iVL can be coordinately measured in PBMC from clinical samples but do not correlate with pVL, CD4 counts, or length of suppressive antiretroviral therapy. Interestingly, a high iVL (but not a high cVL) in patients with undetectable pVL was associated with subsequent treatment failure.
Surveillance Cultures and Duration of Carriage of Multidrug-Resistant
Acinetobacter baumannii
Authors: Marchaim Dror , Navon-Venezia Shiri , Schwartz David , Tarabeia Jalal , Fefer Iris , Schwaber Mitchell J. , Carmeli Yehuda
Published: February 2007

Isolating carriers of multidrug-resistant (MDR)
Acinetobacter baumannii
is the main measure to prevent its spread. Identification of carriers accompanied by contact precautions is essential. We aimed to determine the appropriate surveillance sampling sites and the duration of carriage of MDR
A. baumannii
. We studied prospectively two groups of patients from whom MDR
A. baumannii
was previously isolated: (i) those with recent clinical isolation (≤10 days) and (ii) those with remote clinical isolation (≥6 months). Screening for carriage was conducted from six sites: nostrils, pharynx, skin, rectum, wounds, and endotracheal aspirates. Strains recovered concurrently from different sites were genotyped using pulsed-field gel electrophoresis. Twelve of 22 with recent clinical isolation of MDR
A. baumannii
had ≥1 positive screening culture, resulting in a sensitivity of 55% when six body sites were sampled. Sensitivities of single sites ranged from 13.5% to 29%. Among 30 patients with remote clinical isolation, screening cultures were positive in 5 (17%), with a mean duration of 17.5 months from the last clinical culture. Remote carriers had positive screening cultures from the skin and pharynx but not from nose, rectum, wounds, or endotracheal aspirates. Eleven strains from five patients were genotyped. In all but one case, isolates from different sites in a given patient were clonal. Current methodology is suboptimal to detect MDR
A. baumannii
carriage. The sensitivity of surveillance cultures is low, even when six different body sites are sampled. The proportion of individuals with previous MDR
A. baumannii
isolation who remain carriers for prolonged periods is substantial. These data should be considered when designing measures to limit the spread of MDR
A. baumannii
.
False-Positive Culture Results from Patient Tissue Specimens Due to Contamination of RPMI Medium with
Cryptococcus albidus
Authors: Winston Lisa G. , Roemer Marguerite , Goodman Carol , Haller Barbara
Published: February 2007

Cryptococcus albidus
, a rare opportunist, was isolated from biopsy specimens from three patients over 4 days. An investigation showed that the specimens had been contaminated by placement in RPMI medium. The importance of rapid communication between the microbiology laboratory, the infectious diseases/infection control division, and other involved parties in the event of unusual occurrences is highlighted.
Graphium basitruncatumFungemia in a Patient with Acute Leukemia
Authors: Kumar Deepali , Sigler Lynne , Gibas Connie Fe C. , Mohan Subhash , Schuh Andre , Medeiros Bruno C. , Peckham Kenneth , Humar Atul
Published: February 2007

We report the first case of infection caused byGraphium basitruncatumin a man with acute leukemia who developed persistent fungemia and skin lesions.G. basitruncatum, a member of theMicroascaceae, is phylogenetically and morphologically distinct fromGraphium penicillioidesand the opportunistic pathogensScedosporium apiospermum(Pseudallescheria boydii) andScedosporium prolificans.
Clonal Distribution of Invasive
Neisseria meningitidis
Serogroup C Strains Circulating from 1976 to 2005 in Greater São Paulo, Brazil
Authors: de Lemos Ana Paula Silva , Yara Teresa Ykuko , Gorla Maria Cecília Outeiro , de Paiva Maria Vaneide , de Souza Adriana Lambert , Gonçalves Maria Inês Cappelletti , de Almeida Samanta Cristine Grassi , do Valle Gloria Regina Feitas , Sacchi Claudio Tavares
Published: February 2007

Meningococcal disease is characterized by cyclic fluctuations in incidence, serogroup distribution, and antigenic profiles. In greater São Paulo, Brazil, there has been a constant increase in the incidence of serogroup C meningococcal disease since the late 1980s. To gain an understanding of changes in serogroup C meningococcal disease over three decades in greater São Paulo, Brazil, 1,059 invasive
Neisseria meningitidis
serogroup C isolates from 1976 and 2005 were analyzed. Three major clone complexes, sequence type (ST)-11, ST-8, and ST-103, were identified by multilocus sequence typing, and the isolates were characterized by serotyping and 16S rRNA typing. During the 30-year period, there were two major antigenic replacements: from 2a:P1.(5,2) to 2b:P1.3 and subsequently to 23:P1.14-6. All strains of clone ST-103 were characterized as serotype 23 and serosubtype P1.14-6. The origin of 23:P1.14-6 ST-103 complex strains is unknown, but efforts are needed to monitor its spread and define its virulence. The antigenic replacements we observed likely represent a mechanism to sustain meningococcal disease in the population as immunity to circulating strains accumulated.
Comparison of the Digene Hybrid Capture System Cytomegalovirus (CMV) DNA (Version 2.0), Roche CMV UL54 Analyte-Specific Reagent, and QIAGEN RealArt CMV LightCycler PCR Reagent Tests Using AcroMetrix OptiQuant CMV DNA Quantification Panels and Specimens from Allogeneic-Stem-Cell Transplant Recipients
Authors: Hanson Kimberly E. , Reller L. Barth , Kurtzberg Joanne , Horwitz Mitchell , Long Gwynn , Alexander Barbara D.
Published: February 2007

The Digene Hybrid Capture system cytomegalovirus (CMV) DNA (version 2.0), Roche CMV UL54 analyte-specific reagent, and QIAGEN RealArt CMV LightCycler PCR reagent tests were compared using whole-virus standards and plasma specimens collected from allogeneic-stem-cell transplant recipients. PCR assays showed better speed, sensitivity, and specificity.
Simian Immunodeficiency Virus (SIV) Infection Influences the Level and Function of Regulatory T Cells in SIV-Infected Rhesus Macaques but Not SIV-Infected Sooty Mangabeys
Authors: Pereira L. E. , Villinger F. , Onlamoon N. , Bryan P. , Cardona A. , Pattanapanysat K. , Mori K. , Hagen S. , Picker L. , Ansari A. A.
Published: February 2007

Differences in clinical outcome of simian immunodeficiency virus (SIV) infection in disease-resistant African sooty mangabeys (SM) and disease-susceptible Asian rhesus macaques (RM) prompted us to examine the role of regulatory T cells (Tregs) in these two animal models. Results from a cross-sectional study revealed maintenance of the frequency and absolute number of peripheral Tregs in chronically SIV-infected SM while a significant loss occurred in chronically SIV-infected RM compared to uninfected animals. A longitudinal study of experimentally SIV-infected animals revealed a transient increase in the frequency of Tregs from baseline values following acute infection in RM, but no change in the frequency of Tregs occurred in SM during this period. Further examination revealed a strong correlation between plasma viral load (VL) and the level of Tregs in SIV-infected RM but not SM. A correlation was also noted in SIV-infected RM that control VL spontaneously or in response to antiretroviral chemotherapy. In addition, immunofluorescent cell count assays showed that while Treg-depleted peripheral blood mononuclear cells from RM led to a significant enhancement of CD4+and CD8+T-cell responses to select pools of SIV peptides, there was no detectable T-cell response to the same pool of SIV peptides in Treg-depleted cells from SIV-infected SM. Our data collectively suggest that while Tregs do appear to play a role in the control of viremia and the magnitude of the SIV-specific immune response in RM, their role in disease resistance in SM remains unclear.
Extensive Intrasubtype Recombination in South African Human Immunodeficiency Virus Type 1 Subtype C Infections
Authors: Rousseau Christine M. , Learn Gerald H. , Bhattacharya Tanmoy , Nickle David C. , Heckerman David , Chetty Senica , Brander Christian , Goulder Philip J. R. , Walker Bruce D. , Kiepiela Photini , Korber Bette T. , Mullins James I.
Published: February 2007

Recombinant human immunodeficiency virus type 1 (HIV-1) strains containing sequences from different viral genetic subtypes (intersubtype) and different lineages from within the same subtype (intrasubtype) have been observed. A consequence of recombination can be the distortion of the phylogenetic signal. Several intersubtype recombinants have been identified; however, less is known about the frequency of intrasubtype recombination. For this study, near-full-length HIV-1 subtype C genomes from 270 individuals were evaluated for the presence of intrasubtype recombination. A sliding window schema (window, 2 kb; step, 385 bp) was used to partition the aligned sequences. The Shimodaira-Hasegawa test detected significant topological incongruence in 99.6% of the comparisons of the maximum-likelihood trees generated from each sequence partition, a result that could be explained by recombination. Using RECOMBINE, we detected significant levels of recombination using five random subsets of the sequences. With a set of 23 topologically consistent sequences used as references, bootscanning followed by the interactive informative site test defined recombination breakpoints. Using two multiple-comparison correction methods, 47% of the sequences showed significant evidence of recombination in both analyses. Estimated evolutionary rates were revised from 0.51%/year (95% confidence interval [CI], 0.39 to 0.53%) with all sequences to 0.46%/year (95% CI, 0.38 to 0.48%) with the putative recombinants removed. The timing of the subtype C epidemic origin was revised from 1961 (95% CI, 1947 to 1962) with all sequences to 1958 (95% CI, 1949 to 1960) with the putative recombinants removed. Thus, intrasubtype recombinants are common within the subtype C epidemic and these impact analyses of HIV-1 evolution.
Analysis of Hepatitis C Virus Hypervariable Region 1 Sequence from Cryoglobulinemic Patients and Associated Controls
Authors: Bianchettin Gabriella , Bonaccini Claudia , Oliva Romina , Tramontano Anna , Cividini Agostino , Casato Milvia , Merlini Giampaolo , Silini Enrico , Mondelli Mario U.
Published: February 2007

Chronic hepatitis C virus (HCV) infection is frequently associated with extrahepatic manifestations, including nonmalignant and malignant B-cell lymphoproliferative disorders. It has been reported that specific changes or recurring motifs in the amino acid sequence of the HCV hypervariable region 1 (HVR1) may be associated with cryoglobulinemia. We searched for specific insertions/deletions and/or amino acid motifs within HVR1 in samples from 80 symptomatic and asymptomatic patients with and 33 patients without detectable cryoglobulins, all with chronic HCV infection. At variance with the results of a previous study which reported a high frequency of insertions at position 385 of HVR1 from cryoglobulinemic patients, we found a 6.2% prevalence of insertions in samples from patients with and a 9.1% prevalence in those without cryoglobulinemia. Moreover, statistical and bioinformatics approaches including Fisher's exact test,
k
-means clustering, Tree determinant-residue identification, correlation of mutations, principal component analysis, and phylogenetic analysis failed to show statistically significant differences between sequences from cryoglobulin-negative and -positive patients. Our findings suggest that cryoglobulinemia may arise by virtue of as-yet-unidentified host- rather than virus-specific factors. Specific changes in HCV envelope sequence distribution are unlikely to be directly involved in the establishment of pathological B-cell monoclonal proliferation.
Relative Fitness and Replication Capacity of a Multinucleoside Analogue-Resistant Clinical Human Immunodeficiency Virus Type 1 Isolate with a Deletion of Codon 69 in the Reverse Transcriptase Coding Region
Authors: Villena Cristina , Prado Julia G. , Puertas Maria Carmen , Martínez Miguel Ángel , Clotet Bonaventura , Ruiz Lidia , Parkin Neil T. , Menéndez-Arias Luis , Martinez-Picado Javier
Published: February 2007

Deletions, insertions, and amino acid substitutions in the β3-β4 hairpin loop-coding region of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) have been associated with resistance to nucleoside RT inhibitors when appearing in combination with other mutations in the RT-coding region. In this work, we have measured the in vivo fitness of HIV-1 variants containing a deletion of 3 nucleotides affecting codon 69 (Δ69) of the viral RT as well as the replication capacity (RC) ex vivo of a series of recombinant HIV-1 variants carrying an RT bearing the Δ69 deletion or the T69A mutation in a multidrug-resistant (MDR) sequence background, including the Q151M complex and substitutions M184V, K103N, Y181C, and G190A. Patient-derived viral clones having RTs with Δ69 together with S163I showed increased RCs under drug pressure. These data were consistent with the viral population dynamics observed in a long-term-treated HIV-1-infected patient. In the absence of drugs, viral clones containing T69A replicated more efficiently than those having Δ69, but only when patient-derived sequences corresponding to RT residues 248 to 527 were present. These effects could be attributed to a functional interaction between the C-terminal domain of the p66 subunit (RNase H domain) and the DNA polymerase domain of the RT. Finally, recombinant HIV-1 clones bearing RTs with MDR-associated mutations, including deletions at codon 69, showed increased susceptibilities to protease inhibitors in phenotypic assays. These effects correlated with impaired Gag cleavage and could be attributed to delayed maturation and decreased production of active protease in those variants.
Involvement of the Oncoprotein c-Myc in Viral Telomerase RNA Gene Regulation during Marek's Disease Virus-Induced Lymphomagenesis
Authors: Shkreli Marina , Dambrine Ginette , Soubieux Denis , Kut Emmanuel , Rasschaert Denis
Published: February 2007

Marek's disease virus (MDV) is an alphaherpesvirus that induces a highly malignant T-lymphoma in chickens. The viral genome encodes two identical copies of a viral telomerase RNA subunit (vTR) that exhibits 88% sequence identity to its chicken ortholog chTR. The minimal telomerase ribonucleoprotein complex consists of a protein subunit with reverse transcriptase activity (TERT) and an RNA subunit (TR). The active complex compensates for the progressive telomere shortening that occurs during mitosis and is involved in the cell immortalization process. We show here that the upregulation of telomerase activity is associated with an increase in vTR gene expression in chickens infected with the highly oncogenic MDV strain RB-1B. A comparative functional analysis of the viral and chicken TR promoters, based on luciferase reporter assays, revealed that the vTR promoter was up to threefold more efficient than the chTR promoter in avian cells. We demonstrated, by directed mutagenesis of the vTR promoter region, that the stronger transcriptional activity of the vTR promoter resulted largely from an E-box located two nucleotides downstream from the transcriptional start site of the vTR gene. Furthermore, transactivation assays and chromatin immunoprecipitation assays demonstrated the involvement of the c-Myc oncoprotein in the transcriptional regulation of vTR. Finally, an Ets binding site was specifically implicated in the transcriptional regulation of vTR in the MDV-transformed lymphoblastoid cell line MSB-1.
Kaposi's Sarcoma-Associated Herpesvirus LANA Protein Downregulates Nuclear Glycogen Synthase Kinase 3 Activity and Consequently Blocks Differentiation
Authors: Liu Jianyong , Martin Heather , Shamay Meir , Woodard Crystal , Tang Qi-Qun , Hayward S. Diane
Published: February 2007

The Kaposi's sarcoma-associated herpesvirus latency-associated nuclear antigen (LANA) protein interacts with glycogen synthase kinase 3 (GSK-3) and relocalizes GSK-3 in a manner that leads to stabilization of β-catenin and upregulation of β-catenin-responsive cell genes. The LANA-GSK-3 interaction was further examined to determine whether there were additional downstream consequences. In the present study, the nuclear GSK-3 bound to LANA in transfected cells and in BCBL1 primary effusion lymphoma cells was found to be enriched for the inactive serine 9-phosphorylated form of GSK-3. The mechanism of inactivation of nuclear GSK-3 involved LANA recruitment of the extracellular signal-regulated kinases 1 and 2 (ERK1/2) and the ribosomal S6 kinase 1 (RSK1). ERK1/2 and RSK1 coprecipitated with LANA, and LANA was a substrate for ERK1 in vitro. A model is proposed for the overall inactivation of nuclear GSK-3 that incorporates the previously described GSK-3 phosphorylation of LANA itself. Functional inactivation of nuclear GSK-3 was demonstrated by the ability of LANA to limit phosphorylation of the known GSK-3 substrates C/EBPβ and C/EBPα. The effect of LANA-mediated ablation of C/EBP phosphorylation on differentiation was modeled in the well-characterized 3T3L1 adipogenesis system. LANA-expressing 3T3L1 cells were impaired in their ability to undergo differentiation and adipogenesis. C/EBPβ induction followed the same time course as that seen in vector-transduced cells, but there was delayed and reduced induction of C/EBPβ transcriptional targets in LANA-expressing cells. We conclude that LANA inactivates nuclear GSK-3 and modifies the function of proteins that are GSK-3 substrates. In the case of C/EBPs, this translates into LANA-mediated inhibition of differentiation.
Primary CD4+T-Cell Responses Provide both Helper and Cytotoxic Functions during Epstein-Barr Virus Infection and Transformation of Fetal Cord Blood B Cells
Authors: MacArthur Georgina J. , Wilson A. Douglas , Birchall Martin A. , Morgan Andrew J.
Published: February 2007

Most humans carry Epstein-Barr virus (EBV) in circulating memory B cells as a latent infection that is controlled by an immune response. When infected by EBV, B lymphocytes in fetal cord blood are readily transformed to lymphoblastoid cell lines (LCL). It is frequently assumed that this high efficiency of transformation is due to the absence of a primary immune response. However, cord blood lymphocytes stimulated with autologous LCL yield CD4+T cells that can completely inhibit the growth of LCL by a major histocompatibility complex-restricted cytotoxic mechanism mediated by granulysin and granzyme B. Because EBV-transformed B cells maintain the phenotype of antigen-activated B-cell blasts, they can potentially receive inhibitory or helper functions from CD4+T cells. To assess these functions, the effect of EBV-specific CD4+T cells on the efficiency of virus transformation of autologous B cells was assayed. Paradoxically, although the cytotoxic CD4+T-cell lines reduced EBV B-cell transformation at a high effector/target ratio of 10:1, they caused a twofold increase in B-cell transformation at the lower effector/target ratio of 1:1. Th1-polarized CD4+T cells were more effective at inhibiting B-cell transformation, but Th2-polarized cell lines had reduced cytotoxic activity, were unable to inhibit LCL growth, and caused a 10-fold increase in transformation efficiency. Tonsil lymphoid follicles lacked NK cells and CD8+T cells but contained CD4+T cells. We propose that CD4+T cells provide helper or cytotoxic functions to EBV-transformed B cells and that the balance of these functions within tonsil compartments is critical in establishing asymptomatic primary EBV infection and maintaining a stable lifelong latent infection.
Prion Infection of Muscle Cells In Vitro
Authors: Dlakic Wendy M. , Grigg Eric , Bessen Richard A.
Published: February 2007

The prion agent has been detected in skeletal muscle of humans and animals with prion diseases. Here we report scrapie infection of murine C2C12 myoblasts and myotubes in vitro following coculture with a scrapie-infected murine neuroblastoma (N2A) cell line but not following incubation with a scrapie-infected nonneuronal cell line or a scrapie brain homogenate. Terminal differentiation of scrapie-infected C2C12 myoblasts into myotubes resulted in an increase in the expression of the disease-specific prion protein, PrPSc. The amount of scrapie infectivity or PrPScin C2C12 myotubes was comparable to the levels found in scrapie-infected N2A cells, indicating that a high level of infection was established in muscle cells. Subclones of scrapie-infected C2C12 cells produced high levels of PrPScin myotubes, and the C-terminal C2 polypeptide fragment of PrPScwas found based on deglycosylation and PrPSc-specific immunoprecipitation of cell lysates. This is the first report of a stable prion infection in muscle cells in vitro and of a long-term prion infection in a nondividing, differentiated peripheral cell type in culture. These in vitro studies also suggest that in vivo prion infection of skeletal muscle requires contact with prion-infected neurons or, possibly, nerve terminals.
Primary Human Immunodeficiency Virus Type 1 Nef Alleles Show Major Differences in Pathogenicity in Transgenic Mice
Authors: Priceputu Elena , Hanna Zaher , Hu Chunyan , Simard Marie-Chantal , Vincent Patrick , Wildum Steffen , Schindler Michael , Kirchhoff Frank , Jolicoeur Paul
Published: February 2007

We previously reported that the human immunodeficiency virus type 1 NL4-3 Nef is necessary and sufficient to induce a severe AIDS-like disease in transgenic (Tg) mice when the protein is expressed under the regulatory sequences of the human CD4 gene. We have now assayed additional Nef alleles (SF2, JR-CSF, YU10x, and NL4-3 [T71R] Nef alleles), including some from long-term nonprogressors (AD-93, 032an, and 039nm alleles) in the same Tg system and compared their pathogenicities. All these Nef alleles downregulated cell surface CD4 in human cells in vitro and also, with the exception of Nef
YU10x
, in Tg CD4
+
T cells. Depletion of double-positive and single-positive thymocytes occurred with all alleles but was less pronounced in Nef
YU10x
Tg mice. A loss of peripheral CD4
+
T cells was observed with all alleles but was minimal in Nef
YU10x
Tg mice. In Nef
032an
and Nef
SF2
Tg mice, T-cell loss was severe despite lower levels of Tg expression, suggesting a higher virulence of these alleles. All Nef alleles except the Nef
YU10x
and Nef
NL4-3(T71R)
alleles induced an enhanced activated memory (CD25
+
CD69
+
CD44
high
CD45RB
low
CD62L
low
) and apoptotic phenotype. Also, all could interact with and/or activate PAK2 except the Nef
JR-CSF
allele. Organ (lung and kidney) diseases were present in Nef
NL4-3(T71R)
, Nef
032an
, Nef
039nm
, and Nef
SF2
Tg mice, despite very low levels of Tg expression for the last strain. However, no organ disease or minimal organ disease developed in Nef
YU10x
and Nef
AD-93
Tg mice and Nef
JR-CSF
Tg mice, respectively, despite high levels of Tg expression. Our data show that important differences in the pathogenicities of various Nef alleles can be scored in Tg mice. Interestingly, our results also revealed that some phenotypes can segregate independently, such as CD4
+
T-cell depletion and activation, as well as severe depletion of thymic CD4
+
T cells and peripheral CD4
+
T cells. Therefore, expression of Nef alleles in Tg mice under the CD4C regulatory elements represents a novel assay for measuring their pathogenicity. Because of the very high similarity of this murine AIDS-like disease to human AIDS, this assay may have a predictive value regarding the behavior of Nef in infected humans.
Complement Contributes to Inflammatory Tissue Destruction in a Mouse Model of Ross River Virus-Induced Disease
Authors: Morrison Thomas E. , Fraser Robert J. , Smith Paul N. , Mahalingam Suresh , Heise Mark T.
Published: February 2007

Arthritogenic alphaviruses, including Ross River virus (RRV) and chikungunya virus, are mosquito-borne viruses that cause significant human disease worldwide, including explosive epidemics that can result in thousands to millions of infected individuals. Similar to infection of humans, infection of C57BL/6 mice with RRV results in severe monocytic inflammation of bone, joint, and skeletal muscle tissues. We demonstrate here that the complement system, an important component of the innate immune response, enhances the severity of RRV-induced disease in mice. Complement activation products were detected in the inflamed tissues and in the serum of RRV-infected wild-type mice. Furthermore, mice deficient in C3 (C3−/−), the central component of the complement system, developed much less severe disease signs than did wild-type mice. Complement-mediated chemotaxis is essential for many inflammatory arthritides; however, RRV-infected wild-type and C3−/−mice had similar numbers and composition of inflammatory infiltrates within hind limb skeletal muscle tissue. Despite similar inflammatory infiltrates, RRV-infected C3−/−mice exhibited far less severe destruction of skeletal muscle tissue. In addition to these studies, complement activation was also detected in synovial fluid from RRV-infected patients. Taken together, these findings indicate that complement activation occurs in the tissues of humans and mice infected with RRV and suggest that complement plays an essential role in the effector phase, but not the inductive phase, of RRV-induced arthritis and myositis.
On the Electronic States of S4+ and S4- Isomers
Authors: Sormova Hanka , Linguerri Roberto , Rosmus Pavel , Fabian Jürgen , Komiha Najia
Published: February 2007

For three energetically most stable structures of tetrasulfur, S4, S4+ and S4- (cis-chain, rectangular, and trans-chain forms), equilibrium geometries, harmonic wavenumbers, ionization energies, electron affinities, electronic vertical and adiabatic excitation energies, and electronic transition moments were calculated by ab initio methods. It was found that similarly to the ground state of S4, the S4+ cis-isomer could interconvert, perturbed, however, by vibronic coupling with a very close-lying excited state and large-amplitude vibrations. Moreover, the cis- and rectangular minima are calculated to be energetically degenerated. The ω values in all three species agree reasonably well with existing experimental and theoretical data. The calculated patterns of harmonic modes suggest the existence of very complex low-lying anharmonic polyads in all three species. The calculated ionization energies reported previously are compared with the present more accurate data. Also the electronic transition moments and the energy positions of the electronic states with higher spin multiplicities are given.
Lateral variability in shallow marine ichnofabrics: implications for the ichnofabric analysis method
Authors: McIlroy Duncan
Published: February 2007

Ichnological analysis, commonly undertaken both in the field and in core studies, is generally carried out in vertical logged successions. This work documents the results of a detailed ichnofabric study of two highly bioturbated sandstone beds separated by a mudstone, within the thick, Lower Jurassic succession of the Yorkshire coast, UK. The two sandstone beds contain relicts of hummocky cross-stratification and rare bioclasts of bivalves and belemnites. Bioturbation of the beds is intense and the diversity of trace fossils is considerable. Trace fossils present include
Teichichnus rectus
,
Teichichnus
isp. A,
Thalassinoides
isp.,
Palaeophycus heberti
,
Diplocraterion parallelum
,
Rhizocorallium
,
Rosselia socialis
,
Schaubcylindrichnus
isp.,
Chondrites
isp.,
Planolites
isp. and
Phycosiphon incertum
. Ichnofabrics were studied at 5 m intervals parallel to the modern cliff-line, which is parallel to the inferred Jurassic palaeo-coastline. The results demonstrate that there is considerable patchiness to ichnofabric even in a comparatively simple depositional setting such as a storm-influenced shelf. This observation is in line with studies of the modern sea floor. The implications of patchiness in ichnofabric are broad-ranging, but most importantly suggest that caution is needed in the use of ichnofabric analysis for intra-regional correlations.