bluuebunny/crossref_metadata_2025 huggingface dataset:
Acceleration of GATE SPECT simulations
Authors: De Beenhouwer Jan , Staelens Steven , Vandenberghe Stefaan , Lemahieu Ignace
Published: April 2008

Geant4 application for tomographic emission (GATE) is a geometry and tracking 4 (Geant4) application toolkit for accurate simulation of positron emission tomography and single photon emission computed tomography (SPECT) scanners. GATE simulations with realistic count levels are very CPU‐intensive as they take up to several days with single‐CPU computers. Therefore, we implemented both standard forced detection (FD) and convolution‐based forced detection (CFD) with multiple projection sampling, which allows the simulation of all projections simultaneously in GATE. In addition, a FD and CFD specialized Geant4 navigator was developed to overcome the detailed but slow tracking algorithms in Geant4. This article is focused on the implementation and validation of these aforementioned developments. The results show a good agreement between the FD and CFD versus analog GATE simulations for Tc‐99m SPECT. These combined developments accelerate GATE by three orders of magnitude in the case of FD. CFD is an additional two orders of magnitude faster than FD. This renders realistic simulations feasible within minutes on a single CPU. Future work will extend our framework to higher energy isotopes, which will require the inclusion of a septal penetration and collimator scatter model.
VMC versus BEAMnrc: A comparison of simulated linear accelerator heads for photon beams
Authors: Hasenbalg F. , Fix M. K. , Born E. J. , Mini R. , Kawrakow I.
Published: April 2008

BEAMnrc, a code for simulating medical linear accelerators based on EGSnrc, has been benchmarked and used extensively in the scientific literature and is therefore often considered to be the gold standard for Monte Carlo simulations for radiotherapy applications. However, its long computation times make it too slow for the clinical routine and often even for research purposes without a large investment in computing resources. VMC is a much faster code thanks to the intensive use of variance reduction techniques and a much faster implementation of the condensed history technique for charged particle transport. A research version of this code is also capable of simulating the full head of linear accelerators operated in photon mode (excluding multileaf collimators, hard and dynamic wedges). In this work, a validation of the full head simulation at 6 and 18 MV is performed, simulating with VMC and BEAMnrc the addition of one head component at a time and comparing the resulting phase space files. For the comparison, photon and electron fluence, photon energy fluence, mean energy, and photon spectra are considered. The largest absolute differences are found in the energy fluences. For all the simulations of the different head components, a very good agreement (differences in energy fluences between VMC and BEAMnrc ) is obtained. Only a particular case at 6 MV shows a somewhat larger energy fluence difference of . Dosimetrically, these phase space differences imply an agreement between both codes at the level, making VMC head module suitable for full head simulations with considerable gain in efficiency and without loss of accuracy.
Development of a QA phantom and automated analysis tool for geometric quality assurance of on‐board MV and kV x‐ray imaging systems
Authors: Mao Weihua , Lee Louis , Xing Lei
Published: April 2008

The medical linear accelerator (linac) integrated with a kilovoltage (kV) flat‐panel imager has been emerging as an important piece of equipment for image‐guided radiation therapy. Due to the sagging of the linac head and the flexing of the robotic arms that mount the x‐ray tube and flat‐panel detector, geometric nonidealities generally exist in the imaging geometry no matter whether it is for the two‐dimensional projection image or three‐dimensional cone‐beam computed tomography. Normally, the geometric parameters are established during the commissioning and incorporated in correction software in respective image formation or reconstruction. A prudent use of an on‐board imaging system necessitates a routine surveillance of the geometric accuracy of the system like the position of the x‐ray source, imager position and orientation, isocenter, rotation trajectory, and source‐to‐imager distance. Here we describe a purposely built phantom and a data analysis software for monitoring these important parameters of the system in an efficient and automated way. The developed tool works equally well for the megavoltage (MV) electronic portal imaging device and hence allows us to measure the coincidence of the isocenters of the MV and kV beams of the linac. This QA tool can detect an angular uncertainty of 0.1° of the x‐ray source. For spatial uncertainties, such as the source position, the imager position, or the kV/MV isocenter misalignment, the demonstrated accuracy of this tool was better than . The developed tool provides us with a simple, robust, and objective way to probe and monitor the geometric status of an imaging system in a fully automatic process and facilitate routine QA workflow in a clinic.
Optimization of the computational efficiency of a 3D, collapsed cone dose calculation algorithm for brachytherapy
Authors: Carlsson Tedgren Åsa , Ahnesjö Anders
Published: April 2008

Brachytherapy dose calculations based on point kernel superposition using the collapsed cone method have been shown to accurately model the influence from finite dimensions of the patient and effects from heterogeneities including those of high atomic numbers. The collapsed cone method is for brachytherapy applications most effectively implemented through a successive‐scattering approach, in which the dose from once and higher order of scattered photons is calculated separately and in successive scatter order. The calculation speed achievable is directly proportional to the number of directions used for point kernel discretization and to the number of voxels in the volume. In this work we investigate how to best divide the total number of directions between the two steps of successive‐scattering dose calculations. Results show that the largest fraction of the total number of directions should be utilized in calculating the first‐scatter dose. Also shown is how the number of directions required for keeping discretization artifacts at acceptably low levels decreases significantly in multiple‐source configurations, as a result of the dose gradients being less steep than those around single sources. Investigating the number of kernel directions required to keep artifacts low enough within the high dose region of an implant (i.e., for dose levels above approximately of the mean central target dose) reveals similar figures for brachytherapy as for external beam applications, where collapsed cone superposition is clinically used. Also shown is that approximating point kernels with their isotropic average leads to small dose differences at low and intermediate energies, implying that the collapsed cone calculations can be done in a single operation common to all sources of the implant at these energies. The current findings show that collapsed cone calculations can be achieved for brachytherapy with the same efficiency as for external beams. This, combined with recent results on gains in efficiency through implementing the algorithm on graphical card parallel hardware indicates that dose can be calculated with account for heterogeneities and finite dimensions within a few seconds for large voxel arrays and is therefore of interest for practical application to treatment planning.
On comparing methods for discriminating between actually negative and actually positive subjects with FROC type data
Authors: Song Tao , Bandos Andriy I. , Rockette Howard E. , Gur David
Published: April 2008

The task of searching and detecting multiple abnormalities depicted on an image, or a series of images, is a common problem in different areas such as military target detection or diagnostic medical imaging. A free response receiver operating characteristic (FROC) approach for assessing performance in many of these scenarios entails marking the locations of suspected abnormalities and indicating a level of suspicion at each of the marked locations. One of the important characteristics of a system being evaluated under the FROC paradigm is its performance in the conventional ROC domain, namely classifying a subject (or a unit of interest) as “negative” or “positive” in regard to the presence of the abnormality (or any of the abnormalities) of interest. With FROC data we can compare subjects by specifying a function of multiple scores within a subject. This approach allows formulating subject‐based ROC type indices that can be estimated using existing ROC concepts. In this article we focus on indices that reflect the ability of the system to discriminate between actually negative and actually positive subjects. We consider a previously proposed index that is based on the comparison of the highest scores on subjects and two new indices that are based on potentially more stable comparison functions, namely comparison of average scores and stochastic dominance. Based on these indices we develop nonparametric procedures for comparing subject‐based discriminative ability of diagnostic systems being evaluated under the FROC paradigm. We also investigate the properties of the statistical procedures in a simulation study.
Episodic-Like Memory in Rats: Is It Based on When or How Long Ago?
Authors: Roberts William A. , Feeney Miranda C. , MacPherson Krista , Petter Mark , McMillan Neil , Musolino Evanya
Published: April 2008

Recent experiments with rats suggest that they show episodic-like or what-where-when memory for a preferred food found on a radial maze. Although memory for when a salient event occurred suggests that rats can mentally travel in time to a moment in the past, an alternative possibility is that they remember how long ago the food was found. Three groups of rats were tested for memory of previously encountered food. The different groups could use only the cues of when, how long ago, or when + how long ago. Only the cue of how long ago food was encountered was used successfully. These results suggest that episodic-like memory in rats is qualitatively different from human episodic memory.
Crystal Structure of a Self-Spliced Group II Intron
Authors: Toor Navtej , Keating Kevin S. , Taylor Sean D. , Pyle Anna Marie
Published: April 2008

Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from
Oceanobacillus iheyensis
at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two–metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.
The Roles of Subsurface Carbon and Hydrogen in Palladium-Catalyzed Alkyne Hydrogenation
Authors: Teschner Detre , Borsodi János , Wootsch Attila , Révay Zsolt , Hävecker Michael , Knop-Gericke Axel , Jackson S. David , Schlögl Robert
Published: April 2008

Alkynes can be selectively hydrogenated into alkenes on solid palladium catalysts. This process requires a strong modification of the near-surface region of palladium, in which carbon (from fragmented feed molecules) occupies interstitial lattice sites. In situ x-ray photoelectron spectroscopic measurements under reaction conditions indicated that much less carbon was dissolved in palladium during unselective, total hydrogenation. Additional studies of hydrogen content using in situ prompt gamma activation analysis, which allowed us to follow the hydrogen content of palladium during catalysis, indicated that unselective hydrogenation proceeds on hydrogen-saturated β-hydride, whereas selective hydrogenation was only possible after decoupling bulk properties from the surface events. Thus, the population of subsurface sites of palladium, by either hydrogen or carbon, governs the hydrogenation events on the surface.
Use of the
Brucella melitensis
Native Hapten To Diagnose Brucellosis in Goats by a Rapid, Simple, and Specific Fluorescence Polarization Assay
Authors: Ramírez-Pfeiffer Carlos , Díaz-Aparicio Efrén , Gomez-Flores Ricardo , Rodríguez-Padilla Cristina , Morales-Loredo Alberto , Álvarez-Ojeda Genoveva
Published: April 2008

The performance of the fluorescence polarization assay (FPA) using the recently described
Brucella melitensis
native hapten and the
Brucella abortus O
-polysaccharide tracer was evaluated and compared with those of The World Organization for Animal Health tests related to indirect and competitive enzyme-linked immunosorbent assays as classification variables for goat sera obtained from a high-prevalence area where vaccination was performed; test series were also evaluated to increase the final specificity of the tests. Our results showed that the respective relative sensitivity and specificity were 99.7% and 32.5% for the rose Bengal test with a 3% cell concentration (RBT3), 92.8% and 68.8% for the rose Bengal test with 8% cell concentration (RBT8), 98.4% and 84.9% for the Canadian complement fixation test (CFT), 83.7% and 65.5% for the Mexican CFT, 98.4% and 81.0% for the buffered plate agglutination test (BPAT), and 78.1% and 89.3% for the fluorescence polarization assay (FPA). The use of the FPA as the secondary test significantly increased the final specificities of test combinations; the screening tests BPAT, RBT3, and RBT8 plus FPA resulted in 90%, 91.2%, and 91.3% final specificities, respectively, whereas for the combinations RBT3 plus Mexican CFT, RBT8 plus Mexican CFT, and BPAT plus Canadian CFT, the specificities were 65.5%, 63.2%, and 91.7%, respectively. The results suggested that the FPA may be routinely applied as an adaptable screening test for diagnosis of goat brucellosis, since its cutoff can be adjusted to improve its sensitivity or specificity, it is a rapid and simple test, it can be the test of choice when specificity is relevant or when an alternative confirmatory test is not available, and it is not affected by vaccination, thus reducing the number of goats wrongly slaughtered due to misdiagnosis.
Oligonucleotide Array-Based Identification of Species in the
Acinetobacter calcoaceticus-A. baumannii
Complex in Isolates from Blood Cultures and Antimicrobial Susceptibility Testing of the Isolates
Authors: Ko Wen-Chien , Lee Nan-Yao , Su Siou Cing , Dijkshoorn Lenie , Vaneechoutte Mario , Wang Li-Rong , Yan Jin-Jou , Chang Tsung Chain
Published: April 2008

Acinetobacter calcoaceticus
,
A. baumannii
,
Acinetobacter
genomic species (gen. sp.) 3, and
Acinetobacter
gen. sp. 13TU, which are included in the
A. calcoaceticus
-
A. baumannii
complex, are difficult to distinguish by phenotypic methods. An array with six oligonucleotide probes based on the 16S-23S rRNA gene intergenic spacer (ITS) region was developed to differentiate species in the
A. calcoaceticus
-
A. baumannii
complex. Validation of the array with a reference collection of 52 strains of the
A. calcoaceticus
-
A. baumannii
complex and 137 strains of other species resulted in an identification sensitivity and specificity of 100%. By using the array, the species distribution of 291 isolates of the
A. calcoaceticus
-
A. baumannii
complex from patients with bacteremia were determined to be
A. baumannii
(221 strains [75.9%]),
Acinetobacter
gen. sp. 3 (67 strains [23.0%]),
Acinetobacter
gen. sp. 13TU (2 strains [0.7%]), and unidentified
Acinetobacter
sp. (1 strain [0.3%]). The identification accuracy of the array for 12 randomly selected isolates from patients with bacteremia was further confirmed by sequence analyses of the ITS region and the 16S rRNA gene. Antimicrobial susceptibility testing of the 291 isolates from patients with bacteremia revealed that
A. baumannii
strains were less susceptible to antimicrobial agents than
Acinetobacter
gen. sp. 3. All
Acinetobacter
gen. sp. 3 strains were susceptible to ampicillin-sulbactam, imipenem, and meropenem; but only 67.4%, 90%, and 86% of the
A. baumannii
strains were susceptible to ampicillin-sulbactam, imipenem, and meropenem, respectively. The observed significant variations in antimicrobial susceptibility among different species in the
A. calcoaceticus
-
A. baumannii
complex emphasize that the differentiation of species within the complex is relevant from a clinical-epidemiological point of view.
Identification of Thermotolerant
Campylobacter
Species by Fluorescence In Situ Hybridization
Authors: Poppert Sven , Haas Michaela , Yildiz Tatjana , Alter Thomas , Bartel Edda , Fricke Ursula , Essig Andreas
Published: April 2008

Thermotolerant
Campylobacter
spp. (
Campylobacter jejuni
,
C. coli
,
C. lari
, and
C. upsaliensis
) are leading causes of food-borne diarrhea in humans. In this study, the usefulness of fluorescence in situ hybridization (FISH) for the identification of
Campylobacter
isolates was investigated. A hierarchical FISH probe set that included six group-, genus-, and species-specific probes was developed and evaluated with 12 reference strains and 94 clinical isolates of
Campylobacter
,
Arcobacter
, and
Helicobacter
. FISH correctly identified all isolates to the genus level and detected all thermotolerant
Campylobacter
isolates. The assay showed high degrees of sensitivity for the identification of
C. jejuni
(90%),
C. coli
(97%),
C. lari
(81%), and
C. upsaliensis
(100%) to the species level.
Performance of HerpeSelect and Kalon Assays in Detection of Antibodies to Herpes Simplex Virus Type 2
Authors: LeGoff Jérôme , Mayaud Philippe , Gresenguet Gérard , Weiss Helen A. , Nzambi Khonde , Frost Eric , Pepin Jacques , Belec Laurent
Published: April 2008

The performances of commercial enzyme-linked immunosorbent assays (ELISAs) in detecting herpes simplex virus type 2 (HSV-2) antibodies have been inconsistent for African and human immunodeficiency virus (HIV)-positive populations. We compared the performances of the HerpeSelect and Kalon glycoprotein G2 ELISAs for patients with genital ulcer disease in Ghana and the Central African Republic. Sera from 434 women were tested with the HerpeSelect assay, and a subsample (
n
= 199) was tested by the Kalon assay. Ulcer swabs and cervicovaginal lavage samples were tested for HSV-2 DNA by PCR. HSV-2-seronegative women with detectable genital HSV-2 DNA were retested for HSV-2 antibodies 14 and 28 days later by the two ELISAs. A total of 346 (80%) women were positive by HerpeSelect at baseline, and 225 (54%) had detectable genital (lesional or cervicovaginal) HSV-2 DNA. Sixty-six (19%) HerpeSelect-positive samples had low-positive index values (1.1 to 3.5), and 58% of these samples had detectable genital HSV-2 DNA. Global agreement between the two serological assays was 86%. Concordance was high (99%) for sera that were negative by HerpeSelect or had high index values (>3.5). Defining infection detected by HSV-2 DNA PCR and/or Kalon assay as true infection, 71% of sera with low-positive index values were associated with true HSV-2 infection. Twenty-five women were identified as having nonprimary first-episode genital HSV-2 infection. Rates of HSV-2 seroconversion at day 14 were 77% (10/13 patients) by HerpeSelect assay and 23% (3/13 patients) by Kalon assay, with four additional seroconversions detected by Kalon assay at day 28. HIV serostatus did not influence assay performance. Low index values obtained with the HerpeSelect assay may correspond to true HSV-2 infection, in particular to nonprimary first episodes of genital HSV-2 infection, and need to be interpreted in the context of clinical history.
Bacterial Profiles of Root Caries in Elderly Patients
Authors: Preza Dorita , Olsen Ingar , Aas Jørn A. , Willumsen Tiril , Grinde Bjørn , Paster Bruce J.
Published: April 2008

Culture-based studies have shown that
Streptococcus mutans
and lactobacilli are associated with root caries (RC). The purpose of the present study was to assess the bacterial diversity of RC in elderly patients by use of culture-independent molecular techniques and to determine the associations of specific bacterial species or bacterial communities with healthy and carious roots. Plaque was collected from root surfaces of 10 control subjects with no RC and from 11 subjects with RC. The bacterial 16S rRNA genes from extracted DNA were PCR amplified, cloned, and sequenced to determine species identity. From a total of 3,544 clones, 245 predominant species or phylotypes were observed, representing eight bacterial phyla. The majority (54%) of the species detected have not yet been cultivated. Species of
Selenomonas
and
Veillonella
were common in all samples. The healthy microbiota included
Fusobacterium nucleatum
subsp.
polymorphum
,
Leptotrichia
spp.,
Selenomonas noxia
,
Streptococcus cristatus
, and
Kingella oralis
. Lactobacilli were absent,
S. mutans
was present in one, and
Actinomyces
spp. were present in 50% of the controls. In contrast, the microbiota of the RC subjects was dominated by
Actinomyces
spp., lactobacilli,
S. mutans
,
Enterococcus faecalis
,
Selenomonas
sp. clone CS002,
Atopobium
and
Olsenella
spp.,
Prevotella multisaccharivorax
,
Pseudoramibacter alactolyticus
, and
Propionibacterium
sp. strain FMA5. The bacterial profiles of RC showed considerable subject-to-subject variation, indicating that the microbial communities are more complex than previously presumed. The data suggest that putative etiological agents of RC include not only
S. mutans
, lactobacilli, and
Actinomyces
but also species of
Atopobium
,
Olsenella
,
Pseudoramibacter
,
Propionibacterium
, and
Selenomonas
.
Pulmonary Paragonimiasis Diagnosed by Fine-Needle Aspiration Biopsy
Authors: Zarrin-Khameh Neda , Citron Deborah R. , Stager Charles E. , Laucirica Rodolfo
Published: April 2008

We report a case of paragonimiasis involving a 12-year-old Latin American boy. The diagnosis was made by fine-needle aspiration biopsy of a pulmonary nodule. Identification of the species by morphometric analysis of the eggs indicated that the infection was caused by
Paragonimus mexicanus
.
Insertion of the Two Cleavage Sites of the Respiratory Syncytial Virus Fusion Protein in Sendai Virus Fusion Protein Leads to Enhanced Cell-Cell Fusion and a Decreased Dependency on the HN Attachment Protein for Activity
Authors: Rawling Joanna , García-Barreno Blanca , Melero José A.
Published: April 2008

Cell entry by paramyxoviruses requires fusion of the viral envelope with the target cell membrane. Fusion is mediated by the viral fusion (F) glycoprotein and usually requires the aid of the attachment glycoprotein (G, H or HN, depending on the virus). Human respiratory syncytial virus F protein (FRSV) is able to mediate membrane fusion in the absence of the attachment G protein and is unique in possessing two multibasic furin cleavage sites, separated by a region of 27 amino acids (pep27). Cleavage at both sites is required for cell-cell fusion. We have investigated the significance of the two cleavage sites and pep27 in the context of Sendai virus F protein (FSeV), which possesses a single monobasic cleavage site and requires both coexpression of the HN attachment protein and trypsin in order to fuse cells. Inclusion of both FRSVcleavage sites in FSeVresulted in a dramatic increase in cell-cell fusion activity in the presence of HN. Furthermore, chimeric FSeVmutants containing both FRSVcleavage sites demonstrated cell-cell fusion in the absence of HN. The presence of two multibasic cleavage sites may therefore represent a strategy to regulate activation of a paramyxovirus F protein for cell-cell fusion in the absence of an attachment protein.
Attenuation of V- or C-Defective Measles Viruses: Infection Control by the Inflammatory and Interferon Responses of Rhesus Monkeys
Authors: Devaux Patricia , Hodge Gregory , McChesney Michael B. , Cattaneo Roberto
Published: April 2008

Patients recruited in virus-based cancer clinical trials and immunocompromised individuals in need of vaccination would profit from viral strains with defined attenuation mechanisms. We generated measles virus (MV) strains defective for the expression of either the V protein, a modulator of the innate immune response, or the C protein, which has multiple functions. The virulence of these strains was compared with that of the parental wild-type MV in a natural host,
Macaca mulatta
. Skin rash, viremia, and the strength of the innate and adaptive immune responses were characterized in groups of six animals. Replication of V- or C-protein-defective viruses was short-lived and reached lower levels in peripheral blood mononuclear cells and lymphatic organs compared to the wild-type virus; none of the mutants reverted to the wild type. The neutralizing antibody titers and MV-specific T-cell responses were equivalent in monkeys infected with the viral strains tested, documenting strong adaptive immune responses. In contrast, the inflammatory response was better controlled by wild-type MV, as revealed by inhibition of interleukin-6 and tumor necrosis factor alpha transcription. The interferon response was also better controlled by the wild-type virus than by the defective viruses. Since V- and C-defective MVs induce strong adaptive immune responses while spreading less efficiently, they may be developed as vaccines for immunocompromised individuals. Moreover, MV unable to interact with single innate immunity proteins may be developed for preferential replication in tumors with specific contexts of vulnerability.
Insulin-Like Growth Factor II mRNA Binding Protein 1 Associates with Gag Protein of Human Immunodeficiency Virus Type 1, and Its Overexpression Affects Virus Assembly
Authors: Zhou Yongdong , Rong Liwei , Lu Jennifer , Pan Qinghua , Liang Chen
Published: April 2008

The assembly of human immunodeficiency virus type 1 (HIV-1) particles is driven by viral Gag protein. This function of Gag not only benefits from its self-multimerization property but also depends on its interaction with a number of cellular factors such as TSG101 and ALIX/AIP1 that promote virus budding and release from cell surfaces. However, interaction with Gag also allows some cellular factors such as APOBEC3G and Trim5α to access viral replication machinery and block viral replication. In this study, we report a new HIV-1 Gag-binding factor named insulin-like growth factor II mRNA binding protein 1 (IMP1). Gag-IMP1 interaction requires the second zinc finger of the nucleocapsid (NC) domain of Gag and the KH3 and KH4 domains of IMP1. A fourfold reduction of HIV-1 infectivity was seen with overexpression of the wild-type IMP1 and its mutant that is able to interact with Gag but not with overexpression of IMP1 mutants exhibiting Gag-binding deficiency. The decreased viral infectivity was further shown as a result of diminished viral RNA packaging, abrogated Gag processing on the cellular membranes, and impeded maturation of virus particles. Together, these results demonstrate that IMP1 interacts with HIV-1 Gag protein and is able to block the formation of infectious HIV-1 particles.
A Novel Mutation in Murine Hepatitis Virus nsp5, the Viral 3C-Like Proteinase, Causes Temperature-Sensitive Defects in Viral Growth and Protein Processing
Authors: Sparks Jennifer S. , Donaldson Eric F. , Lu Xiaotao , Baric Ralph S. , Denison Mark R.
Published: April 2008

Sequencing and reversion analysis of murine hepatitis virus (MHV) temperature-sensitive (
ts
) viruses has identified putative
ts
mutations in the replicase nonstructural proteins (nsp's) of these coronaviruses. In this study, reverse transcriptase PCR sequencing of the RNA genome of an isolate of the MHV
ts
virus Alb
ts
6, referred to as Alb/ts/nsp5/V148A, identified a putative
ts
mutation in nsp5 (T10651C, Val148Ala), the viral 3C-like proteinase (3CLpro). The introduction of the T10651C mutation into the infectious MHV clone resulted in the recovery of a mutant virus, the nsp5/V148A virus, that demonstrated reduced growth and nsp5 proteinase activity identical to that of Alb/ts/nsp5/V148A at the nonpermissive temperature. Sequence analysis of 40°C revertants of Alb/ts/nsp5/V148A identified primary reversion to Ala148Val in nsp5, as well as two independent second-site mutations resulting in Ser133Asn and His134Tyr substitutions in nsp5. The introduction of the Ser133Asn or His134Tyr substitution into the cloned nsp5/V148A mutant virus background resulted in the recovery of viruses with increased growth fitness and the partial restoration of nsp5 activity at the nonpermissive temperature. Modeling of the nsp5 structure of Alb/ts/nsp5/V148A predicted that the Val148Ala mutation alters residue 148 interactions with residues of the substrate binding S1 subsite of the nsp5 active-site cavity. This study identifies novel residues in nsp5 that may be important for regulating substrate specificity and nsp5 proteinase activity.
Comprehensive Immunological Evaluation Reveals Surprisingly Few Differences between Elite Controller and ProgressorMamu-B*17-Positive Simian Immunodeficiency Virus-Infected Rhesus Macaques
Authors: Maness Nicholas J. , Yant Levi J. , Chung Chungwon , Loffredo John T. , Friedrich Thomas C. , Piaskowski Shari M. , Furlott Jessica , May Gemma E. , Soma Taeko , León Enrique J. , Wilson Nancy A. , Piontkivska Helen , Hughes Austin L. , Sidney John , Sette Alessandro , Watkins David I.
Published: April 2008

The association between particular major histocompatibility complex class I (MHC-I) alleles and control of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication implies that certain CD8+T-lymphocyte (CD8-TL) responses are better able than others to control viral replication in vivo. However, possession of favorable alleles does not guarantee improved prognosis or viral control. In rhesus macaques, the MHC-I alleleMamu-B*17is correlated with reduced viremia and is overrepresented in macaques that control SIVmac239, termed elite controllers (ECs). However, there is so far no mechanistic explanation for this phenomenon. Here we show that the chronic-phase Mamu-B*17-restricted repertoire is focused primarily against just five epitopes—VifHW8, EnvFW9, NefIW9, NefMW9, andenvARFcRW9—in both ECs and progressors. Interestingly, Mamu-B*17-restricted CD8-TL do not target epitopes in Gag. CD8-TL escape variation occurred in all targeted Mamu-B*17-restricted epitopes. However, recognition of escape variant peptides was commonly observed in both ECs and progressors. Wild-type sequences in the VifHW8 epitope tended to be conserved in ECs, but there was no evidence that this enhances viral control. In fact, no consistent differences were detected between ECs and progressors in any measured parameter. Our data suggest that the narrowly focused Mamu-B*17-restricted repertoire suppresses virus replication and drives viral evolution. It is, however, insufficient in the majority of individuals that express the “protective” Mamu-B*17 molecule. Most importantly, our data indicate that the important differences betweenMamu-B*17-positive ECs and progressors are not readily discernible using standard assays to measure immune responses.
Human Immunodeficiency Virus Type 1 Vpr Binds to the N Lobe of the Wee1 Kinase Domain and Enhances Kinase Activity for Cdc2
Authors: Kamata Masakazu , Watanabe Nobumoto , Nagaoka Yoshiko , Chen Irvin S. Y.
Published: April 2008

Human immunodeficiency virus type 1 Vpr is a virion-associated accessory protein that has multiple activities within an infected cell. One of the most dramatic effects of Vpr is the induction of cell cycle arrest at the G
2
/M boundary, followed by apoptosis. This effect has implications for CD4
+
cell loss in AIDS. In normal cell cycle regulation, Wee1, a key regulator for G
2
-M progression, phosphorylates Tyr15 on Cdc2 and thereby blocks the progression of cells into M phase. We demonstrate that Vpr physically interacts with Wee1 at the N lobe of the kinase domain analogous to that present in other kinases. This interaction with Vpr enhances Wee1 kinase activity for Cdc2. Overexpression of Wee1 kinase-deficient mutants competes for Vpr-mediated cell cycle arrest, and deletion of the region of Wee1 that binds Vpr abrogates that competition. However, the Vpr mutants I74P and I81P, which fail to induce G
2
arrest, can bind to and increase the kinase activity of Wee1 to the same extent as wild-type Vpr. Therefore, we conclude that the binding of Vpr to Wee1 is not sufficient for Vpr to activate the G
2
checkpoint, and it may reflect an independent function of Vpr.
Tumor Antigen LRRC15 Impedes Adenoviral Infection: Implications for Virus-Based Cancer Therapy
Authors: O'Prey Jim , Wilkinson Simon , Ryan Kevin M.
Published: April 2008

Adenoviruses for gene or oncolytic therapy are under development. Notable among these strategies is adenoviral delivery of the tumor suppressor p53. Since all therapeutics have limitations in certain settings, we have undertaken retroviral suppressor screens to identify genes conferring resistance to adenovirus-delivered p53. These studies identified the tumor antigen LRRC15, which is frequently overexpressed in multiple tumor types, as a repressor of cell death due to adenoviral p53. LRRC15, however, does not impede p53 function per se but impedes adenoviral infection. Specifically, LRRC15 causes redistribution of the coxsackievirus-adenovirus receptor away from the cell surface. This effect is manifested in less adenoviral binding to the surfaces of LRRC15-expressing cells. This discovery, therefore, not only is important for understanding adenoviral biology but also has potentially important implications for adenovirus-based anticancer therapeutics.
Structural and Functional Constraints Limit Options for Cytotoxic T-Lymphocyte Escape in the Immunodominant HLA-B27-Restricted Epitope in Human Immunodeficiency Virus Type 1 Capsid
Authors: Schneidewind Arne , Brockman Mark A. , Sidney John , Wang Yaoyu E. , Chen Huabiao , Suscovich Todd J. , Li Bin , Adam Rahma I. , Allgaier Rachel L. , Mothé Bianca R. , Kuntzen Thomas , Oniangue-Ndza Cesar , Trocha Alicja , Yu Xu G. , Brander Christian , Sette Alessandro , Walker Bruce D. , Allen Todd M.
Published: April 2008

Control of human immunodeficiency virus type 1 (HIV-1) by HLA-B27-positive subjects has been linked to an immunodominant CD8+cytotoxic T-lymphocyte (CTL) response targeting the conserved KK10 epitope (KRWIILGLNK263-272) in p24/Gag. Viral escape in KK10 typically occurs through development of an R264K substitution in conjunction with the upstream compensatory mutation S173A, and the difficulty of the virus to escape from the immune response against the KK10 epitope until late in infection has been associated with slower clinical progression. Rare alternative escape mutations at R264have been observed, but factors dictating the preferential selection of R264K remain unclear. Here we illustrate that while all observed R264mutations (K, G, Q, and T) reduced peptide binding to HLA-B27 and impaired viral replication, the replicative defects of the alternative mutants were actually less pronounced than those for R264K. Importantly, however, none of these mutants replicated as well as an R264K variant containing the compensatory mutation S173A. In assessing the combined effects of viral replication and CTL escape using an in vitro coculture assay, we further observed that the compensated R264K mutant also displayed the highest replication capacity in the presence of KK10-specific CTLs. Comparisons of codon usage for the respective variants indicated that generation of the R264K mutation may also be favored due to a G-to-A bias in nucleotide substitutions during HIV-1 replication. Together, these data suggest that the preference for R264K is due primarily to the ability of the S173A-compensated virus to replicate better than alternative variants in the presence of CTLs, suggesting that viral fitness is a key contributor for the selection of immune escape variants.
A Direct Comparison of Human Papillomavirus Type 16 L1 Particles Reveals a Lower Immunogenicity of Capsomeres than Viruslike Particles with Respect to the Induced Antibody Response
Authors: Thönes Nadja , Herreiner Anna , Schädlich Lysann , Piuko Konrad , Müller Martin
Published: April 2008

Capsomeres are considered to be an alternative to viruslike particle (VLP)-based vaccines as they can be produced in prokaryotic expression systems. So far, no detailed side-by-side comparison of VLPs and capsomeres has been performed. In the present study, we immunized mice with insect cell-derived human papillomavirus type 16 VLPs and capsomeres. VLPs induced consistently higher antibody titers than capsomeres but the two forms induced similar CD8 T-cell responses after subcutaneous, intranasal, and oral immunization, and at least 20 to 40 times more L1 in the form of capsomeres than in the form of VLPs was needed to achieve comparable antibody responses. These results were confirmed by DNA immunization. The lower immunogenicity of capsomeres was independent of the isotype switch, as it was also observed for the early immunoglobulin M responses. Although there were differences in the display of surface epitopes between the L1 particles, these did not contribute significantly to the differences in the immune responses. capsomeres were less immunogenic than VLPs in Toll-like receptor 4 (TLR4)-deficient mice, suggesting that the lower immunogenicity is not due to a failure of capsomeres to trigger TLR4. We observed better correlation between antibody results from enzyme-linked immunosorbent assays and neutralization assays for sera from VLP-immunized mice than for sera from capsomere-immunized mice, suggesting qualitative differences between VLPs and capsomeres. We also showed that the lower immunogenicity of capsomeres could be compensated by the use of an adjuvant system containing MPL. Taken together, these results suggest that, presumably because of the lower degree of complexity of the antigen organization, capsomeres are significantly less immunogenic than VLPs with respect to the humoral immune response and that this characteristic should be considered in the design of putative capsomere-based prophylactic vaccines.
Identification of a Highly Conserved, Functional Nuclear Localization Signal within the N-Terminal Region of Herpes Simplex Virus Type 1 VP1-2 Tegument Protein
Authors: Abaitua F. , O'Hare P.
Published: April 2008

VP1-2 is a large structural protein assembled into the tegument compartment of the virion, conserved across the herpesviridae, and essential for virus replication. In herpes simplex virus (HSV) and pseudorabies virus, VP1-2 is tightly associated with the capsid. Studies of its assembly and function remain incomplete, although recent data indicate that in HSV, VP1-2 is recruited onto capsids in the nucleus, with this being required for subsequent recruitment of additional structural proteins. Here we have developed an antibody to characterize VP1-2 localization, observing the protein in both cytoplasmic and nuclear compartments, frequently in clusters in both locations. Within the nucleus, a subpopulation of VP1-2 colocalized with VP26 and VP5, though VP1-2-positive foci devoid of these components were observed. We note a highly conserved basic motif adjacent to the previously identified N-terminal ubiquitin hydrolase domain (DUB). The DUB domain in isolation exhibited no specific localization, but when extended to include the adjacent motif, it efficiently accumulated in the nucleus. Transfer of the isolated motif to a test protein, β-galactosidase, conferred specific nuclear localization. Substitution of a single amino acid within the motif abolished the nuclear localization function. Deletion of the motif from intact VP1-2 abrogated its nuclear localization. Moreover, in a functional assay examining the ability of VP1-2 to complement growth of a VP1-2-ve mutant, deletion of the nuclear localization signal abolished complementation. The nuclear localization signal may be involved in transport of VP1-2 early in infection or to late assembly sites within the nucleus or, considering the potential existence of VP1-2 cleavage products, in selective localization of subdomains to different compartments.
Association between walking distance and percentiles of body mass index in older and younger men
Authors: Williams P T
Published: April 2008

Objective:

To assess the association of weekly walking distance to body weight and waist circumference in elderly (age ⩾75 years), senior (55⩽ age <75 years), middle-aged (35⩽ age <55 years), and younger men (18⩽ age <35 years old).

Design:

Cross-sectional analyses of baseline questionnaires from 7082 male participants of the National Walkers’ Health Study.

Results:

Standard regression analyses showed that body mass index (BMI) was inversely and significantly associated with walking distance (kg/m2per km/week) in elderly (slope (SE): −0.032 (0.008)), senior (−0.045 (0.005)) and middle-aged men (−0.037 (0.007)), as were their waist circumferences (−0.090 (0.025), −0.122 (0.012) and −0.091 (0.015) cm per km/week, respectively), and that these slopes remained significant when adjusted statistically for reported weekly servings of meat, fish, fruit and alcohol. However, percentile regression analyses showed that the declines in BMI per km/week walked were greater at the higher than the lower percentiles of the BMI distribution. In men ⩾74 years old the decline per km walked was 4.9-fold greater among the heaviest men (that is, 90th BMI percentile; −0.076 kg/m2per km/week) than among the leanest men (that is, 10th BMI percentile; −0.015 kg/m2per km/week). The differences in slope at the 90th compared to the 10th BMI percentile were 5.4-fold among men 55–74 years old and sixfold among men 35–54 years old. Per km/week walked, the declines at the 90th percentile of waist circumference were also greater than at its 10th percentile, and intermediate for percentiles in between. Whereas standard regression analyses suggest that the average declines in BMI per km/week walked reported here are consistent with those reported previously per km/week run in male runners 35–54 years old (−0.036 (0.001) kg/m2per km/week) and ⩾50 years old (−0.038 (0.001) kg/m2per km/week), percentile regression analyses showed that when adjusted to the leaner body weights of the runners the declines per km walked were between 49% and 59% less for walkers than runners.

Conclusions:

Declines in BMI and waist circumferences with walking distance depend upon the percentile of the BMI distribution, with the decline per km walked being significantly greater among heavier men.
Regular Tai Chi Chuan exercise improves T cell helper function of patients with type 2 diabetes mellitus with an increase in T-bet transcription factor and IL-12 production
Authors: Yeh S-H , Chuang H , Lin L-W , Hsiao C-Y , Wang P-W , Liu R-T , Yang K D
Published: April 2008

Background:

Exercise has been shown to be beneficial in the treatment of type 2 diabetes mellitus (DM); its benefit to immune function, however, remains to be determined.

Objective:

This study investigated the effect of a 12-week course of Tai Chi Chuan (TCC) exercise on T cell helper (Th) reaction in patients with type 2 DM.

Methods:

A case-control study was performed in 30 pairs of patients with type 2 DM and normal age-matched adults. Fasting blood glucose, HbA1c, mediators (interleukin (IL)-12, IL-4 and transforming growth factor (TGF)β) and transcription factors (T-bet, GATA-3 and FoxP3) of Th1/Th2/T regulatory (Treg) reaction were measured before and after a 12-week TCC exercise programme.

Results:

Fasting glucose and HbA1c levels in the patients with type 2 DM were significantly higher than in age-matched controls before exercise. After TCC exercise, HbA1c levels in patients with type 2 DM significantly decreased (7.59 (0.32)% vs 7.16 (0.22)%; p = 0.047) and blood levels of IL-12 increased significantly (5.96 (1.10) vs 12.96 (3.07); p = 0.035). To study the molecular Th1/Th2/Treg reaction, patients with type 2 DM were found to have lower T-bet but not GATA-3 or FoxP3 expression than normal controls before TCC exercise. After the 12-week TCC exercise T-bet expression significantly increased in patients with type 2 DM.

Conclusions:

A 12-week TCC exercise programme decreases HbA1c levels along with an increase in the Th1 reaction. A combination of TCC with medication may provide an even better improvement in both metabolism and immunity of patients with type 2 DM.
Comparison of fat oxidation during exercise in lean and obese pubertal boys: clinical implications
Authors: Zunquin G , Theunynck D , Sesboüé B , Arhan P , Bouglé D
Published: April 2008

Objective:

To examine fat oxidation rates during exercise in lean and obese pubescent children.

Design:

A graded leg cycle ergometry test was performed by two groups of pubescent boys (13 lean: mean (SD) age 12.0 (0.5) years, body mass index (BMI) 18.56 (1.12) kg/m2; 17 obese: mean (SD) age 12.1 (0.1) years, BMI 26.68 (3.37) kg/m2; p<0.001). The first step of the test was fixed at 30 W and power was gradually increased by 20 W every 3.5 min. The mean ventilatory gas measurement was obtained during the last 30 s of each step for calculation of fat oxidation rate vs exercise intensity.

Results:

At low intensity (0–30% of peak oxygen consumption) when fat-free mass is considered, the fat oxidation rate was identical for the two groups. At higher intensities (40%, 50% and 60% of peak oxygen consumption) the fat oxidation rate was significantly higher in lean boys than in obese boys.

Conclusion:

These results confirm that obese pubertal boys have fat-free mass decreased capacities to use fat during moderate exercise. The findings suggest that obese boys need to practise physical activity at a lower intensity than healthy boys to enhance lipolysis and diminish adipose tissue and the consequences of obesity.
Randomized controlled trial of ionization and photoelectric smoke alarm functionality
Authors: Mueller B A , Sidman E A , Alter H , Perkins R , Grossman D C
Published: April 2008

Objective:

To compare functionality, reasons for non-function, and nuisance alarm levels of two common types of smoke alarms after installation in low- to mid-level income households in King County, Washington.

Methods:

Randomized controlled trial of 761 households. An ionization or photoelectric smoke alarm was installed between June 1, 2000 and July 31, 2002. Main outcome measures were: percentage of study alarms that were working, observed reasons for non-functional status, and self-reported frequency of nuisance alarms at 9 and 15 months of follow-up.

Results:

At 9 months after installation, 20% of ionization, vs 5% of photoelectric alarms were non-functional, a difference that persisted at 15 months, with the most common reasons for both types being a disconnected or absent battery. The risk ratio for ionization, relative to photoelectric alarms, being non-functional or removed was 2.7 (95% CI 1.8 to 4.1) at 15 months of follow-up. These findings were not altered by educational level, or the presence of smokers, children <5 years, or adults ⩾65 years.

Conclusions:

Burn prevention efforts are geared towards increasing smoke alarm ownership and improving maintenance of functional status. Results suggest that the selective use of photoelectric alarms by fire injury prevention programs or consumers may provide longer-term protection in similar populations. Designing smoke alarms that minimize nuisance alarming may also result in longer term functionality.